Publications
2024
Selig, Keegan R.; López-Torres, Sergi; Burrows, Anne M.; Silcox, Mary T.; Meng, Jin
Dental caries in living and extinct strepsirrhines with insights into diet Journal Article
In: The Anatomical Record, vol. n/a, no. n/a, 2024.
@article{https://doi.org/10.1002/ar.25420,
title = {Dental caries in living and extinct strepsirrhines with insights into diet},
author = {Keegan R. Selig and Sergi López-Torres and Anne M. Burrows and Mary T. Silcox and Jin Meng},
url = {https://anatomypubs.onlinelibrary.wiley.com/doi/abs/10.1002/ar.25420},
doi = {https://doi.org/10.1002/ar.25420},
year = {2024},
date = {2024-03-11},
journal = {The Anatomical Record},
volume = {n/a},
number = {n/a},
abstract = {Abstract Dental caries is one of the most common diseases afflicting modern humans and occurs in both living and extinct non-human primates, as well as other mammalian species. Compared to other primates, less is known about the etiology or frequency of caries among the Strepsirrhini. Given the link between caries and diet, caries frequency may be informative about the dietary ecology of a given animal. Understanding rates of caries in wild populations is also critical to assessing dental health in captive populations. Here, we examine caries frequency in a sample of 36 extant strepsirrhine species (n = 316 individuals) using odontological collections of wild-, non-captive animals housed at the American Museum of Natural History by counting the number of specimens characterized by the disease. Additionally, in the context of studying caries lesions in strepsirrhines, case studies were also conducted to test if similar lesions were found in their fossil relatives. In particular, two fossil strepsirrhine species were analyzed: the earliest Late Eocene Karanisia clarki, and the subfossil lemur Megaladapis madagascariensis. Our results suggest that caries affects 13.92% of the extant individuals we examined. The frugivorous and folivorous taxa were characterized by the highest overall frequency of caries, whereas the insectivores, gummivores, and omnivores had much lower caries frequencies. Our results suggest that caries may be common among wild populations of strepsirrhines, and in fact is more prevalent than in many catarrhines and platyrrhines. These findings have important implications for understanding caries, diet, and health in living and fossil taxa.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract Dental caries is one of the most common diseases afflicting modern humans and occurs in both living and extinct non-human primates, as well as other mammalian species. Compared to other primates, less is known about the etiology or frequency of caries among the Strepsirrhini. Given the link between caries and diet, caries frequency may be informative about the dietary ecology of a given animal. Understanding rates of caries in wild populations is also critical to assessing dental health in captive populations. Here, we examine caries frequency in a sample of 36 extant strepsirrhine species (n = 316 individuals) using odontological collections of wild-, non-captive animals housed at the American Museum of Natural History by counting the number of specimens characterized by the disease. Additionally, in the context of studying caries lesions in strepsirrhines, case studies were also conducted to test if similar lesions were found in their fossil relatives. In particular, two fossil strepsirrhine species were analyzed: the earliest Late Eocene Karanisia clarki, and the subfossil lemur Megaladapis madagascariensis. Our results suggest that caries affects 13.92% of the extant individuals we examined. The frugivorous and folivorous taxa were characterized by the highest overall frequency of caries, whereas the insectivores, gummivores, and omnivores had much lower caries frequencies. Our results suggest that caries may be common among wild populations of strepsirrhines, and in fact is more prevalent than in many catarrhines and platyrrhines. These findings have important implications for understanding caries, diet, and health in living and fossil taxa.
Sulej, Tomasz; Machalski, Marcin; Tałanda, Mateusz
New finds of Olenekian, Early Triassic, trematosaurid amphibians and prolocophonid reptiles from Poland Journal Article
In: Acta Palaeontologica Polonica, vol. 69, no. 1, pp. 49–56, 2024.
@article{sulej2024new,
title = {New finds of Olenekian, Early Triassic, trematosaurid amphibians and prolocophonid reptiles from Poland},
author = {Tomasz Sulej and Marcin Machalski and Mateusz Tałanda},
url = {https://www.app.pan.pl/article/item/app011092023.html},
doi = {10.4202/app.01109.2023},
year = {2024},
date = {2024-03-08},
urldate = {2024-03-08},
journal = {Acta Palaeontologica Polonica},
volume = {69},
number = {1},
pages = {49–56},
abstract = {The continental Lower Triassic (Middle Buntsandstein) siliciclastic deposits exposed along the margins of the Holy Cross Mountains, Poland, yield locally abundant vertebrate footprints and bones. Although the footprints have been described in a number of studies, providing, for example, new insights into the origin of dinosaurs, there are few studies focusing on the bones. Here, we describe new amphibian and reptile material from the Buntsandstein fluvial sandstones of early Olenekian age exposed at Stryczowice on the north-eastern margin of the Holy Cross Mountains. These finds include fragmentary cranial specimens referred to as Trematosauridae gen. et sp. indet. and Procolophonidae gen. et sp. indet. Faunal differences between Stryczowice and the best-known Polish Olenekian vertebrate-bearing site of Czatkowice 1 near Kraków support heterogeneity in the Early Triassic vertebrate distribution across Pangea.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The continental Lower Triassic (Middle Buntsandstein) siliciclastic deposits exposed along the margins of the Holy Cross Mountains, Poland, yield locally abundant vertebrate footprints and bones. Although the footprints have been described in a number of studies, providing, for example, new insights into the origin of dinosaurs, there are few studies focusing on the bones. Here, we describe new amphibian and reptile material from the Buntsandstein fluvial sandstones of early Olenekian age exposed at Stryczowice on the north-eastern margin of the Holy Cross Mountains. These finds include fragmentary cranial specimens referred to as Trematosauridae gen. et sp. indet. and Procolophonidae gen. et sp. indet. Faunal differences between Stryczowice and the best-known Polish Olenekian vertebrate-bearing site of Czatkowice 1 near Kraków support heterogeneity in the Early Triassic vertebrate distribution across Pangea.
Ciach, Michał Aleksander; Pawłowska, Julia; Górecki, Paweł; Muszewska, Anna
The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities Journal Article
In: Evolution Letters, vol. 03, pp. qrae009, 2024, ISSN: 2056-3744.
@article{Ciach24,
title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities},
author = {Ciach, Michał Aleksander and Pawłowska, Julia and Górecki, Paweł and Muszewska, Anna},
url = {https://doi.org/10.1093/evlett/qrae009},
doi = {10.1093/evlett/qrae009},
issn = {2056-3744},
year = {2024},
date = {2024-03-05},
urldate = {2024-03-05},
journal = {Evolution Letters},
volume = {03},
pages = {qrae009},
abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts’ metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins’ functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.Horizontal gene transfer is a transmission of genes between organisms, distinct from vertical inheritance from parents to offspring. HGT seems to occur among all living forms. Our study focuses on horizontally transferred genes present in early diverging fungi (EDF). EDF is a relatively understudied group of organisms with vastly diverse lifestyles and tremendous ecological importance. They include arbuscular mycorrhizal Glomeromycota, the gut-dwelling symbionts of herbivores Neocallimastigomycota, or the parasitic Batrachochytrium. HGT has been reported to contribute to this diversity by facilitating niche adaptations in certain lineages. In our work, we have analyzed horizontally acquired genes in 44 fungal genomes, focusing on cases with clear phylogenetic evidence. We have designed a computational pipeline that detects a statistical sample of reliable HGTs. The pipeline is published alongside the article. We have analyzed the donors, acceptors, and properties of the transferred genes. We found transfers of genes that can expand the metabolic, adaptive, and immune capabilities of fungi.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts’ metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins’ functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.Horizontal gene transfer is a transmission of genes between organisms, distinct from vertical inheritance from parents to offspring. HGT seems to occur among all living forms. Our study focuses on horizontally transferred genes present in early diverging fungi (EDF). EDF is a relatively understudied group of organisms with vastly diverse lifestyles and tremendous ecological importance. They include arbuscular mycorrhizal Glomeromycota, the gut-dwelling symbionts of herbivores Neocallimastigomycota, or the parasitic Batrachochytrium. HGT has been reported to contribute to this diversity by facilitating niche adaptations in certain lineages. In our work, we have analyzed horizontally acquired genes in 44 fungal genomes, focusing on cases with clear phylogenetic evidence. We have designed a computational pipeline that detects a statistical sample of reliable HGTs. The pipeline is published alongside the article. We have analyzed the donors, acceptors, and properties of the transferred genes. We found transfers of genes that can expand the metabolic, adaptive, and immune capabilities of fungi.
Jankowska, Katarzyna; Łukomska-Kowalczyk, Maja; Milanowski, Rafał; Fells, Alicja; Zakryś, Bożena
Biodiversity of autotrophic euglenids based on the group specific DNA metabarcoding approach Journal Article
In: Protist, vol. 175, no. 3, pp. 126024, 2024, ISSN: 1434-4610.
@article{JANKOWSKA2024126024,
title = {Biodiversity of autotrophic euglenids based on the group specific DNA metabarcoding approach},
author = {Katarzyna Jankowska and Maja Łukomska-Kowalczyk and Rafał Milanowski and Alicja Fells and Bożena Zakryś},
url = {https://www.sciencedirect.com/science/article/pii/S1434461024000166},
doi = {https://doi.org/10.1016/j.protis.2024.126024},
issn = {1434-4610},
year = {2024},
date = {2024-03-04},
urldate = {2024-01-01},
journal = {Protist},
volume = {175},
number = {3},
pages = {126024},
abstract = {This study reports a comprehensive analysis of photoautotrophic euglenids’ distribution and biodiversity in 16 small water bodies of various types (including fish ponds, field ponds, rural ponds and park ponds) located in three regions of Poland: Masovia, Masuria and Pomerania during a period of three years. By employing a euglenid specific barcode marker and a curated database of V2 18S rDNA sequences it was possible to identify 97.7 % of euglenid reads at species level. A total of 152 species classified in 13 genera were identified. The number of euglenid species found in one pond varied from 40 to 102. The most common species were Euglena agilis and Euglenaria caudata, found in every analysed waterbody. The highest number of observed species belonged to Trachelomonas and Phacus. Certain species exhibited a tendency to coexist, suggesting the presence of distinct species assemblages. Among them, the most distinctive cluster was associated with water bodies located in the Masuria region, characterized also by the greatest species richness, including many very rare species: Euglenaformis chlorophoenicea, Lepocinclis autumnalis, L. marssonii, Trachelomonas eurystoma, T. manschurica, T. mucosa, T. zuberi, T. zuberi var. nepos.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This study reports a comprehensive analysis of photoautotrophic euglenids’ distribution and biodiversity in 16 small water bodies of various types (including fish ponds, field ponds, rural ponds and park ponds) located in three regions of Poland: Masovia, Masuria and Pomerania during a period of three years. By employing a euglenid specific barcode marker and a curated database of V2 18S rDNA sequences it was possible to identify 97.7 % of euglenid reads at species level. A total of 152 species classified in 13 genera were identified. The number of euglenid species found in one pond varied from 40 to 102. The most common species were Euglena agilis and Euglenaria caudata, found in every analysed waterbody. The highest number of observed species belonged to Trachelomonas and Phacus. Certain species exhibited a tendency to coexist, suggesting the presence of distinct species assemblages. Among them, the most distinctive cluster was associated with water bodies located in the Masuria region, characterized also by the greatest species richness, including many very rare species: Euglenaformis chlorophoenicea, Lepocinclis autumnalis, L. marssonii, Trachelomonas eurystoma, T. manschurica, T. mucosa, T. zuberi, T. zuberi var. nepos.
Łaska, Weronika; Rodríguez-Tovar, Francisco J; Uchman, Alfred
New insights into endolithic palaeocommunity development in mobile hard substrate using CT imaging of bioeroded clasts from the Pliocene (Almería, SE Spain) Journal Article
In: The Science of Nature, vol. 111, no. 1, pp. 1–25, 2024.
@article{laska2024new,
title = {New insights into endolithic palaeocommunity development in mobile hard substrate using CT imaging of bioeroded clasts from the Pliocene (Almería, SE Spain)},
author = {Weronika Łaska and Francisco J Rodríguez-Tovar and Alfred Uchman},
year = {2024},
date = {2024-02-08},
urldate = {2024-01-01},
journal = {The Science of Nature},
volume = {111},
number = {1},
pages = {1–25},
publisher = {Springer},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Skawina, Aleksandra; Dąbrowska, Agnieszka; Bonk, Agata; Paterczyk, Bohdan; Nowakowska, Julita
Tracking the micro-and nanoplastics in the terrestrial-freshwater food webs. Bivalves as sentinel species Journal Article
In: Science of The Total Environment, pp. 170468, 2024.
@article{skawina2024tracking,
title = {Tracking the micro-and nanoplastics in the terrestrial-freshwater food webs. Bivalves as sentinel species},
author = {Aleksandra Skawina and Agnieszka Dąbrowska and Agata Bonk and Bohdan Paterczyk and Julita Nowakowska},
year = {2024},
date = {2024-02-05},
urldate = {2024-01-01},
journal = {Science of The Total Environment},
pages = {170468},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2023
Ajijah, Nur; Fiodor, Angelika; Dziurzynski, Mikolaj; Stasiuk, Robert; Pawlowska, Julia; Dziewit, Lukasz; Pranaw, Kumar
In: Frontiers in Plant Science, vol. 14, 2023, ISSN: 1664-462X.
@article{10.3389/fpls.2023.1288408,
title = {Biocontrol potential of Pseudomonas protegens ML15 against Botrytis cinerea causing gray mold on postharvest tomato (Solanum lycopersicum var. cerasiforme)},
author = {Nur Ajijah and Angelika Fiodor and Mikolaj Dziurzynski and Robert Stasiuk and Julia Pawlowska and Lukasz Dziewit and Kumar Pranaw},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1288408},
doi = {10.3389/fpls.2023.1288408},
issn = {1664-462X},
year = {2023},
date = {2023-12-15},
urldate = {2023-01-01},
journal = {Frontiers in Plant Science},
volume = {14},
abstract = {Gray mold, caused by Botrytis cinerea is a major cause of post-harvest rot of fresh fruits and vegetables. The utilization of selected microorganisms as biocontrol agents is a promising alternative to effectively control gray mold on tomatoes. The current study was conducted to explore potential biocontrol mechanisms of the Pseudomonas strain to control infections on post-harvest tomatoes. Among the 8 tested bacterial isolates, Pseudomonas protegens ML15 demonstrated antagonistic activity to Botrytis cinerea. Moreover, P. protegens ML15 exhibited the production of siderophores, hydrogen cyanide, ammonia, exopolysaccharides, lipase, biosurfactant, 2,4-diacetylphloroglucinol, and several other antifungal compounds, such as 1-tetradecanol, cyclododecane, 2,4-di-tert-butylphenol, and 2-methyl-1-hexadecanol. A comprehensive genomic analysis of P. protegens ML15 unravels 18 distinct genetic regions with the potential for biosynthesizing secondary metabolites, known for their pivotal role in biocontrol responses against plant pathogens. In vivo, experiments showed that both culture suspension and cell-free supernatant of P. protegens ML15 significantly reduced fungal growth (53.0 ± 0.63%) and mitigated disease development (52.8 ± 1.5%) in cherry tomatoes at four days post-B. cinerea inoculation. During the infection, the application of P. protegens ML15 resulted in the augmentation of total antioxidant, phenolic content, and ascorbic acids content. Thus, our results suggested that P. protegens ML15’s role as a biocontrol agent against B. cinerea-induced postharvest tomato decay achieved through the secretion of antifungal substances, induction of tomato defense responses, and inhibition of mycelial growth of B. cinerea. These findings provide a significant contribution to the ongoing search for alternative, eco-friendly methods of controlling gray mold in fresh products. The utilization of P. protegens ML15 as a biocontrol agent could help to reduce the reliance on chemical fungicides and promote sustainable agriculture practices.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gray mold, caused by Botrytis cinerea is a major cause of post-harvest rot of fresh fruits and vegetables. The utilization of selected microorganisms as biocontrol agents is a promising alternative to effectively control gray mold on tomatoes. The current study was conducted to explore potential biocontrol mechanisms of the Pseudomonas strain to control infections on post-harvest tomatoes. Among the 8 tested bacterial isolates, Pseudomonas protegens ML15 demonstrated antagonistic activity to Botrytis cinerea. Moreover, P. protegens ML15 exhibited the production of siderophores, hydrogen cyanide, ammonia, exopolysaccharides, lipase, biosurfactant, 2,4-diacetylphloroglucinol, and several other antifungal compounds, such as 1-tetradecanol, cyclododecane, 2,4-di-tert-butylphenol, and 2-methyl-1-hexadecanol. A comprehensive genomic analysis of P. protegens ML15 unravels 18 distinct genetic regions with the potential for biosynthesizing secondary metabolites, known for their pivotal role in biocontrol responses against plant pathogens. In vivo, experiments showed that both culture suspension and cell-free supernatant of P. protegens ML15 significantly reduced fungal growth (53.0 ± 0.63%) and mitigated disease development (52.8 ± 1.5%) in cherry tomatoes at four days post-B. cinerea inoculation. During the infection, the application of P. protegens ML15 resulted in the augmentation of total antioxidant, phenolic content, and ascorbic acids content. Thus, our results suggested that P. protegens ML15’s role as a biocontrol agent against B. cinerea-induced postharvest tomato decay achieved through the secretion of antifungal substances, induction of tomato defense responses, and inhibition of mycelial growth of B. cinerea. These findings provide a significant contribution to the ongoing search for alternative, eco-friendly methods of controlling gray mold in fresh products. The utilization of P. protegens ML15 as a biocontrol agent could help to reduce the reliance on chemical fungicides and promote sustainable agriculture practices.
Campo, Javier; Carlos-Oliveira, Maria; Čepička, Ivan; Hehenberger, Elisabeth; Horák, Aleš; Karnkowska, Anna; Kolisko, Martin; Lara, Enrique; Lukeš, Julius; Pánek, Tomáš; Piwosz, Kasia; Richter, Daniel J.; Škaloud, Pavel; Sutak, Robert; Tachezy, Jan; Hampl, Vladimír
The protist cultural renaissance Journal Article
In: Trends in Microbiology, 2023, ISSN: 0966-842X.
@article{DELCAMPO2023,
title = {The protist cultural renaissance},
author = {Javier Campo and Maria Carlos-Oliveira and Ivan Čepička and Elisabeth Hehenberger and Aleš Horák and Anna Karnkowska and Martin Kolisko and Enrique Lara and Julius Lukeš and Tomáš Pánek and Kasia Piwosz and Daniel J. Richter and Pavel Škaloud and Robert Sutak and Jan Tachezy and Vladimír Hampl},
url = {https://www.sciencedirect.com/science/article/pii/S0966842X23003281},
doi = {https://doi.org/10.1016/j.tim.2023.11.010},
issn = {0966-842X},
year = {2023},
date = {2023-12-14},
urldate = {2023-01-01},
journal = {Trends in Microbiology},
abstract = {Protists are key players in the biosphere. Here, we provide a perspective on integrating protist culturing with omics approaches, imaging, and high-throughput single-cell manipulation strategies, concluding with actions required for a successful return of the golden age of protist culturing.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Protists are key players in the biosphere. Here, we provide a perspective on integrating protist culturing with omics approaches, imaging, and high-throughput single-cell manipulation strategies, concluding with actions required for a successful return of the golden age of protist culturing.
Klug, Christian; Stevens, Kevin; Hoffmann, René; Zatoń, Michał; Clements, Thomas; Košťák, Martin; Weis, Robert; De Baets, Kenneth; Lehmann, Jens; Vinther, Jakob; Fuchs, Dirk
Revisiting the identification of Syllipsimopodi bideni and timing of the decabrachian-octobrachian divergence Journal Article
In: Nature Communications, vol. 14, no. 1, pp. 8094, 2023, ISSN: 2041-1723.
@article{klug_revisiting_2023,
title = {Revisiting the identification of Syllipsimopodi bideni and timing of the decabrachian-octobrachian divergence},
author = {Christian Klug and Kevin Stevens and René Hoffmann and Michał Zatoń and Thomas Clements and Martin Košťák and Robert Weis and De Baets, Kenneth and Jens Lehmann and Jakob Vinther and Dirk Fuchs},
url = {https://www.nature.com/articles/s41467-023-42842-x},
doi = {10.1038/s41467-023-42842-x},
issn = {2041-1723},
year = {2023},
date = {2023-12-07},
urldate = {2023-12-07},
journal = {Nature Communications},
volume = {14},
number = {1},
pages = {8094},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Novák, Lukáš V. F.; Treitli, Sebastian C.; Pyrih, Jan; Hałakuc, Paweł; Pipaliya, Shweta V.; Vacek, Vojtěch; Brzoň, Ondřej; Soukal, Petr; Eme, Laura; Dacks, Joel B.; Karnkowska, Anna; Eliáš, Marek; Hampl, Vladimír
Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria Journal Article
In: PLOS Genetics, vol. 19, no. 12, pp. 1-30, 2023.
@article{10.1371/journal.pgen.1011050,
title = {Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria},
author = {Lukáš V. F. Novák and Sebastian C. Treitli and Jan Pyrih and Paweł Hałakuc and Shweta V. Pipaliya and Vojtěch Vacek and Ondřej Brzoň and Petr Soukal and Laura Eme and Joel B. Dacks and Anna Karnkowska and Marek Eliáš and Vladimír Hampl},
url = {https://doi.org/10.1371/journal.pgen.1011050},
doi = {10.1371/journal.pgen.1011050},
year = {2023},
date = {2023-12-07},
urldate = {2023-12-07},
journal = {PLOS Genetics},
volume = {19},
number = {12},
pages = {1-30},
publisher = {Public Library of Science},
abstract = {The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the genera Trimastix and Paratrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-living Paratrimastix pyriformis and the oxymonad Blattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis, B. nauphoetae, and Streblomastix strix), suggesting the amitochondriate status is common to a large part if not the whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the genera Trimastix and Paratrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-living Paratrimastix pyriformis and the oxymonad Blattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis, B. nauphoetae, and Streblomastix strix), suggesting the amitochondriate status is common to a large part if not the whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.
KD, Hyde; MA, Abdel-Wahab; J, Abdollahzadeh; PD, Abeywickrama; S, Absalan; N, Afshari; AM, Ainsworth; (...),; J, Pawłowska; (...),; L, Zucconi
Global consortium for the classification of fungi and fungus-like taxa Journal Article
In: Mycosphere, vol. 14, iss. 1, pp. 1960-2012, 2023.
@article{nokey,
title = {Global consortium for the classification of fungi and fungus-like taxa},
author = {Hyde KD and Abdel-Wahab MA and Abdollahzadeh J and Abeywickrama PD and Absalan S and Afshari N and Ainsworth AM and (...) and Pawłowska J and (...) and Zucconi L},
url = {https://www.mycosphere.org/pdf/MYCOSPHERE_14_1_23-1.pdf},
doi = {Doi:10.5943/mycosphere/14/1/23 },
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {Mycosphere},
volume = {14},
issue = {1},
pages = {1960-2012},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sheard, Catherine; Street, Sally E.; Healy, Susan D.; Troisi, Camille A.; Clark, Andrew D.; Yovcheva, Antonia; Trébaol, Alexis; Vanadzina, Karina; Lala, Kevin N.
Nest traits for the world's birds Journal Article
In: Global Ecology and Biogeography, vol. n/a, no. n/a, 2023.
@article{https://doi.org/10.1111/geb.13783,
title = {Nest traits for the world's birds},
author = {Catherine Sheard and Sally E. Street and Susan D. Healy and Camille A. Troisi and Andrew D. Clark and Antonia Yovcheva and Alexis Trébaol and Karina Vanadzina and Kevin N. Lala},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/geb.13783},
doi = {https://doi.org/10.1111/geb.13783},
year = {2023},
date = {2023-11-27},
journal = {Global Ecology and Biogeography},
volume = {n/a},
number = {n/a},
abstract = {Abstract Motivation A well-constructed nest is a key element of successful reproduction in most species of birds, and nest morphology varies widely across the class. Macroecological and macroevolutionary studies tend to group nest design into a small number of discrete categories, often based on taxonomic inference. In reality, however, many species display considerable intraspecific variation in their nest-building behaviour, and broad-level categories may include several functionally distinct nest types. To address this imprecision in the literature and facilitate future studies of broad-scale variation in avian parental care, we here introduce a detailed, global comparative database of nest building in birds, together with preliminary correlations between these traits and species-level environmental variables. Main types of variables contained We present species-level data for nest structure, location, height, material composition, sex of builder, building time and nest dimensions. Spatial location and grain Global. Maps are presented at the 10 × 10 level. Time period and grain Included species are generally extant, although we present some data for recently extinct taxa. The data were collected in 2017–2021 and was drawn from secondary sources published in 1992–2021. Major taxa and level of measurement Partial or complete trait data is presented for 8601 species of birds, representing 36 of 36 orders and 239 of 243 families. Software format Data have been uploaded as Supplementary Material in .csv format and are separated by species and source for all traits (Dataset S1, and Metadata) as well as summarized at the species level for the major structure and location variables (Dataset S2, and Metadata).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract Motivation A well-constructed nest is a key element of successful reproduction in most species of birds, and nest morphology varies widely across the class. Macroecological and macroevolutionary studies tend to group nest design into a small number of discrete categories, often based on taxonomic inference. In reality, however, many species display considerable intraspecific variation in their nest-building behaviour, and broad-level categories may include several functionally distinct nest types. To address this imprecision in the literature and facilitate future studies of broad-scale variation in avian parental care, we here introduce a detailed, global comparative database of nest building in birds, together with preliminary correlations between these traits and species-level environmental variables. Main types of variables contained We present species-level data for nest structure, location, height, material composition, sex of builder, building time and nest dimensions. Spatial location and grain Global. Maps are presented at the 10 × 10 level. Time period and grain Included species are generally extant, although we present some data for recently extinct taxa. The data were collected in 2017–2021 and was drawn from secondary sources published in 1992–2021. Major taxa and level of measurement Partial or complete trait data is presented for 8601 species of birds, representing 36 of 36 orders and 239 of 243 families. Software format Data have been uploaded as Supplementary Material in .csv format and are separated by species and source for all traits (Dataset S1, and Metadata) as well as summarized at the species level for the major structure and location variables (Dataset S2, and Metadata).
Świś, Przemysław
Anagenetic evolution and peramorphosis of a latest Devonian conodont from Holy Cross Mountain (Poland) Journal Article
In: Journal of Micropalaeontology, vol. 42, no. 2, pp. 193–210, 2023.
@article{jm-42-193-2023,
title = {Anagenetic evolution and peramorphosis of a latest Devonian conodont from Holy Cross Mountain (Poland)},
author = {Przemysław Świś},
url = {https://jm.copernicus.org/articles/42/193/2023/},
doi = {10.5194/jm-42-193-2023},
year = {2023},
date = {2023-11-20},
urldate = {2023-01-01},
journal = {Journal of Micropalaeontology},
volume = {42},
number = {2},
pages = {193–210},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Barido-Sottani, Joëlle; Pohle, Alexander; De Baets, Kenneth; Murdock, Duncan; Warnock, Rachel C. M.
Putting the F into FBD analysis: tree constraints or morphological data? Journal Article
In: Palaeontology, vol. 66, no. 6, pp. e12679, 2023.
@article{https://doi.org/10.1111/pala.12679,
title = {Putting the F into FBD analysis: tree constraints or morphological data?},
author = {Joëlle Barido-Sottani and Alexander Pohle and De Baets, Kenneth and Duncan Murdock and Rachel C. M. Warnock},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pala.12679},
doi = {https://doi.org/10.1111/pala.12679},
year = {2023},
date = {2023-11-12},
urldate = {2023-11-12},
journal = {Palaeontology},
volume = {66},
number = {6},
pages = {e12679},
abstract = {Abstract The fossilized birth–death (FBD) process provides an ideal model for inferring phylogenies from both extant and fossil taxa. Using this approach, fossils are directly integrated into the tree, leading to a statistically coherent prior on divergence times. Since fossils are typically not associated with molecular sequences, additional information is required to place fossils in the tree. We use simulations to evaluate two different approaches to handling fossil placement in FBD analyses: using topological constraints, where the user specifies monophyletic clades based on established taxonomy, or using total-evidence analyses, which use a morphological data matrix in addition to the molecular alignment. We also explore how rate variation in fossil recovery or diversification rates impacts these approaches. We find that the extant topology is well recovered under all methods of fossil placement. Divergence times are similarly well recovered across all methods, with the exception of constraints which contain errors. We see similar patterns in datasets which include rate variation, however, relative errors in extant divergence times increase when more variation is included in the dataset, for all approaches using topological constraints, and particularly for constraints with errors. Finally, we show that trees recovered under the FBD model are more accurate than those estimated using non-time calibrated inference. Overall, we show that both fossil placement approaches are reliable even when including uncertainty. Our results underscore the importance of core taxonomic research, including morphological data collection and species descriptions, irrespective of the approach to handling phylogenetic uncertainty using the FBD process.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract The fossilized birth–death (FBD) process provides an ideal model for inferring phylogenies from both extant and fossil taxa. Using this approach, fossils are directly integrated into the tree, leading to a statistically coherent prior on divergence times. Since fossils are typically not associated with molecular sequences, additional information is required to place fossils in the tree. We use simulations to evaluate two different approaches to handling fossil placement in FBD analyses: using topological constraints, where the user specifies monophyletic clades based on established taxonomy, or using total-evidence analyses, which use a morphological data matrix in addition to the molecular alignment. We also explore how rate variation in fossil recovery or diversification rates impacts these approaches. We find that the extant topology is well recovered under all methods of fossil placement. Divergence times are similarly well recovered across all methods, with the exception of constraints which contain errors. We see similar patterns in datasets which include rate variation, however, relative errors in extant divergence times increase when more variation is included in the dataset, for all approaches using topological constraints, and particularly for constraints with errors. Finally, we show that trees recovered under the FBD model are more accurate than those estimated using non-time calibrated inference. Overall, we show that both fossil placement approaches are reliable even when including uncertainty. Our results underscore the importance of core taxonomic research, including morphological data collection and species descriptions, irrespective of the approach to handling phylogenetic uncertainty using the FBD process.
Abarenkov, Kessy; Nilsson, R Henrik; Larsson, Karl-Henrik; Taylor, Andy F S; May, Tom W; Frøslev, Tobias Guldberg; Pawlowska, Julia; Lindahl, Björn; Põldmaa, Kadri; Truong, Camille; Vu, Duong; Hosoya, Tsuyoshi; Niskanen, Tuula; Piirmann, Timo; Ivanov, Filipp; Zirk, Allan; Peterson, Marko; Cheeke, Tanya E; Ishigami, Yui; Jansson, Arnold Tobias; Jeppesen, Thomas Stjernegaard; Kristiansson, Erik; Mikryukov, Vladimir; Miller, Joseph T; Oono, Ryoko; Ossandon, Francisco J; Paupério, Joana; Saar, Irja; Schigel, Dmitry; Suija, Ave; Tedersoo, Leho; Kõljalg, Urmas
In: Nucleic Acids Research, pp. gkad1039, 2023, ISBN: 0305-1048.
@article{nokey,
title = {The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered},
author = {Abarenkov, Kessy and Nilsson, R Henrik and Larsson, Karl-Henrik and Taylor, Andy F S and May, Tom W and Frøslev, Tobias Guldberg and Pawlowska, Julia and Lindahl, Björn and Põldmaa, Kadri and Truong, Camille and Vu, Duong and Hosoya, Tsuyoshi and Niskanen, Tuula and Piirmann, Timo and Ivanov, Filipp and Zirk, Allan and Peterson, Marko and Cheeke, Tanya E and Ishigami, Yui and Jansson, Arnold Tobias and Jeppesen, Thomas Stjernegaard and Kristiansson, Erik and Mikryukov, Vladimir and Miller, Joseph T and Oono, Ryoko and Ossandon, Francisco J and Paupério, Joana and Saar, Irja and Schigel, Dmitry and Suija, Ave and Tedersoo, Leho and Kõljalg, Urmas},
url = {https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad1039/53343664/gkad1039.pdf},
doi = {https://doi.org/10.1093/nar/gkad1039},
isbn = {0305-1048},
year = {2023},
date = {2023-11-12},
journal = {Nucleic Acids Research},
pages = {gkad1039},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sokołowska, Blanka; Orłowska, Małgorzata; Okrasińska, Alicja; Piłsyk, Sebastian; Pawłowska, Julia; Muszewska, Anna
What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota Journal Article
In: IMA Fungus, vol. 14, iss. 22, 2023.
@article{Sokolowska23,
title = {What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota},
author = {Blanka Sokołowska and Małgorzata Orłowska and Alicja Okrasińska and Sebastian Piłsyk and Julia Pawłowska and Anna Muszewska},
doi = {https://doi.org/10.1186/s43008-023-00127-4},
year = {2023},
date = {2023-11-06},
journal = {IMA Fungus},
volume = {14},
issue = {22},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Czepiński, Łukasz; Pawlak, Wojciech; Rytel, Adam; Tałanda, Mateusz; Szczygielski, Tomasz; Sulej, Tomasz
A new Middle Triassic vertebrate assemblage from Miedary (southern Poland) Journal Article
In: Journal of Vertebrate Paleontology, vol. 0, no. 0, pp. e2265445, 2023.
@article{doi:10.1080/02724634.2023.2265445,
title = {A new Middle Triassic vertebrate assemblage from Miedary (southern Poland)},
author = {Łukasz Czepiński and Wojciech Pawlak and Adam Rytel and Mateusz Tałanda and Tomasz Szczygielski and Tomasz Sulej},
url = {https://doi.org/10.1080/02724634.2023.2265445},
doi = {10.1080/02724634.2023.2265445},
year = {2023},
date = {2023-10-27},
urldate = {2023-10-27},
journal = {Journal of Vertebrate Paleontology},
volume = {0},
number = {0},
pages = {e2265445},
publisher = {Taylor & Francis},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Siedlecki, Igor; Piątek, Marcin; Majchrowska, Maria; Okrasińska, Alicja; Owczarek-Kościelniak, Magdalena; Pawłowska, Julia
In: Fungal Biology, 2023, ISSN: 1878-6146.
@article{SIEDLECKI2023,
title = {Discovery of Formicomyces microglobosus gen. et sp. nov. strengthens the hypothesis of independent evolution of ant-associated fungi in Trichomeriaceae},
author = {Igor Siedlecki and Marcin Piątek and Maria Majchrowska and Alicja Okrasińska and Magdalena Owczarek-Kościelniak and Julia Pawłowska},
url = {https://www.sciencedirect.com/science/article/pii/S1878614623001083},
doi = {https://doi.org/10.1016/j.funbio.2023.10.005},
issn = {1878-6146},
year = {2023},
date = {2023-10-24},
urldate = {2023-10-24},
journal = {Fungal Biology},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ostrowski, Grzegorz; Jaworska, Danuta; Płecha, Magdalena; Przybylski, Wiesław; Sałek, Piotr; Sawicki, Krzysztof; Pawłowska, Julia
Cold adapted and closely related mucoraceae species colonise dry-aged beef (DAB) Journal Article
In: Fungal Biology, 2023, ISSN: 1878-6146.
@article{OSTROWSKI2023,
title = {Cold adapted and closely related mucoraceae species colonise dry-aged beef (DAB)},
author = {Grzegorz Ostrowski and Danuta Jaworska and Magdalena Płecha and Wiesław Przybylski and Piotr Sałek and Krzysztof Sawicki and Julia Pawłowska},
url = {https://www.sciencedirect.com/science/article/pii/S1878614623001034},
doi = {https://doi.org/10.1016/j.funbio.2023.09.005},
issn = {1878-6146},
year = {2023},
date = {2023-10-23},
urldate = {2023-01-01},
journal = {Fungal Biology},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abramczyk, Beniamin; Ławicki, Szymon; Pyter, Weronika; Bluszcz, Agata; Piszczek, Ignacy; Audycki, Jonatan; Pawłowska, Julia
Microbiological awareness among upper-secondary school students in the context of covid-19 vaccination Journal Article
In: Journal of Baltic Science Education, vol. 22, iss. 5, pp. 749-766, 2023, ISSN: 1648-3898.
@article{1316b,
title = {Microbiological awareness among upper-secondary school students in the context of covid-19 vaccination},
author = {Beniamin Abramczyk and Szymon Ławicki and Weronika Pyter and Agata Bluszcz and Ignacy Piszczek and Jonatan Audycki and Julia Pawłowska},
url = {https://oaji.net/articles/2023/987-1697653260.pdf},
doi = {https://doi.org/10.33225/jbse/23.22.749},
issn = {1648-3898},
year = {2023},
date = {2023-10-01},
urldate = {2023-10-01},
journal = {Journal of Baltic Science Education},
volume = {22},
issue = {5},
pages = {749-766},
chapter = {749-766},
abstract = {There is evidence that education levels have an impact on people's attitudes toward vaccination. The recent COVID-19 pandemic has highlighted the need to maximize vaccinations - one of the most efficient ways to prevent the spread of infectious diseases. Young individuals play a major role in disease transmission due to their intense social life and frequent asymptomatic infections. In this study, a survey of upper secondary school students in Poland was conducted to assess their microbiological awareness depending on subjects that they studied on the extended level and COVID-19 vaccination willingness. Participants learning biology and chemistry on the extended level had significantly higher microbiological awareness. Clear proof of microbiological awareness's influence on vaccination willingness was not found. Although studying biology did not significantly influence students' willingness to be vaccinated, their place of residence did. Students from bigger cities were more willing to get vaccinated. These results show that while science education raises microbiological awareness among upper secondary school students, place of residence, likely through social pressure, is a more important factor influencing vaccination willingness. It is suggested that more effort should be put into educating society as a whole and encouraging vaccination particularly.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
There is evidence that education levels have an impact on people's attitudes toward vaccination. The recent COVID-19 pandemic has highlighted the need to maximize vaccinations - one of the most efficient ways to prevent the spread of infectious diseases. Young individuals play a major role in disease transmission due to their intense social life and frequent asymptomatic infections. In this study, a survey of upper secondary school students in Poland was conducted to assess their microbiological awareness depending on subjects that they studied on the extended level and COVID-19 vaccination willingness. Participants learning biology and chemistry on the extended level had significantly higher microbiological awareness. Clear proof of microbiological awareness's influence on vaccination willingness was not found. Although studying biology did not significantly influence students' willingness to be vaccinated, their place of residence did. Students from bigger cities were more willing to get vaccinated. These results show that while science education raises microbiological awareness among upper secondary school students, place of residence, likely through social pressure, is a more important factor influencing vaccination willingness. It is suggested that more effort should be put into educating society as a whole and encouraging vaccination particularly.
Skawina, Aleksandra
X-rays and invisible sand: two new methods for designing burrowing behavioral experiments with juvenile unionoids Journal Article
In: Hydrobiologia, 2023.
@article{Skawina_23_hydro,
title = {X-rays and invisible sand: two new methods for designing burrowing behavioral experiments with juvenile unionoids},
author = {Aleksandra Skawina},
doi = {10.1007/s10750-023-05362-9},
year = {2023},
date = {2023-09-20},
urldate = {2023-09-20},
journal = {Hydrobiologia},
abstract = {Unionoids are in global decline, which may be associated with their complex life cycle. Their juveniles are unique because while hidden (burrowed deeply in bottom sediments) they undergo critical anatomical changes (also developing a characteristic juvenile shell sculpture). Currently, the juveniles’ period of life is believed to be both the least known and one of the most vulnerable—thus the possibility of obtaining any biological knowledge is essential for establishing conservation strategies and addressing functional or evolutionary questions. I propose two new methods for visualization of the burrowing behavior of unionoid juveniles within deposits that are cheap and easy: (1) laminated deposits of quartz–aragonite sand for time-stepped X-ray images of bivalve traces, and (2) silica gel serving as 'invisible sand' for direct observations and video recording of behavior within sediments. Both deposits in a pilot study were accepted by the juvenile unionoids—they were stable enough and penetrable, with no observable signs of harmful effects on animals’ behavior during trials. In both, juveniles were clearly visible, settled within the top 1 cm layer of deposits. Both methods are promising tools for future in situ within the deposits research on the biology of this much unexplored and vulnerable unionoids' life stage.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Unionoids are in global decline, which may be associated with their complex life cycle. Their juveniles are unique because while hidden (burrowed deeply in bottom sediments) they undergo critical anatomical changes (also developing a characteristic juvenile shell sculpture). Currently, the juveniles’ period of life is believed to be both the least known and one of the most vulnerable—thus the possibility of obtaining any biological knowledge is essential for establishing conservation strategies and addressing functional or evolutionary questions. I propose two new methods for visualization of the burrowing behavior of unionoid juveniles within deposits that are cheap and easy: (1) laminated deposits of quartz–aragonite sand for time-stepped X-ray images of bivalve traces, and (2) silica gel serving as 'invisible sand' for direct observations and video recording of behavior within sediments. Both deposits in a pilot study were accepted by the juvenile unionoids—they were stable enough and penetrable, with no observable signs of harmful effects on animals’ behavior during trials. In both, juveniles were clearly visible, settled within the top 1 cm layer of deposits. Both methods are promising tools for future in situ within the deposits research on the biology of this much unexplored and vulnerable unionoids' life stage.
Vanadzina, Karina; Street, Sally E; Sheard, Catherine
The evolution of enclosed nesting in passerines is shaped by competition, energetic costs, and predation threat Journal Article
In: Ornithology, vol. 141, pp. 1-15, 2023, ISSN: 0004-8038.
@article{10.1093/ornithology/ukad048,
title = {The evolution of enclosed nesting in passerines is shaped by competition, energetic costs, and predation threat},
author = {Karina Vanadzina and Sally E Street and Catherine Sheard},
url = {https://doi.org/10.1093/ornithology/ukad048},
doi = {10.1093/ornithology/ukad048},
issn = {0004-8038},
year = {2023},
date = {2023-09-11},
urldate = {2023-01-01},
journal = {Ornithology},
volume = {141},
pages = {1-15},
abstract = {Many avian species breed in enclosed nests that may provide better protection against predation and climatic conditions compared to open nests and are generally associated with larger clutch sizes and slower offspring growth. Here we show that different enclosed nesting strategies are each linked to behaviors with very different costs and benefits on a macroevolutionary scale. Using a detailed dataset of nest structure and location from the order Passeriformes, we employed phylogenetic comparative methods to evaluate (1) how predation, competition, design complexity, and energetic costs have shaped evolutionary transitions between different nesting strategies, and (2) whether these strategies also have distinct relationships with life-history traits. We find that flexible strategies (i.e., nesting in both open and enclosed sites) as well as energetically demanding strategies are evolutionarily unstable, indicating the presence of underlying ecological tradeoffs between antipredator protections, construction costs, and competition. We confirm that species with enclosed nests have larger clutch sizes and longer development and nestling periods compared to open nesters, but only species that construct enclosed nests rather than compete for preexisting cavities spend more time incubating and are concentrated in the tropics. Flexible strategies prevail in seasonal environments and are linked to larger clutches—but not longer development—compared to nesting in the open. Overall, our results suggest that predation, competition, and energetic costs affect the evolution of nesting strategies, but via distinct pathways, and that caution is warranted when generalizing about the functions of enclosed nest designs in birds.• Many birds raise their young in enclosed nests, which likely offer protection from predators and climatic conditions. We currently know little, however, about why some species build their own enclosed nests, while others adopt existing cavities.• Using a broad-scale, comparative approach with data from more than 4,000 passerine species (order Passeriformes), we evaluate how predation, competition, nest complexity, and energetic costs have shaped the evolution of these different enclosed nesting strategies.• We find that both flexible and energetically costly enclosed nesting strategies are disfavored on evolutionary timescales. We also show that enclosed nesters have larger clutches and longer developmental periods irrespective of whether they compete for or build their nests.• Our study highlights that different types of enclosed nesting strategies are linked to different sets of evolutionary costs and benefits.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Many avian species breed in enclosed nests that may provide better protection against predation and climatic conditions compared to open nests and are generally associated with larger clutch sizes and slower offspring growth. Here we show that different enclosed nesting strategies are each linked to behaviors with very different costs and benefits on a macroevolutionary scale. Using a detailed dataset of nest structure and location from the order Passeriformes, we employed phylogenetic comparative methods to evaluate (1) how predation, competition, design complexity, and energetic costs have shaped evolutionary transitions between different nesting strategies, and (2) whether these strategies also have distinct relationships with life-history traits. We find that flexible strategies (i.e., nesting in both open and enclosed sites) as well as energetically demanding strategies are evolutionarily unstable, indicating the presence of underlying ecological tradeoffs between antipredator protections, construction costs, and competition. We confirm that species with enclosed nests have larger clutch sizes and longer development and nestling periods compared to open nesters, but only species that construct enclosed nests rather than compete for preexisting cavities spend more time incubating and are concentrated in the tropics. Flexible strategies prevail in seasonal environments and are linked to larger clutches—but not longer development—compared to nesting in the open. Overall, our results suggest that predation, competition, and energetic costs affect the evolution of nesting strategies, but via distinct pathways, and that caution is warranted when generalizing about the functions of enclosed nest designs in birds.• Many birds raise their young in enclosed nests, which likely offer protection from predators and climatic conditions. We currently know little, however, about why some species build their own enclosed nests, while others adopt existing cavities.• Using a broad-scale, comparative approach with data from more than 4,000 passerine species (order Passeriformes), we evaluate how predation, competition, nest complexity, and energetic costs have shaped the evolution of these different enclosed nesting strategies.• We find that both flexible and energetically costly enclosed nesting strategies are disfavored on evolutionary timescales. We also show that enclosed nesters have larger clutches and longer developmental periods irrespective of whether they compete for or build their nests.• Our study highlights that different types of enclosed nesting strategies are linked to different sets of evolutionary costs and benefits.
Kyrychenko, A. M.; Burkot, V. M.; Shcherbatenko, I. S.
Giant DNA Viruses Infecting Unicellular Protists Journal Article
In: Microbiological Journal, vol. 85, no. 4, pp. 72—82, 2023.
@article{nokey,
title = {Giant DNA Viruses Infecting Unicellular Protists},
author = {A.M. Kyrychenko and V.M. Burkot and I.S. Shcherbatenko},
doi = {10.15407/microbiolj85.04.072},
year = {2023},
date = {2023-08-16},
urldate = {2023-08-16},
journal = {Microbiological Journal},
volume = {85},
number = {4},
pages = {72—82},
abstract = {Giant viruses (GV) are widespread in various ecosystems and ecological niches of the biosphere, most commonly in marine and freshwater aquatic ecosystems and soils. These viruses infect protists, a paraphyletic group of various unicellular, syncytial, and protozoan multicellular eukaryotes that are not true animals, plants, or fungus. The morphologically and functionally diverse group of protists includes parasites, commensals, or mutualistic symbionts of eukaryots, as well as heterotrophs, autotrophs, and mixotrophs. These giant viruses are currently classified into several families: Mimiviridae, Pithoviridae, Pandoraviridae, Phycodnaviridae, and the Mollivirus genus. GVs of unicellular protists belonging to the Mimiviridae family mainly infect the species of the Acanthamoeba genus. In this review, we provide the available information concerning giant viruses of the Mimiviridae family infecting other protists. These viruses include: Phaeocystis globosa virus PgV-16T (PgV), Aureococcus anophagefferens virus (AaV), Bodo saltans virus (BsV), Chrysochromulina ericina virus (CeV), and Phaeocystis pouchetii virus (PpV), which infect phytoplanktonic protists, as well as a giant virus of microzooplanktonic species, the Cafeteria roenbergensis virus (CroV). The review focuses on the major differences between these viruses and typical objects of current virology, their importance for understanding the evolutionary processes of genomes, genes, proteins, the biosynthetic and defense systems of organisms, as well as the important role of GV in regulating the aquatic microorganisms abundance and species diversity, carbon transfer and nutrient recycling in marine and freshwater reservoirs. Writing this review was motivated by the intention to inspire the interest of scientists in studying viruses as the most widespread biological creatures on Earth and ubiquitous symbiotic partners of all three domains of life.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Giant viruses (GV) are widespread in various ecosystems and ecological niches of the biosphere, most commonly in marine and freshwater aquatic ecosystems and soils. These viruses infect protists, a paraphyletic group of various unicellular, syncytial, and protozoan multicellular eukaryotes that are not true animals, plants, or fungus. The morphologically and functionally diverse group of protists includes parasites, commensals, or mutualistic symbionts of eukaryots, as well as heterotrophs, autotrophs, and mixotrophs. These giant viruses are currently classified into several families: Mimiviridae, Pithoviridae, Pandoraviridae, Phycodnaviridae, and the Mollivirus genus. GVs of unicellular protists belonging to the Mimiviridae family mainly infect the species of the Acanthamoeba genus. In this review, we provide the available information concerning giant viruses of the Mimiviridae family infecting other protists. These viruses include: Phaeocystis globosa virus PgV-16T (PgV), Aureococcus anophagefferens virus (AaV), Bodo saltans virus (BsV), Chrysochromulina ericina virus (CeV), and Phaeocystis pouchetii virus (PpV), which infect phytoplanktonic protists, as well as a giant virus of microzooplanktonic species, the Cafeteria roenbergensis virus (CroV). The review focuses on the major differences between these viruses and typical objects of current virology, their importance for understanding the evolutionary processes of genomes, genes, proteins, the biosynthetic and defense systems of organisms, as well as the important role of GV in regulating the aquatic microorganisms abundance and species diversity, carbon transfer and nutrient recycling in marine and freshwater reservoirs. Writing this review was motivated by the intention to inspire the interest of scientists in studying viruses as the most widespread biological creatures on Earth and ubiquitous symbiotic partners of all three domains of life.
Fells, Alicja; Jiang, Xiaodie; Jankowska, Katarzyna; Łukomska-Kowalczyk, Maja; Milanowski, Rafał; Wang, Quanxi; Zakryś, Bożena
In: TAXON, vol. 72, no. 4, pp. 733-750, 2023.
@article{https://doi.org/10.1002/tax.12937,
title = {Molecular and morphological delimitation of species in Strombomonas (Euglenaceae) including a protocol for DNA isolation utilising a chelating resin},
author = {Alicja Fells and Xiaodie Jiang and Katarzyna Jankowska and Maja Łukomska-Kowalczyk and Rafał Milanowski and Quanxi Wang and Bożena Zakryś},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/tax.12937},
doi = {https://doi.org/10.1002/tax.12937},
year = {2023},
date = {2023-08-11},
urldate = {2023-01-01},
journal = {TAXON},
volume = {72},
number = {4},
pages = {733-750},
abstract = {Abstract Although Strombomonas verrucosa has been the type of the genus name for almost 100 years, its lack of clear diagnostic traits has rendered morphological distinction from its congeners almost impossible. As such, a study was conducted combining previously unused morphological data (chloroplast characters) with molecular data (sequences of nuclear SSU, LSU and plastid-encoded SSU rDNA) and extensive literature review. The study focused on environmental samples obtained from Poland and China and resulted in 51 new sequences representing three molecular markers (17 nSSU, 16 nLSU and 18 cpSSU rDNA). Revised delimitations of the genus Strombomonas and its type S. verrucosa are presented that include new and detailed diagnostic characters. In addition to the type, we recognize nine species: S. acuminata, S. borystheniensis, S. eurystoma, S. fluviatilis, S. gibberosa, S. maxima, S. ovalis, S. schauinslandii, S. triquetra. Three of these are incorporated into a phylogeny for the first time (S. fluviatilis, S. gibberosa, S. schauinslandii). To improve the efficiency of DNA isolation from loricate cells, a protocol utilising a chelating resin for DNA isolation – following the lead of diatomologists – has been adjusted for Euglenaceae and is also presented.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract Although Strombomonas verrucosa has been the type of the genus name for almost 100 years, its lack of clear diagnostic traits has rendered morphological distinction from its congeners almost impossible. As such, a study was conducted combining previously unused morphological data (chloroplast characters) with molecular data (sequences of nuclear SSU, LSU and plastid-encoded SSU rDNA) and extensive literature review. The study focused on environmental samples obtained from Poland and China and resulted in 51 new sequences representing three molecular markers (17 nSSU, 16 nLSU and 18 cpSSU rDNA). Revised delimitations of the genus Strombomonas and its type S. verrucosa are presented that include new and detailed diagnostic characters. In addition to the type, we recognize nine species: S. acuminata, S. borystheniensis, S. eurystoma, S. fluviatilis, S. gibberosa, S. maxima, S. ovalis, S. schauinslandii, S. triquetra. Three of these are incorporated into a phylogeny for the first time (S. fluviatilis, S. gibberosa, S. schauinslandii). To improve the efficiency of DNA isolation from loricate cells, a protocol utilising a chelating resin for DNA isolation – following the lead of diatomologists – has been adjusted for Euglenaceae and is also presented.
Žliobaitė, Indrė; Fortelius, Mikael; Bernor, Raymond L.; Ostende, Lars W. Hoek; Janis, Christine M.; Lintulaakso, Kari; Säilä, Laura K.; Werdelin, Lars; Casanovas-Vilar, Isaac; Croft, Darin A.; Flynn, Lawrence J.; Hopkins, Samantha S. B.; Kaakinen, Anu; Kordos, László; Kostopoulos, Dimitris S.; Pandolfi, Luca; Rowan, John; Tesakov, Alexey; Vislobokova, Innessa; Zhang, Zhaoqun; Aiglstorfer, Manuela; Alba, David M.; Arnal, Michelle; Antoine, Pierre-Olivier; Belmaker, Miriam; Bilgin, Melike; Boisserie, Jean-Renaud; Borths, Matthew R.; Cooke, Siobhán B.; Dam, Jan A.; Delson, Eric; Eronen, Jussi T.; Fox, David; Friscia, Anthony R.; Furió, Marc; Giaourtsakis, Ioannis X.; Holbrook, Luke; Hunter, John; López-Torres, Sergi; Ludtke, Joshua; Minwer-Barakat, Raef; Made, Jan; Mennecart, Bastien; Pushkina, Diana; Rook, Lorenzo; Saarinen, Juha; Samuels, Joshua X.; Sanders, William; Silcox, Mary T.; Vepsäläinen, Jouni
The NOW Database of Fossil Mammals Book Chapter
In: Casanovas-Vilar, Isaac; Ostende, Lars W. Hoek; Janis, Christine M.; Saarinen, Juha (Ed.): Evolution of Cenozoic Land Mammal Faunas and Ecosystems: 25 Years of the NOW Database of Fossil Mammals, pp. 33–42, Springer International Publishing, Cham, 2023, ISBN: 978-3-031-17491-9.
@inbook{Žliobaitė2023,
title = {The NOW Database of Fossil Mammals},
author = {Indrė Žliobaitė and Mikael Fortelius and Raymond L. Bernor and Lars W. Hoek Ostende and Christine M. Janis and Kari Lintulaakso and Laura K. Säilä and Lars Werdelin and Isaac Casanovas-Vilar and Darin A. Croft and Lawrence J. Flynn and Samantha S. B. Hopkins and Anu Kaakinen and László Kordos and Dimitris S. Kostopoulos and Luca Pandolfi and John Rowan and Alexey Tesakov and Innessa Vislobokova and Zhaoqun Zhang and Manuela Aiglstorfer and David M. Alba and Michelle Arnal and Pierre-Olivier Antoine and Miriam Belmaker and Melike Bilgin and Jean-Renaud Boisserie and Matthew R. Borths and Siobhán B. Cooke and Jan A. Dam and Eric Delson and Jussi T. Eronen and David Fox and Anthony R. Friscia and Marc Furió and Ioannis X. Giaourtsakis and Luke Holbrook and John Hunter and Sergi López-Torres and Joshua Ludtke and Raef Minwer-Barakat and Jan Made and Bastien Mennecart and Diana Pushkina and Lorenzo Rook and Juha Saarinen and Joshua X. Samuels and William Sanders and Mary T. Silcox and Jouni Vepsäläinen},
editor = {Isaac Casanovas-Vilar and Lars W. Hoek Ostende and Christine M. Janis and Juha Saarinen},
url = {https://doi.org/10.1007/978-3-031-17491-9_3},
doi = {10.1007/978-3-031-17491-9_3},
isbn = {978-3-031-17491-9},
year = {2023},
date = {2023-08-09},
urldate = {2023-01-01},
booktitle = {Evolution of Cenozoic Land Mammal Faunas and Ecosystems: 25 Years of the NOW Database of Fossil Mammals},
pages = {33–42},
publisher = {Springer International Publishing},
address = {Cham},
abstract = {NOW (New and Old Worlds) is a global database of fossil mammal occurrences, currently containing around 68,000 locality-species entries. The database spans the last 66 million years, with its primary focus on the last 23 million years. Whereas the database contains recordsNOW Databaserecords from all continents, the main focus and coverage of the database historically has been on Eurasia. The database includes primarily, but not exclusively, terrestrial mammals. It covers a large part of the currently known mammalian fossil record, focusing on classical and actively researched fossil localities. The database is managed in collaboration with an international advisory board of experts. Rather than a static archive, it emphasizes the continuous integration of new knowledge of the communityNOW Databasedatacuration in, data curationDatacuration, and consistencyNOW Databaseconsistency of scientific interpretations. The database records species occurrences at localities worldwide, as well as ecologicalEcological characteristics of fossil species, geological contextsGeologic/geologicalcontext of localities and more. The NOW database is primarily used for two purposes: (1) queries about occurrences of particular taxa, their characteristics and properties of localities in the spirit of an encyclopedia; and (2) large scale research and quantitative analyses of evolutionary processes, patterns, reconstructing past environments, as well as interpreting evolutionary contexts. The data are fully open, no logging in or community membership is necessary for using the data for any purpose.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
NOW (New and Old Worlds) is a global database of fossil mammal occurrences, currently containing around 68,000 locality-species entries. The database spans the last 66 million years, with its primary focus on the last 23 million years. Whereas the database contains recordsNOW Databaserecords from all continents, the main focus and coverage of the database historically has been on Eurasia. The database includes primarily, but not exclusively, terrestrial mammals. It covers a large part of the currently known mammalian fossil record, focusing on classical and actively researched fossil localities. The database is managed in collaboration with an international advisory board of experts. Rather than a static archive, it emphasizes the continuous integration of new knowledge of the communityNOW Databasedatacuration in, data curationDatacuration, and consistencyNOW Databaseconsistency of scientific interpretations. The database records species occurrences at localities worldwide, as well as ecologicalEcological characteristics of fossil species, geological contextsGeologic/geologicalcontext of localities and more. The NOW database is primarily used for two purposes: (1) queries about occurrences of particular taxa, their characteristics and properties of localities in the spirit of an encyclopedia; and (2) large scale research and quantitative analyses of evolutionary processes, patterns, reconstructing past environments, as well as interpreting evolutionary contexts. The data are fully open, no logging in or community membership is necessary for using the data for any purpose.
Szczygielski, Tomasz; Piechowski, Rafał
Limb anatomy of the Triassic turtles: appendicular osteology of Proterochersis (Testudinata, Proterochersidae) Journal Article
In: Zoological Journal of the Linnean Society, pp. zlad057, 2023, ISSN: 0024-4082.
@article{10.1093/zoolinnean/zlad057,
title = {Limb anatomy of the Triassic turtles: appendicular osteology of Proterochersis (Testudinata, Proterochersidae)},
author = {Tomasz Szczygielski and Rafał Piechowski},
url = {https://doi.org/10.1093/zoolinnean/zlad057},
doi = {10.1093/zoolinnean/zlad057},
issn = {0024-4082},
year = {2023},
date = {2023-07-25},
urldate = {2023-01-01},
journal = {Zoological Journal of the Linnean Society},
pages = {zlad057},
abstract = {The turtle locomotor system is heavily modified owing to the severe impact of development of the shell on the body plan of these reptiles. Although limb and girdle osteology of the earliest, Triassic turtles is relatively well understood in general, the exact impacts of variability, ontogeny and preservation (e.g. deformation) on the observed morphologies have rarely been considered in detail. Here, we describe in detail and document the osteology and intraspecific variability of the limbs and girdles of Proterochersis spp., the basalmost true turtles (Testudinata). We also provide a synthesis of currently available data and detailed comparisons with other Triassic stem turtles to gain a better understanding of the diagnostic value of the early turtle appendicular skeleton and to pave the way for future biomechanical and functional studies. Our data suggest that Proterochersis spp. could be at least partly aquatic and could change their preferred habitat during ontogeny, with larger (and, presumably, older) specimens presenting more characters suggestive of a more terrestrial environment.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The turtle locomotor system is heavily modified owing to the severe impact of development of the shell on the body plan of these reptiles. Although limb and girdle osteology of the earliest, Triassic turtles is relatively well understood in general, the exact impacts of variability, ontogeny and preservation (e.g. deformation) on the observed morphologies have rarely been considered in detail. Here, we describe in detail and document the osteology and intraspecific variability of the limbs and girdles of Proterochersis spp., the basalmost true turtles (Testudinata). We also provide a synthesis of currently available data and detailed comparisons with other Triassic stem turtles to gain a better understanding of the diagnostic value of the early turtle appendicular skeleton and to pave the way for future biomechanical and functional studies. Our data suggest that Proterochersis spp. could be at least partly aquatic and could change their preferred habitat during ontogeny, with larger (and, presumably, older) specimens presenting more characters suggestive of a more terrestrial environment.
Gryganskyi, Andrii P.; Golan, Jacob; Muszewska, Anna; Idnurm, Alexander; Dolatabadi, Somayeh; Mondo, Stephen J.; Kutovenko, Vira B.; Kutovenko, Volodymyr O.; Gajdeczka, Michael T.; Anishchenko, Iryna M.; Pawlowska, Julia; Tran, Ngoc Vinh; Ebersberger, Ingo; Voigt, Kerstin; Wang, Yan; Chang, Ying; Pawlowska, Teresa E.; Heitman, Joseph; Vilgalys, Rytas; Bonito, Gregory; Benny, Gerald L.; Smith, Matthew E.; Reynolds, Nicole; James, Timothy Y.; Grigoriev, Igor V.; Spatafora, Joseph W.; Stajich, Jason E.
Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? Journal Article
In: Microorganisms, vol. 11(7), pp. 1830, 2023.
@article{Gryganskyi2023,
title = {Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?},
author = {Andrii P. Gryganskyi and Jacob Golan and Anna Muszewska and Alexander Idnurm and Somayeh Dolatabadi and Stephen J. Mondo and Vira B. Kutovenko and Volodymyr O. Kutovenko and Michael T. Gajdeczka and Iryna M. Anishchenko and Julia Pawlowska and Ngoc Vinh Tran and Ingo Ebersberger and Kerstin Voigt and Yan Wang and Ying Chang and Teresa E. Pawlowska and Joseph Heitman and Rytas Vilgalys and Gregory Bonito and Gerald L. Benny and Matthew E. Smith and Nicole Reynolds and Timothy Y. James and Igor V. Grigoriev and Joseph W. Spatafora and Jason E. Stajich},
url = {https://www.mdpi.com/2076-2607/11/7/1830},
doi = {https://doi.org/10.3390/microorganisms11071830 },
year = {2023},
date = {2023-07-18},
urldate = {2023-07-18},
journal = {Microorganisms},
volume = {11(7)},
pages = {1830},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nätscher, Paulina S.; Gliwa, Jana; De Baets, Kenneth; Ghaderi, Abbas; Korn, Dieter
Exceptions to the temperature–size rule: no Lilliput Effect in end-Permian ostracods (Crustacea) from Aras Valley (northwest Iran) Journal Article
In: Palaeontology, vol. 66, no. 4, pp. e12667, 2023.
@article{https://doi.org/10.1111/pala.12667,
title = {Exceptions to the temperature–size rule: no Lilliput Effect in end-Permian ostracods (Crustacea) from Aras Valley (northwest Iran)},
author = {Paulina S. Nätscher and Jana Gliwa and De Baets, Kenneth and Abbas Ghaderi and Dieter Korn},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pala.12667},
doi = {https://doi.org/10.1111/pala.12667},
year = {2023},
date = {2023-07-11},
urldate = {2023-01-01},
journal = {Palaeontology},
volume = {66},
number = {4},
pages = {e12667},
abstract = {Abstract The body size of marine ectotherms is often negatively correlated with ambient water temperature, as seen in many clades during the hyperthermal crisis of the end-Permian mass extinction (c. 252 Ma). However, in the case of ostracods, size changes during ancient hyperthermal events are rarely quantified. In this study, we evaluate the body size changes of ostracods in the Aras Valley section (northwest Iran) in response to the drastic warming during the end-Permian mass extinction at three taxonomic levels: class, order, species. At the assemblage level, the warming triggers a complete species turnover in the Aras Valley section, with larger, newly emerging species dominating the immediate post-extinction assemblage for a short time. Individual ostracod species and instars do not show dwarfing or a change in body size as an adaptation to the temperature stress during the end-Permian crisis. This may indicate that the ostracods in the Aras Valley section might have been exceptions to the temperature–size rule (TSR), using an adaptation mechanism that does not involve a decrease in body size. This adaptation might be similar to the accelerated development despite constant instar body sizes that can be observed in some recent experimental studies of ostracod responses to thermal stress.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract The body size of marine ectotherms is often negatively correlated with ambient water temperature, as seen in many clades during the hyperthermal crisis of the end-Permian mass extinction (c. 252 Ma). However, in the case of ostracods, size changes during ancient hyperthermal events are rarely quantified. In this study, we evaluate the body size changes of ostracods in the Aras Valley section (northwest Iran) in response to the drastic warming during the end-Permian mass extinction at three taxonomic levels: class, order, species. At the assemblage level, the warming triggers a complete species turnover in the Aras Valley section, with larger, newly emerging species dominating the immediate post-extinction assemblage for a short time. Individual ostracod species and instars do not show dwarfing or a change in body size as an adaptation to the temperature stress during the end-Permian crisis. This may indicate that the ostracods in the Aras Valley section might have been exceptions to the temperature–size rule (TSR), using an adaptation mechanism that does not involve a decrease in body size. This adaptation might be similar to the accelerated development despite constant instar body sizes that can be observed in some recent experimental studies of ostracod responses to thermal stress.
Allaire, Ninon; Ginot, Samuel; De Baets, Kenneth; Korn, Dieter; Goudemand, Nicolas; Monnet, Claude; Crônier, Catherine
Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry Journal Article
In: Acta Palaeontologica Polonica, vol. 68, no. 2, pp. 193–212, 2023.
@article{allaire2023morphological,
title = {Morphological disparity of early ammonoids: A geometric morphometric approach to investigate conch geometry},
author = {Ninon Allaire and Samuel Ginot and De Baets, Kenneth and Dieter Korn and Nicolas Goudemand and Claude Monnet and Catherine Crônier},
url = {https://www.app.pan.pl/article/item/app010332022.html},
doi = {10.4202/app.01033.2022},
year = {2023},
date = {2023-07-03},
urldate = {2023-07-03},
journal = {Acta Palaeontologica Polonica},
volume = {68},
number = {2},
pages = {193–212},
abstract = {Fossils of Devonian ammonoids are abundant and well-preserved in the Anti-Atlas of Morocco; as such they provide an invaluable record of regional morphological disparity changes (diversity of shapes) that characterise the first steps of ammonoid evolution. However, they were rarely analysed quantitatively with respect to their morphological spectrum. Here, we investigated the morphological disparity of the Early–Middle Devonian ammonoids of the Moroccan Anti- Atlas by analysing the shape of their whorl profile. A geometric morphometric approach based on the acquisition of outline semilandmark coordinates was used to analyse the whorl profiles. For comparison, morphometric ratios based on classical conch measurements were also analysed to investigate the overall conch geometry. Several standard disparity estimators were computed to measure different aspects of morphological disparity fluctuations through time. It appears that a major increase in disparity occurred throughout the Early Devonian, followed by fluctuating disparity during the Middle Devonian constituting a general decreasing trend. Only the end-Eifelian Kačák Event shows a significant decrease in disparity. Thus, the ammonoids explored the range of possible shapes fairly quickly during their initial radiation; however, we found no evidence for an early burst of shape diversity (i.e., the rise does not exceed the expectations given diversity). Nevertheless, correlation tests between diversity and disparity time series support that they are partially decoupled. The highly resolved biozone record highlights that the increase in disparity began earlier than the increase in diversity that characterises the late Emsian.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fossils of Devonian ammonoids are abundant and well-preserved in the Anti-Atlas of Morocco; as such they provide an invaluable record of regional morphological disparity changes (diversity of shapes) that characterise the first steps of ammonoid evolution. However, they were rarely analysed quantitatively with respect to their morphological spectrum. Here, we investigated the morphological disparity of the Early–Middle Devonian ammonoids of the Moroccan Anti- Atlas by analysing the shape of their whorl profile. A geometric morphometric approach based on the acquisition of outline semilandmark coordinates was used to analyse the whorl profiles. For comparison, morphometric ratios based on classical conch measurements were also analysed to investigate the overall conch geometry. Several standard disparity estimators were computed to measure different aspects of morphological disparity fluctuations through time. It appears that a major increase in disparity occurred throughout the Early Devonian, followed by fluctuating disparity during the Middle Devonian constituting a general decreasing trend. Only the end-Eifelian Kačák Event shows a significant decrease in disparity. Thus, the ammonoids explored the range of possible shapes fairly quickly during their initial radiation; however, we found no evidence for an early burst of shape diversity (i.e., the rise does not exceed the expectations given diversity). Nevertheless, correlation tests between diversity and disparity time series support that they are partially decoupled. The highly resolved biozone record highlights that the increase in disparity began earlier than the increase in diversity that characterises the late Emsian.
P.W., Crous; Osieck, E. R.; Shivas, R. G.; Tan, Y. P.; Bishop-Hurley, S. L.; Esteve-Raventós, F.; Larsson, E.; Luangsa-ard, J. J.; Pancorbo, F.; Balashov, S.; Baseia, I. G.; Boekhout, T.; Chandranayaka, S.; Cowan, D. A.; Cruz, R. H. S. F.; Czachura, P.; De la Peña-Lastra, S.; Dovana, F.; Drury, B.; Fell, J.; Flakus, A.; Fotedar, R.; Jurjević, Ž.; Kolecka, A.; Mack, J.; Maggs-Kölling, G.; Mahadevakumar, S.; Mateos, A.; Mongkolsamrit, S.; Noisripoom, W.; Plaza, M.; Overy, D. P.; Piątek, M.; Sandoval-Denis, M.; Vauras, J.; Wingfield, M. J.; Abell, S. E.; Ahmadpour, A.; Akulov, A.; Alavi, F.; Alavi, Z.; Altes, A.; Alvarado, P.; Anand, G.; Ashtekar, N.; Assyov, B.; Banc-Prandi, G.; Barbosa, K. D.; Barreto, G. G.; Bellanger, J. -M.; Bezerra, J. L.; Bhat, D. J.; Bilanski, P.; Bose, T.; Bozok, F.; Chaves, J.; Costa-Rezende, D. H.; Danteswari, C.; Darmostuk, V.; Delgado, G.; Denman, S.; Eichmeier, A.; Etayo, J.; Eyssartier, G.; Faulwetter, S.; Ganga, K. G. G.; Ghosta, Y.; Goh, J.; Góis, J. S.; Gramaje, D.; Granit, L.; Groenewald, M.; Gulden, G.; Gusmão, L. F. P.; Hammerbacher, A.; Heidarian, Z.; Hywel-Jones, N.; Jankowiak, R.; Kaliyaperumal, M.; Kaygusuz, O.; Kezo, K.; Khonsanit, A.; Kumar, S.; Kuo, C. H.; Læssøe, T.; Latha, K. P. D.; Loizides, M.; Luo, S. M.; Maciá-Vicente, J. G.; Manimohan, P.; Marbach, P. A. S.; Marinho, P.; Marney, T. S.; Marques, G.; Martín, M. P.; Miller, A. N.; Mondello, F.; Moreno, G.; Mufeeda, K. T.; Mun, H. Y.; Nau, T.; Nkomo, T.; Okrasińska, A.; Oliveira, J. P. A. F.; Oliveira, R. L.; Ortiz, D. A.; Pawłowska, J.; Pérez-De-Gregorio, M. À.; Podile, A. R.; Portugal, A.; Privitera, N.; Rajeshkumar, K. C.; Rauf, I.; Rian, B.; Rigueiro-Rodríguez, A.; Rivas-Torres, G. F.; Rodriguez-Flakus, P.; Romero-Gordillo, M.; Saar, I.; Saba, M.; Santos, C. D.; Sarma, P. V. S. R. N.; Siquier, J. L.; Sleiman, S.; Spetik, M.; Sridhar, K. R.; Stryjak-Bogacka, M.; Szczepańska, K.; Taşkın, H.; Tennakoon, D. S.; Thanakitpipattana, D.; Trovao, J.; Türkekul, İ.; van Iperen, A. L.; van 't Hof, P.; Vasquez, G.; Visagie, C. M.; Wingfield, B. D.; Wong, P. T. W.; Yang, W. X.; Yarar, M.; Yarden, O.; Yilmaz, N.; Zhang, N.; Zhu, Y. N.; Groenewald, J. Z.
Fungal Planet description sheets: 1478–1549 Journal Article
In: Persoonia - Molecular Phylogeny and Evolution of Fungi, vol. 50, pp. 158-310, 2023.
@article{CrousEtAl2023,
title = {Fungal Planet description sheets: 1478–1549},
author = {Crous P.W. and Osieck, E.R. and Shivas, R.G. and Tan, Y.P. and Bishop-Hurley, S.L. and Esteve-Raventós, F. and Larsson, E. and Luangsa-ard, J.J. and Pancorbo, F. and Balashov, S. and Baseia, I.G. and Boekhout, T. and Chandranayaka, S. and Cowan, D.A. and Cruz, R.H.S.F. and Czachura, P. and De la Peña-Lastra, S. and Dovana, F. and Drury, B. and Fell, J. and Flakus, A. and Fotedar, R. and Jurjević, Ž. and Kolecka, A. and Mack, J. and Maggs-Kölling, G. and Mahadevakumar, S. and Mateos, A. and Mongkolsamrit, S. and Noisripoom, W. and Plaza, M. and Overy, D.P. and Piątek, M. and Sandoval-Denis, M. and Vauras, J. and Wingfield, M.J. and Abell, S.E. and Ahmadpour, A. and Akulov, A. and Alavi, F. and Alavi, Z. and Altes, A. and Alvarado, P. and Anand, G. and Ashtekar, N. and Assyov, B. and Banc-Prandi, G. and Barbosa, K.D. and Barreto, G.G. and Bellanger, J.-M. and Bezerra, J.L. and Bhat, D.J. and Bilanski, P. and Bose, T. and Bozok, F. and Chaves, J. and Costa-Rezende, D.H. and Danteswari, C. and Darmostuk, V. and Delgado, G. and Denman, S. and Eichmeier, A. and Etayo, J. and Eyssartier, G. and Faulwetter, S. and Ganga, K.G.G. and Ghosta, Y. and Goh, J. and Góis, J.S. and Gramaje, D. and Granit, L. and Groenewald, M. and Gulden, G. and Gusmão, L.F.P. and Hammerbacher, A. and Heidarian, Z. and Hywel-Jones, N. and Jankowiak, R. and Kaliyaperumal, M. and Kaygusuz, O. and Kezo, K. and Khonsanit, A. and Kumar, S. and Kuo, C.H. and Læssøe, T. and Latha, K.P.D. and Loizides, M. and Luo, S.M. and Maciá-Vicente, J.G. and Manimohan, P. and Marbach, P.A.S. and Marinho, P. and Marney, T.S. and Marques, G. and Martín, M.P. and Miller, A.N. and Mondello, F. and Moreno, G. and Mufeeda, K.T. and Mun, H.Y. and Nau, T. and Nkomo, T. and Okrasińska, A. and Oliveira, J.P.A.F. and Oliveira, R.L. and Ortiz, D.A. and Pawłowska, J. and Pérez-De-Gregorio, M.À. and Podile, A.R. and Portugal, A. and Privitera, N. and Rajeshkumar, K.C. and Rauf, I. and Rian, B. and Rigueiro-Rodríguez, A. and Rivas-Torres, G.F. and Rodriguez-Flakus, P. and Romero-Gordillo, M. and Saar, I. and Saba, M. and Santos, C.D. and Sarma, P.V.S.R.N. and Siquier, J.L. and Sleiman, S. and Spetik, M. and Sridhar, K.R. and Stryjak-Bogacka, M. and Szczepańska, K. and Taşkın, H. and Tennakoon, D.S. and Thanakitpipattana, D. and Trovao, J. and Türkekul, İ. and van Iperen, A.L. and van 't Hof, P. and Vasquez, G. and Visagie, C.M. and Wingfield, B.D. and Wong, P.T.W. and Yang, W.X. and Yarar, M. and Yarden, O. and Yilmaz, N. and Zhang, N. and Zhu, Y.N. and Groenewald, J.Z.},
url = {https://www.ingentaconnect.com/content/nhn/pimj/pre-prints/content-nbc-persoonia-0661#},
doi = {https://doi.org/10.3767/persoonia.2023.50.05},
year = {2023},
date = {2023-07-03},
urldate = {2023-07-03},
journal = {Persoonia - Molecular Phylogeny and Evolution of Fungi},
volume = {50},
pages = {158-310},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
De Baets, Kenneth; Vanadzina, Karina; Schiffbauer, James
Parasitic Relationships: Trapped in time Journal Article
In: eLife, vol. 12, pp. e90008, 2023, ISSN: 2050-084X.
@article{10.7554/eLife.90008,
title = {Parasitic Relationships: Trapped in time},
author = {De Baets, Kenneth and Karina Vanadzina and James Schiffbauer},
url = {https://doi.org/10.7554/eLife.90008},
doi = {10.7554/eLife.90008},
issn = {2050-084X},
year = {2023},
date = {2023-07-01},
urldate = {2023-07-01},
journal = {eLife},
volume = {12},
pages = {e90008},
publisher = {eLife Sciences Publications, Ltd},
abstract = {Analysis of specimens preserved in amber from the Cretaceous period suggests that nematodes changed their host preference towards insects with a complete metamorphosis more recently.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Analysis of specimens preserved in amber from the Cretaceous period suggests that nematodes changed their host preference towards insects with a complete metamorphosis more recently.
Czepiński, Łukasz
Skull of a dromaeosaurid Shri devi from the Upper Cretaceous of the Gobi Desert suggests convergence to the North American forms Journal Article
In: Acta Palaeontologica Polonica, vol. 68, 2023.
@article{Czepiński_2023,
title = {Skull of a dromaeosaurid Shri devi from the Upper Cretaceous of the Gobi Desert suggests convergence to the North American forms},
author = {Łukasz Czepiński},
doi = {10.4202/app.01065.2023},
year = {2023},
date = {2023-06-21},
urldate = {2023-06-21},
journal = {Acta Palaeontologica Polonica},
volume = {68},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jagielska, Maria; Hałakuc, Paweł; Płecha, Magdalena; Milanowski, Rafał
Mitochondrial genomes – unity and diversity Journal Article
In: Postępy Biochemii, vol. 69, no. 2, pp. 113-121, 2023.
@article{Jagielska23_1,
title = {Mitochondrial genomes – unity and diversity},
author = {Maria Jagielska and Paweł Hałakuc and Magdalena Płecha and Rafał Milanowski},
url = {https://postepybiochemii.ptbioch.edu.pl/index.php/PB/article/view/486},
doi = {10.18388/pb.2021_486 },
year = {2023},
date = {2023-06-19},
journal = {Postępy Biochemii},
volume = {69},
number = {2},
pages = {113-121},
abstract = {The emergence of mitochondria was one of the most important events in the history of life on Earth. The engulfed bacterial cell, transformed into a mitochondrion, retained its genome, which then underwent numerous modifications. Through massive loss and numerous gene trans-fers into the nuclear genome, the autonomous bacterium eventually evolved into the organelle we know today. As a result of changes taking place independently in different evolutionary lineages, we observe a great diversity of mitochondrial genomes with respect to structure and gene content. In most cases, mitochondrial DNA has a circular shape, but linear molecules of mitochondrial DNA are also observed in some eukaryotes. In extreme cases, such as in reduced mitochondrial-derived organelles, the genome has been completely lost. In this article, we discuss the diversity of mitochondrial genome structures within the largest groups of Eukarya.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The emergence of mitochondria was one of the most important events in the history of life on Earth. The engulfed bacterial cell, transformed into a mitochondrion, retained its genome, which then underwent numerous modifications. Through massive loss and numerous gene trans-fers into the nuclear genome, the autonomous bacterium eventually evolved into the organelle we know today. As a result of changes taking place independently in different evolutionary lineages, we observe a great diversity of mitochondrial genomes with respect to structure and gene content. In most cases, mitochondrial DNA has a circular shape, but linear molecules of mitochondrial DNA are also observed in some eukaryotes. In extreme cases, such as in reduced mitochondrial-derived organelles, the genome has been completely lost. In this article, we discuss the diversity of mitochondrial genome structures within the largest groups of Eukarya.
Vinn, Olev; De Baets, Kenneth; Isakar, Mare; Toom, Ursula
Parasite-induced shell damage in brachiopod Porambonites (Porambonites) laticaudata from the Late Ordovician (Sandbian) of Estonia Journal Article
In: Estonian Journal of Earth Sciences, vol. 72, no. 1, pp. 110–113, 2023.
@article{vinn2023parasite,
title = {Parasite-induced shell damage in brachiopod Porambonites (Porambonites) laticaudata from the Late Ordovician (Sandbian) of Estonia},
author = {Vinn, Olev and De Baets, Kenneth and Isakar, Mare and Toom, Ursula },
url = {https://kirj.ee/wp-content/plugins/kirj/pub/earth-1-2023-110-113_20230610122825.pdf},
year = {2023},
date = {2023-06-14},
urldate = {2023-06-14},
journal = {Estonian Journal of Earth Sciences},
volume = {72},
number = {1},
pages = {110–113},
abstract = {A new type of shell damage has been described in Ordovician brachiopods in Porambonites (Porambonites) laticaudata. There is a pair of small pits with somewhat different outline in the shell surface at the anterior commissure of the brachiopod. These pits are oriented in lateral direction, about 40o from the direction of the sulcus on the anterior commissure. Previously known shell damage has resulted from failed predatory attacks by durophagous predators and differ from the shell damage in P. (P.) laticaudata. The pits in the shell margin are most likely the result of shell malformation caused by the presence of symbionts. It is plausible that the symbionts of the P. (P.) laticaudata benefitted from inhalant currents and were cleptoparasites. The symbionts caused damage to the host brachiopod, which also suggests a parasitic relationship.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A new type of shell damage has been described in Ordovician brachiopods in Porambonites (Porambonites) laticaudata. There is a pair of small pits with somewhat different outline in the shell surface at the anterior commissure of the brachiopod. These pits are oriented in lateral direction, about 40o from the direction of the sulcus on the anterior commissure. Previously known shell damage has resulted from failed predatory attacks by durophagous predators and differ from the shell damage in P. (P.) laticaudata. The pits in the shell margin are most likely the result of shell malformation caused by the presence of symbionts. It is plausible that the symbionts of the P. (P.) laticaudata benefitted from inhalant currents and were cleptoparasites. The symbionts caused damage to the host brachiopod, which also suggests a parasitic relationship.
Hehenberger, Elisabeth; Boscaro, Vittorio; James, Erick R.; Hirakawa, Yoshihisa; Trznadel, Morelia; Mtawali, Mahara; Fiorito, Rebecca; Campo, Javier; Karnkowska, Anna; Kolisko, Martin; Irwin, Nicholas A. T.; Mathur, Varsha; Scheffrahn, Rudolf H.; Keeling, Patrick J.
In: Journal of Eukaryotic Microbiology, vol. 70, no. 5, pp. e12987, 2023.
@article{Hehenberger2023,
title = {New Parabasalia symbionts Snyderella spp. and Daimonympha gen. nov. from South American Rugitermes termites and the parallel evolution of a cell with a rotating “head”},
author = {Elisabeth Hehenberger and Vittorio Boscaro and Erick R. James and Yoshihisa Hirakawa and Morelia Trznadel and Mahara Mtawali and Rebecca Fiorito and Javier Campo and Anna Karnkowska and Martin Kolisko and Nicholas A. T. Irwin and Varsha Mathur and Rudolf H. Scheffrahn and Patrick J. Keeling},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85162158230&doi=10.1111%2fjeu.12987&partnerID=40&md5=fa6e625d9458584ab89cd3c3f0943aa3},
doi = {10.1111/jeu.12987},
year = {2023},
date = {2023-06-06},
urldate = {2023-01-01},
journal = {Journal of Eukaryotic Microbiology},
volume = {70},
number = {5},
pages = {e12987},
abstract = {Most Parabasalia are symbionts in the hindgut of “lower” (non-Termitidae) termites, where they widely vary in morphology and degree of morphological complexity. Large and complex cells in the class Cristamonadea evolved by replicating a fundamental unit, the karyomastigont, in various ways. We describe here four new species of Calonymphidae (Cristamonadea) from Rugitermes hosts, assigned to the genus Snyderella based on diagnostic features (including the karyomastigont pattern) and molecular phylogeny. We also report a new genus of Calonymphidae, Daimonympha, from Rugitermes laticollis. Daimonympha's morphology does not match that of any known Parabasalia, and its SSU rRNA gene sequence corroborates this distinction. Daimonympha does however share a puzzling feature with a few previously described, but distantly related, Cristamonadea: a rapid, smooth, and continuous rotation of the anterior end of the cell, including the many karyomastigont nuclei. The function of this rotatory movement, the cellular mechanisms enabling it, and the way the cell deals with the consequent cell membrane shear, are all unknown. “Rotating wheel” structures are famously rare in biology, with prokaryotic flagella being the main exception; these mysterious spinning cells found only among Parabasalia are another, far less understood, example.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Most Parabasalia are symbionts in the hindgut of “lower” (non-Termitidae) termites, where they widely vary in morphology and degree of morphological complexity. Large and complex cells in the class Cristamonadea evolved by replicating a fundamental unit, the karyomastigont, in various ways. We describe here four new species of Calonymphidae (Cristamonadea) from Rugitermes hosts, assigned to the genus Snyderella based on diagnostic features (including the karyomastigont pattern) and molecular phylogeny. We also report a new genus of Calonymphidae, Daimonympha, from Rugitermes laticollis. Daimonympha's morphology does not match that of any known Parabasalia, and its SSU rRNA gene sequence corroborates this distinction. Daimonympha does however share a puzzling feature with a few previously described, but distantly related, Cristamonadea: a rapid, smooth, and continuous rotation of the anterior end of the cell, including the many karyomastigont nuclei. The function of this rotatory movement, the cellular mechanisms enabling it, and the way the cell deals with the consequent cell membrane shear, are all unknown. “Rotating wheel” structures are famously rare in biology, with prokaryotic flagella being the main exception; these mysterious spinning cells found only among Parabasalia are another, far less understood, example.
Žárský, Vojtečh; Karnkowska, Anna; Boscaro, Vittorio; Trznadel, Morelia; Whelan, Thomas A.; Hiltunen-Thorén, Markus; Onut-Brännström, Ioana; Abbott, Cathryn L.; Fast, Naomi M.; Burki, Fabien; Keeling, Patrick J.
Contrasting outcomes of genome reduction in mikrocytids and microsporidians Journal Article
In: BMC Biology, vol. 21, pp. 137, 2023.
@article{Žárský2023,
title = {Contrasting outcomes of genome reduction in mikrocytids and microsporidians},
author = {Vojtečh Žárský and Anna Karnkowska and Vittorio Boscaro and Morelia Trznadel and Thomas A. Whelan and Markus Hiltunen-Thorén and Ioana Onut-Brännström and Cathryn L. Abbott and Naomi M. Fast and Fabien Burki and Patrick J. Keeling},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85161033094&doi=10.1186%2fs12915-023-01635-w&partnerID=40&md5=066566bc7a7a1389a8f244241f133482},
doi = {10.1186/s12915-023-01635-w},
year = {2023},
date = {2023-06-06},
urldate = {2023-01-01},
journal = {BMC Biology},
volume = {21},
pages = {137},
abstract = {Background
Intracellular symbionts often undergo genome reduction, losing both coding and non-coding DNA in a process that ultimately produces small, gene-dense genomes with few genes. Among eukaryotes, an extreme example is found in microsporidians, which are anaerobic, obligate intracellular parasites related to fungi that have the smallest nuclear genomes known (except for the relic nucleomorphs of some secondary plastids). Mikrocytids are superficially similar to microsporidians: they are also small, reduced, obligate parasites; however, as they belong to a very different branch of the tree of eukaryotes, the rhizarians, such similarities must have evolved in parallel. Since little genomic data are available from mikrocytids, we assembled a draft genome of the type species, Mikrocytos mackini, and compared the genomic architecture and content of microsporidians and mikrocytids to identify common characteristics of reduction and possible convergent evolution.
Results
At the coarsest level, the genome of M. mackini does not exhibit signs of extreme genome reduction; at 49.7 Mbp with 14,372 genes, the assembly is much larger and gene-rich than those of microsporidians. However, much of the genomic sequence and most (8075) of the protein-coding genes code for transposons, and may not contribute much of functional relevance to the parasite. Indeed, the energy and carbon metabolism of M. mackini share several similarities with those of microsporidians. Overall, the predicted proteome involved in cellular functions is quite reduced and gene sequences are extremely divergent. Microsporidians and mikrocytids also share highly reduced spliceosomes that have retained a strikingly similar subset of proteins despite having reduced independently. In contrast, the spliceosomal introns in mikrocytids are very different from those of microsporidians in that they are numerous, conserved in sequence, and constrained to an exceptionally narrow size range (all 16 or 17 nucleotides long) at the shortest extreme of known intron lengths.
Conclusions
Nuclear genome reduction has taken place many times and has proceeded along different routes in different lineages. Mikrocytids show a mix of similarities and differences with other extreme cases, including uncoupling the actual size of a genome with its functional reduction.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background
Intracellular symbionts often undergo genome reduction, losing both coding and non-coding DNA in a process that ultimately produces small, gene-dense genomes with few genes. Among eukaryotes, an extreme example is found in microsporidians, which are anaerobic, obligate intracellular parasites related to fungi that have the smallest nuclear genomes known (except for the relic nucleomorphs of some secondary plastids). Mikrocytids are superficially similar to microsporidians: they are also small, reduced, obligate parasites; however, as they belong to a very different branch of the tree of eukaryotes, the rhizarians, such similarities must have evolved in parallel. Since little genomic data are available from mikrocytids, we assembled a draft genome of the type species, Mikrocytos mackini, and compared the genomic architecture and content of microsporidians and mikrocytids to identify common characteristics of reduction and possible convergent evolution.
Results
At the coarsest level, the genome of M. mackini does not exhibit signs of extreme genome reduction; at 49.7 Mbp with 14,372 genes, the assembly is much larger and gene-rich than those of microsporidians. However, much of the genomic sequence and most (8075) of the protein-coding genes code for transposons, and may not contribute much of functional relevance to the parasite. Indeed, the energy and carbon metabolism of M. mackini share several similarities with those of microsporidians. Overall, the predicted proteome involved in cellular functions is quite reduced and gene sequences are extremely divergent. Microsporidians and mikrocytids also share highly reduced spliceosomes that have retained a strikingly similar subset of proteins despite having reduced independently. In contrast, the spliceosomal introns in mikrocytids are very different from those of microsporidians in that they are numerous, conserved in sequence, and constrained to an exceptionally narrow size range (all 16 or 17 nucleotides long) at the shortest extreme of known intron lengths.
Conclusions
Nuclear genome reduction has taken place many times and has proceeded along different routes in different lineages. Mikrocytids show a mix of similarities and differences with other extreme cases, including uncoupling the actual size of a genome with its functional reduction.
Intracellular symbionts often undergo genome reduction, losing both coding and non-coding DNA in a process that ultimately produces small, gene-dense genomes with few genes. Among eukaryotes, an extreme example is found in microsporidians, which are anaerobic, obligate intracellular parasites related to fungi that have the smallest nuclear genomes known (except for the relic nucleomorphs of some secondary plastids). Mikrocytids are superficially similar to microsporidians: they are also small, reduced, obligate parasites; however, as they belong to a very different branch of the tree of eukaryotes, the rhizarians, such similarities must have evolved in parallel. Since little genomic data are available from mikrocytids, we assembled a draft genome of the type species, Mikrocytos mackini, and compared the genomic architecture and content of microsporidians and mikrocytids to identify common characteristics of reduction and possible convergent evolution.
Results
At the coarsest level, the genome of M. mackini does not exhibit signs of extreme genome reduction; at 49.7 Mbp with 14,372 genes, the assembly is much larger and gene-rich than those of microsporidians. However, much of the genomic sequence and most (8075) of the protein-coding genes code for transposons, and may not contribute much of functional relevance to the parasite. Indeed, the energy and carbon metabolism of M. mackini share several similarities with those of microsporidians. Overall, the predicted proteome involved in cellular functions is quite reduced and gene sequences are extremely divergent. Microsporidians and mikrocytids also share highly reduced spliceosomes that have retained a strikingly similar subset of proteins despite having reduced independently. In contrast, the spliceosomal introns in mikrocytids are very different from those of microsporidians in that they are numerous, conserved in sequence, and constrained to an exceptionally narrow size range (all 16 or 17 nucleotides long) at the shortest extreme of known intron lengths.
Conclusions
Nuclear genome reduction has taken place many times and has proceeded along different routes in different lineages. Mikrocytids show a mix of similarities and differences with other extreme cases, including uncoupling the actual size of a genome with its functional reduction.
López-Torres, Sergi; Bertrand, Ornella C.; Lang, Madlen M.; Fostowicz-Frelik, Łucja; Silcox, Mary T.; Meng, Jin
Cranial endocast of Anagale gobiensis (Anagalidae) and its implications for early brain evolution in Euarchontoglires Journal Article
In: Palaeontology, vol. 66, no. 3, pp. e12650, 2023.
@article{https://doi.org/10.1111/pala.12650,
title = {Cranial endocast of Anagale gobiensis (Anagalidae) and its implications for early brain evolution in Euarchontoglires},
author = {Sergi López-Torres and Ornella C. Bertrand and Madlen M. Lang and Łucja Fostowicz-Frelik and Mary T. Silcox and Jin Meng},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pala.12650},
doi = {https://doi.org/10.1111/pala.12650},
year = {2023},
date = {2023-06-01},
urldate = {2023-06-01},
journal = {Palaeontology},
volume = {66},
number = {3},
pages = {e12650},
abstract = {Abstract Anagalids are an extinct group of primitive mammals from the Asian Palaeogene thought to be possible basal members of Glires. Anagalid material is rare, with only a handful of crania known. Here we describe the first virtual endocast of an anagalid, based on the holotype of Anagale gobiensis (AMNH 26079; late Eocene, China), which allows for comparison with published endocasts from fossil members of modern euarchontogliran lineages (i.e. primates, rodents, lagomorphs). The endocast displays traits often observed in fossorial mammals, such as relatively small petrosal lobules and a low neocortical ratio, which would be consistent with previous inferences about use of subterranean food sources based on heavy dental wear. In fact, Anagale gobiensis has the lowest neocortical ratio yet recorded for a euarchontogliran. This species was olfaction-driven, based on the relatively large olfactory bulbs and laterally expansive palaeocortex. The endocast supports previous inferences that relatively large olfactory bulbs, partial midbrain exposure and low encephalization quotient are ancestral for Euarchontoglires, although the likely fossorial adaptations of Anagale gobiensis may also partly explain these traits. While Anagale gobiensis is a primitive mammal in many aspects, some of its derived endocranial traits point towards a new, different trajectory of brain evolution within Euarchontoglires.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract Anagalids are an extinct group of primitive mammals from the Asian Palaeogene thought to be possible basal members of Glires. Anagalid material is rare, with only a handful of crania known. Here we describe the first virtual endocast of an anagalid, based on the holotype of Anagale gobiensis (AMNH 26079; late Eocene, China), which allows for comparison with published endocasts from fossil members of modern euarchontogliran lineages (i.e. primates, rodents, lagomorphs). The endocast displays traits often observed in fossorial mammals, such as relatively small petrosal lobules and a low neocortical ratio, which would be consistent with previous inferences about use of subterranean food sources based on heavy dental wear. In fact, Anagale gobiensis has the lowest neocortical ratio yet recorded for a euarchontogliran. This species was olfaction-driven, based on the relatively large olfactory bulbs and laterally expansive palaeocortex. The endocast supports previous inferences that relatively large olfactory bulbs, partial midbrain exposure and low encephalization quotient are ancestral for Euarchontoglires, although the likely fossorial adaptations of Anagale gobiensis may also partly explain these traits. While Anagale gobiensis is a primitive mammal in many aspects, some of its derived endocranial traits point towards a new, different trajectory of brain evolution within Euarchontoglires.
Karnkowska, Anna; Yubuki, Naoji; Maruyama, Moe; Yamaguchi, Aika; Kashiyama, Yuichiro; Suzaki, Toshinobu; Keeling, Patrick J.; Hampl, Vladimír; Leander, Brian S.
Euglenozoan kleptoplasty illuminates the early evolution of photoendosymbiosis Journal Article
In: Proceedings of the National Academy of Sciences, vol. 120, no. 12, 2023, ISSN: 0027-8424.
@article{Karnkowska2023,
title = {Euglenozoan kleptoplasty illuminates the early evolution of photoendosymbiosis},
author = {Anna Karnkowska and Naoji Yubuki and Moe Maruyama and Aika Yamaguchi and Yuichiro Kashiyama and Toshinobu Suzaki and Patrick J. Keeling and Vladimír Hampl and Brian S. Leander},
url = {https://pnas.org/doi/10.1073/pnas.2220100120},
doi = {10.1073/pnas.2220100120},
issn = {0027-8424},
year = {2023},
date = {2023-03-27},
urldate = {2023-03-16},
journal = {Proceedings of the National Academy of Sciences},
volume = {120},
number = {12},
abstract = {Kleptoplasts (kP) are distinct among photosynthetic organelles in eukaryotes (i.e., plastids) because they are routinely sequestered from prey algal cells and function only temporarily in the new host cell. Therefore, the hosts of kleptoplasts benefit from photosynthesis without constitutive photoendosymbiosis. Here, we report that the euglenozoan Rapaza viridis has only kleptoplasts derived from a specific strain of green alga, Tetraselmis sp., but no canonical plastids like those found in its sister group, the Euglenophyceae. R. viridis showed a dynamic change in the accumulation of cytosolic polysaccharides in response to light–dark cycles, and 13 C isotopic labeling of ambient bicarbonate demonstrated that these polysaccharides originate in situ via photosynthesis; these data indicate that the kleptoplasts of R. viridis are functionally active. We also identified 276 sequences encoding putative plastid-targeting proteins and 35 sequences of presumed kleptoplast transporters in the transcriptome of R. viridis . These genes originated in a wide range of algae other than Tetraselmis sp., the source of the kleptoplasts, suggesting a long history of repeated horizontal gene transfer events from different algal prey cells. Many of the kleptoplast proteins, as well as the protein-targeting system, in R. viridis were shared with members of the Euglenophyceae, providing evidence that the early evolutionary stages in the green alga-derived secondary plastids of euglenophytes also involved kleptoplasty.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kleptoplasts (kP) are distinct among photosynthetic organelles in eukaryotes (i.e., plastids) because they are routinely sequestered from prey algal cells and function only temporarily in the new host cell. Therefore, the hosts of kleptoplasts benefit from photosynthesis without constitutive photoendosymbiosis. Here, we report that the euglenozoan Rapaza viridis has only kleptoplasts derived from a specific strain of green alga, Tetraselmis sp., but no canonical plastids like those found in its sister group, the Euglenophyceae. R. viridis showed a dynamic change in the accumulation of cytosolic polysaccharides in response to light–dark cycles, and 13 C isotopic labeling of ambient bicarbonate demonstrated that these polysaccharides originate in situ via photosynthesis; these data indicate that the kleptoplasts of R. viridis are functionally active. We also identified 276 sequences encoding putative plastid-targeting proteins and 35 sequences of presumed kleptoplast transporters in the transcriptome of R. viridis . These genes originated in a wide range of algae other than Tetraselmis sp., the source of the kleptoplasts, suggesting a long history of repeated horizontal gene transfer events from different algal prey cells. Many of the kleptoplast proteins, as well as the protein-targeting system, in R. viridis were shared with members of the Euglenophyceae, providing evidence that the early evolutionary stages in the green alga-derived secondary plastids of euglenophytes also involved kleptoplasty.
Przybylski, Wiesław; Jaworska, Danuta; Płecha, Magdalena; Dukaczewska, Karina; Ostrowski, Grzegorz; Sałek, Piotr; Sawicki, Krzysztof; Pawłowska, Julia
Fungal Biostarter Effect on the Quality of Dry-Aged Beef Journal Article
In: Foods, vol. 12, no. 6, pp. 1330, 2023, ISSN: 2304-8158.
@article{Przybylski2023,
title = {Fungal Biostarter Effect on the Quality of Dry-Aged Beef},
author = {Przybylski, Wiesław and Jaworska, Danuta and Płecha, Magdalena and Dukaczewska, Karina and Ostrowski, Grzegorz and Sałek, Piotr and Sawicki, Krzysztof and Pawłowska, Julia},
url = {https://www.mdpi.com/2304-8158/12/6/1330},
doi = {10.3390/foods12061330},
issn = {2304-8158},
year = {2023},
date = {2023-03-21},
urldate = {2023-03-21},
journal = {Foods},
volume = {12},
number = {6},
pages = {1330},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
López-Torres, Sergi; Bhagat, Raj; Bertrand, Ornella C.; Silcox, Mary T.; Fostowicz-Frelik, Łucja
Locomotor behavior and hearing sensitivity in an early lagomorph reconstructed from the bony labyrinth Journal Article
In: Ecology and Evolution, vol. 13, no. 3, pp. e9890, 2023.
@article{LopezE&E2023,
title = {Locomotor behavior and hearing sensitivity in an early lagomorph reconstructed from the bony labyrinth},
author = {Sergi López-Torres and Raj Bhagat and Ornella C. Bertrand and Mary T. Silcox and Łucja Fostowicz-Frelik},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.9890},
doi = {https://doi.org/10.1002/ece3.9890},
year = {2023},
date = {2023-03-18},
urldate = {2023-03-18},
journal = {Ecology and Evolution},
volume = {13},
number = {3},
pages = {e9890},
abstract = {Abstract The structure of the bony labyrinth is highly informative with respect to locomotor agility (semicircular canals [SCC]) and hearing sensitivity (cochlear and oval windows). Here, we reconstructed the agility and hearing sensitivity of the stem lagomorph Megalagus turgidus from the early Oligocene of the Brule Formation of Nebraska (USA). Megalagus has proportionally smaller SCCs with respect to its body mass compared with most extant leporids but within the modern range of variability, suggesting that it was less agile than most of its modern relatives. A level of agility for Megalagus within the range of modern rabbits is consistent with the evidence from postcranial elements. The hearing sensitivity for Megalagus is in the range of extant lagomorphs for both low- and high-frequency sounds. Our data show that by the early Oligocene stem lagomorphs had already attained fundamentally rabbit-like hearing sensitivity and locomotor behavior, even though Megalagus was not a particularly agile lagomorph. This is likely because Megalagus was more of a woodland dweller than an open-habitat runner. The study of sensory evolution in Lagomorpha is practically unknown, and these results provide first advances in understanding the primitive stages for the order and how the earliest members of this clade perceived their environment.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract The structure of the bony labyrinth is highly informative with respect to locomotor agility (semicircular canals [SCC]) and hearing sensitivity (cochlear and oval windows). Here, we reconstructed the agility and hearing sensitivity of the stem lagomorph Megalagus turgidus from the early Oligocene of the Brule Formation of Nebraska (USA). Megalagus has proportionally smaller SCCs with respect to its body mass compared with most extant leporids but within the modern range of variability, suggesting that it was less agile than most of its modern relatives. A level of agility for Megalagus within the range of modern rabbits is consistent with the evidence from postcranial elements. The hearing sensitivity for Megalagus is in the range of extant lagomorphs for both low- and high-frequency sounds. Our data show that by the early Oligocene stem lagomorphs had already attained fundamentally rabbit-like hearing sensitivity and locomotor behavior, even though Megalagus was not a particularly agile lagomorph. This is likely because Megalagus was more of a woodland dweller than an open-habitat runner. The study of sensory evolution in Lagomorpha is practically unknown, and these results provide first advances in understanding the primitive stages for the order and how the earliest members of this clade perceived their environment.
Silcox, Mary T.; López-Torres, Sergi
Primate Origins: The Earliest Primates and Euprimates and Their Role in the Evolution of the Order Book Chapter
In: Chapter 22, pp. 365-380, John Wiley & Sons, Ltd, 2023, ISBN: 9781119828075.
@inbook{Sergi2023,
title = {Primate Origins: The Earliest Primates and Euprimates and Their Role in the Evolution of the Order},
author = {Mary T. Silcox and Sergi López-Torres},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119828075.ch22},
doi = {https://doi.org/10.1002/9781119828075.ch22},
isbn = {9781119828075},
year = {2023},
date = {2023-03-15},
urldate = {2023-03-15},
pages = {365-380},
publisher = {John Wiley & Sons, Ltd},
chapter = {22},
abstract = {This chapter provides an overview of the fossil record for the key early euprimate groups, and for the plesiadapiforms, and discusses how this record relates to Primate Origins and to the origins of Strepsirrhini and Anthropoidea. Adapis was the first fossil primate to be named, although the reference in its name to Apis, the sacred Egyptian bull, implies some initial confusion about its identity. Primitive adapoids and omomyoids are very similar dentally, although adapoids do possess two apparently derived features of the dentition that allows them to be distinguished. Traditionally, omomyoids have been viewed as tarsier-like, in contrast to the lemur-like adapoids. The endocasts of plesiadapiforms indicate that the brain had not yet evolved a euprimate-like expansion of the neocortex, with notably larger olfactory bulbs relative to the overall size of the brain compared to even the most primitive euprimates.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
This chapter provides an overview of the fossil record for the key early euprimate groups, and for the plesiadapiforms, and discusses how this record relates to Primate Origins and to the origins of Strepsirrhini and Anthropoidea. Adapis was the first fossil primate to be named, although the reference in its name to Apis, the sacred Egyptian bull, implies some initial confusion about its identity. Primitive adapoids and omomyoids are very similar dentally, although adapoids do possess two apparently derived features of the dentition that allows them to be distinguished. Traditionally, omomyoids have been viewed as tarsier-like, in contrast to the lemur-like adapoids. The endocasts of plesiadapiforms indicate that the brain had not yet evolved a euprimate-like expansion of the neocortex, with notably larger olfactory bulbs relative to the overall size of the brain compared to even the most primitive euprimates.
Hsieh, Shannon; Łaska, Weronika; Uchman, Alfred
Intermittent and temporally variable bioturbation by some terrestrial invertebrates: implications for ichnology Journal Article
In: The Science of Nature, vol. 110, no. 2, pp. 11, 2023.
@article{hsieh2023intermittent,
title = {Intermittent and temporally variable bioturbation by some terrestrial invertebrates: implications for ichnology},
author = {Shannon Hsieh and Weronika Łaska and Alfred Uchman},
year = {2023},
date = {2023-03-07},
urldate = {2023-01-01},
journal = {The Science of Nature},
volume = {110},
number = {2},
pages = {11},
publisher = {Springer},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Leonhard, Isabella; Agiadi, Konstantina
Addressing challenges in marine conservation with fish otoliths and their death assemblages Journal Article
In: Geological Society, London, Special Publications, vol. 529, no. 1, 2023.
@article{leonhard2023addressing,
title = {Addressing challenges in marine conservation with fish otoliths and their death assemblages},
author = {Isabella Leonhard and Konstantina Agiadi},
url = {https://www.lyellcollection.org/doi/10.1144/SP529-2022-132},
doi = {10.1144/SP529-2022-132},
year = {2023},
date = {2023-02-16},
urldate = {2023-01-01},
journal = {Geological Society, London, Special Publications},
volume = {529},
number = {1},
publisher = {The Geological Society of London},
abstract = {Otolith death assemblages provide a valuable source of biological and ecological information that can help address three main problems in marine conservation: a) the lack of pre-industrial, pre-human-impact baselines for evaluating change; b) the inefficiency of survey methods for recording small and cryptic fish species; and c) the absence of long-term data on environmental change impacts on marine ecosystems and fishes. We review here the current knowledge on the formation and preservation of otoliths and their death assemblages, and the methods to obtain, date and analyse them in order to detect changes in the species traits and ecology, the fish population structure and the palaeoceanographic shifts that drove them.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Otolith death assemblages provide a valuable source of biological and ecological information that can help address three main problems in marine conservation: a) the lack of pre-industrial, pre-human-impact baselines for evaluating change; b) the inefficiency of survey methods for recording small and cryptic fish species; and c) the absence of long-term data on environmental change impacts on marine ecosystems and fishes. We review here the current knowledge on the formation and preservation of otoliths and their death assemblages, and the methods to obtain, date and analyse them in order to detect changes in the species traits and ecology, the fish population structure and the palaeoceanographic shifts that drove them.
Dziurzynski, Mikolaj; Gorecki, Adrian; Pawlowska, Julia; Istel, Lukasz; Decewicz, Przemyslaw; Golec, Piotr; Styczynski, Michal; Poszytek, Krzysztof; Rokowska, Anna; Gorniak, Dorota; Dziewit, Lukasz
In: Science of The Total Environment, vol. 856, no. 2, pp. 159072, 2023, ISSN: 0048-9697.
@article{DZIURZYNSKI2022159072,
title = {Revealing the diversity of bacteria and fungi in the active layer of permafrost at Spitsbergen island (Arctic) – Combining classical microbiology and metabarcoding for ecological and bioprospecting exploration},
author = {Mikolaj Dziurzynski and Adrian Gorecki and Julia Pawlowska and Lukasz Istel and Przemyslaw Decewicz and Piotr Golec and Michal Styczynski and Krzysztof Poszytek and Anna Rokowska and Dorota Gorniak and Lukasz Dziewit},
url = {https://www.sciencedirect.com/science/article/pii/S004896972206171X},
doi = {https://doi.org/10.1016/j.scitotenv.2022.159072},
issn = {0048-9697},
year = {2023},
date = {2023-01-15},
journal = {Science of The Total Environment},
volume = {856},
number = {2},
pages = {159072},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Silcox, Mary T; Bertrand, Ornella C; Harrington, Arianna R; Lang, Madlen M; Martin-Flores, Gabriela A San; López-Torres, Sergi
Early Evolution of the Brain in Primates and Their Close Kin Book Chapter
In: Dozo, María Teresa; Paulina-Carabajal, Ariana; Macrini, Thomas E; Walsh, Stig (Ed.): Chapter 12, pp. 457–506, Springer Cham, Switzerland, 2023, ISBN: 978-3-031-13983-3.
@inbook{Silcox_Bertrand_Harrington_Lang_SanMartin-Flores_Lopez-Torres_2023,
title = {Early Evolution of the Brain in Primates and Their Close Kin},
author = {Mary T Silcox and Ornella C Bertrand and Arianna R Harrington and Madlen M Lang and Gabriela A San Martin-Flores and Sergi López-Torres},
editor = {María Teresa Dozo and Ariana Paulina-Carabajal and Thomas E Macrini and Stig Walsh},
url = {https://link.springer.com/chapter/10.1007/978-3-031-13983-3_12},
isbn = {978-3-031-13983-3},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
pages = {457–506},
publisher = {Springer Cham},
address = {Switzerland},
chapter = {12},
abstract = {The interpretation of early primate endocasts can be framed around four critical questions: (1) What are accurate estimates of endocranial capacity for known euprimate specimens? (2) What does the available data for stem primates tell us with respect to the earliest phases of primate brain evolution? (3) How should relative brain size be assessed? and (4) What is the appropriate comparative context for interpreting fossil primate endocasts? The widespread availability of CT data has allowed for better estimates of endocranial volume (#1), and for more data from stem primates (#2). From these data it is clear that the earliest primates had brains that were little differentiated in terms of form or size from their ancestors, although there might have been some modest increase in the relative size of the neocortex. Major changes in shape occurred at the euprimate node, with expansions in the temporal and occipital lobes (reflected in an expanded neocortex), and a lack of expansion in the olfactory bulbs. The brain of early fossil euprimates nonetheless still displayed primitive features such as narrow frontal lobes. Questions #3 and #4 remain contentious, although a much-expanded comparative sample of fossil endocasts allows for new perspectives on these issues.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
The interpretation of early primate endocasts can be framed around four critical questions: (1) What are accurate estimates of endocranial capacity for known euprimate specimens? (2) What does the available data for stem primates tell us with respect to the earliest phases of primate brain evolution? (3) How should relative brain size be assessed? and (4) What is the appropriate comparative context for interpreting fossil primate endocasts? The widespread availability of CT data has allowed for better estimates of endocranial volume (#1), and for more data from stem primates (#2). From these data it is clear that the earliest primates had brains that were little differentiated in terms of form or size from their ancestors, although there might have been some modest increase in the relative size of the neocortex. Major changes in shape occurred at the euprimate node, with expansions in the temporal and occipital lobes (reflected in an expanded neocortex), and a lack of expansion in the olfactory bulbs. The brain of early fossil euprimates nonetheless still displayed primitive features such as narrow frontal lobes. Questions #3 and #4 remain contentious, although a much-expanded comparative sample of fossil endocasts allows for new perspectives on these issues.
Scott, Craig S; López-Torres, Sergi; Silcox, Mary T; Fox, Richard C
New paromomyids (Mammalia, Primates) from the Paleocene of southwestern Alberta, Canada, and an analysis of paromomyid interrelationships Journal Article
In: Journal of Paleontology, pp. 1–22, 2023.
@article{scott2023new,
title = {New paromomyids (Mammalia, Primates) from the Paleocene of southwestern Alberta, Canada, and an analysis of paromomyid interrelationships},
author = {Craig S Scott and Sergi López-Torres and Mary T Silcox and Richard C Fox},
url = {https://www.cambridge.org/core/journals/journal-of-paleontology/article/new-paromomyids-mammalia-primates-from-the-paleocene-of-southwestern-alberta-canada-and-an-analysis-of-paromomyid-interrelationships/85328AE223A9AE66A2948F6FB06712CD},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Journal of Paleontology},
pages = {1--22},
publisher = {Cambridge University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2022
Domian, Grażyna; Konik, Judyta; Kudławiec, Barbara; Kujawa, Anna; Lożek, Marcin; Naser, Grażyna; Pawłowska, Julia; Piskorski, Sebastian; Rosa-Gruszecka, Aleksandra; Stasińska, Małgorzata; Stokłosa, Natalia
Mycological reports of the Fungal Diversity and Conservation Section of the Polish Mycological Society. Part 2. Journal Article
In: Przegląd Przyrodniczy, vol. XXXIII, no. 4, pp. 12-59, 2022.
@article{PawlowskaPrzeglad2022,
title = {Mycological reports of the Fungal Diversity and Conservation Section of the Polish Mycological Society. Part 2.},
author = {Grażyna Domian and Judyta Konik and Barbara Kudławiec and Anna Kujawa and Marcin Lożek and Grażyna Naser and Julia Pawłowska and Sebastian Piskorski and Aleksandra Rosa-Gruszecka and Małgorzata Stasińska and Natalia Stokłosa},
url = {https://www.kp.org.pl/images/pp/artykuły_od_2019/4_2022_XXXIII_4/Domian%20et%20al_2022_Obserwacje%20mykologiczne.pdf},
year = {2022},
date = {2022-12-31},
urldate = {2022-12-31},
journal = {Przegląd Przyrodniczy},
volume = {XXXIII},
number = {4},
pages = {12-59},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
De Baets, Kenneth; Jarochowska, Emilia; Buchwald, Stella Zora; Klug, Christian; Korn, Dieter
Lithology controls ammonoid size distributions Journal Article
In: PALAIOS, vol. 37, iss. 12, pp. 744-754, 2022, ISSN: 0883-1351.
@article{deBaets2022.12.30,
title = {Lithology controls ammonoid size distributions},
author = {De Baets, Kenneth and Jarochowska, Emilia and Buchwald, Stella Zora and Klug, Christian and Korn, Dieter},
url = {https://doi.org/10.2110/palo.2021.063
https://pubs.geoscienceworld.org/sepm/palaios/article-pdf/37/12/744/5758729/i1938-5323-37-12-744.pdf},
doi = {10.2110/palo.2021.063},
issn = {0883-1351},
year = {2022},
date = {2022-12-30},
urldate = {2022-12-30},
journal = {PALAIOS},
volume = {37},
issue = {12},
pages = {744-754},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Baczyński, Jakub; Celep, Ferhat; Spalik, Krzysztof; Claßen-Bockhoff, Regine
Flower-like meristem conditions and spatial constraints shape architecture of floral pseudanthia in Apioideae Journal Article
In: EvoDevo, vol. 13, pp. 19, 2022.
@article{Baczyński2022,
title = {Flower-like meristem conditions and spatial constraints shape architecture of floral pseudanthia in Apioideae},
author = {Baczyński, Jakub and Celep, Ferhat and Spalik, Krzysztof and Claßen-Bockhoff, Regine},
url = {https://doi.org/10.1186/s13227-022-00204-6},
doi = {10.1186/s13227-022-00204-6},
year = {2022},
date = {2022-12-19},
journal = {EvoDevo},
volume = {13},
pages = {19},
abstract = {Pseudanthia are multiflowered units that resemble single flowers, frequently by association with pseudocorollas formed by enlarged peripheral florets (ray flowers). Such resemblance is not only superficial, because numerous pseudanthia originate from peculiar reproductive meristems with flower-like characteristics, i.e. floral unit meristems (FUMs). Complex FUM-derived pseudanthia with ray flowers are especially common in Apiaceae, but our knowledge about their patterning is limited. In this paper, we aimed to investigate both the genetic and morphological basis of their development.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pseudanthia are multiflowered units that resemble single flowers, frequently by association with pseudocorollas formed by enlarged peripheral florets (ray flowers). Such resemblance is not only superficial, because numerous pseudanthia originate from peculiar reproductive meristems with flower-like characteristics, i.e. floral unit meristems (FUMs). Complex FUM-derived pseudanthia with ray flowers are especially common in Apiaceae, but our knowledge about their patterning is limited. In this paper, we aimed to investigate both the genetic and morphological basis of their development.
Rackevei, A. S.; Karnkowska, A.; Wolf, M.
18S rDNA sequence–structure phylogeny of the Euglenophyceae (Euglenozoa, Euglenida) Journal Article
In: Journal of Eukaryotic Microbiology, 2022.
@article{Rackevei2022,
title = {18S rDNA sequence–structure phylogeny of the Euglenophyceae (Euglenozoa, Euglenida)},
author = {A. S. Rackevei and A. Karnkowska and M. Wolf},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85144112638&doi=10.1111%2fjeu.12959&partnerID=40&md5=9bf67781c977866a8dd5baa9a03d9f4c},
doi = {10.1111/jeu.12959},
year = {2022},
date = {2022-12-07},
urldate = {2022-12-07},
journal = {Journal of Eukaryotic Microbiology},
abstract = {The phylogeny of Euglenophyceae (Euglenozoa, Euglenida) has been discussed for decades with new genera being described in the last few years. In this study, we reconstruct a phylogeny using 18S rDNA sequence and structural data simultaneously. Using homology modeling, individual secondary structures were predicted. Sequence–structure data are encoded and automatically aligned. Here, we present a sequence–structure neighbor-joining tree of more than 300 taxa classified as Euglenophyceae. Profile neighbor-joining was used to resolve the basal branching pattern. Neighbor-joining, maximum parsimony, and maximum likelihood analyses were performed using sequence–structure information for manually chosen subsets. All analyses supported the monophyly of Eutreptiella, Discoplastis, Lepocinclis, Strombomonas, Cryptoglena, Monomorphina, Euglenaria, and Colacium. Well-supported topologies were generally consistent with previous studies using a combined dataset of genetic markers. Our study supports the simultaneous use of sequence and structural data to reconstruct more accurate and robust trees. The average bootstrap value is significantly higher than the average bootstrap value obtained from sequence-only analyses, which is promising for resolving relationships between more closely related taxa.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The phylogeny of Euglenophyceae (Euglenozoa, Euglenida) has been discussed for decades with new genera being described in the last few years. In this study, we reconstruct a phylogeny using 18S rDNA sequence and structural data simultaneously. Using homology modeling, individual secondary structures were predicted. Sequence–structure data are encoded and automatically aligned. Here, we present a sequence–structure neighbor-joining tree of more than 300 taxa classified as Euglenophyceae. Profile neighbor-joining was used to resolve the basal branching pattern. Neighbor-joining, maximum parsimony, and maximum likelihood analyses were performed using sequence–structure information for manually chosen subsets. All analyses supported the monophyly of Eutreptiella, Discoplastis, Lepocinclis, Strombomonas, Cryptoglena, Monomorphina, Euglenaria, and Colacium. Well-supported topologies were generally consistent with previous studies using a combined dataset of genetic markers. Our study supports the simultaneous use of sequence and structural data to reconstruct more accurate and robust trees. The average bootstrap value is significantly higher than the average bootstrap value obtained from sequence-only analyses, which is promising for resolving relationships between more closely related taxa.
Hohmann, Niklas
In: Frontiers in Earth Science, vol. 10, pp. 1013174, 2022.
@article{Hohmann2022,
title = {Global compilation of surface mixed layer parameters (sedimentation rate, bioturbation depth, mixing intensity) from marine environments: The SMLBase v1.0},
author = {Niklas Hohmann},
url = {https://www.frontiersin.org/articles/10.3389/feart.2022.1013174/full},
doi = {10.3389/feart.2022.1013174},
year = {2022},
date = {2022-12-06},
urldate = {2023-12-06},
journal = {Frontiers in Earth Science},
volume = {10},
pages = {1013174},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Maciszewski, K.; Fells, A.; Karnkowska, A.
Challenging the Importance of Plastid Genome Structure Conservation: New Insights From Euglenophytes Journal Article
In: Molecular biology and evolution, vol. 39, no. 12, pp. msac255, 2022.
@article{Maciszewski2022,
title = {Challenging the Importance of Plastid Genome Structure Conservation: New Insights From Euglenophytes},
author = {K. Maciszewski and A. Fells and A. Karnkowska},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85143644275&doi=10.1093%2fmolbev%2fmsac255&partnerID=40&md5=e63da87baf5864bd2b41415366ed82b3},
doi = {10.1093/molbev/msac255},
year = {2022},
date = {2022-12-05},
urldate = {2022-12-05},
journal = {Molecular biology and evolution},
volume = {39},
number = {12},
pages = {msac255},
abstract = {Plastids, similar to mitochondria, are organelles of endosymbiotic origin, which retained their vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the quadripartite (four-part) structure, is considered to be strictly conserved; however, the bulk of our knowledge on their variability and evolutionary transformations comes from studies of the primary plastids of green algae and land plants. To broaden our perspective, we obtained seven new ptDNA sequences from freshwater species of photosynthetic euglenids-a group that obtained secondary plastids, known to have dynamically evolving genome structure, via endosymbiosis with a green alga. Our analyses have demonstrated that the evolutionary history of euglenid plastid genome structure is exceptionally convoluted, with a patchy distribution of inverted ribosomal operon (rDNA) repeats, as well as several independent acquisitions of tandemly repeated rDNA copies. Moreover, we have shown that inverted repeats in euglenid ptDNA do not share their genome-stabilizing property documented in chlorophytes. We hypothesize that the degeneration of the quadripartite structure of euglenid plastid genomes is connected to the group II intron expansion. These findings challenge the current global paradigms of plastid genome architecture evolution and underscore the often-underestimated divergence between the functionality of shared traits in primary and complex plastid organelles.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Plastids, similar to mitochondria, are organelles of endosymbiotic origin, which retained their vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the quadripartite (four-part) structure, is considered to be strictly conserved; however, the bulk of our knowledge on their variability and evolutionary transformations comes from studies of the primary plastids of green algae and land plants. To broaden our perspective, we obtained seven new ptDNA sequences from freshwater species of photosynthetic euglenids-a group that obtained secondary plastids, known to have dynamically evolving genome structure, via endosymbiosis with a green alga. Our analyses have demonstrated that the evolutionary history of euglenid plastid genome structure is exceptionally convoluted, with a patchy distribution of inverted ribosomal operon (rDNA) repeats, as well as several independent acquisitions of tandemly repeated rDNA copies. Moreover, we have shown that inverted repeats in euglenid ptDNA do not share their genome-stabilizing property documented in chlorophytes. We hypothesize that the degeneration of the quadripartite structure of euglenid plastid genomes is connected to the group II intron expansion. These findings challenge the current global paradigms of plastid genome architecture evolution and underscore the often-underestimated divergence between the functionality of shared traits in primary and complex plastid organelles.
Uhlik, Marcin; Brzeziński, Tomasz
In: Crustaceana, vol. 95, iss. 8-9, pp. 907-923, 2022.
@article{Uhlik_2022,
title = {Embryogeny of Bosmina longirostris (O. F. Müller, 1785) (Bosminidae) confirms a close relationship to the superfamily Eurycercoidea (Branchiopoda, Cladocera, Anomopoda)},
author = {Marcin Uhlik and Tomasz Brzeziński},
doi = {10.1163/15685403-bja10236},
year = {2022},
date = {2022-11-18},
urldate = {2022-11-18},
journal = {Crustaceana},
volume = {95},
issue = {8-9},
pages = {907-923},
abstract = {The embryonic stages of the anomopod Bosmina longirostris of the family Bosminidae were elucidated by scanning electron microscopy. Along with the corresponding stages of Bosmina coregoni described by Kotov (2001), these findings have enabled a comparison to Dunhevedia crassa, as a representative species of the family Chydoridae, and to Eurycercus lamellatus of the family Eurycercidae. In general, the developmental patterns are similar in these four species, particularly from blastulation to the first instar. The principal difference during embryogenesis is that in D. crassa and B. longirostris five thoracopods (six in E. lamellatus) are differentiated already with endo- and exopodites.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The embryonic stages of the anomopod Bosmina longirostris of the family Bosminidae were elucidated by scanning electron microscopy. Along with the corresponding stages of Bosmina coregoni described by Kotov (2001), these findings have enabled a comparison to Dunhevedia crassa, as a representative species of the family Chydoridae, and to Eurycercus lamellatus of the family Eurycercidae. In general, the developmental patterns are similar in these four species, particularly from blastulation to the first instar. The principal difference during embryogenesis is that in D. crassa and B. longirostris five thoracopods (six in E. lamellatus) are differentiated already with endo- and exopodites.
Ebenezer, T. E.; Low, R. S.; O'Neill, E. C.; Huang, I.; DeSimone, A.; Farrow, S. C.; Field, R. A.; Ginger, M. L.; Guerrero, S. A.; Hammond, M.; Hampl, V.; Horst, G.; Ishikawa, T.; Karnkowska, A.; Linton, E. W.; Myler, P.; Nakazawa, M.; Cardol, P.; Sánchez-Thomas, R.; Saville, B. J.; Shah, M. R.; Simpson, A. G. B.; Sur, A.; Suzuki, K.; Tyler, K. M.; Zimba, P. V.; Hall, N.; Field, M. C.
Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world Journal Article
In: Biology open, vol. 11, no. 11, pp. bio059561, 2022.
@article{Ebenezer2022,
title = {Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world},
author = {T. E. Ebenezer and R. S. Low and E. C. O'Neill and I. Huang and A. DeSimone and S. C. Farrow and R. A. Field and M. L. Ginger and S. A. Guerrero and M. Hammond and V. Hampl and G. Horst and T. Ishikawa and A. Karnkowska and E. W. Linton and P. Myler and M. Nakazawa and P. Cardol and R. Sánchez-Thomas and B. J. Saville and M. R. Shah and A. G. B. Simpson and A. Sur and K. Suzuki and K. M. Tyler and P. V. Zimba and N. Hall and M. C. Field},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85142345726&doi=10.1242%2fbio.059561&partnerID=40&md5=314fa8ff81384509cf02182000cbfe04},
doi = {10.1242/bio.059561},
year = {2022},
date = {2022-11-01},
urldate = {2022-11-01},
journal = {Biology open},
volume = {11},
number = {11},
pages = {bio059561},
abstract = {Euglenoids (Euglenida) are unicellular flagellates possessing exceptionally wide geographical and ecological distribution. Euglenoids combine a biotechnological potential with a unique position in the eukaryotic tree of life. In large part these microbes owe this success to diverse genetics including secondary endosymbiosis and likely additional sources of genes. Multiple euglenoid species have translational applications and show great promise in production of biofuels, nutraceuticals, bioremediation, cancer treatments and more exotically as robotics design simulators. An absence of reference genomes currently limits these applications, including development of efficient tools for identification of critical factors in regulation, growth or optimization of metabolic pathways. The Euglena International Network (EIN) seeks to provide a forum to overcome these challenges. EIN has agreed specific goals, mobilized scientists, established a clear roadmap (Grand Challenges), connected academic and industry stakeholders and is currently formulating policy and partnership principles to propel these efforts in a coordinated and efficient manner.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Euglenoids (Euglenida) are unicellular flagellates possessing exceptionally wide geographical and ecological distribution. Euglenoids combine a biotechnological potential with a unique position in the eukaryotic tree of life. In large part these microbes owe this success to diverse genetics including secondary endosymbiosis and likely additional sources of genes. Multiple euglenoid species have translational applications and show great promise in production of biofuels, nutraceuticals, bioremediation, cancer treatments and more exotically as robotics design simulators. An absence of reference genomes currently limits these applications, including development of efficient tools for identification of critical factors in regulation, growth or optimization of metabolic pathways. The Euglena International Network (EIN) seeks to provide a forum to overcome these challenges. EIN has agreed specific goals, mobilized scientists, established a clear roadmap (Grand Challenges), connected academic and industry stakeholders and is currently formulating policy and partnership principles to propel these efforts in a coordinated and efficient manner.
Tałanda, Mateusz; Fernandez, Vincent; Panciroli, Elsa; Evans, Susan E; Benson, Roger J
Synchrotron tomography of a stem lizard elucidates early squamate anatomy Journal Article
In: Nature, vol. 611, no. 7934, pp. 99-104, 2022.
@article{talanda2022synchrotron,
title = {Synchrotron tomography of a stem lizard elucidates early squamate anatomy},
author = {Mateusz Tałanda and Vincent Fernandez and Elsa Panciroli and Susan E Evans and Roger J Benson},
doi = {10.1038/s41586-022-05332-6},
year = {2022},
date = {2022-10-26},
urldate = {2022-01-01},
journal = {Nature},
volume = {611},
number = {7934},
pages = {99-104},
publisher = {Nature Publishing Group},
abstract = {Squamates (lizards and snakes) include more than 10,000 living species, descended from an ancestor that diverged more than 240 million years ago from that of their closest living relative, Sphenodon. However, a deficiency of fossil evidence1,2,3,4,5,6,7, combined with serious conflicts between molecular and morphological accounts of squamate phylogeny8,9,10,11,12,13 (but see ref. 14), has caused uncertainty about the origins and evolutionary assembly of squamate anatomy. Here we report the near-complete skeleton of a stem squamate, Bellairsia gracilis, from the Middle Jurassic epoch of Scotland, documented using high-resolution synchrotron phase-contrast tomography. Bellairsia shares numerous features of the crown group, including traits related to cranial kinesis (an important functional feature of many extant squamates) and those of the braincase and shoulder girdle. Alongside these derived traits, Bellairsia also retains inferred ancestral features including a pterygoid–vomer contact and the presence of both cervical and dorsal intercentra. Phylogenetic analyses return strong support for Bellairsia as a stem squamate, suggesting that several features that it shares with extant gekkotans are plesiomorphies, consistent with the molecular phylogenetic hypothesis that gekkotans are early-diverging squamates. We also provide confident support of stem squamate affinities for the enigmatic Oculudentavis. Our findings indicate that squamate-like functional features of the suspensorium, braincase and shoulder girdle preceded the origin of their palatal and vertebral traits and indicate the presence of advanced stem squamates as persistent components of terrestrial assemblages up to at least the middle of the Cretaceous period.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Squamates (lizards and snakes) include more than 10,000 living species, descended from an ancestor that diverged more than 240 million years ago from that of their closest living relative, Sphenodon. However, a deficiency of fossil evidence1,2,3,4,5,6,7, combined with serious conflicts between molecular and morphological accounts of squamate phylogeny8,9,10,11,12,13 (but see ref. 14), has caused uncertainty about the origins and evolutionary assembly of squamate anatomy. Here we report the near-complete skeleton of a stem squamate, Bellairsia gracilis, from the Middle Jurassic epoch of Scotland, documented using high-resolution synchrotron phase-contrast tomography. Bellairsia shares numerous features of the crown group, including traits related to cranial kinesis (an important functional feature of many extant squamates) and those of the braincase and shoulder girdle. Alongside these derived traits, Bellairsia also retains inferred ancestral features including a pterygoid–vomer contact and the presence of both cervical and dorsal intercentra. Phylogenetic analyses return strong support for Bellairsia as a stem squamate, suggesting that several features that it shares with extant gekkotans are plesiomorphies, consistent with the molecular phylogenetic hypothesis that gekkotans are early-diverging squamates. We also provide confident support of stem squamate affinities for the enigmatic Oculudentavis. Our findings indicate that squamate-like functional features of the suspensorium, braincase and shoulder girdle preceded the origin of their palatal and vertebral traits and indicate the presence of advanced stem squamates as persistent components of terrestrial assemblages up to at least the middle of the Cretaceous period.
Wilczynski, Wojciech; Babkiewicz, Ewa; Pukos, Szymon; Wawrzeńczak, Julia; Zebrowski, Marcin Lukasz; Banasiak, Łukasz; Kudriashov, Mark; Maszczyk, Piotr
The Effects of Hypoxia on Threshold Food Concentrations in Different Daphnia Species Journal Article
In: Water, vol. 14, no. 20, 2022, ISSN: 2073-4441.
@article{w14203213,
title = {The Effects of Hypoxia on Threshold Food Concentrations in Different Daphnia Species},
author = {Wojciech Wilczynski and Ewa Babkiewicz and Szymon Pukos and Julia Wawrzeńczak and Marcin Lukasz Zebrowski and Łukasz Banasiak and Mark Kudriashov and Piotr Maszczyk},
url = {https://www.mdpi.com/2073-4441/14/20/3213},
doi = {10.3390/w14203213},
issn = {2073-4441},
year = {2022},
date = {2022-10-13},
urldate = {2022-01-01},
journal = {Water},
volume = {14},
number = {20},
abstract = {Numerous studies have revealed a negative correlation between the body size and temperature among a variety of aquatic ectotherms. Many studies at individual and population levels indicated that this mechanism may be explained by the decrease of competitive abilities of larger- over smaller-bodied individuals, as the production of larger-bodied individuals is more limited due to greater susceptibility to decreased oxygen concentrations (i.e., environmental hypoxia) at elevated temperatures. However, this hypothesis is still not tested at the community level. To test this, we performed several experiments on the food thresholds (which is a proxy for competitive ability) of 6 zooplankton (Daphnia) species varying in body size, at high or low oxygen concentrations. Contrary to the hypothesis tested, hypoxia increased threshold food concentrations to a relatively greater extent in smaller species than in larger ones. This may be attributed to the better evolutionary adaptations of larger-bodied daphnids to oxygen-poor environments manifested in higher production of haemoglobin. The results obtained in this study cannot exclude the possibility that environmental hypoxia is responsible for the temperature-size pattern in aquatic ectotherms, as our experiments did not take into account the long-term energetic costs of expedited haemoglobin synthesis, which could shift size-dependent competitive power.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Numerous studies have revealed a negative correlation between the body size and temperature among a variety of aquatic ectotherms. Many studies at individual and population levels indicated that this mechanism may be explained by the decrease of competitive abilities of larger- over smaller-bodied individuals, as the production of larger-bodied individuals is more limited due to greater susceptibility to decreased oxygen concentrations (i.e., environmental hypoxia) at elevated temperatures. However, this hypothesis is still not tested at the community level. To test this, we performed several experiments on the food thresholds (which is a proxy for competitive ability) of 6 zooplankton (Daphnia) species varying in body size, at high or low oxygen concentrations. Contrary to the hypothesis tested, hypoxia increased threshold food concentrations to a relatively greater extent in smaller species than in larger ones. This may be attributed to the better evolutionary adaptations of larger-bodied daphnids to oxygen-poor environments manifested in higher production of haemoglobin. The results obtained in this study cannot exclude the possibility that environmental hypoxia is responsible for the temperature-size pattern in aquatic ectotherms, as our experiments did not take into account the long-term energetic costs of expedited haemoglobin synthesis, which could shift size-dependent competitive power.
López-Torres, Sergi
Primate Evolution and the Emergence of Humans (Vertebrate Life 11th ed.) Book Chapter
In: Pough, Harvey; Bemis, William E.; McGuire, Betty Anne; Janis, Christine M. (Ed.): Chapter 24, pp. 557-585, Oxford University Press, New York, 11, 2022, ISBN: 978-0197564882.
@inbook{Lopez_primates_2022,
title = {Primate Evolution and the Emergence of Humans (Vertebrate Life 11th ed.)},
author = {Sergi López-Torres},
editor = { Harvey Pough and William E. Bemis and Betty Anne McGuire and Christine M. Janis },
url = {https://global.oup.com/academic/product/vertebrate-life-9780197564882?cc=us&lang=en#},
isbn = {978-0197564882},
year = {2022},
date = {2022-10-01},
urldate = {2022-10-01},
pages = {557-585},
publisher = {Oxford University Press},
address = {New York},
edition = {11},
chapter = {24},
abstract = {Primates have been a moderately successful group for most of the Cenozoic, although since the end of the Eocene they have been largely confined to tropical latitudes (with the exception of humans). Primates include not only the anthropoids—the group of apes and monkeys to which humans belong—but also the prosimians, animals such as bush babies and lemurs, and earlier less derived forms known only from the fossil record. Molecular techniques show that chimpanzees are the closest extant relatives of humans, and both molecular data and the fossil record indicate that the separation of humans from the African great apes occurred about 6.6 Ma. Fossils of Australopithecus—the sister taxon to our own genus, Homo—clearly show that bipedal walking arose before the appearance of a large brain. A diversity of new fossils has shown that early human evolution was much more complex and diverse than previously thought.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
Primates have been a moderately successful group for most of the Cenozoic, although since the end of the Eocene they have been largely confined to tropical latitudes (with the exception of humans). Primates include not only the anthropoids—the group of apes and monkeys to which humans belong—but also the prosimians, animals such as bush babies and lemurs, and earlier less derived forms known only from the fossil record. Molecular techniques show that chimpanzees are the closest extant relatives of humans, and both molecular data and the fossil record indicate that the separation of humans from the African great apes occurred about 6.6 Ma. Fossils of Australopithecus—the sister taxon to our own genus, Homo—clearly show that bipedal walking arose before the appearance of a large brain. A diversity of new fossils has shown that early human evolution was much more complex and diverse than previously thought.
Mulvey, Laura PA; Warnock, Rachel CM; De Baets, Kenneth
Where traditional extinction estimates fall flat: using novel cophylogenetic methods to estimate extinction risk in platyhelminths Journal Article
In: Proceedings of the Royal Society B: Biological Sciences, vol. 289, no. 1981, pp. 20220432, 2022.
@article{doi:10.1098/rspb.2022.0432,
title = {Where traditional extinction estimates fall flat: using novel cophylogenetic methods to estimate extinction risk in platyhelminths},
author = {Laura PA Mulvey and Rachel CM Warnock and De Baets, Kenneth},
url = {https://royalsocietypublishing.org/doi/abs/10.1098/rspb.2022.0432},
doi = {10.1098/rspb.2022.0432},
year = {2022},
date = {2022-08-31},
urldate = {2022-08-31},
journal = {Proceedings of the Royal Society B: Biological Sciences},
volume = {289},
number = {1981},
pages = {20220432},
abstract = {Today parasites comprise a huge proportion of living biodiversity and play a major role in shaping community structure. Given their ecological significance, parasite extinctions could result in massive cascading effects across ecosystems. It is therefore crucial that we have a way of estimating their extinction risk. Attempts to do this have often relied on information about host extinction risk, without explicitly incorporating information about the parasites. However, assuming an identical risk may be misleading. Here, we apply a novel metric to estimate the cophylogenetic extinction rate, Ec, of parasites with their hosts. This metric incorporates information about the evolutionary history of parasites and hosts that can be estimated using event-based cophylogenetic methods. To explore this metric, we investigated the use of different cophylogenetic methods to inform the Ec rate, based on the analysis of polystome parasites and their anuran hosts. We show using both parsimony- and model-based approaches that different methods can have a large effect on extinction risk estimation. Further, we demonstrate that model-based approaches offer greater potential to provide insights into cophylogenetic history and extinction risk.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Today parasites comprise a huge proportion of living biodiversity and play a major role in shaping community structure. Given their ecological significance, parasite extinctions could result in massive cascading effects across ecosystems. It is therefore crucial that we have a way of estimating their extinction risk. Attempts to do this have often relied on information about host extinction risk, without explicitly incorporating information about the parasites. However, assuming an identical risk may be misleading. Here, we apply a novel metric to estimate the cophylogenetic extinction rate, Ec, of parasites with their hosts. This metric incorporates information about the evolutionary history of parasites and hosts that can be estimated using event-based cophylogenetic methods. To explore this metric, we investigated the use of different cophylogenetic methods to inform the Ec rate, based on the analysis of polystome parasites and their anuran hosts. We show using both parsimony- and model-based approaches that different methods can have a large effect on extinction risk estimation. Further, we demonstrate that model-based approaches offer greater potential to provide insights into cophylogenetic history and extinction risk.
Okamura, Beth; Gruhl, Alexander; De Baets, Kenneth
Evolutionary Transitions of Parasites between Freshwater and Marine Environments Journal Article
In: Integrative and Comparative Biology, vol. 62, no. 2, pp. 345–356, 2022, ISSN: 1540-7063.
@article{deBaets2022,
title = {Evolutionary Transitions of Parasites between Freshwater and Marine Environments},
author = {Beth Okamura and Alexander Gruhl and Kenneth De Baets},
url = {https://doi.org/10.1093/icb/icac050},
doi = {10.1093/icb/icac050},
issn = {1540-7063},
year = {2022},
date = {2022-08-02},
journal = {Integrative and Comparative Biology},
volume = {62},
number = {2},
pages = {345–356},
abstract = {Evolutionary transitions of organisms between environments have long fascinated biologists, but attention has been focused almost exclusively on free-living organisms and challenges to achieve such transitions. This bias requires addressing because parasites are a major component of biodiversity. We address this imbalance by focusing on transitions of parasitic animals between marine and freshwater environments. We highlight parasite traits and processes that may influence transition likelihood (e.g., transmission mode, life cycle, host use), and consider mechanisms and directions of transitions. Evidence for transitions in deep time and at present are described, and transitions in our changing world are considered. We propose that environmental transitions may be facilitated for endoparasites because hosts reduce exposure to physiologically challenging environments and argue that adoption of an endoparasitic lifestyle entails an equivalent transitioning process as organisms switch from living in one environment (e.g., freshwater, seawater, or air) to living symbiotically within hosts. Environmental transitions of parasites have repeatedly resulted in novel forms and diversification, contributing to the tree of life. Recognizing the potential processes underlying present-day and future environmental transitions is crucial in view of our changing world and the current biodiversity crisis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Evolutionary transitions of organisms between environments have long fascinated biologists, but attention has been focused almost exclusively on free-living organisms and challenges to achieve such transitions. This bias requires addressing because parasites are a major component of biodiversity. We address this imbalance by focusing on transitions of parasitic animals between marine and freshwater environments. We highlight parasite traits and processes that may influence transition likelihood (e.g., transmission mode, life cycle, host use), and consider mechanisms and directions of transitions. Evidence for transitions in deep time and at present are described, and transitions in our changing world are considered. We propose that environmental transitions may be facilitated for endoparasites because hosts reduce exposure to physiologically challenging environments and argue that adoption of an endoparasitic lifestyle entails an equivalent transitioning process as organisms switch from living in one environment (e.g., freshwater, seawater, or air) to living symbiotically within hosts. Environmental transitions of parasites have repeatedly resulted in novel forms and diversification, contributing to the tree of life. Recognizing the potential processes underlying present-day and future environmental transitions is crucial in view of our changing world and the current biodiversity crisis.
Kaszecki, E.; Kennedy, V.; Shah, M.; Maciszewski, K.; Karnkowska, A.; Linton, E.; Ginger, M. L.; Farrow, S.; Ebenezer, T. E.
Meeting Report: Euglenids in the Age of Symbiogenesis: Origins, Innovations, and Prospects, November 8–11, 2021 Journal Article
In: Protist, vol. 173, no. 4, pp. 125894, 2022.
@article{Kaszecki2022,
title = {Meeting Report: Euglenids in the Age of Symbiogenesis: Origins, Innovations, and Prospects, November 8–11, 2021},
author = {E. Kaszecki and V. Kennedy and M. Shah and K. Maciszewski and A. Karnkowska and E. Linton and M. L. Ginger and S. Farrow and T. E. Ebenezer},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85132872051&doi=10.1016%2fj.protis.2022.125894&partnerID=40&md5=214bcd7e2241e36052f570507753a3da},
doi = {10.1016/j.protis.2022.125894},
year = {2022},
date = {2022-08-01},
urldate = {2022-08-01},
journal = {Protist},
volume = {173},
number = {4},
pages = {125894},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Grau-Camats, Montserrat; Bertrand, Ornella C; Prieto, Jérome; López-Torres, Sergi; Silcox, Mary T; Casanovas-Vilar, Isaac
A Miopetaurista (Rodentia, Sciuridae) cranium from the Middle Miocene of Bavaria (Germany) and brain evolution in flying squirrels Journal Article
In: Papers in Palaeontology, vol. 8, no. 4, pp. e1454, 2022.
@article{grau2022miopetaurista,
title = {A Miopetaurista (Rodentia, Sciuridae) cranium from the Middle Miocene of Bavaria (Germany) and brain evolution in flying squirrels},
author = {Montserrat Grau-Camats and Ornella C Bertrand and Jérome Prieto and Sergi López-Torres and Mary T Silcox and Isaac Casanovas-Vilar},
doi = {10.1002/spp2.1454},
year = {2022},
date = {2022-07-25},
journal = {Papers in Palaeontology},
volume = {8},
number = {4},
pages = {e1454},
publisher = {Wiley Online Library},
abstract = {Flying squirrels (Sciurinae, Pteromyini) are the most successful group of gliding mammals. However, their fossil record mostly consists of isolated dental remains that provide very limited insights into their palaeobiology and evolution. The first skeleton of a fossil flying squirrel, belonging to the species Miopetaurista neogrivensis, has been described only recently. It presents all the diagnostic gliding-related postcranial features of its extant relatives and shows that this group has undergone very little morphological change for almost 12 myr. However, the associated cranium is badly crushed, and particular details of the cranial morphology cannot be described. Here, we describe a well-preserved cranium of the closely related Miopetaurista crusafonti from 12.5–12.0 Ma from Bavaria (Germany). Its cranial morphology is found to be almost identical to extant large flying squirrels, even in details such as the position of the foramina. The virtual endocast also shows close affinities to living large flying squirrels in morphology and in the relative volume of different brain regions, showing diagnostic features such as the size reduction of petrosal lobules and olfactory bulbs. However, the encephalization quotient (EQ) and neocortical ratio are lower than observed in extant flying squirrels. EQ is known to increase through time in squirrels, but might also be related to locomotion, given that arboreal and gliding squirrels display higher EQs than terrestrial ones. Because Miopetaurista was certainly a glider, its comparatively lower EQ and neocortical size support the existence of an independent trend of increasing EQ and neocortical complexity in this flying squirrel subclade.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Flying squirrels (Sciurinae, Pteromyini) are the most successful group of gliding mammals. However, their fossil record mostly consists of isolated dental remains that provide very limited insights into their palaeobiology and evolution. The first skeleton of a fossil flying squirrel, belonging to the species Miopetaurista neogrivensis, has been described only recently. It presents all the diagnostic gliding-related postcranial features of its extant relatives and shows that this group has undergone very little morphological change for almost 12 myr. However, the associated cranium is badly crushed, and particular details of the cranial morphology cannot be described. Here, we describe a well-preserved cranium of the closely related Miopetaurista crusafonti from 12.5–12.0 Ma from Bavaria (Germany). Its cranial morphology is found to be almost identical to extant large flying squirrels, even in details such as the position of the foramina. The virtual endocast also shows close affinities to living large flying squirrels in morphology and in the relative volume of different brain regions, showing diagnostic features such as the size reduction of petrosal lobules and olfactory bulbs. However, the encephalization quotient (EQ) and neocortical ratio are lower than observed in extant flying squirrels. EQ is known to increase through time in squirrels, but might also be related to locomotion, given that arboreal and gliding squirrels display higher EQs than terrestrial ones. Because Miopetaurista was certainly a glider, its comparatively lower EQ and neocortical size support the existence of an independent trend of increasing EQ and neocortical complexity in this flying squirrel subclade.
Gumińska, Natalia; Milanowski, Rafał
Charakterystyka kolistych DNA u Eukarya Journal Article
In: Postępy Biochemii, vol. 68, no. 2, pp. 129-141, 2022, ISSN: 2720-5959.
@article{Gumin2022Char,
title = {Charakterystyka kolistych DNA u Eukarya},
author = {Natalia Gumińska and Rafał Milanowski},
url = {https://postepybiochemii.ptbioch.edu.pl/index.php/PB/article/view/423},
doi = {10.18388/pb.2021_423 },
issn = {2720-5959},
year = {2022},
date = {2022-07-06},
journal = {Postępy Biochemii},
volume = {68},
number = {2},
pages = {129-141},
abstract = {W komórkach eukariotycznych DNA występuje głównie w formie liniowej, upakowanej w chromosomy. Poza tym może też przybierać postać kolistych cząsteczek. Najdokładniej zbadane zostały koliste DNA odgrywające rolę genomów mitochondriów i chloroplastów. Niemniej zasób kolistych DNA u Eukarya jest znacznie szerszy. Obejmuje również pozachromosomowe cząsteczki (ang. extrachromosomal circular DNA; eccDNA): koliste formy rDNA, pierścienie telomerowe, małe polidyspersyjne DNA, mikroDNA oraz inne typy kolistych DNA o pochodzeniu jądrowym. Występowanie eccDNA potwierdzono u wszystkich organizmów testowanych w tym zakresie. Dotychczasowe badania wykazały, że niektóre eccDNA są obecne na każdym etapie cyklu komórkowego, podczas gdy inne pojawiają się i/lub ulegają nagromadzeniu w szczególnych okolicznościach. Dowiedziono, że akumulacja eccDNA nierzadko zachodzi w następstwie poważnej destabilizacji genomu, będącej wynikiem stanów chorobowych czy stresu. Choć w środowisku naukowym wzrasta zainteresowanie eccDNA, pozostają one słabo poznanym składnikiem genomów eukariotycznych. Nadal niewiele wiadomo na temat mechanizmów ich formowania, ewolucji oraz ich funkcji biologicznych.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
W komórkach eukariotycznych DNA występuje głównie w formie liniowej, upakowanej w chromosomy. Poza tym może też przybierać postać kolistych cząsteczek. Najdokładniej zbadane zostały koliste DNA odgrywające rolę genomów mitochondriów i chloroplastów. Niemniej zasób kolistych DNA u Eukarya jest znacznie szerszy. Obejmuje również pozachromosomowe cząsteczki (ang. extrachromosomal circular DNA; eccDNA): koliste formy rDNA, pierścienie telomerowe, małe polidyspersyjne DNA, mikroDNA oraz inne typy kolistych DNA o pochodzeniu jądrowym. Występowanie eccDNA potwierdzono u wszystkich organizmów testowanych w tym zakresie. Dotychczasowe badania wykazały, że niektóre eccDNA są obecne na każdym etapie cyklu komórkowego, podczas gdy inne pojawiają się i/lub ulegają nagromadzeniu w szczególnych okolicznościach. Dowiedziono, że akumulacja eccDNA nierzadko zachodzi w następstwie poważnej destabilizacji genomu, będącej wynikiem stanów chorobowych czy stresu. Choć w środowisku naukowym wzrasta zainteresowanie eccDNA, pozostają one słabo poznanym składnikiem genomów eukariotycznych. Nadal niewiele wiadomo na temat mechanizmów ich formowania, ewolucji oraz ich funkcji biologicznych.
Cho, A.; Tikhonenkov, D. V.; Hehenberger, E.; Karnkowska, A.; Mylnikov, A. P.; Keeling, P. J.
Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles Journal Article
In: Molecular Phylogenetics and Evolution, vol. 171, pp. 107468, 2022.
@article{Cho2022,
title = {Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles},
author = {A. Cho and D. V. Tikhonenkov and E. Hehenberger and A. Karnkowska and A. P. Mylnikov and P. J. Keeling},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85127804129&doi=10.1016%2fj.ympev.2022.107468&partnerID=40&md5=4e9dc68e0f03addf392f1cf1b24bbcfc},
doi = {10.1016/j.ympev.2022.107468},
year = {2022},
date = {2022-06-01},
urldate = {2022-06-01},
journal = {Molecular Phylogenetics and Evolution},
volume = {171},
pages = {107468},
abstract = {Stramenopiles are a diverse but relatively well-studied eukaryotic supergroup with considerable genomic information available (Sibbald and Archibald, 2017). Nevertheless, the relationships between major stramenopile subgroups remain unresolved, in part due to a lack of data from small nanoflagellates that make up a lot of the genetic diversity of the group. This is most obvious in Bigyromonadea, which is one of four major stramenopile subgroups but represented by a single transcriptome. To examine the diversity of Bigyromonadea and how the lack of data affects the tree, we generated transcriptomes from seven novel bigyromonada species described in this study: Develocauda condao n. gen. n. sp., Develocanicus komovi n. gen. n. sp., Develocanicus vyazemskyi n. sp., Cubaremonas variflagellatum n. gen. n. sp., Pirsonia chemainus nom. prov., Feodosia pseudopoda nom. prov., and Koktebelia satura nom. prov. Both maximum likelihood and Bayesian phylogenomic trees based on a 247 gene-matrix recovered a monophyletic Bigyromonadea that includes two diverse subgroups, Developea and Pirsoniales, that were not previously related based on single gene trees. Maximum likelihood analyses show Bigyromonadea related to oomycetes, whereas Bayesian analyses and topology testing were inconclusive. We observed similarities between the novel bigyromonad species and motile zoospores of oomycetes in morphology and the ability to self-aggregate. Rare formation of pseudopods and fused cells were also observed, traits that are also found in members of labyrinthulomycetes, another osmotrophic stramenopiles. Furthermore, we report the first case of eukaryovory in the flagellated stages of Pirsoniales. These analyses reveal new diversity of Bigyromonadea, and altogether suggest their monophyly with oomycetes, collectively known as Pseudofungi, is the most likely topology of the stramenopile tree.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Stramenopiles are a diverse but relatively well-studied eukaryotic supergroup with considerable genomic information available (Sibbald and Archibald, 2017). Nevertheless, the relationships between major stramenopile subgroups remain unresolved, in part due to a lack of data from small nanoflagellates that make up a lot of the genetic diversity of the group. This is most obvious in Bigyromonadea, which is one of four major stramenopile subgroups but represented by a single transcriptome. To examine the diversity of Bigyromonadea and how the lack of data affects the tree, we generated transcriptomes from seven novel bigyromonada species described in this study: Develocauda condao n. gen. n. sp., Develocanicus komovi n. gen. n. sp., Develocanicus vyazemskyi n. sp., Cubaremonas variflagellatum n. gen. n. sp., Pirsonia chemainus nom. prov., Feodosia pseudopoda nom. prov., and Koktebelia satura nom. prov. Both maximum likelihood and Bayesian phylogenomic trees based on a 247 gene-matrix recovered a monophyletic Bigyromonadea that includes two diverse subgroups, Developea and Pirsoniales, that were not previously related based on single gene trees. Maximum likelihood analyses show Bigyromonadea related to oomycetes, whereas Bayesian analyses and topology testing were inconclusive. We observed similarities between the novel bigyromonad species and motile zoospores of oomycetes in morphology and the ability to self-aggregate. Rare formation of pseudopods and fused cells were also observed, traits that are also found in members of labyrinthulomycetes, another osmotrophic stramenopiles. Furthermore, we report the first case of eukaryovory in the flagellated stages of Pirsoniales. These analyses reveal new diversity of Bigyromonadea, and altogether suggest their monophyly with oomycetes, collectively known as Pseudofungi, is the most likely topology of the stramenopile tree.
Okrasińska, Alicja; Decewicz, Przemyslaw; Majchrowska, Maria; Dziewit, Lukasz; Muszewska, Anna; Dolatabadi, Somayeh; Kruszewski, Łukasz; Błocka, Zuzanna; Pawłowska, Julia
Marginal lands and fungi – linking the type of soil contamination with fungal community composition Journal Article
In: Environmental Microbiology, 2022.
@article{https://doi.org/10.1111/1462-2920.16007,
title = {Marginal lands and fungi – linking the type of soil contamination with fungal community composition},
author = {Alicja Okrasińska and Przemyslaw Decewicz and Maria Majchrowska and Lukasz Dziewit and Anna Muszewska and Somayeh Dolatabadi and Łukasz Kruszewski and Zuzanna Błocka and Julia Pawłowska},
url = {https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.16007},
doi = {https://doi.org/10.1111/1462-2920.16007},
year = {2022},
date = {2022-05-31},
journal = {Environmental Microbiology},
abstract = {Summary Fungi can be found in almost all ecosystems. Some of them can even survive in harsh, anthropogenically transformed environments, such as post-industrial soils. In order to verify how the soil fungal diversity may be changed by pollution, two soil samples from each of the 28 post-industrial sites were collected. Each soil sample was characterized in terms of concentration of heavy metals and petroleum derivatives. To identify soil fungal communities, fungal internal transcribed spacer 2 (ITS2) amplicon was sequenced for each sample using Illumina MiSeq platform. There were significant differences in the community structure and taxonomic diversity among the analysed samples. The highest taxon richness and evenness were observed in the non-polluted sites, and lower numbers of taxa were identified in multi-polluted soils. The presence of monocyclic aromatic hydrocarbons, gasoline and mineral oil was determined as the factors driving the differences in the mycobiome. Furthermore, in the culture-based selection experiment, two main groups of fungi growing on polluted media were identified – generalists able to live in the presence of pollution, and specialists adapted to the usage of BTEX as a sole source of energy. Our selection experiment proved that it is long-term soil contamination that shapes the community, rather than temporary addition of pollutant.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Summary Fungi can be found in almost all ecosystems. Some of them can even survive in harsh, anthropogenically transformed environments, such as post-industrial soils. In order to verify how the soil fungal diversity may be changed by pollution, two soil samples from each of the 28 post-industrial sites were collected. Each soil sample was characterized in terms of concentration of heavy metals and petroleum derivatives. To identify soil fungal communities, fungal internal transcribed spacer 2 (ITS2) amplicon was sequenced for each sample using Illumina MiSeq platform. There were significant differences in the community structure and taxonomic diversity among the analysed samples. The highest taxon richness and evenness were observed in the non-polluted sites, and lower numbers of taxa were identified in multi-polluted soils. The presence of monocyclic aromatic hydrocarbons, gasoline and mineral oil was determined as the factors driving the differences in the mycobiome. Furthermore, in the culture-based selection experiment, two main groups of fungi growing on polluted media were identified – generalists able to live in the presence of pollution, and specialists adapted to the usage of BTEX as a sole source of energy. Our selection experiment proved that it is long-term soil contamination that shapes the community, rather than temporary addition of pollutant.
Hałakuc, Paweł; Karnkowska, Anna; Milanowski, Rafał
Typical structure of rRNA coding genes in diplonemids points to two independent origins of the bizarre rDNA structures of euglenozoans Journal Article
In: BMC Ecology and Evolution, vol. 22, no. 1, pp. 59, 2022, ISSN: 2730-7182.
@article{Haakuc2022,
title = {Typical structure of rRNA coding genes in diplonemids points to two independent origins of the bizarre rDNA structures of euglenozoans},
author = {Paweł Hałakuc and Anna Karnkowska and Rafał Milanowski},
url = {https://doi.org/10.1186/s12862-022-02014-9
https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-022-02014-9},
doi = {10.1186/s12862-022-02014-9},
issn = {2730-7182},
year = {2022},
date = {2022-05-09},
journal = {BMC Ecology and Evolution},
volume = {22},
number = {1},
pages = {59},
abstract = {Members of Euglenozoa (Discoba) are known for unorthodox rDNA organization. In Euglenida rDNA is located on extrachromosomal circular DNA. In Kinetoplastea and Euglenida the core of the large ribosomal subunit, typically formed by the 28S rRNA, consists of several smaller rRNAs. They are the result of the presence of additional internal transcribed spacers (ITSs) in the rDNA. Diplonemea is the third of the main groups of Euglenozoa and its members are known to be among the most abundant and diverse protists in the oceans. Despite that, the rRNA of only one diplonemid species, Diplonema papillatum, has been examined so far and found to exhibit continuous 28S rRNA. Currently, the rDNA organization has not been researched for any diplonemid. Herein we investigate the structure of rRNA genes in classical (Diplonemidae) and deep-sea diplonemids (Eupelagonemidae), representing the majority of known diplonemid diversity. The results fill the gap in knowledge about diplonemid rDNA and allow better understanding of the evolution of the fragmented structure of the rDNA in Euglenozoa.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Members of Euglenozoa (Discoba) are known for unorthodox rDNA organization. In Euglenida rDNA is located on extrachromosomal circular DNA. In Kinetoplastea and Euglenida the core of the large ribosomal subunit, typically formed by the 28S rRNA, consists of several smaller rRNAs. They are the result of the presence of additional internal transcribed spacers (ITSs) in the rDNA. Diplonemea is the third of the main groups of Euglenozoa and its members are known to be among the most abundant and diverse protists in the oceans. Despite that, the rRNA of only one diplonemid species, Diplonema papillatum, has been examined so far and found to exhibit continuous 28S rRNA. Currently, the rDNA organization has not been researched for any diplonemid. Herein we investigate the structure of rRNA genes in classical (Diplonemidae) and deep-sea diplonemids (Eupelagonemidae), representing the majority of known diplonemid diversity. The results fill the gap in knowledge about diplonemid rDNA and allow better understanding of the evolution of the fragmented structure of the rDNA in Euglenozoa.
Dzik, Jerzy; Phong, Nguyen Duc; Thuy, Nguyen Thi; Swiś, Przemyslaw
Evolution and migration of conodonts and ammonoids near the end of Devonian recorded in distant localities Journal Article
In: Stratigraphy, vol. 19, no. 1, pp. 27-50, 2022.
@article{Dzik2022,
title = {Evolution and migration of conodonts and ammonoids near the end of Devonian recorded in distant localities},
author = {Jerzy Dzik and Nguyen Duc Phong and Nguyen Thi Thuy and Przemyslaw Swiś},
url = {https://www.micropress.org/microaccess/check/2272},
year = {2022},
date = {2022-03-15},
journal = {Stratigraphy},
volume = {19},
number = {1},
pages = {27-50},
abstract = {The Devonian-Carboniferous boundary is allegedly marked by one of the most catastrophic global extinctions associated with sedimentation of the Hangenberg black shale. A dense sampling of the Kowala section in the Holy Cross Mountains, Poland, challenges this view, showing that the faunal dynamics across the Hangenberg black shalewas not more dramatic than that across the preceding Kowala black shale. Quantitative analysis and biologically meaningful conodont apparatus study of the Kowala material offer probably the most complete record of faunal change in the latest Famennian and earliest Tournaisian among those sampled bed-by-bed for ammonoids and conodonts. It appears that the faunal dynamics of both cephalopods and conodonts was controlled by environmental changes that resulted in numerous immigrations and disappearances of particular lineages. Only a small fraction of lineages persisted long enough at the place, and transformed their morphology fast enough, to leave a record of their evolution. Most of the evolution apparently took place elsewhere. Locations of remote refugia where these lineages evolved in the time span bracketed by the Kowala and Hangenberg black shale events remain to be identified. Conodont apparatus study on geographically distant Vietnamese locality Cat Ba provides evidence that at least in the latest Famennian some conodont species unknown from Poland were present in Vietnam. Moreover, the contribution of species known from both localities to Polish and Vietnamese fossil assemblages was dramatically different.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The Devonian-Carboniferous boundary is allegedly marked by one of the most catastrophic global extinctions associated with sedimentation of the Hangenberg black shale. A dense sampling of the Kowala section in the Holy Cross Mountains, Poland, challenges this view, showing that the faunal dynamics across the Hangenberg black shalewas not more dramatic than that across the preceding Kowala black shale. Quantitative analysis and biologically meaningful conodont apparatus study of the Kowala material offer probably the most complete record of faunal change in the latest Famennian and earliest Tournaisian among those sampled bed-by-bed for ammonoids and conodonts. It appears that the faunal dynamics of both cephalopods and conodonts was controlled by environmental changes that resulted in numerous immigrations and disappearances of particular lineages. Only a small fraction of lineages persisted long enough at the place, and transformed their morphology fast enough, to leave a record of their evolution. Most of the evolution apparently took place elsewhere. Locations of remote refugia where these lineages evolved in the time span bracketed by the Kowala and Hangenberg black shale events remain to be identified. Conodont apparatus study on geographically distant Vietnamese locality Cat Ba provides evidence that at least in the latest Famennian some conodont species unknown from Poland were present in Vietnam. Moreover, the contribution of species known from both localities to Polish and Vietnamese fossil assemblages was dramatically different.
NN, Wijayawardene; KD, Hyde; DQ, Dai; M, Sánchez-García; BT, Goto; RK, Saxena; M, Erdoğdu; F, Selçuk; KC, Rajeshkumar; A, Aptroot; J, Błaszkowski; N, Boonyuen; da Silva GA,; de Souza FA,; W, Dong; D, Ertz; D, Haelewaters; EBG, Jones; SC, Karunarathna; PM, Kirk; M, Kukwa; J, Kumla; DV, Leontyev; HT, Lumbsch; SSN, Maharachchikumbura; F, Marguno; P, Martínez-Rodríguez; A, Mešić; JS, Monteiro; F, Oehl; J, Pawłowska; D, Pem; WP, Pfliegler; AJL, Phillips; A, Pošta; MQ, He; JX, Li; M, Raza; OP, Sruthi; S, Suetrong; N, Suwannarach; L, Tedersoo; V, Thiyagaraja; S, Tibpromma; Z, Tkalčec; YS, Tokarev; DN, Wanasinghe; DSA, Wijesundara; SDMK, Wimalaseana; H, Madrid; GQ, Zhang; Y, Gao; I, Sánchez-Castro; LZ, Tang; M, Stadler; A, Yurkov; M, Thines
Outline of Fungi and fungus-like taxa – 2021 Journal Article
In: Mycosphere, vol. 13, no. 1, pp. 53-453, 2022.
@article{Wijayawardene2022,
title = {Outline of Fungi and fungus-like taxa – 2021},
author = {Wijayawardene NN and Hyde KD and Dai DQ and Sánchez-García M and Goto BT and Saxena RK and Erdoğdu M and Selçuk F and Rajeshkumar KC and Aptroot A and Błaszkowski J and Boonyuen N and da Silva GA and de Souza FA and Dong W and Ertz D and Haelewaters D and Jones EBG and Karunarathna SC and Kirk PM and Kukwa M and Kumla J and Leontyev DV and Lumbsch HT and Maharachchikumbura SSN and Marguno F and Martínez-Rodríguez P and Mešić A and Monteiro JS and Oehl F and Pawłowska J and Pem D and Pfliegler WP and Phillips AJL and Pošta A and He MQ and Li JX and Raza M and Sruthi OP and Suetrong S and Suwannarach N and Tedersoo L and Thiyagaraja V and Tibpromma S and Tkalčec Z and Tokarev YS and Wanasinghe DN and Wijesundara DSA and Wimalaseana SDMK and Madrid H and Zhang GQ and Gao Y and Sánchez-Castro I and Tang LZ and Stadler M and Yurkov A and Thines M},
url = {https://www.mycosphere.org/pdf/MYCOSPHERE_13_1_2.pdf},
doi = {Doi 10.5943/mycosphere/13/1/2},
year = {2022},
date = {2022-02-23},
journal = {Mycosphere},
volume = {13},
number = {1},
pages = {53-453},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pawlak, Wojciech; Rozwalak, Piotr; Sulej, Tomasz
Triassic fish faunas from Miedary (Upper Silesia, Poland) and their implications for understanding paleosalinity Journal Article
In: Palaeogeography, Palaeoclimatology, Palaeoecology, vol. 590, pp. 110860, 2022, ISSN: 0031-0182.
@article{Pawlak_2022,
title = {Triassic fish faunas from Miedary (Upper Silesia, Poland) and their implications for understanding paleosalinity},
author = {Wojciech Pawlak and Piotr Rozwalak and Tomasz Sulej},
url = {https://www.sciencedirect.com/science/article/abs/pii/S003101822200030X},
issn = {0031-0182},
year = {2022},
date = {2022-02-09},
urldate = {2022-01-01},
journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
volume = {590},
pages = {110860},
abstract = {We describe two new fish-dominated faunas from the Middle Triassic (Ladinian) Miedary site, Upper Silesia, Poland, and present a comparative analysis of Middle-to-Late Triassic vertebrate assemblages from the Germanic Basin, in order to explore the influence of salinity on faunal composition. The composition of the assemblage from dolomite beds at Miedary is similar to those from the Muschalkalk facies, whereas the assemblage from glauconite beds appears to be the first brackish vertebrate assemblage of the Serrolepis lake-type recognized from the eastern Germanic Basin. Comparative analysis of all sites, using hierarchical clustering, nonmetric multidimensional scaling, and principal component approaches, revealed the existence of vertebrate taxa associated withfreshwater, brackish and marine conditions, as well as euryhaline taxa with wide salinity preferences. Moreover, it confirms the brackish nature of Serrolepis-bearing assemblages, and suggests that Serrolepis suevicus is a brackish specialist, indicative of oligohaline to miohaline paleosalinities. The Middle-Late Triassic vertebrate faunas appear dominated by stenohaline taxa, with a conspicuous separation of species living in the freshwater and marine conditions. The euryhaline taxa are rare, and comprise Acrodus lateralis, Eusauropterygia, Lissodus nodosus, and Saurichthyiformes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We describe two new fish-dominated faunas from the Middle Triassic (Ladinian) Miedary site, Upper Silesia, Poland, and present a comparative analysis of Middle-to-Late Triassic vertebrate assemblages from the Germanic Basin, in order to explore the influence of salinity on faunal composition. The composition of the assemblage from dolomite beds at Miedary is similar to those from the Muschalkalk facies, whereas the assemblage from glauconite beds appears to be the first brackish vertebrate assemblage of the Serrolepis lake-type recognized from the eastern Germanic Basin. Comparative analysis of all sites, using hierarchical clustering, nonmetric multidimensional scaling, and principal component approaches, revealed the existence of vertebrate taxa associated withfreshwater, brackish and marine conditions, as well as euryhaline taxa with wide salinity preferences. Moreover, it confirms the brackish nature of Serrolepis-bearing assemblages, and suggests that Serrolepis suevicus is a brackish specialist, indicative of oligohaline to miohaline paleosalinities. The Middle-Late Triassic vertebrate faunas appear dominated by stenohaline taxa, with a conspicuous separation of species living in the freshwater and marine conditions. The euryhaline taxa are rare, and comprise Acrodus lateralis, Eusauropterygia, Lissodus nodosus, and Saurichthyiformes.
Karlicki, Michał; Antonowicz, Stanisław; Karnkowska, Anna
Tiara: deep learning-based classification system for eukaryotic sequences Journal Article
In: Bioinformatics, vol. 38, no. 2, pp. 344–350, 2022.
@article{Karlicki_2021,
title = {Tiara: deep learning-based classification system for eukaryotic sequences},
author = {Michał Karlicki and Stanisław Antonowicz and Anna Karnkowska},
editor = {Inanc Birol},
url = {https://doi.org/10.1093%2Fbioinformatics%2Fbtab672},
doi = {10.1093/bioinformatics/btab672},
year = {2022},
date = {2022-01-07},
journal = {Bioinformatics},
volume = {38},
number = {2},
pages = {344–350},
publisher = {Oxford University Press (OUP)},
abstract = {Abstract
Motivation
With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of eukaryotic diversity.
Results
We developed Tiara, a deep-learning-based approach for the identification of eukaryotic sequences in the metagenomic datasets. Its two-step classification process enables the classification of nuclear and organellar eukaryotic fractions and subsequently divides organellar sequences into plastidial and mitochondrial. Using the test dataset, we have shown that Tiara performed similarly to EukRep for prokaryotes classification and outperformed it for eukaryotes classification with lower calculation time. In the tests on the real data, Tiara performed better than EukRep in analyzing the small dataset representing eukaryotic cell microbiome and large dataset from the pelagic zone of oceans. Tiara is also the only available tool correctly classifying organellar sequences, which was confirmed by the recovery of nearly complete plastid and mitochondrial genomes from the test data and real metagenomic data.
Availability and implementation
Tiara is implemented in python 3.8, available at https://github.com/ibe-uw/tiara and tested on Unix-based systems. It is released under an open-source MIT license and documentation is available at https://ibe-uw.github.io/tiara. Version 1.0.1 of Tiara has been used for all benchmarks.
Supplementary information
Supplementary data are available at Bioinformatics online.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract
Motivation
With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of eukaryotic diversity.
Results
We developed Tiara, a deep-learning-based approach for the identification of eukaryotic sequences in the metagenomic datasets. Its two-step classification process enables the classification of nuclear and organellar eukaryotic fractions and subsequently divides organellar sequences into plastidial and mitochondrial. Using the test dataset, we have shown that Tiara performed similarly to EukRep for prokaryotes classification and outperformed it for eukaryotes classification with lower calculation time. In the tests on the real data, Tiara performed better than EukRep in analyzing the small dataset representing eukaryotic cell microbiome and large dataset from the pelagic zone of oceans. Tiara is also the only available tool correctly classifying organellar sequences, which was confirmed by the recovery of nearly complete plastid and mitochondrial genomes from the test data and real metagenomic data.
Availability and implementation
Tiara is implemented in python 3.8, available at https://github.com/ibe-uw/tiara and tested on Unix-based systems. It is released under an open-source MIT license and documentation is available at https://ibe-uw.github.io/tiara. Version 1.0.1 of Tiara has been used for all benchmarks.
Supplementary information
Supplementary data are available at Bioinformatics online.
Motivation
With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of eukaryotic diversity.
Results
We developed Tiara, a deep-learning-based approach for the identification of eukaryotic sequences in the metagenomic datasets. Its two-step classification process enables the classification of nuclear and organellar eukaryotic fractions and subsequently divides organellar sequences into plastidial and mitochondrial. Using the test dataset, we have shown that Tiara performed similarly to EukRep for prokaryotes classification and outperformed it for eukaryotes classification with lower calculation time. In the tests on the real data, Tiara performed better than EukRep in analyzing the small dataset representing eukaryotic cell microbiome and large dataset from the pelagic zone of oceans. Tiara is also the only available tool correctly classifying organellar sequences, which was confirmed by the recovery of nearly complete plastid and mitochondrial genomes from the test data and real metagenomic data.
Availability and implementation
Tiara is implemented in python 3.8, available at https://github.com/ibe-uw/tiara and tested on Unix-based systems. It is released under an open-source MIT license and documentation is available at https://ibe-uw.github.io/tiara. Version 1.0.1 of Tiara has been used for all benchmarks.
Supplementary information
Supplementary data are available at Bioinformatics online.
Maciszewski, Kacper; Dabbagh, Nadja; Preisfeld, Angelika; Karnkowska, Anna
Maturyoshka: A maturase inside a maturase, and other peculiarities of the novel chloroplast genomes of marine euglenophytes Journal Article
In: Molecular Phylogenetics and Evolution, vol. 170, pp. 107441, 2022, ISSN: 1055-7903.
@article{MACISZEWSKI2022107441,
title = {Maturyoshka: A maturase inside a maturase, and other peculiarities of the novel chloroplast genomes of marine euglenophytes},
author = {Kacper Maciszewski and Nadja Dabbagh and Angelika Preisfeld and Anna Karnkowska},
url = {https://www.sciencedirect.com/science/article/pii/S1055790322000549},
doi = {https://doi.org/10.1016/j.ympev.2022.107441},
issn = {1055-7903},
year = {2022},
date = {2022-01-01},
journal = {Molecular Phylogenetics and Evolution},
volume = {170},
pages = {107441},
abstract = {Organellar genomes often carry group II introns, which occasionally encode proteins called maturases that are important for splicing. The number of introns varies substantially among various organellar genomes, and bursts of introns have been observed in multiple eukaryotic lineages, including euglenophytes, with more than 100 introns in their plastid genomes. To examine the evolutionary diversity and history of maturases, an essential gene family among euglenophytes, we searched for their homologs in newly sequenced and published plastid genomes representing all major euglenophyte lineages. We found that maturase content in plastid genomes has a patchy distribution, with a maximum of eight of them present in Eutreptiella eupharyngea. The most basal lineages of euglenophytes, Eutreptiales, share the highest number of maturases, but the lowest number of introns. We also identified a peculiar convoluted structure of a gene located in an intron, in a gene within an intron, within yet another gene, present in some Eutreptiales. Further investigation of functional domains of identified maturases show that most of them lost at least one of the functional domains, which implies that the patchy maturase distribution is due to frequent inactivation and eventual loss over time. Finally, we identified the diversified evolutionary origin of analysed maturases, which were acquired along with the green algal plastid or horizontally transferred. These findings indicate that euglenophytes' plastid maturases have experienced a surprisingly dynamic history due to gains from diversified donors, their retention, and loss.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Organellar genomes often carry group II introns, which occasionally encode proteins called maturases that are important for splicing. The number of introns varies substantially among various organellar genomes, and bursts of introns have been observed in multiple eukaryotic lineages, including euglenophytes, with more than 100 introns in their plastid genomes. To examine the evolutionary diversity and history of maturases, an essential gene family among euglenophytes, we searched for their homologs in newly sequenced and published plastid genomes representing all major euglenophyte lineages. We found that maturase content in plastid genomes has a patchy distribution, with a maximum of eight of them present in Eutreptiella eupharyngea. The most basal lineages of euglenophytes, Eutreptiales, share the highest number of maturases, but the lowest number of introns. We also identified a peculiar convoluted structure of a gene located in an intron, in a gene within an intron, within yet another gene, present in some Eutreptiales. Further investigation of functional domains of identified maturases show that most of them lost at least one of the functional domains, which implies that the patchy maturase distribution is due to frequent inactivation and eventual loss over time. Finally, we identified the diversified evolutionary origin of analysed maturases, which were acquired along with the green algal plastid or horizontally transferred. These findings indicate that euglenophytes' plastid maturases have experienced a surprisingly dynamic history due to gains from diversified donors, their retention, and loss.
Miłobedzka, Aleksandra; Ferreira, Catarina; Vaz-Moreira, Ivone; Calderón-Franco, David; Gorecki, Adrian; Purkrtova, Sabina; Bartacek, Jan; Dziewit, Lukasz; Singleton, Caitlin M; Nielsen, Per Halkjær; Weissbrodt, David Gregory; Manaia, Célia M
Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle Journal Article
In: Journal of Hazardous Materials, vol. 424, pp. 127407, 2022, ISSN: 0304-3894.
@article{MILOBEDZKA2022127407,
title = {Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle},
author = {Aleksandra Miłobedzka and Catarina Ferreira and Ivone Vaz-Moreira and David Calderón-Franco and Adrian Gorecki and Sabina Purkrtova and Jan Bartacek and Lukasz Dziewit and Caitlin M Singleton and Per Halkjær Nielsen and David Gregory Weissbrodt and Célia M Manaia},
url = {https://www.sciencedirect.com/science/article/pii/S030438942102375X},
doi = {https://doi.org/10.1016/j.jhazmat.2021.127407},
issn = {0304-3894},
year = {2022},
date = {2022-01-01},
journal = {Journal of Hazardous Materials},
volume = {424},
pages = {127407},
abstract = {Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion.
Chaber, Katarzyna; Łukomska-Kowalczyk, Maja; Fells, Alicja; Milanowski, Rafał; Zakryś, Bożena
Toward the robust resolution of taxonomic ambiguity within Lepocinclis (Euglenida) based on DNA sequencing and morphology Journal Article
In: Journal of Phycology, vol. 58, no. 1, pp. 105-120, 2022.
@article{https://doi.org/10.1111/jpy.13220,
title = {Toward the robust resolution of taxonomic ambiguity within Lepocinclis (Euglenida) based on DNA sequencing and morphology},
author = {Katarzyna Chaber and Maja Łukomska-Kowalczyk and Alicja Fells and Rafał Milanowski and Bożena Zakryś},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13220},
doi = {https://doi.org/10.1111/jpy.13220},
year = {2022},
date = {2022-01-01},
journal = {Journal of Phycology},
volume = {58},
number = {1},
pages = {105-120},
abstract = {DNA sequences were analyzed for three groups of species from the Lepocinclis genus (L. acus-like, L. oxyuris-like, and L. tripteris-like) along with cellular morphology. Phylogenetic analyses were based on nuclear SSU rDNA, LSU rDNA, and plastid-encoded LSU rDNA. DNA sequences were obtained from species available in culture collections (L. acus SAG 1224-1a and UTEX 1316) and those isolated directly from the environment in Poland (48 isolates), resulting in 79 new sequences. The obtained phylogenetic tree of Lepocinclis included 27 taxa, five of which are presented for the first time (L. convoluta, L. gracillimoides, L. longissima, L. pseudospiroides, and L. torta) and nine taxonomically verified and described. Based on morphology, literature data, and phylogenetic analyses, the following species were distinguished: in the L. acus-like group, L. longissima and L. acus; in the L. tripteris-like group, L. pseudospiroides, L. torta, and L. tripteris; in the L. oxyuris-like group, L. gracillimoides, L. oxyuris var. oxyuris, and L. oxyuris var. helicoidea. For all verified species, diagnostic descriptions were emended, nomenclatural adjustments were made, and epitypes were designated.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
DNA sequences were analyzed for three groups of species from the Lepocinclis genus (L. acus-like, L. oxyuris-like, and L. tripteris-like) along with cellular morphology. Phylogenetic analyses were based on nuclear SSU rDNA, LSU rDNA, and plastid-encoded LSU rDNA. DNA sequences were obtained from species available in culture collections (L. acus SAG 1224-1a and UTEX 1316) and those isolated directly from the environment in Poland (48 isolates), resulting in 79 new sequences. The obtained phylogenetic tree of Lepocinclis included 27 taxa, five of which are presented for the first time (L. convoluta, L. gracillimoides, L. longissima, L. pseudospiroides, and L. torta) and nine taxonomically verified and described. Based on morphology, literature data, and phylogenetic analyses, the following species were distinguished: in the L. acus-like group, L. longissima and L. acus; in the L. tripteris-like group, L. pseudospiroides, L. torta, and L. tripteris; in the L. oxyuris-like group, L. gracillimoides, L. oxyuris var. oxyuris, and L. oxyuris var. helicoidea. For all verified species, diagnostic descriptions were emended, nomenclatural adjustments were made, and epitypes were designated.
Frankiewicz, Kamil E; Banasiak, Łukasz; Oskolski, Alexei; Reduron, Jean-Pierre; Reyes-Betancort, Jorge Alfredo; Alsarraf, Mohammed; Trzeciak, Paulina; Spalik, Krzysztof
Long-distance dispersal events rather than growth habit and life-history traits affect diversification rate in tribe Apieae (Apiaceae) Journal Article
In: Botanical Journal of the Linnean Society, vol. 198, no. 1, pp. 1–25, 2022, ISSN: 0024-4074, (boab032).
@article{10.1093/botlinnean/boab032,
title = {Long-distance dispersal events rather than growth habit and life-history traits affect diversification rate in tribe Apieae (Apiaceae)},
author = {Kamil E Frankiewicz and Łukasz Banasiak and Alexei Oskolski and Jean-Pierre Reduron and Jorge Alfredo Reyes-Betancort and Mohammed Alsarraf and Paulina Trzeciak and Krzysztof Spalik},
url = {https://doi.org/10.1093/botlinnean/boab032},
doi = {10.1093/botlinnean/boab032},
issn = {0024-4074},
year = {2022},
date = {2022-01-01},
journal = {Botanical Journal of the Linnean Society},
volume = {198},
number = {1},
pages = {1–25},
abstract = {Factors influencing diversification rates may be of intrinsic (e.g. morphological novelties) or extrinsic (e.g. long-distance dispersal, availability of ecological niches) nature. Growth habit may influence diversification rates because herbaceous plants often have shorter generation times and a more pronounced r reproductive strategy than their woody relatives. We examined life history and habit evolution, wood anatomy and biogeographical history of Apiaceae tribe Apieae in conjunction with diversification rate analysis to explore which factors may have affected clade species richness and to elucidate the constraints on the evolution of secondary woodiness in this group. We demonstrate that diversification rates are similar in morphologically homogeneous and diverse clades and in herbaceous and woody lineages. The only clade with a significantly elevated diversification rate is Southern Hemisphere Apium, in which diversity probably resulted from several long-distance dispersal events. We also show that wood anatomy in herbaceous and woody species does not differ considerably regardless of their continental or insular origin, but it is affected by stem architecture and plant reproductive strategy. As the taxonomy of Apieae suffers from inflation with numerous monotypic genera, we propose to include Canaria in Rutheopsis, and Foeniculum, Schoenoselinum, Ridolfia and Pseudoridolfia in Anethum.},
note = {boab032},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Factors influencing diversification rates may be of intrinsic (e.g. morphological novelties) or extrinsic (e.g. long-distance dispersal, availability of ecological niches) nature. Growth habit may influence diversification rates because herbaceous plants often have shorter generation times and a more pronounced r reproductive strategy than their woody relatives. We examined life history and habit evolution, wood anatomy and biogeographical history of Apiaceae tribe Apieae in conjunction with diversification rate analysis to explore which factors may have affected clade species richness and to elucidate the constraints on the evolution of secondary woodiness in this group. We demonstrate that diversification rates are similar in morphologically homogeneous and diverse clades and in herbaceous and woody lineages. The only clade with a significantly elevated diversification rate is Southern Hemisphere Apium, in which diversity probably resulted from several long-distance dispersal events. We also show that wood anatomy in herbaceous and woody species does not differ considerably regardless of their continental or insular origin, but it is affected by stem architecture and plant reproductive strategy. As the taxonomy of Apieae suffers from inflation with numerous monotypic genera, we propose to include Canaria in Rutheopsis, and Foeniculum, Schoenoselinum, Ridolfia and Pseudoridolfia in Anethum.
Baczyński, Jakub; Sauquet, Hervé; Spalik, Krzysztof
Exceptional evolutionary lability of flower-like inflorescences (pseudanthia) in Apiaceae subfamily Apioideae Journal Article
In: American Journal of Botany, vol. 109, no. 3, pp. 437-455, 2022.
@article{https://doi.org/10.1002/ajb2.1819,
title = {Exceptional evolutionary lability of flower-like inflorescences (pseudanthia) in Apiaceae subfamily Apioideae},
author = {Jakub Baczyński and Hervé Sauquet and Krzysztof Spalik},
url = {https://bsapubs.onlinelibrary.wiley.com/doi/abs/10.1002/ajb2.1819},
doi = {https://doi.org/10.1002/ajb2.1819},
year = {2022},
date = {2022-01-01},
journal = {American Journal of Botany},
volume = {109},
number = {3},
pages = {437-455},
abstract = {Abstract Premise Pseudanthia are widespread and have long been postulated to be a key innovation responsible for some of the angiosperm radiations. The aim of our study was to analyze macroevolutionary patterns of these flower-like inflorescences and their potential correlation with diversification rates in Apiaceae subfamily Apioideae. In particular, we were interested to investigate evolvability of pseudanthia and evaluate their potential association with changes in the size of floral display. Methods The framework for our analyses consisted of a time-calibrated phylogeny of 1734 representatives of Apioideae and a morphological matrix of inflorescence traits encoded for 847 species. Macroevolutionary patterns in pseudanthia were inferred using Markov models of discrete character evolution and stochastic character mapping, and a principal component analysis was used to visualize correlations in inflorescence architecture. The interdependence between net diversification rates and the occurrence of pseudocorollas was analyzed with trait-independent and trait-dependent approaches. Results Pseudanthia evolved in 10 major clades of Apioideae with at least 36 independent origins and 46 reversals. The morphospace analysis recovered differences in color and compactness between floral and hyperfloral pseudanthia. A correlation between pseudocorollas and size of inflorescence was also strongly supported. Contrary to our predictions, pseudanthia are not responsible for variation in diversification rates identified in this subfamily. Conclusions Our results suggest that pseudocorollas evolve as an answer to the trade-off between enlargement of floral display and costs associated with production of additional flowers. The high evolvability and architectural differences in apioid pseudanthia may be explained on the basis of adaptive wandering and evolutionary developmental biology.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract Premise Pseudanthia are widespread and have long been postulated to be a key innovation responsible for some of the angiosperm radiations. The aim of our study was to analyze macroevolutionary patterns of these flower-like inflorescences and their potential correlation with diversification rates in Apiaceae subfamily Apioideae. In particular, we were interested to investigate evolvability of pseudanthia and evaluate their potential association with changes in the size of floral display. Methods The framework for our analyses consisted of a time-calibrated phylogeny of 1734 representatives of Apioideae and a morphological matrix of inflorescence traits encoded for 847 species. Macroevolutionary patterns in pseudanthia were inferred using Markov models of discrete character evolution and stochastic character mapping, and a principal component analysis was used to visualize correlations in inflorescence architecture. The interdependence between net diversification rates and the occurrence of pseudocorollas was analyzed with trait-independent and trait-dependent approaches. Results Pseudanthia evolved in 10 major clades of Apioideae with at least 36 independent origins and 46 reversals. The morphospace analysis recovered differences in color and compactness between floral and hyperfloral pseudanthia. A correlation between pseudocorollas and size of inflorescence was also strongly supported. Contrary to our predictions, pseudanthia are not responsible for variation in diversification rates identified in this subfamily. Conclusions Our results suggest that pseudocorollas evolve as an answer to the trade-off between enlargement of floral display and costs associated with production of additional flowers. The high evolvability and architectural differences in apioid pseudanthia may be explained on the basis of adaptive wandering and evolutionary developmental biology.
2021
Pedro, Crous; Osieck, E. R; (...) Pawłowska, Julia; Portugal, A; (...),; Trovão, João; (...) Groenewald, J. Z.
Fungal Planet description sheets: 1284–1382 Journal Article
In: Persoonia, vol. 47, pp. 309, 2021, ISSN: 1878-9080.
@article{Trovão2021,
title = {Fungal Planet description sheets: 1284–1382},
author = {Crous Pedro and Osieck, E.R and (...) Pawłowska, Julia and Portugal, A and (...) and Trovão, João and (...) Groenewald, J.Z.},
url = {https://www.ingentaconnect.com/contentone/nhn/pimj/2021/00000047/00000001/art00006},
doi = {https://doi.org/10.3767/persoonia.2021.47.06},
issn = {1878-9080},
year = {2021},
date = {2021-12-24},
journal = {Persoonia},
volume = {47},
pages = {309},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Treitli, Sebastian Cristian; Peña-Diaz, Priscila; Hałakuc, Paweł; Karnkowska, Anna; Hampl, Vladimír
High quality genome assembly of the amitochondriate eukaryote Monocercomonoides exilis Journal Article
In: Microbial Genomics, vol. 7, no. 12, pp. 000745, 2021, ISSN: 2057-5858.
@article{mbs:/content/journal/mgen/10.1099/mgen.0.000745,
title = {High quality genome assembly of the amitochondriate eukaryote Monocercomonoides exilis},
author = {Sebastian Cristian Treitli and Priscila Peña-Diaz and Paweł Hałakuc and Anna Karnkowska and Vladimír Hampl},
url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000745},
doi = {https://doi.org/10.1099/mgen.0.000745},
issn = {2057-5858},
year = {2021},
date = {2021-12-24},
journal = {Microbial Genomics},
volume = {7},
number = {12},
pages = {000745},
publisher = {Microbiology Society},
abstract = {Monocercomonoides exilis is considered the first known eukaryote to completely lack mitochondria. This conclusion is based primarily on a genomic and transcriptomic study which failed to identify any mitochondrial hallmark proteins. However, the available genome assembly has limited contiguity and around 1.5 % of the genome sequence is represented by unknown bases. To improve the contiguity, we re-sequenced the genome and transcriptome of M. exilis using Oxford Nanopore Technology (ONT). The resulting draft genome is assembled in 101 contigs with an N50 value of 1.38 Mbp, almost 20 times higher than the previously published assembly. Using a newly generated ONT transcriptome, we further improve the gene prediction and add high quality untranslated region (UTR) annotations, in which we identify two putative polyadenylation signals present in the 3′UTR regions and characterise the Kozak sequence in the 5′UTR regions. All these improvements are reflected by higher BUSCO genome completeness values. Regardless of an overall more complete genome assembly without missing bases and a better gene prediction, we still failed to identify any mitochondrial hallmark genes, thus further supporting the hypothesis on the absence of mitochondrion.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Monocercomonoides exilis is considered the first known eukaryote to completely lack mitochondria. This conclusion is based primarily on a genomic and transcriptomic study which failed to identify any mitochondrial hallmark proteins. However, the available genome assembly has limited contiguity and around 1.5 % of the genome sequence is represented by unknown bases. To improve the contiguity, we re-sequenced the genome and transcriptome of M. exilis using Oxford Nanopore Technology (ONT). The resulting draft genome is assembled in 101 contigs with an N50 value of 1.38 Mbp, almost 20 times higher than the previously published assembly. Using a newly generated ONT transcriptome, we further improve the gene prediction and add high quality untranslated region (UTR) annotations, in which we identify two putative polyadenylation signals present in the 3′UTR regions and characterise the Kozak sequence in the 5′UTR regions. All these improvements are reflected by higher BUSCO genome completeness values. Regardless of an overall more complete genome assembly without missing bases and a better gene prediction, we still failed to identify any mitochondrial hallmark genes, thus further supporting the hypothesis on the absence of mitochondrion.
Leonhard, Isabella; Shirley, Bryan; Murdock, Duncan J E; Repetski, John; Jarochowska, Emilia
Growth and feeding ecology of coniform conodonts Journal Article
In: PeerJ, vol. 9, pp. e12505, 2021, ISSN: 2167-8359.
@article{Leonhard2021,
title = {Growth and feeding ecology of coniform conodonts},
author = {Isabella Leonhard and Bryan Shirley and Duncan J E Murdock and John Repetski and Emilia Jarochowska},
doi = {10.7717/peerj.12505},
issn = {2167-8359},
year = {2021},
date = {2021-12-15},
journal = {PeerJ},
volume = {9},
pages = {e12505},
abstract = {<p> Conodonts were the first vertebrates to develop mineralized dental tools, known as elements. Recent research suggests that conodonts were macrophagous predators and/or scavengers but we do not know how this feeding habit emerged in the earliest coniform conodonts, since most studies focus on the derived, ‘complex’ conodonts. Previous modelling of element position and mechanical properties indicate they were capable of food processing. A direct test would be provided through evidence of <italic>in vivo</italic> element crown tissue damage or through <italic>in vivo</italic> incorporated chemical proxies for a shift in their trophic position during ontogeny. Here we focus on coniform elements from two conodont taxa, the phylogenetically primitive <italic>Proconodontus muelleri</italic> Miller, 1969 from the late Cambrian and the more derived <italic>Panderodus equicostatus</italic> Rhodes, 1954 from the Silurian. Proposing that this extremely small sample is, however, representative for these taxa, we aim to describe in detail the growth of an element from each of these taxa in order to the test the following hypotheses: (1) <italic>Panderodus</italic> and <italic>Proconodontus</italic> processed hard food, which led to damage of their elements consistent with prey capture function; and (2) both genera shifted towards higher trophic levels during ontogeny. We employed backscatter electron (BSE) imaging, energy-dispersive X-ray spectroscopy (EDX) and synchrotron radiation X-ray tomographic microscopy (SRXTM) to identify growth increments, wear and damage surfaces, and the Sr/Ca ratio in bioapatite as a proxy for the trophic position. Using these data, we can identify whether they exhibit determinate or indeterminate growth and whether both species followed linear or allometric growth dynamics. Growth increments (27 in <italic>Pa. equicostatus</italic> and 58 in <italic>Pr. muelleri</italic> ) were formed in bundles of 4–7 increments in <italic>Pa. equicostatus</italic> and 7–9 in <italic>Pr. muelleri</italic> . We interpret the bundles as analogous to Retzius periodicity in vertebrate teeth. Based on applied optimal resource allocation models, internal periodicity might explain indeterminate growth in both species. They also allow us to interpret the almost linear growth of both individuals as an indicator that there was no size-dependent increase in mortality in the ecosystems where they lived <italic>e.g</italic> ., as would be the case in the presence of larger predators. Our findings show that periodic growth was present in early conodonts and preceded tissue repair in response to wear and damage. We found no microwear and the Sr/Ca ratio, and therefore the trophic position, did not change substantially during the lifetimes of either individual. Trophic ecology of coniform conodonts differed from the predatory and/or scavenger lifestyle documented for “complex” conodonts. We propose that conodonts adapted their life histories to top-down controlled ecosystems during the Nekton Revolution. </p>},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
<p> Conodonts were the first vertebrates to develop mineralized dental tools, known as elements. Recent research suggests that conodonts were macrophagous predators and/or scavengers but we do not know how this feeding habit emerged in the earliest coniform conodonts, since most studies focus on the derived, ‘complex’ conodonts. Previous modelling of element position and mechanical properties indicate they were capable of food processing. A direct test would be provided through evidence of <italic>in vivo</italic> element crown tissue damage or through <italic>in vivo</italic> incorporated chemical proxies for a shift in their trophic position during ontogeny. Here we focus on coniform elements from two conodont taxa, the phylogenetically primitive <italic>Proconodontus muelleri</italic> Miller, 1969 from the late Cambrian and the more derived <italic>Panderodus equicostatus</italic> Rhodes, 1954 from the Silurian. Proposing that this extremely small sample is, however, representative for these taxa, we aim to describe in detail the growth of an element from each of these taxa in order to the test the following hypotheses: (1) <italic>Panderodus</italic> and <italic>Proconodontus</italic> processed hard food, which led to damage of their elements consistent with prey capture function; and (2) both genera shifted towards higher trophic levels during ontogeny. We employed backscatter electron (BSE) imaging, energy-dispersive X-ray spectroscopy (EDX) and synchrotron radiation X-ray tomographic microscopy (SRXTM) to identify growth increments, wear and damage surfaces, and the Sr/Ca ratio in bioapatite as a proxy for the trophic position. Using these data, we can identify whether they exhibit determinate or indeterminate growth and whether both species followed linear or allometric growth dynamics. Growth increments (27 in <italic>Pa. equicostatus</italic> and 58 in <italic>Pr. muelleri</italic> ) were formed in bundles of 4–7 increments in <italic>Pa. equicostatus</italic> and 7–9 in <italic>Pr. muelleri</italic> . We interpret the bundles as analogous to Retzius periodicity in vertebrate teeth. Based on applied optimal resource allocation models, internal periodicity might explain indeterminate growth in both species. They also allow us to interpret the almost linear growth of both individuals as an indicator that there was no size-dependent increase in mortality in the ecosystems where they lived <italic>e.g</italic> ., as would be the case in the presence of larger predators. Our findings show that periodic growth was present in early conodonts and preceded tissue repair in response to wear and damage. We found no microwear and the Sr/Ca ratio, and therefore the trophic position, did not change substantially during the lifetimes of either individual. Trophic ecology of coniform conodonts differed from the predatory and/or scavenger lifestyle documented for “complex” conodonts. We propose that conodonts adapted their life histories to top-down controlled ecosystems during the Nekton Revolution. </p>
Frankiewicz, Kamil E; Oskolski, Alexei A; Reduron, Jean-Pierre; Banasiak, Łukasz; Reyes-Betancort, Jorge-Alfredo; Trzeciak, Paulina; Spalik, Krzysztof
Stem anatomy of Apioideae (Apiaceae): effects of habit and reproductive strategy Journal Article
In: IAWA Journal, vol. 43, no. 1-2, pp. 42-65, 2021, ISSN: 0928-1541 .
@article{Stem2021,
title = {Stem anatomy of Apioideae (Apiaceae): effects of habit and reproductive strategy },
author = {Kamil E Frankiewicz and Alexei A Oskolski and Jean-Pierre Reduron and Łukasz Banasiak and Jorge-Alfredo Reyes-Betancort and Paulina Trzeciak and Krzysztof Spalik},
doi = {https://doi.org/10.1163/22941932-bja10078},
issn = {0928-1541 },
year = {2021},
date = {2021-12-03},
journal = {IAWA Journal},
volume = {43},
number = {1-2},
pages = {42-65},
abstract = {Apioideae is the biggest and the most diverse of four subfamilies recognised within Apiaceae. Except for a few, likely derived, woody clades, most representatives of this subfamily are herbaceous. In the present study, we assessed stem anatomy of 87, mostly therophytic and hemicryptophytic, species from at least 20 distinct lineages of Apioideae, and juxtaposed them with 67 species from our previous anatomical projects also focused on this subfamily. Comparing our data with the literature, we found that wood anatomy does not allow for a distinction between apioids and their close relatives (Azorelloideae, Saniculoideae), but more distantly related Mackinlayoideae differ from Apioideae in their perforation plate type. Vessel element and fibre length, and vessel diameter were positively correlated with plant height: phenomena already reported in literature. Similar pattern was retrieved for vertical intervessel pit diameter. Wood ground tissue in apioids ranges from entirely fibrous to parenchymatous. The shortening of internodes seems to favour the formation of parenchymatic ground tissue, whereas the early shift to flowering promotes the deposition of fibrous wood in monocarpic species. These results support a hypothesis on interdependence among internode length, reproductive strategy, and wood ground tissue type.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Apioideae is the biggest and the most diverse of four subfamilies recognised within Apiaceae. Except for a few, likely derived, woody clades, most representatives of this subfamily are herbaceous. In the present study, we assessed stem anatomy of 87, mostly therophytic and hemicryptophytic, species from at least 20 distinct lineages of Apioideae, and juxtaposed them with 67 species from our previous anatomical projects also focused on this subfamily. Comparing our data with the literature, we found that wood anatomy does not allow for a distinction between apioids and their close relatives (Azorelloideae, Saniculoideae), but more distantly related Mackinlayoideae differ from Apioideae in their perforation plate type. Vessel element and fibre length, and vessel diameter were positively correlated with plant height: phenomena already reported in literature. Similar pattern was retrieved for vertical intervessel pit diameter. Wood ground tissue in apioids ranges from entirely fibrous to parenchymatous. The shortening of internodes seems to favour the formation of parenchymatic ground tissue, whereas the early shift to flowering promotes the deposition of fibrous wood in monocarpic species. These results support a hypothesis on interdependence among internode length, reproductive strategy, and wood ground tissue type.
Soukal, Petr; Hrdá, Štěpánka; Karnkowska, Anna; Milanowski, Rafał; Szabová, Jana; Hradilová, Miluše; Strnad, Hynek; Vlček, Čestmír; Čepička, Ivan; Hampl, Vladimír
Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology Journal Article
In: Scientific Reports, vol. 11, no. 1, pp. 13070, 2021, ISSN: 2045-2322.
@article{Soukal2021,
title = {Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology},
author = {Petr Soukal and Štěpánka Hrdá and Anna Karnkowska and Rafał Milanowski and Jana Szabová and Miluše Hradilová and Hynek Strnad and Čestmír Vlček and Ivan Čepička and Vladimír Hampl},
url = {https://doi.org/10.1038/s41598-021-92174-3
http://www.nature.com/articles/s41598-021-92174-3},
doi = {10.1038/s41598-021-92174-3},
issn = {2045-2322},
year = {2021},
date = {2021-12-01},
journal = {Scientific Reports},
volume = {11},
number = {1},
pages = {13070},
abstract = {Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting genomic and transcriptomic drafts of a primary osmotroph, Rhabdomonas costata . The current genomic assembly length of 100 Mbp is 14× smaller than that of E. gracilis . Despite being too fragmented for comprehensive gene prediction it provided fragments of the mitochondrial genome and comparison of the transcriptomic and genomic data revealed features of its introns, including several candidates for nonconventional types. A set of 39,456 putative R. costata proteins was predicted from the transcriptome. Annotation of the mitochondrial core metabolism provides the first data on the facultatively anaerobic mitochondrion of R. costata , which in most respects resembles the mitochondrion of E. gracilis with a certain level of streamlining. R. costata can synthetise thiamine by enzymes of heterogenous provenances and haem by a mitochondrial-cytoplasmic C4 pathway with enzymes orthologous to those found in E. gracilis . The low percentage of green algae-affiliated genes supports the ancestrally osmotrophic status of this species.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting genomic and transcriptomic drafts of a primary osmotroph, Rhabdomonas costata . The current genomic assembly length of 100 Mbp is 14× smaller than that of E. gracilis . Despite being too fragmented for comprehensive gene prediction it provided fragments of the mitochondrial genome and comparison of the transcriptomic and genomic data revealed features of its introns, including several candidates for nonconventional types. A set of 39,456 putative R. costata proteins was predicted from the transcriptome. Annotation of the mitochondrial core metabolism provides the first data on the facultatively anaerobic mitochondrion of R. costata , which in most respects resembles the mitochondrion of E. gracilis with a certain level of streamlining. R. costata can synthetise thiamine by enzymes of heterogenous provenances and haem by a mitochondrial-cytoplasmic C4 pathway with enzymes orthologous to those found in E. gracilis . The low percentage of green algae-affiliated genes supports the ancestrally osmotrophic status of this species.
P.W., Crous; D.A., Cowan; G., Maggs-Kölling; N., Yilmaz; R., Thangavel; M.J., Wingfield; M.E., Noordeloos; B., Dima; T.E., Brandrud; G.M., Jansen; O.V., Morozova; J., Vila; R.G., Shivas; Y.P., Tan; S., Bishop-Hurley; E., Lacey; T.S., Marney; E., Larsson; G., Le Floch; L., Lombard; P., Nodet; V., Hubka; P., Alvarado; A., Berraf-Tebbal; J.D., Reyes; G., Delgado; A., Eichmeier; J.B., Jordal; A.V., Kachalkin; A., Kubátová; J.G., Maciá-Vicente; E.F., Malysheva; V., Papp; K.C., Rajeshkumar; A., Sharma; M., Spetik; D., Szabóová; M.A., Tomashevskaya; J.A., Abad; Z.G., Abad; A.V., Alexandrova; G., Anand; F., Arenas; N., Ashtekar; S., Balashov; Á., Bañares; R., Baroncelli; I., Bera; A.Yu., Biketova; C.L., Blomquist; T., Boekhout; D., Boertmann; T.M., Bulyonkova; T.I., Burgess; A.J., Carnegie; J.F., Cobo-Diaz; G., Corriol; J.H., Cunnington; da Cruz M.O.,; U., Damm; N., Davoodian; de A. Santiago A.L.C.M.,; J., Dearnaley; de Freitas L.W.S.,; K., Dhileepan; R., Dimitrov; S., Di Piazza; S., Fatima; F., Fuljer; H., Galera; A., Ghosh; A., Giraldo; (...), Glushakova A. M.; M., Gorczak; D.E., Gouliamova; D., Gramaje; M., Groenewald; C.K., Gunsch; A., Gutiérrez; D., Holdom; J., Houbraken; A.B., Ismailov; Ł., Istel; T., Iturriaga; M., Jeppson; Ž., Jurjević; L.B., Kalinina; V.I., Kapitonov; I., Kautmanova; A.N., Khalid; M., Kiran; L., Kiss; Á., Kovács; D., Kurose; I., Kusan; S., Lad; T., Læssøe; H.B., Lee; J.J., Luangsa-ard; M., Lynch; A.E., Mahamedi; V.F., Malysheva; A., Mateos; N., Matočec; A., Mešić; A.N., Miller; S., Mongkolsamrit; G., Moreno; A., Morte; R., Mostowfizadeh-Ghalamfarsa; A., Naseer; A., Navarro-Ródenas; T.T.T., Nguyen; W., Noisripoom; J.E., Ntandu; J., Nuytinck; V., Ostrý; T.A., Pankratov; J., Pawłowska; J., Pecenka; T.H.G., Pham; A., Polhorský; A., Posta; D.B., Raudabaugh; K., Reschke; A., Rodríguez; M., Romero; S., Rooney-Latham; J., Roux; M., Sandoval-Denis; M.Th., Smith; T.V., Steinrucken; T.Y., Svetasheva; Z., Tkalčec; van der Linde E.J.,; v.d. Vegte M.,; J., Vauras; A., Verbeken; C.M., Visagie; J.S., Vitelli; S.V., Volobuev; A., Weill; M., Wrzosek; I.V., Zmitrovich; E.A., Zvyagina; J.Z., Groenewald
Fungal Planet description sheets: 1182–1283 Journal Article
In: Persoonia, vol. 46, no. 11, pp. 313-528, 2021.
@article{Crous2021,
title = {Fungal Planet description sheets: 1182–1283},
author = {Crous P.W. and Cowan D.A. and Maggs-Kölling G. and Yilmaz N. and Thangavel R. and Wingfield M.J. and Noordeloos M.E. and Dima B. and Brandrud T.E. and Jansen G.M. and Morozova O.V. and Vila J. and Shivas R.G. and Tan Y.P. and Bishop-Hurley S. and Lacey E. and Marney T.S. and Larsson E. and Le Floch G. and Lombard L. and Nodet P. and Hubka V. and Alvarado P. and Berraf-Tebbal A. and Reyes J.D. and Delgado G. and Eichmeier A. and Jordal J.B. and Kachalkin A.V. and Kubátová A. and Maciá-Vicente J.G. and Malysheva E.F. and Papp V. and Rajeshkumar K.C. and Sharma A. and Spetik M. and Szabóová D. and Tomashevskaya M.A. and Abad J.A. and Abad Z.G. and Alexandrova A.V. and Anand G. and Arenas F. and Ashtekar N. and Balashov S. and Bañares Á. and Baroncelli R. and Bera I. and Biketova A.Yu. and Blomquist C.L. and Boekhout T. and Boertmann D. and Bulyonkova T.M. and Burgess T.I. and Carnegie A.J. and Cobo-Diaz J.F. and Corriol G. and Cunnington J.H. and da Cruz M.O. and Damm U. and Davoodian N. and de A. Santiago A.L.C.M. and Dearnaley J. and de Freitas L.W.S. and Dhileepan K. and Dimitrov R. and Di Piazza S. and Fatima S. and Fuljer F. and Galera H. and Ghosh A. and Giraldo A. and Glushakova A.M. (...) and Gorczak M. and Gouliamova D.E. and Gramaje D. and Groenewald M. and Gunsch C.K. and Gutiérrez A. and Holdom D. and Houbraken J. and Ismailov A.B. and Istel Ł. and Iturriaga T. and Jeppson M. and Jurjević Ž. and Kalinina L.B. and Kapitonov V.I. and Kautmanova I. and Khalid A.N. and Kiran M. and Kiss L. and Kovács Á. and Kurose D. and Kusan I. and Lad S. and Læssøe T. and Lee H.B. and Luangsa-ard J.J. and Lynch M. and Mahamedi A.E. and Malysheva V.F. and Mateos A. and Matočec N. and Mešić A. and Miller A.N. and Mongkolsamrit S. and Moreno G. and Morte A. and Mostowfizadeh-Ghalamfarsa R. and Naseer A. and Navarro-Ródenas A. and Nguyen T.T.T. and Noisripoom W. and Ntandu J.E. and Nuytinck J. and Ostrý V. and Pankratov T.A. and Pawłowska J. and Pecenka J. and Pham T.H.G. and Polhorský A. and Posta A. and Raudabaugh D.B. and Reschke K. and Rodríguez A. and Romero M. and Rooney-Latham S. and Roux J. and Sandoval-Denis M. and Smith M.Th. and Steinrucken T.V. and Svetasheva T.Y. and Tkalčec Z. and van der Linde E.J. and v.d. Vegte M. and Vauras J. and Verbeken A. and Visagie C.M. and Vitelli J.S. and Volobuev S.V. and Weill A. and Wrzosek M. and Zmitrovich I.V. and Zvyagina E.A. and Groenewald J.Z.},
url = {https://www.ingentaconnect.com/content/nhn/pimj/pre-prints/content-nbc-persoonia-0595},
doi = {https://doi.org/10.3767/persoonia.2021.46.11},
year = {2021},
date = {2021-07-31},
journal = {Persoonia},
volume = {46},
number = {11},
pages = {313-528},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gorczak, Michał; Trigos-Peral, Gema
Solving a long-standing enigma: Myrmicinosporidium durum belongs to Blastocladiomycota, a phylum of primarily aquatic fungi Journal Article
In: Journal of Invertebrate Pathology, pp. 107640, 2021, ISSN: 0022-2011.
@article{GORCZAK2021107640,
title = {Solving a long-standing enigma: Myrmicinosporidium durum belongs to Blastocladiomycota, a phylum of primarily aquatic fungi},
author = {Michał Gorczak and Gema Trigos-Peral},
url = {https://www.sciencedirect.com/science/article/pii/S0022201121001075},
doi = {https://doi.org/10.1016/j.jip.2021.107640},
issn = {0022-2011},
year = {2021},
date = {2021-06-22},
journal = {Journal of Invertebrate Pathology},
pages = {107640},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Czepiński, Łukasz; Dróżdż, Dawid; Szczygielski, Tomasz; Tałanda, Mateusz; Pawlak, Wojciech; Lewczuk, Antoni; Rytel, Adam; Sulej, Tomasz
An Upper Triassic Terrestrial Vertebrate Assemblage from the Forgotten Kocury Locality (Poland) with a New Aetosaur Taxon Journal Article
In: Journal of Vertebrate Paleontology, pp. e1898977, 2021.
@article{Czepinski2021,
title = {An Upper Triassic Terrestrial Vertebrate Assemblage from the Forgotten Kocury Locality (Poland) with a New Aetosaur Taxon},
author = {Łukasz Czepiński and Dawid Dróżdż and Tomasz Szczygielski and Mateusz Tałanda and Wojciech Pawlak and Antoni Lewczuk and Adam Rytel and Tomasz Sulej},
url = {https://doi.org/10.1080/02724634.2021.1898977},
doi = {10.1080/02724634.2021.1898977},
year = {2021},
date = {2021-04-14},
journal = {Journal of Vertebrate Paleontology},
pages = {e1898977},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Koczyk, Grzegorz; Pawłowska, Julia; Muszewska, Anna
Terpenoid Biosynthesis Dominates among Secondary Metabolite Clusters in Mucoromycotina Genomes Journal Article
In: Journal of Fungi, vol. 7, no. 4, pp. 285, 2021, ISSN: 2309-608X.
@article{jof7040285,
title = {Terpenoid Biosynthesis Dominates among Secondary Metabolite Clusters in Mucoromycotina Genomes},
author = {Grzegorz Koczyk and Julia Pawłowska and Anna Muszewska},
url = {https://www.mdpi.com/2309-608X/7/4/285},
doi = {10.3390/jof7040285},
issn = {2309-608X},
year = {2021},
date = {2021-04-09},
journal = {Journal of Fungi},
volume = {7},
number = {4},
pages = {285},
abstract = {Early-diverging fungi harbour unprecedented diversity in terms of living forms, biological traits and genome architecture. Before the sequencing era, non-Dikarya fungi were considered unable to produce secondary metabolites (SM); however, this perspective is changing. The main classes of secondary metabolites in fungi include polyketides, nonribosomal peptides, terpenoids and siderophores that serve different biological roles, including iron chelation and plant growth promotion. The same classes of SM are reported for representatives of early-diverging fungal lineages. Encouraged by the advancement in the field, we carried out a systematic survey of SM in Mucoromycotina and corroborated the presence of various SM clusters (SMCs) within the phylum. Among the core findings, considerable representation of terpene and nonribosomal peptide synthetase (NRPS)-like candidate SMCs was found. Terpene clusters with diverse domain composition and potentially highly variable products dominated the landscape of candidate SMCs. A uniform low-copy distribution of siderophore clusters was observed among most assemblies. Mortierellomycotina are highlighted as the most potent SMC producers among the Mucoromycota and as a source of novel peptide products. SMC identification is dependent on gene model quality and can be successfully performed on a batch scale with genomes of different quality and completeness.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Early-diverging fungi harbour unprecedented diversity in terms of living forms, biological traits and genome architecture. Before the sequencing era, non-Dikarya fungi were considered unable to produce secondary metabolites (SM); however, this perspective is changing. The main classes of secondary metabolites in fungi include polyketides, nonribosomal peptides, terpenoids and siderophores that serve different biological roles, including iron chelation and plant growth promotion. The same classes of SM are reported for representatives of early-diverging fungal lineages. Encouraged by the advancement in the field, we carried out a systematic survey of SM in Mucoromycotina and corroborated the presence of various SM clusters (SMCs) within the phylum. Among the core findings, considerable representation of terpene and nonribosomal peptide synthetase (NRPS)-like candidate SMCs was found. Terpene clusters with diverse domain composition and potentially highly variable products dominated the landscape of candidate SMCs. A uniform low-copy distribution of siderophore clusters was observed among most assemblies. Mortierellomycotina are highlighted as the most potent SMC producers among the Mucoromycota and as a source of novel peptide products. SMC identification is dependent on gene model quality and can be successfully performed on a batch scale with genomes of different quality and completeness.
Gumińska, Natalia; Łukomska-Kowalczyk, Maja; Chaber, Katarzyna; Zakryś, Bożena; Milanowski, Rafał
In: Environmental Microbiology, vol. 23, no. 6, pp. 2992–3008 , 2021.
@article{https://doi.org/10.1111/1462-2920.15495,
title = {Evaluation of V2 18S rDNA barcode marker and assessment of sample collection and DNA extraction methods for metabarcoding of autotrophic euglenids},
author = {Natalia Gumińska and Maja Łukomska-Kowalczyk and Katarzyna Chaber and Bożena Zakryś and Rafał Milanowski},
url = {https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15495},
doi = {https://doi.org/10.1111/1462-2920.15495},
year = {2021},
date = {2021-04-08},
journal = {Environmental Microbiology},
volume = {23},
number = {6},
pages = {2992–3008 },
abstract = {Summary Even though the interest in metabarcoding in environmental studies is growing, euglenids are still underrepresented in both sea and freshwater bodies researches. The reason for this situation could be the unsuitability of universal eukaryotic DNA barcodes and primers as well as the lack of a verified protocol, suitable to assess euglenid diversity. In this study, using specific primers for the V2 hypervariable region of 18S rDNA for metabarcoding resulted in obtaining a high fraction (85%) of euglenid reads and species-level identification of almost 90% of them. Fifty species were detected by the metabarcoding method, including almost all species observed using a light microscope. We investigated three biomass harvesting methods (filtering, centrifugation and scraping the side of a collection vessel) and determined that centrifugation and filtration outperformed scrapes, but the choice between them is not crucial for the reliability of the analysis. In addition, eight DNA extraction methods were evaluated. We compared five commercially available DNA isolation kits, two CTAB-based protocols and a chelating resin. For this purpose, the efficiency of extraction, quality of obtained DNA, preparation time and generated costs were taken into consideration. After examination of the aforementioned criteria, we chose the GeneMATRIX Soil DNA Purification Kit as the most suitable for DNA isolation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Summary Even though the interest in metabarcoding in environmental studies is growing, euglenids are still underrepresented in both sea and freshwater bodies researches. The reason for this situation could be the unsuitability of universal eukaryotic DNA barcodes and primers as well as the lack of a verified protocol, suitable to assess euglenid diversity. In this study, using specific primers for the V2 hypervariable region of 18S rDNA for metabarcoding resulted in obtaining a high fraction (85%) of euglenid reads and species-level identification of almost 90% of them. Fifty species were detected by the metabarcoding method, including almost all species observed using a light microscope. We investigated three biomass harvesting methods (filtering, centrifugation and scraping the side of a collection vessel) and determined that centrifugation and filtration outperformed scrapes, but the choice between them is not crucial for the reliability of the analysis. In addition, eight DNA extraction methods were evaluated. We compared five commercially available DNA isolation kits, two CTAB-based protocols and a chelating resin. For this purpose, the efficiency of extraction, quality of obtained DNA, preparation time and generated costs were taken into consideration. After examination of the aforementioned criteria, we chose the GeneMATRIX Soil DNA Purification Kit as the most suitable for DNA isolation.
Świś, Przemysław
A new Devonian species of the enigmatic Carboniferous conodont Dollymae Journal Article
In: Palaeoworld, 2021, ISSN: 1871-174X.
@article{SWIS2021,
title = {A new Devonian species of the enigmatic Carboniferous conodont Dollymae},
author = {Przemysław Świś},
url = {https://www.sciencedirect.com/science/article/pii/S1871174X21000251},
doi = {https://doi.org/10.1016/j.palwor.2021.03.003},
issn = {1871-174X},
year = {2021},
date = {2021-03-30},
journal = {Palaeoworld},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gorczak, Michał; Siedlecki, Igor; Błocka, Zuzanna; Cullen, Maria; Daniele, Inita; Fox, Howard; Harder, Christoffer; Kinnunen, Juha; Kochanowski, Michał; Krisai-Greilhuber, Irmgard; Majchrowska, Maria; Meiere, Diana; Oberhofer, Martina; Schigel, Dmitry; Senn-Irlet, Beatrice; Wiktorowicz, Dorota; Wrzosek, Marta; Pawłowska, Julia
In: Acta Mycologica, vol. 55, no. 2, pp. 55211, 2021.
@article{Gorczak2021,
title = {18th Congress of European Mycologists Bioblitz 2019 – Naturalists Contribute to the Knowledge of Mycobiota and Lichenobiota of Białowieża Primeval Forest},
author = {Michał Gorczak and Igor Siedlecki and Zuzanna Błocka and Maria Cullen and Inita Daniele and Howard Fox and Christoffer Harder and Juha Kinnunen and Michał Kochanowski and Irmgard Krisai-Greilhuber and Maria Majchrowska and Diana Meiere and Martina Oberhofer and Dmitry Schigel and Beatrice Senn-Irlet and Dorota Wiktorowicz and Marta Wrzosek and Julia Pawłowska},
url = {https://pbsociety.org.pl/journals/index.php/am/article/view/am.55211/8039},
doi = {DOI: https://doi.org/10.5586/am.55211},
year = {2021},
date = {2021-02-25},
journal = {Acta Mycologica},
volume = {55},
number = {2},
pages = {55211},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Muszewska, Anna; Okrasińska, Alicja; Steczkiewicz, Kamil; Drgas, Olga; Orłowska, Małgorzata; Perlińska-Lenart, Urszula; Aleksandrzak-Piekarczyk, Tamara; Szatraj, Katarzyna; Zielenkiewicz, Urszula; Piłsyk, Sebastian; Malc, Ewa; Mieczkowski, Piotr; Kruszewska, Joanna S.; Bernat, Przemysław; Pawłowska, Julia
Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina Journal Article
In: Frontiers in Microbiology, vol. 12, pp. 239, 2021.
@article{muszewska2021,
title = {Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina},
author = {Anna Muszewska and Alicja Okrasińska and Kamil Steczkiewicz and Olga Drgas and Małgorzata Orłowska and Urszula Perlińska-Lenart and Tamara Aleksandrzak-Piekarczyk and Katarzyna Szatraj and Urszula Zielenkiewicz and Sebastian Piłsyk and Ewa Malc and Piotr Mieczkowski and Joanna S. Kruszewska and Przemysław Bernat and Julia Pawłowska},
url = {https://www.frontiersin.org/article/10.3389/fmicb.2021.636986},
doi = {10.3389/fmicb.2021.636986},
year = {2021},
date = {2021-02-15},
journal = {Frontiers in Microbiology},
volume = {12},
pages = {239},
abstract = {Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.
Gumińska, Natalia; Zakryś, Bożena; Milanowski, Rafał
A New Type of Circular RNA derived from Nonconventional Introns in Nuclear Genes of Euglenids Journal Article
In: Journal of Molecular Biology, vol. 433, no. 3, pp. 166758, 2021.
@article{GUMINSKA2021166758,
title = {A New Type of Circular RNA derived from Nonconventional Introns in Nuclear Genes of Euglenids},
author = {Natalia Gumińska and Bożena Zakryś and Rafał Milanowski},
url = {https://www.sciencedirect.com/science/article/pii/S0022283620306835?via%3Dihub},
doi = {https://doi.org/10.1016/j.jmb.2020.166758},
year = {2021},
date = {2021-02-05},
journal = {Journal of Molecular Biology},
volume = {433},
number = {3},
pages = {166758},
abstract = {Nuclear protein-coding genes of euglenids (Discoba, Euglenozoa, Euglenida) contain conventional (spliceosomal) and nonconventional introns. The latter have been found only in euglenozoans. A unique feature of nonconventional introns is the ability to form a stable and slightly conserved RNA secondary structure bringing together intron ends and placing adjacent exons in proximity. To date, little is known about the mechanism of their excision (e.g. whether it involves the spliceosome or not). The tubA gene of Euglena gracilis harbors three conventional and three nonconventional introns. While the conventional introns are excised as lariats, nonconventional introns are present in the cell solely as circular RNAs with full-length ends. Based on this discovery as well as on previous observations indicating that nonconventional introns are observed frequently at unique positions of genes, we suggest that this new type of intronic circRNA might play a role in intron mobility.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nuclear protein-coding genes of euglenids (Discoba, Euglenozoa, Euglenida) contain conventional (spliceosomal) and nonconventional introns. The latter have been found only in euglenozoans. A unique feature of nonconventional introns is the ability to form a stable and slightly conserved RNA secondary structure bringing together intron ends and placing adjacent exons in proximity. To date, little is known about the mechanism of their excision (e.g. whether it involves the spliceosome or not). The tubA gene of Euglena gracilis harbors three conventional and three nonconventional introns. While the conventional introns are excised as lariats, nonconventional introns are present in the cell solely as circular RNAs with full-length ends. Based on this discovery as well as on previous observations indicating that nonconventional introns are observed frequently at unique positions of genes, we suggest that this new type of intronic circRNA might play a role in intron mobility.
Chachuła, Piotr; Domian, Grażyna; Gierczyk, Błażej; Halama, Marek; Kałucka, Izabela; Kujawa, Anna; Ławrynowicz, Maria; Łuszczyński, Janusz; Mleczko, Piotr; Okrasińska, Alicja; Pawłowska, Julia; Piskorski, Sebastian; Ronikier, Anna; Ruszkiewicz-Michalska, Małgorzata; Rutkowski, Ryszard; Skoczek, Barbara; Stasińska, Małgorzata; Szczepkowski, Andrzej; Ślusarczyk, Dominika; Ślusarczyk, Tomasz
Grzyby chronione Polski. Rozmieszczenie, zagrożenia, rekomendacje ochronne Book
Instytut Środowiska Rolniczego i Leśnego Polskiej Akademii Nauk, Poznań, 2021, ISBN: 978-83-938379-8-4.
@book{Kujawa2021,
title = {Grzyby chronione Polski. Rozmieszczenie, zagrożenia, rekomendacje ochronne},
author = {Piotr Chachuła and Grażyna Domian and Błażej Gierczyk and Marek Halama and Izabela Kałucka and Anna Kujawa and Maria Ławrynowicz and Janusz Łuszczyński and Piotr Mleczko and Alicja Okrasińska and Julia Pawłowska and Sebastian Piskorski and Anna Ronikier and Małgorzata Ruszkiewicz-Michalska and Ryszard Rutkowski and Barbara Skoczek and Małgorzata Stasińska and Andrzej Szczepkowski and Dominika Ślusarczyk and Tomasz Ślusarczyk},
editor = {Anna Kujawa and Małgorzata Ruszkiewicz-Michalska and Izabela Kałucka},
isbn = {978-83-938379-8-4},
year = {2021},
date = {2021-02-01},
publisher = {Instytut Środowiska Rolniczego i Leśnego Polskiej Akademii Nauk},
address = {Poznań},
keywords = {},
pubstate = {published},
tppubtype = {book}
}
Baczyński, Jakub; Miłobędzka, Aleksandra; Banasiak, Łukasz
Morphology of pollen in Apiales (Asterids, Eudicots) Journal Article
In: Phytotaxa, vol. 478, no. 1, pp. 001-032, 2021.
@article{PTphytotaxa.478.1.1,
title = {Morphology of pollen in Apiales (Asterids, Eudicots)},
author = {Jakub Baczyński and Aleksandra Miłobędzka and Łukasz Banasiak},
url = {https://www.biotaxa.org/Phytotaxa/article/view/phytotaxa.478.1.1},
doi = {https://doi.org/10.11646/phytotaxa.478.1.1},
year = {2021},
date = {2021-01-05},
journal = {Phytotaxa},
volume = {478},
number = {1},
pages = {001-032},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Siedlecki, Igor; Gorczak, Michał; Okrasińska, Alicja; Wrzosek, Marta
Chance or Necessity—The Fungi Co−Occurring with Formica polyctena Ants Journal Article
In: Insects, vol. 12, no. 3, 2021.
@article{insects12030204,
title = {Chance or Necessity—The Fungi Co−Occurring with Formica polyctena Ants},
author = {Igor Siedlecki and Michał Gorczak and Alicja Okrasińska and Marta Wrzosek},
url = {https://www.mdpi.com/2075-4450/12/3/204},
doi = {10.3390/insects12030204},
year = {2021},
date = {2021-01-01},
journal = {Insects},
volume = {12},
number = {3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Singh, Racquel A; Boscaro, Vittorio; James, Erick R; Karnkowska, Anna; Kolisko, Martin; Gavelis, Gregory S; Okamoto, Noriko; Campo, Javier Del; Fiorito, Rebecca; Hehenberger, Elisabeth; Irwin, Nicholas A T; Mathur, Varsha; Scheffrahn, Rudolf H; Keeling, Patrick J
Characterization of new cristamonad species from kalotermitid termites including a novel genus, Runanympha Journal Article
In: Scientific reports, vol. 11, no. 1, pp. 7270, 2021, ISSN: 20452322.
@article{Singh2021,
title = {Characterization of new cristamonad species from kalotermitid termites including a novel genus, Runanympha},
author = {Racquel A Singh and Vittorio Boscaro and Erick R James and Anna Karnkowska and Martin Kolisko and Gregory S Gavelis and Noriko Okamoto and Javier {Del Campo} and Rebecca Fiorito and Elisabeth Hehenberger and Nicholas A T Irwin and Varsha Mathur and Rudolf H Scheffrahn and Patrick J Keeling},
url = {https://doi.org/10.1038/s41598-021-86645-w},
doi = {10.1038/s41598-021-86645-w},
issn = {20452322},
year = {2021},
date = {2021-01-01},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7270},
publisher = {Nature Publishing Group UK},
abstract = {Cristamonadea is a large class of parabasalian protists that reside in the hindguts of wood-feeding insects, where they play an essential role in the digestion of lignocellulose. This group of symbionts boasts an impressive array of complex morphological characteristics, many of which have evolved multiple times independently. However, their diversity is understudied and molecular data remain scarce. Here we describe seven new species of cristamonad symbionts from Comatermes, Calcaritermes, and Rugitermes termites from Peru and Ecuador. To classify these new species, we examined cells by light and scanning electron microscopy, sequenced the symbiont small subunit ribosomal RNA (rRNA) genes, and carried out barcoding of the mitochondrial large subunit rRNA gene of the hosts to confirm host identification. Based on these data, five of the symbionts characterized here represent new species within described genera: Devescovina sapara n. sp., Devescovina aymara n. sp., Macrotrichomonas ashaninka n. sp., Macrotrichomonas secoya n. sp., and Macrotrichomonas yanesha n. sp. Additionally, two symbionts with overall morphological characteristics similar to the poorly-studied and probably polyphyletic 'joeniid' Parabasalia are classified in a new genus Runanympha n. gen.: Runanympha illapa n. sp., and Runanympha pacha n. sp.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cristamonadea is a large class of parabasalian protists that reside in the hindguts of wood-feeding insects, where they play an essential role in the digestion of lignocellulose. This group of symbionts boasts an impressive array of complex morphological characteristics, many of which have evolved multiple times independently. However, their diversity is understudied and molecular data remain scarce. Here we describe seven new species of cristamonad symbionts from Comatermes, Calcaritermes, and Rugitermes termites from Peru and Ecuador. To classify these new species, we examined cells by light and scanning electron microscopy, sequenced the symbiont small subunit ribosomal RNA (rRNA) genes, and carried out barcoding of the mitochondrial large subunit rRNA gene of the hosts to confirm host identification. Based on these data, five of the symbionts characterized here represent new species within described genera: Devescovina sapara n. sp., Devescovina aymara n. sp., Macrotrichomonas ashaninka n. sp., Macrotrichomonas secoya n. sp., and Macrotrichomonas yanesha n. sp. Additionally, two symbionts with overall morphological characteristics similar to the poorly-studied and probably polyphyletic 'joeniid' Parabasalia are classified in a new genus Runanympha n. gen.: Runanympha illapa n. sp., and Runanympha pacha n. sp.
Łukomska-Kowalczyk, Maja; Chaber, Katarzyna; Fells, Alicja; Milanowski, Rafał; Zakryś, Bożena
Description of Flexiglena gen. nov. and new members of Discoplastis and Euglenaformis (Euglenida) Journal Article
In: Journal of Phycology, vol. 57, no. 3, pp. 766-779, 2021.
@article{https://doi.org/10.1111/jpy.13107,
title = {Description of Flexiglena gen. nov. and new members of Discoplastis and Euglenaformis (Euglenida)},
author = {Maja Łukomska-Kowalczyk and Katarzyna Chaber and Alicja Fells and Rafał Milanowski and Bożena Zakryś},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13107},
doi = {https://doi.org/10.1111/jpy.13107},
year = {2021},
date = {2021-01-01},
journal = {Journal of Phycology},
volume = {57},
number = {3},
pages = {766-779},
abstract = {Environmental sampling in Poland and the United States and phylogenetic analyses based on 567 sequences of four genes (155 sequences of nuclear SSU rDNA, 139 of nuclear LSU rDNA, 135 of plastid-encoded SSU rDNA, and 138 of plastid-encoded LSU rDNA) resulted in description of the new genus Flexiglena, which has been erected by accommodating Euglena variabilis, and enriching the Discoplastis and Euglenaformis genera with five new species. Four of them have joined the Discoplastis genus, currently consisting of six representatives: D. adunca, D. angusta (=Euglena angusta), D. constricta (=Lepocinclis constricta), D. excavata (=E. excavata), D. gasterosteus (=E. gasterosteus), and D. spathirhyncha. One of them has enriched the Euglenaformis genus, currently represented by two species: Euf. chlorophoenicea (= E. chlorophoenicea) and Euf. proxima. For most studied species, the diagnostic descriptions have been emended and epitypes were designated. Furthermore, the emending of Discoplastis and Euglenaformis diagnoses was performed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Environmental sampling in Poland and the United States and phylogenetic analyses based on 567 sequences of four genes (155 sequences of nuclear SSU rDNA, 139 of nuclear LSU rDNA, 135 of plastid-encoded SSU rDNA, and 138 of plastid-encoded LSU rDNA) resulted in description of the new genus Flexiglena, which has been erected by accommodating Euglena variabilis, and enriching the Discoplastis and Euglenaformis genera with five new species. Four of them have joined the Discoplastis genus, currently consisting of six representatives: D. adunca, D. angusta (=Euglena angusta), D. constricta (=Lepocinclis constricta), D. excavata (=E. excavata), D. gasterosteus (=E. gasterosteus), and D. spathirhyncha. One of them has enriched the Euglenaformis genus, currently represented by two species: Euf. chlorophoenicea (= E. chlorophoenicea) and Euf. proxima. For most studied species, the diagnostic descriptions have been emended and epitypes were designated. Furthermore, the emending of Discoplastis and Euglenaformis diagnoses was performed.
Kostygov, Alexei Y; Karnkowska, Anna; Votypka, Jan; Tashyreva, Daria; Maciszewski, Kacper; Yurchenko, Vyacheslav; Lukes, Julius
Euglenozoa : taxonomy, diversity and ecology, symbioses and viruses Journal Article
In: Open Biology, vol. 11, no. 3, pp. 200407-200407, 2021, ISBN: 0000000337.
@article{Kostygov2021,
title = {Euglenozoa : taxonomy, diversity and ecology, symbioses and viruses},
author = {Alexei Y Kostygov and Anna Karnkowska and Jan Votypka and Daria Tashyreva and Kacper Maciszewski and Vyacheslav Yurchenko and Julius Lukes},
url = {https://royalsocietypublishing.org/doi/pdf/10.1098/rsob.200407},
doi = {https://doi.org/10.1098/rsob.200407},
isbn = {0000000337},
year = {2021},
date = {2021-01-01},
journal = {Open Biology},
volume = {11},
number = {3},
pages = {200407-200407},
abstract = {Euglenozoa is a species-rich group of protists, which have extremely diverse
lifestyles and a range of features that distinguish them from other eukaryotes. They are composed of free-living and parasitic kinetoplastids,
mostly free-living diplonemids, heterotrophic and photosynthetic euglenids,
as well as deep-sea symbiontids. Although they form a well-supported
monophyletic group, these morphologically rather distinct groups are
almost never treated together in a comparative manner, as attempted here.
We present an updated taxonomy, complemented by photos of representative species, with notes on diversity, distribution and biology of
euglenozoans. For kinetoplastids, we propose a significantly modified taxonomy that reflects the latest findings. Finally, we summarize what is
known about viruses infecting euglenozoans, as well as their relationships
with ecto- and endosymbiotic bacteria.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Euglenozoa is a species-rich group of protists, which have extremely diverse
lifestyles and a range of features that distinguish them from other eukaryotes. They are composed of free-living and parasitic kinetoplastids,
mostly free-living diplonemids, heterotrophic and photosynthetic euglenids,
as well as deep-sea symbiontids. Although they form a well-supported
monophyletic group, these morphologically rather distinct groups are
almost never treated together in a comparative manner, as attempted here.
We present an updated taxonomy, complemented by photos of representative species, with notes on diversity, distribution and biology of
euglenozoans. For kinetoplastids, we propose a significantly modified taxonomy that reflects the latest findings. Finally, we summarize what is
known about viruses infecting euglenozoans, as well as their relationships
with ecto- and endosymbiotic bacteria.
lifestyles and a range of features that distinguish them from other eukaryotes. They are composed of free-living and parasitic kinetoplastids,
mostly free-living diplonemids, heterotrophic and photosynthetic euglenids,
as well as deep-sea symbiontids. Although they form a well-supported
monophyletic group, these morphologically rather distinct groups are
almost never treated together in a comparative manner, as attempted here.
We present an updated taxonomy, complemented by photos of representative species, with notes on diversity, distribution and biology of
euglenozoans. For kinetoplastids, we propose a significantly modified taxonomy that reflects the latest findings. Finally, we summarize what is
known about viruses infecting euglenozoans, as well as their relationships
with ecto- and endosymbiotic bacteria.
Lax, G.; Kolisko, M.; Eglit, Y.; Lee, W. J.; Yubuki, N.; Karnkowska, A.; Leander, B. S.; Burger, G.; Keeling, P. J.; Simpson, A. G. B.
Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs Journal Article
In: Molecular Phylogenetics and Evolution, vol. 159, pp. 107088, 2021, ISSN: 1055-7903.
@article{LAX2021107088b,
title = {Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs},
author = {G. Lax and M. Kolisko and Y. Eglit and W.J. Lee and N. Yubuki and A. Karnkowska and B.S. Leander and G. Burger and P.J. Keeling and A.G.B. Simpson},
url = {https://www.sciencedirect.com/science/article/pii/S105579032100021X},
doi = {https://doi.org/10.1016/j.ympev.2021.107088},
issn = {1055-7903},
year = {2021},
date = {2021-01-01},
journal = {Molecular Phylogenetics and Evolution},
volume = {159},
pages = {107088},
abstract = {Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid Olkasia as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by Ploeotia spp.), Lentomonas, and Keelungia form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes Rapaza, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (Anisonema and Dinema spp.), ‘Heteronema II’ (represented by H. vittatum), and a clade of Neometanema plus Aphagea. Among ‘peranemid’ phagotrophs, Chasmostoma branches with included Urceolus, and Peranema with the undescribed ‘Jenningsia II’, while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that Entosiphon is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid Olkasia as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by Ploeotia spp.), Lentomonas, and Keelungia form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes Rapaza, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (Anisonema and Dinema spp.), ‘Heteronema II’ (represented by H. vittatum), and a clade of Neometanema plus Aphagea. Among ‘peranemid’ phagotrophs, Chasmostoma branches with included Urceolus, and Peranema with the undescribed ‘Jenningsia II’, while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that Entosiphon is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.
Okrasińska, Alicja; Bokus, Aleksandra; Duk, Katarzyna; Gęsiorska, Aleksandra; Sokołowska, Blanka; Miłobędzka, Aleksandra; Wrzosek, Marta; Pawłowska, Julia
New Endohyphal Relationships between Mucoromycota and Burkholderiaceae Representatives Journal Article
In: Applied and Environmental Microbiology, vol. 87, no. 7, 2021, ISSN: 0099-2240.
@article{Okrasińskae02707-20,
title = {New Endohyphal Relationships between Mucoromycota and Burkholderiaceae Representatives},
author = {Alicja Okrasińska and Aleksandra Bokus and Katarzyna Duk and Aleksandra Gęsiorska and Blanka Sokołowska and Aleksandra Miłobędzka and Marta Wrzosek and Julia Pawłowska},
editor = {Maia Kivisaar},
url = {https://aem.asm.org/content/87/7/e02707-20},
doi = {10.1128/AEM.02707-20},
issn = {0099-2240},
year = {2021},
date = {2021-01-01},
journal = {Applied and Environmental Microbiology},
volume = {87},
number = {7},
publisher = {American Society for Microbiology Journals},
abstract = {Mucoromycota representatives are known to harbor two types of endohyphal bacteria (EHB)—Burkholderia-related endobacteria (BRE) and Mycoplasma-related endobacteria (MRE). While both BRE and MRE occur in fungi representing all subphyla of Mucoromycota, their distribution is not well studied. Therefore, it is difficult to resolve the evolutionary history of these associations in favor of one of the following two alternative hypotheses explaining their origin: textquotedblleftearly invasiontextquotedblright and textquotedblleftlate invasion.textquotedblright Our main goal was to fill this knowledge gap by surveying Mucoromycota fungi for the presence of EHB. We screened 196 fungal strains from 16 genera using a PCR-based approach to detect bacterial 16S rRNA genes, complemented with fluorescence in situ hybridization (FISH) imaging to confirm the presence of bacteria within the hyphae. We detected Burkholderiaceae in ca. 20% of fungal strains. Some of these bacteria clustered phylogenetically with previously described BRE clades, whereas others grouped with free-living Paraburkholderia. Importantly, the latter were detected in Umbelopsidales, which previously were not known to harbor endobacteria. Our results suggest that this group of EHB is recruited from the environment, supporting the late invasion scenario. This pattern complements the early invasion scenario apparent in the BRE clade of EHB.IMPORTANCE Bacteria living within fungal hyphae present an example of one of the most intimate relationships between fungi and bacteria. Even though there are several well-described examples of such partnerships, their prevalence within the fungal kingdom remains unknown. Our study focused on early divergent terrestrial fungi in the phylum Mucoromycota. We found that ca. 20% of the strains tested harbored bacteria from the family Burkholderiaceae. Not only did we confirm the presence of bacteria from previously described endosymbiont clades, we also identified a new group of endohyphal Burkholderiaceae representing the genus Paraburkholderia. We established that more than half of the screened Umbelopsis strains were positive for bacteria from this new group. We also determined that, while previously described BRE codiverged with their fungal hosts, Paraburkholderia symbionts did not.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mucoromycota representatives are known to harbor two types of endohyphal bacteria (EHB)—Burkholderia-related endobacteria (BRE) and Mycoplasma-related endobacteria (MRE). While both BRE and MRE occur in fungi representing all subphyla of Mucoromycota, their distribution is not well studied. Therefore, it is difficult to resolve the evolutionary history of these associations in favor of one of the following two alternative hypotheses explaining their origin: textquotedblleftearly invasiontextquotedblright and textquotedblleftlate invasion.textquotedblright Our main goal was to fill this knowledge gap by surveying Mucoromycota fungi for the presence of EHB. We screened 196 fungal strains from 16 genera using a PCR-based approach to detect bacterial 16S rRNA genes, complemented with fluorescence in situ hybridization (FISH) imaging to confirm the presence of bacteria within the hyphae. We detected Burkholderiaceae in ca. 20% of fungal strains. Some of these bacteria clustered phylogenetically with previously described BRE clades, whereas others grouped with free-living Paraburkholderia. Importantly, the latter were detected in Umbelopsidales, which previously were not known to harbor endobacteria. Our results suggest that this group of EHB is recruited from the environment, supporting the late invasion scenario. This pattern complements the early invasion scenario apparent in the BRE clade of EHB.IMPORTANCE Bacteria living within fungal hyphae present an example of one of the most intimate relationships between fungi and bacteria. Even though there are several well-described examples of such partnerships, their prevalence within the fungal kingdom remains unknown. Our study focused on early divergent terrestrial fungi in the phylum Mucoromycota. We found that ca. 20% of the strains tested harbored bacteria from the family Burkholderiaceae. Not only did we confirm the presence of bacteria from previously described endosymbiont clades, we also identified a new group of endohyphal Burkholderiaceae representing the genus Paraburkholderia. We established that more than half of the screened Umbelopsis strains were positive for bacteria from this new group. We also determined that, while previously described BRE codiverged with their fungal hosts, Paraburkholderia symbionts did not.
Dzik, Jerzy
Protaspis larva of an aglaspidid-like arthropod from the Ordovician of Siberia and its habitat Journal Article
In: Arthropod Structure & Development, vol. 61, pp. 101026, 2021, ISSN: 1467-8039.
@article{DZIK2021101026,
title = {Protaspis larva of an aglaspidid-like arthropod from the Ordovician of Siberia and its habitat},
author = {Jerzy Dzik},
url = {https://www.sciencedirect.com/science/article/pii/S1467803920301493},
doi = {https://doi.org/10.1016/j.asd.2020.101026},
issn = {1467-8039},
year = {2021},
date = {2021-01-01},
journal = {Arthropod Structure & Development},
volume = {61},
pages = {101026},
abstract = {A fossil larva lacking segmentation of the calcified carapace, closely resembling the trilobite protaspis, has been found associated with other skeletal elements of an angarocaridid Girardevia species in the mid Darriwilian of central Siberia. The presence of protaspis larvae in the angarocaridids, generally believed to represent a branch of the Aglaspidida, supports their proximity to trilobites and proves a low position on the arthropod phylogenetic tree but does not necessarily contradict the chelicerate affinity. The cephalic appendages of angarocaridids bore massive gnathobases with detachable spines, closely similar to those known in extant xiphosurans and in their probable Cambrian relatives. The stratigraphic succession of the angarocaridids, their phosphatized cuticle pieces being abundant in the Ordovician strata of Siberia, shows a gradual improvement of mechanical resistance of their carapaces, eventually resulting in a honeycomb structure. The associated benthic mollusc assemblage is dominated with the bellerophontids showing high mortality at metamorphosis and only the limpet-like Pterotheca, infaunal bivalves, and scaphopods being able to survive this in a substantial number. This suggests a strong selective pressure from predators equipped with well-skeletonised oral apparatuses able to crush mineralized body covers of their prey. Possibly, these were some of the associated conodonts of appropriate size and co-evolving towards their ability to crush more and more resistant cuticle. Less likely candidates for durophagy are endoceratid or orthoceratid cephalopods. Also the angarocaridids themselves, equipped with robust gnathobases of cephalic appendages, apparently predated on benthic shelly animals.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A fossil larva lacking segmentation of the calcified carapace, closely resembling the trilobite protaspis, has been found associated with other skeletal elements of an angarocaridid Girardevia species in the mid Darriwilian of central Siberia. The presence of protaspis larvae in the angarocaridids, generally believed to represent a branch of the Aglaspidida, supports their proximity to trilobites and proves a low position on the arthropod phylogenetic tree but does not necessarily contradict the chelicerate affinity. The cephalic appendages of angarocaridids bore massive gnathobases with detachable spines, closely similar to those known in extant xiphosurans and in their probable Cambrian relatives. The stratigraphic succession of the angarocaridids, their phosphatized cuticle pieces being abundant in the Ordovician strata of Siberia, shows a gradual improvement of mechanical resistance of their carapaces, eventually resulting in a honeycomb structure. The associated benthic mollusc assemblage is dominated with the bellerophontids showing high mortality at metamorphosis and only the limpet-like Pterotheca, infaunal bivalves, and scaphopods being able to survive this in a substantial number. This suggests a strong selective pressure from predators equipped with well-skeletonised oral apparatuses able to crush mineralized body covers of their prey. Possibly, these were some of the associated conodonts of appropriate size and co-evolving towards their ability to crush more and more resistant cuticle. Less likely candidates for durophagy are endoceratid or orthoceratid cephalopods. Also the angarocaridids themselves, equipped with robust gnathobases of cephalic appendages, apparently predated on benthic shelly animals.
Piwczyński, Marcin; Trzeciak, Paulina; Popa, Madalina-Oana; Pabijan, Maciej; Corral, José María; Spalik, Krzysztof; Grzywacz, Andrzej
Using RAD seq for reconstructing phylogenies of highly diverged taxa: A test using the tribe Scandiceae (Apiaceae) Journal Article
In: Journal of Systematics and Evolution, vol. 59, no. 1, pp. 58-72, 2021.
@article{https://doi.org/10.1111/jse.12580,
title = {Using RAD seq for reconstructing phylogenies of highly diverged taxa: A test using the tribe Scandiceae (Apiaceae)},
author = {Marcin Piwczyński and Paulina Trzeciak and Madalina-Oana Popa and Maciej Pabijan and José María Corral and Krzysztof Spalik and Andrzej Grzywacz},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jse.12580},
doi = {https://doi.org/10.1111/jse.12580},
year = {2021},
date = {2021-01-01},
journal = {Journal of Systematics and Evolution},
volume = {59},
number = {1},
pages = {58-72},
abstract = {Abstract The angiosperm Apiaceae tribe Scandiceae includes four major clades—subtribes Daucinae, Ferulinae, Torilidinae, and Scandicinae—that originated ca. 20 Mya. Although all four subtribes are highly supported in molecular analyses, and morphological data indicate a sister relationship between Daucinae and Torilidinae, their branching order has not been resolved using standard Sanger multilocus data. Therefore, in this study, we test the utility of genomic RAD seq data in resolving deep phylogenetic relationships (up to 20 Mya) in Apiaceae subfamily Apioideae, with special emphasis on tribe Scandiceae using 12 representative species. We used two bioinformatic pipelines, pyRAD and RADIS (based on STACKS), to assemble RAD seq data and we tested the influence of various combinations of parameters on the robustness of the inferred tree topologies. Although different data processing approaches produced alignments with various amounts of missing data, they converged to two well-supported topologies, irrespective of the phylogenetic method applied. Highly supported trees showed Scandicinae as sister to all other clades and indicated that Daucinae and Torilidinae are sister groups, thus confirming the relationship inferred from morphology. We conclude that the RAD seq method can be successfully used to resolve deep relationships formed 20 Mya within Apiaceae. We provide recommendations for parameter settings in RADIS and pyRAD for the analysis of taxa that have accumulated considerable genomic divergence.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract The angiosperm Apiaceae tribe Scandiceae includes four major clades—subtribes Daucinae, Ferulinae, Torilidinae, and Scandicinae—that originated ca. 20 Mya. Although all four subtribes are highly supported in molecular analyses, and morphological data indicate a sister relationship between Daucinae and Torilidinae, their branching order has not been resolved using standard Sanger multilocus data. Therefore, in this study, we test the utility of genomic RAD seq data in resolving deep phylogenetic relationships (up to 20 Mya) in Apiaceae subfamily Apioideae, with special emphasis on tribe Scandiceae using 12 representative species. We used two bioinformatic pipelines, pyRAD and RADIS (based on STACKS), to assemble RAD seq data and we tested the influence of various combinations of parameters on the robustness of the inferred tree topologies. Although different data processing approaches produced alignments with various amounts of missing data, they converged to two well-supported topologies, irrespective of the phylogenetic method applied. Highly supported trees showed Scandicinae as sister to all other clades and indicated that Daucinae and Torilidinae are sister groups, thus confirming the relationship inferred from morphology. We conclude that the RAD seq method can be successfully used to resolve deep relationships formed 20 Mya within Apiaceae. We provide recommendations for parameter settings in RADIS and pyRAD for the analysis of taxa that have accumulated considerable genomic divergence.
Frankiewicz, Kamil E; Banasiak, Łukasz; Oskolski, Alexei A; Magee, Anthony R; Alsarraf, Mohammad; Trzeciak, Paulina; Spalik, Krzysztof
Derived woodiness and annual habit evolved in African umbellifers as alternative solutions for coping with drought Journal Article
In: BMC Plant Biology, vol. 21, no. 1, pp. 383, 2021, ISSN: 1471-2229.
@article{Frankiewicz2021,
title = {Derived woodiness and annual habit evolved in African umbellifers as alternative solutions for coping with drought},
author = {Kamil E Frankiewicz and {Ł}ukasz Banasiak and Alexei A Oskolski and Anthony R Magee and Mohammad Alsarraf and Paulina Trzeciak and Krzysztof Spalik},
url = {https://doi.org/10.1186/s12870-021-03151-x},
doi = {10.1186/s12870-021-03151-x},
issn = {1471-2229},
year = {2021},
date = {2021-01-01},
journal = {BMC Plant Biology},
volume = {21},
number = {1},
pages = {383},
abstract = {One of the major trends in angiosperm evolution was the shift from woody to herbaceous habit. However, reversals known as derived woodiness have also been reported in numerous, distantly related clades. Among theories evoked to explain the factors promoting the evolution of derived woodiness are moderate climate theory and cavitation theory. The first assumes that woody habit evolves in response to mild climate allowing for prolonged life span, which in turn leads to bigger and woodier bodies. The second sees woodiness as a result of natural selection for higher cavitation resistance in seasonally dry environments. Here, we compare climatic niches of woody and herbaceous, mostly southern African, umbellifers from the Lefebvrea clade to assess whether woody taxa in fact occur in markedly drier habitats. We also calibrate their phylogeny to estimate when derived woodiness evolved. Finally, we describe the wood anatomy of selected woody and herbaceous taxa to see if life forms are linked to any particular wood traits.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
One of the major trends in angiosperm evolution was the shift from woody to herbaceous habit. However, reversals known as derived woodiness have also been reported in numerous, distantly related clades. Among theories evoked to explain the factors promoting the evolution of derived woodiness are moderate climate theory and cavitation theory. The first assumes that woody habit evolves in response to mild climate allowing for prolonged life span, which in turn leads to bigger and woodier bodies. The second sees woodiness as a result of natural selection for higher cavitation resistance in seasonally dry environments. Here, we compare climatic niches of woody and herbaceous, mostly southern African, umbellifers from the Lefebvrea clade to assess whether woody taxa in fact occur in markedly drier habitats. We also calibrate their phylogeny to estimate when derived woodiness evolved. Finally, we describe the wood anatomy of selected woody and herbaceous taxa to see if life forms are linked to any particular wood traits.
Haelewaters, Danny; Gorczak, Michał; Kaishian, Patricia; Kesel, André De; Blackwell, Meredith
Laboulbeniomycetes, enigmatic fungi with a turbulent taxonomic history Book Section
In: Zaragoza, Óscar; Casadevall, Arturo (Ed.): Encyclopedia of mycology, vol. 1, pp. 263–283, Elsevier, 2021, ISBN: 9780323851800.
@incollection{8714384,
title = {Laboulbeniomycetes, enigmatic fungi with a turbulent taxonomic history},
author = {Danny Haelewaters and Michał Gorczak and Patricia Kaishian and André De Kesel and Meredith Blackwell},
editor = {Óscar Zaragoza and Arturo Casadevall},
url = {http://dx.doi.org/10.1016/b978-0-12-819990-9.00049-4},
isbn = {9780323851800},
year = {2021},
date = {2021-01-01},
booktitle = {Encyclopedia of mycology},
volume = {1},
pages = {263--283},
publisher = {Elsevier},
series = {Encyclopedia of Mycology},
abstract = {Phylogenetic studies of Laboulbeniomycetes support recognition of three orders (Herpomycetales, Laboulbeniales, Pyxidiophorales) and two unnamed clades containing conidial, arthropod-associated fungi and a poorly known perithecial genus, Subbaromyces. Herpomycetales and Laboulbeniales include obligate arthropod-associated biotrophs characterized by a parenchymatous thallus of several thousand cells. Pyxidiophorales are hyphal mycoparasites with an unusual three-morph life cycle. The two-celled ascospore with a distinctive apparatus for attachment to arthropods ties together all Laboulbeniomycetes. The complex morphologies and life histories of these fungi are described as a background for research directions that will rely heavily on molecular methods, including phylogenomics, with emphasis on host–parasite relations.},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Phylogenetic studies of Laboulbeniomycetes support recognition of three orders (Herpomycetales, Laboulbeniales, Pyxidiophorales) and two unnamed clades containing conidial, arthropod-associated fungi and a poorly known perithecial genus, Subbaromyces. Herpomycetales and Laboulbeniales include obligate arthropod-associated biotrophs characterized by a parenchymatous thallus of several thousand cells. Pyxidiophorales are hyphal mycoparasites with an unusual three-morph life cycle. The two-celled ascospore with a distinctive apparatus for attachment to arthropods ties together all Laboulbeniomycetes. The complex morphologies and life histories of these fungi are described as a background for research directions that will rely heavily on molecular methods, including phylogenomics, with emphasis on host–parasite relations.
2020
Kayama, Motoki; Maciszewski, Kacper; Yabuki, Akinori; Miyashita, Hideaki; Karnkowska, Anna; Kamikawa, Ryoma
In: Frontiers in Plant Science, vol. 11, pp. 1859 , 2020.
@article{Kayama2020,
title = {Highly reduced plastid genomes of the non-photosynthetic dictyochophyceans Pteridomonas spp. (Ochrophyta, SAR) are retained for tRNA-Glu-based organellar heme biosynthesis.},
author = {Motoki Kayama and Kacper Maciszewski and Akinori Yabuki and Hideaki Miyashita and Anna Karnkowska and Ryoma Kamikawa },
url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.602455/full},
doi = {https://doi.org/10.3389/fpls.2020.602455},
year = {2020},
date = {2020-11-27},
journal = {Frontiers in Plant Science},
volume = {11},
pages = {1859 },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kolisko, Martin; Flegontova, Olga; Karnkowska, Anna; Lax, Gordon; Maritz, Julia M.; Pánek, Tomáš; Táborský, Petr; Carlton, Jane M.; Čepička, Ivan; Horák, Aleš; Lukeš, Julius; Simpson, Alastair G. B.; Tai, Vera
EukRef-excavates: seven curated SSU ribosomal RNA gene databases Journal Article
In: Database (Oxford), pp. baaa080, 2020.
@article{Kolisko2020,
title = {EukRef-excavates: seven curated SSU ribosomal RNA gene databases},
author = {Martin Kolisko and Olga Flegontova and Anna Karnkowska and Gordon Lax and Julia M. Maritz and Tomáš Pánek and Petr Táborský and Jane M. Carlton and Ivan Čepička and Aleš Horák and Julius Lukeš and Alastair G. B. Simpson and Vera Tai},
url = {https://pubmed.ncbi.nlm.nih.gov/33216898},
doi = {doi: 10.1093/database/baaa080},
year = {2020},
date = {2020-11-20},
journal = {Database (Oxford)},
pages = {baaa080},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Põlme, Sergei; Abarenkov, Kessy; Nilsson, Henrik R.; Lindahl, Björn D.; Clemmensen, Karina Engelbrecht; Kauserud, Havard; Nguyen, Nhu; Kjøller, Rasmus; Bates, Scott T.; Baldrian, Petr; Frøslev, Tobias Guldberg; Adojaan, Kristjan; Vizzini, Alfredo; Suija, Ave; Pfister, Donald; Baral, Hans Otto; Järv, Helle; Madrid, Hugo; Nordén, Jenni; Liu, Jian Kui; Pawłowska, Julia; Põldmaa, Kadri; Pärtel, Kadri; Runnel, Kadri; Hansen, Karen; Larsson, Karl Henrik; Hyde, Kevin David; Denis, Marcelo Sandoval; Smith, Matthew E.; Heller, Merje Toome; Wijayawardene, Nalin N.; Menolli, Nelson; Reynolds, Nicole K.; Drenkhan, Rein; Maharachchikumbura, Sajeewa S. N.; Gibertoni, Tatiana B.; Læssøe, Thomas; Davis, William; Tokarev, Yuri; Corrales, Adriana; Soares, Adriene Mayra; Agan, Ahto; Machado, Alexandre Reis; Moyao, Andrés Argüelles; Detheridge, Andrew; de Meiras Ottoni, Angelina; Verbeken, Annemieke; Dutta, Arun Kumar; Cui, Bao Kai; Pradeep, C. K.; Marín, César; Stanton, Daniel; Gohar, Daniyal; Wanasinghe, Dhanushka N.; Otsing, Eveli; Aslani, Farzad; Griffith, Gareth W.; Lumbsch, Thorsten H.; Grossart, Hans Peter; Masigol, Hossein; Timling, Ina; Hiiesalu, Inga; Oja, Jane; Kupagme, John Y.; Geml, József; Manjarrez, Julieta Alvarez; Ilves, Kai; Loit, Kaire; Adamson, Kalev; Nara, Kazuhide; Küngas, Kati; Jimenez, Keilor Rojas; Bitenieks, Krišs; Irinyi, Laszlo; Nagy, László Laszlo; Soonvald, Liina; Zhou, LiWei; Wagner, Lysett; Aime, M. Catherine; Öpik, Maarja; Mujica, María Isabel; Metsoja, Martin; Ryberg, Martin; Vasar, Martti; Murata, Masao; Nelsen, Matthew P.; Cleary, Michelle; Samarakoon, Milan C.; Doilom, Mingkwan; Bahram, Mohammad; Doust, Niloufar Hagh; Dulya, Olesya; Johnston, Peter; Kohout, Petr; Chen, Qian; Tian, Qing; Nandi, Rajasree; Amiri, Rasekh; Perera, Rekhani Hansika; dos Santos Chikowski, Renata; MendesAlvarenga, Renato L.; Orijel, Roberto Garibay; Gielen, Robin; Phookamsak, Rungtiwa; Jayawardena, Ruvishika S.; Rahimlou, Saleh; Karunarathna, Samantha C.; Tibpromma, Saowaluck; Brown, Shawn P.; Sepp, Siim Kaarel; Mundra, Sunil; Luo, Zhu Hua; Bose, Tanay; Vahter, Tanel; Netherway, Tarquin; Yang, Teng; May, Tom; Varga, Torda; Li, Wei; Coimbra, Victor Rafael Matos; de Oliveira, Virton Rodrigo Targino; de Lima, Vitor Xavier; Mikryukov, Vladimir S.; Lu, Yongzhong; Matsuda, Yosuke; Miyamoto, Yumiko; Kõljalg, Urmas; Tedersoo, Leho
FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles Journal Article
In: Fungal Diversity, vol. 105, no. 1, 2020.
@article{Põlme2020,
title = {FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles},
author = {Sergei Põlme and Kessy Abarenkov and Henrik R. Nilsson and Björn D. Lindahl and Karina Engelbrecht Clemmensen and Havard Kauserud and Nhu Nguyen and Rasmus Kjøller and Scott T. Bates and Petr Baldrian and Tobias Guldberg Frøslev and Kristjan Adojaan and Alfredo Vizzini and Ave Suija and Donald Pfister and Hans Otto Baral and Helle Järv and Hugo Madrid and Jenni Nordén and Jian Kui Liu and Julia Pawłowska and Kadri Põldmaa and Kadri Pärtel and Kadri Runnel and Karen Hansen and Karl Henrik Larsson and Kevin David Hyde and Marcelo Sandoval Denis and Matthew E. Smith and Merje Toome Heller and Nalin N. Wijayawardene and Nelson Menolli and Nicole K. Reynolds and Rein Drenkhan and Sajeewa S. N. Maharachchikumbura and Tatiana B. Gibertoni and Thomas Læssøe and William Davis and Yuri Tokarev and Adriana Corrales and Adriene Mayra Soares and Ahto Agan and Alexandre Reis Machado and Andrés Argüelles Moyao and Andrew Detheridge and Angelina de Meiras Ottoni and Annemieke Verbeken and Arun Kumar Dutta and Bao Kai Cui and C. K. Pradeep and César Marín and Daniel Stanton and Daniyal Gohar and Dhanushka N. Wanasinghe and Eveli Otsing and Farzad Aslani and Gareth W. Griffith and Thorsten H. Lumbsch and Hans Peter Grossart and Hossein Masigol and Ina Timling and Inga Hiiesalu and Jane Oja and John Y. Kupagme and József Geml and Julieta Alvarez Manjarrez and Kai Ilves and Kaire Loit and Kalev Adamson and Kazuhide Nara and Kati Küngas and Keilor Rojas Jimenez and Krišs Bitenieks and Laszlo Irinyi and László Laszlo Nagy and Liina Soonvald and LiWei Zhou and Lysett Wagner and M. Catherine Aime and Maarja Öpik
and María Isabel Mujica and Martin Metsoja and Martin Ryberg and Martti Vasar and Masao Murata and Matthew P. Nelsen and Michelle Cleary and Milan C. Samarakoon and Mingkwan Doilom and Mohammad Bahram
and Niloufar Hagh Doust and Olesya Dulya and Peter Johnston and Petr Kohout and Qian Chen and Qing Tian and Rajasree Nandi and Rasekh Amiri and Rekhani Hansika Perera and Renata dos Santos Chikowski and Renato L. MendesAlvarenga and Roberto Garibay Orijel and Robin Gielen and Rungtiwa Phookamsak and Ruvishika S. Jayawardena and Saleh Rahimlou and Samantha C. Karunarathna and Saowaluck Tibpromma and Shawn P. Brown and Siim Kaarel Sepp and Sunil Mundra and Zhu Hua Luo and Tanay Bose and Tanel Vahter and Tarquin Netherway and Teng Yang and Tom May and Torda Varga and Wei Li and Victor Rafael Matos Coimbra and Virton Rodrigo Targino de Oliveira and Vitor Xavier de Lima and Vladimir S. Mikryukov and Yongzhong Lu and Yosuke Matsuda and Yumiko Miyamoto and Urmas Kõljalg and Leho Tedersoo},
url = {https://link.springer.com/article/10.1007/s13225-020-00466-2#citeas},
doi = {https://doi.org/10.1007/s13225-020-00466-2},
year = {2020},
date = {2020-11-16},
journal = {Fungal Diversity},
volume = {105},
number = {1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sulej, Tomasz; Krzesiński, Grzegorz; Tałanda, Mateusz; Wolniewicz, Andrzej S.; Błażejowski, Błażej; Bonde, Niels; Gutowski, Piotr; Sienkiewicz, Maksymilian; Niedźwiedzki, Grzegorz
The earliest-known mammaliaform fossil from Greenland sheds light on origin of mammals Journal Article
In: Proceedings of the National Academy of Sciences, vol. 117, no. 43, pp. 26861-26867, 2020.
@article{Sulej26861,
title = {The earliest-known mammaliaform fossil from Greenland sheds light on origin of mammals},
author = {Tomasz Sulej and Grzegorz Krzesiński and Mateusz Tałanda and Andrzej S. Wolniewicz and Błażej Błażejowski and Niels Bonde and Piotr Gutowski and Maksymilian Sienkiewicz and Grzegorz Niedźwiedzki},
url = {https://www.pnas.org/content/117/43/26861},
doi = {https://doi.org/10.1073/pnas.2012437117 },
year = {2020},
date = {2020-10-27},
journal = {Proceedings of the National Academy of Sciences},
volume = {117},
number = {43},
pages = {26861-26867},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bakuła, Zofia; Gromadka, Robert; Gawor, Jan; Siedlecki, Paweł; Pomorski, Jan J.; Maciszewski, Kacper; Gromadka, Agnieszka; Karnkowska, Anna; Jagielski, Tomasz
Sequencing and Analysis of the Complete Organellar Genomes of Prototheca wickerhamii Journal Article
In: Frontiers in Plant Science, vol. 11, pp. 1296, 2020.
@article{10.3389/fpls.2020.01296,
title = {Sequencing and Analysis of the Complete Organellar Genomes of Prototheca wickerhamii},
author = {Zofia Bakuła and Robert Gromadka and Jan Gawor and Paweł Siedlecki and Jan J. Pomorski and Kacper Maciszewski and Agnieszka Gromadka and Anna Karnkowska and Tomasz Jagielski},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.01296/full},
doi = {10.3389/fpls.2020.01296},
year = {2020},
date = {2020-09-01},
journal = {Frontiers in Plant Science},
volume = {11},
pages = {1296},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Frankiewicz, Kamil E; Chau, John H; Oskolski, Alexei A
Wood and bark of Buddleja: uniseriate phellem, and systematic and ecological patterns Journal Article
In: IAWA Journal, vol. 42, no. 1, pp. 3–30, 2020, ISBN: 0928-1541.
@article{Woodandbark,
title = {Wood and bark of Buddleja: uniseriate phellem, and systematic and ecological patterns},
author = {Frankiewicz, Kamil E and Chau, John H and Oskolski, Alexei A},
url = {https://brill.com/view/journals/iawa/42/1/article-p3{\\_}2.xml},
doi = {10.1163/22941932-bja10020},
isbn = {0928-1541},
year = {2020},
date = {2020-07-20},
journal = {IAWA Journal},
volume = {42},
number = {1},
pages = {3--30},
abstract = {Wood anatomy of Buddleja is well-explored but not in many southern African members, which form a grade of species and small clades that form successive sister groups to the rest of the genus, and its bark structure has not been studied at all. We provide new descriptions of wood anatomy for twelve species, including nearly all Buddleja from southern Africa and two species of Freylinia in the sister group of Buddleja . We also describe bark structure from fifteen species. To assess if wood anatomy provides phylogenetic and/or ecological signal, we compiled data on wood traits and climatic variables from the distributions of 53 species. Wood traits counteracting cavitation correlated with higher temperature and precipitation seasonality; simultaneously they were better expressed in species with smaller maximal plant height. It is likely that hotter and drier areas harbour smaller plants which have traits conveying higher conductance safety. Bark structure varies considerably. In bark of Buddleja section Gomphostigma , periderm is initiated in the outer cortex and develops thin-walled phellem, and sclerification of their phloem does not occur. This resembles bark in Freylinia , supporting the position of section Gomphostigma as sister to the rest of Buddleja . In the remaining Buddleja species, bark is characterised by formation of periderm with phelloid cells in the secondary phloem. The phellem is often uniseriate, a condition not reported elsewhere. Its formation occurs close in time to solid sclerification of the cut-off phloem, suggesting a possible novel ontogenetic mechanism.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wood anatomy of Buddleja is well-explored but not in many southern African members, which form a grade of species and small clades that form successive sister groups to the rest of the genus, and its bark structure has not been studied at all. We provide new descriptions of wood anatomy for twelve species, including nearly all Buddleja from southern Africa and two species of Freylinia in the sister group of Buddleja . We also describe bark structure from fifteen species. To assess if wood anatomy provides phylogenetic and/or ecological signal, we compiled data on wood traits and climatic variables from the distributions of 53 species. Wood traits counteracting cavitation correlated with higher temperature and precipitation seasonality; simultaneously they were better expressed in species with smaller maximal plant height. It is likely that hotter and drier areas harbour smaller plants which have traits conveying higher conductance safety. Bark structure varies considerably. In bark of Buddleja section Gomphostigma , periderm is initiated in the outer cortex and develops thin-walled phellem, and sclerification of their phloem does not occur. This resembles bark in Freylinia , supporting the position of section Gomphostigma as sister to the rest of Buddleja . In the remaining Buddleja species, bark is characterised by formation of periderm with phelloid cells in the secondary phloem. The phellem is often uniseriate, a condition not reported elsewhere. Its formation occurs close in time to solid sclerification of the cut-off phloem, suggesting a possible novel ontogenetic mechanism.
PW, Crous; MJ, Wingfield; YH, Chooi; (...),; and, Gorczak M
Fungal Planet description sheets: 1042-1111 Journal Article
In: Persoonia, vol. 44, pp. 301-459, 2020.
@article{FungPlanet1042,
title = {Fungal Planet description sheets: 1042-1111},
author = {Crous PW and Wingfield MJ and Chooi YH and (...) and Gorczak M and et al.},
url = {https://www.ingentaconnect.com/content/nhn/pimj/2020/00000044/00000001/art00011},
doi = {10.3767/persoonia.2020.44.11},
year = {2020},
date = {2020-06-01},
journal = {Persoonia},
volume = {44},
pages = {301-459},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.)from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa. Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae. UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis. USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.)on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.)from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.)from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa. Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae. UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis. USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.)on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.)from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes.
Łukomska-Kowalczyk, Maja; Fells, Alicja; Chaber, Katarzyna; Milanowski, Rafał; Zakryś, Bożena
Taxon‐rich phylogeny and taxonomy of the genus Phacus (Euglenida) based on morphological and molecular data Journal Article
In: Journal of Phycology, vol. 56, no. 5, pp. 1135-1156, 2020.
@article{https://doi.org/10.1111/jpy.13028,
title = {Taxon‐rich phylogeny and taxonomy of the genus Phacus (Euglenida) based on morphological and molecular data },
author = {Maja Łukomska-Kowalczyk and Alicja Fells and Katarzyna Chaber and Rafał Milanowski and Bożena Zakryś},
url = {https://onlinelibrary.wiley.com/doi/10.1111/jpy.13028},
doi = { https://doi.org/10.1111/jpy.13028},
year = {2020},
date = {2020-05-19},
journal = {Journal of Phycology},
volume = {56},
number = {5},
pages = {1135-1156},
abstract = {Morphological and molecular features were analyzed for a species of Phacus to better understand the phylogenetic relationships among them and establish the taxonomy. Phylogenetic analyses were based on nSSU rDNA and the research resulted in 55 new sequences. The study included species available in algal collections and those isolated directly from the environment in Poland and the Czech Republic. As a result, the obtained phylogenetic tree of Phacus includes 50 species, out of which 7 are represented on a tree for the first time (Phacus anacoelus, P. anomalus, P. curvicauda, P. elegans, P. lismorensis, P. minutus and P. stokesii) and many have been taxonomically verified. For all verified species, diagnostic descriptions were amended, the naming was reordered and epitypes were designated.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Morphological and molecular features were analyzed for a species of Phacus to better understand the phylogenetic relationships among them and establish the taxonomy. Phylogenetic analyses were based on nSSU rDNA and the research resulted in 55 new sequences. The study included species available in algal collections and those isolated directly from the environment in Poland and the Czech Republic. As a result, the obtained phylogenetic tree of Phacus includes 50 species, out of which 7 are represented on a tree for the first time (Phacus anacoelus, P. anomalus, P. curvicauda, P. elegans, P. lismorensis, P. minutus and P. stokesii) and many have been taxonomically verified. For all verified species, diagnostic descriptions were amended, the naming was reordered and epitypes were designated.
Bajer, Anna; Alsarraf, Mohammed; Dwużnik, Dorota; Mierzejewska, Ewa J.; Kołodziej-Sobocińska, Marta; Behnke-Borowczyk, Jolanta; Banasiak, Łukasz; Grzybek, Maciej; Tołkacz, Katarzyna; Kartawik, Natalia; Stańczak, Łukasz; Opalińsk, Patrycja; Krokowska-Paluszak, Małgorzata; Górecki, Grzegorz; Alsarraf, Mustafa; Behnke, Jerzy M.
In: Parasites & Vectors, vol. 13, no. 1, pp. 95, 2020.
@article{Bajer2020,
title = {Rodents as intermediate hosts of cestode parasites of mammalian carnivores and birds of prey in Poland, with the first data on the life-cycle of Mesocestoides melesi},
author = {Anna Bajer and Mohammed Alsarraf and Dorota Dwużnik and Ewa J. Mierzejewska and Marta Kołodziej-Sobocińska and Jolanta Behnke-Borowczyk and Łukasz Banasiak and Maciej Grzybek and Katarzyna Tołkacz and Natalia Kartawik and Łukasz Stańczak and Patrycja Opalińsk and Małgorzata Krokowska-Paluszak and Grzegorz Górecki and Mustafa Alsarraf and Jerzy M. Behnke},
url = {https://parasitesandvectors.biomedcentral.com/articles/10.1186/s13071-020-3961-2#citeas},
doi = {https://doi.org/10.1186/s13071-020-3961-2},
year = {2020},
date = {2020-02-22},
journal = {Parasites & Vectors},
volume = {13},
number = {1},
pages = {95},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Keeling, Patrick J; Boscaro, Vittorio; Bardell, Floyd; Burki, Fabien; Cho, Anna; Cooney, Elizabeth C; del Campo, Javier; Fast, Naomi M; Fiorito, Rebecca; Gavelis, Greg S; Gawryluk, Ryan M R; George, Emma E; Gomm-Kolisko, Rachael N; Grisdale, Cameron J; Heger, Thierry; Hehenberger, Elisabeth; Herranz, Maria; Hirakawa, Yoshihisa; Husnik, Filip; Imanian, Behzad; Irwin, Nicholas A T; James, Erick R; Janouskovec, Jan; Karnkowska, Anna; Kolisko, Martin; Kwong, Waldan; Leander, Brian S; Mathur, Varsha; Nawar, Ferdous; Okamoto, Noriko; Parfrey, Laura; Pittis, Alexandros; Pan, Jingwen; Pombert, Jean-Francois; Sabetrasekh, Mona; Saldarriaga, Juan F; Sanders, Rhea; Singh, Racquel A; Smith, David R; Strassert, Jürgen F H; Stephenson, India; Syberg-Olsen, Mitchell J; Tai, Vera; Tikhonenkov, Denis V; Steenkiste, Niels W L Van; Whalen, Matthew; Whelan, Thomas A; Wong, Donald K
A letter to Denis Lynn Journal Article
In: Aquatic Ecosystem Health & Management, vol. 23, no. 1, pp. 17–18, 2020, ISSN: 1463-4988.
@article{Keeling202017,
title = {A letter to Denis Lynn},
author = {Patrick J Keeling and Vittorio Boscaro and Floyd Bardell and Fabien Burki and Anna Cho and Elizabeth C Cooney and Javier del Campo and Naomi M Fast and Rebecca Fiorito and Greg S Gavelis and Ryan M R Gawryluk and Emma E George and Rachael N Gomm-Kolisko and Cameron J Grisdale and Thierry Heger and Elisabeth Hehenberger and Maria Herranz and Yoshihisa Hirakawa and Filip Husnik and Behzad Imanian and Nicholas A T Irwin and Erick R James and Jan Janouskovec and Anna Karnkowska and Martin Kolisko and Waldan Kwong and Brian S Leander and Varsha Mathur and Ferdous Nawar and Noriko Okamoto and Laura Parfrey and Alexandros Pittis and Jingwen Pan and Jean-Francois Pombert and Mona Sabetrasekh and Juan F Saldarriaga and Rhea Sanders and Racquel A Singh and David R Smith and Jürgen F H Strassert and India Stephenson and Mitchell J Syberg-Olsen and Vera Tai and Denis V Tikhonenkov and Niels W L {Van Steenkiste} and Matthew Whalen and Thomas A Whelan and Donald K Wong},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85086834910&doi=10.1080%2F14634988.2020.1717827&partnerID=40&md5=d8becb6d97fbe286c3b7a36a05eb19e0 https://bioone.org/journals/aquatic-ecosystem-health-and-management/volume-23/issue-1/14634988.2020.1717827/A-letter-to-Denis-Lynn/10.1080/14634988.2020.1717827.full},
doi = {10.1080/14634988.2020.1717827},
issn = {1463-4988},
year = {2020},
date = {2020-01-02},
journal = {Aquatic Ecosystem Health & Management},
volume = {23},
number = {1},
pages = {17--18},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sulej, Tomasz; Niedźwiedzki, Grzegorz; Tałanda, Mateusz; Dróżdż, Dawid; Hara, Ewa
A new early Late Triassic non-mammaliaform eucynodont from Poland Journal Article
In: Historical Biology, vol. 32, no. 1, pp. 80-92, 2020.
@article{doi:10.1080/08912963.2018.1471477,
title = {A new early Late Triassic non-mammaliaform eucynodont from Poland},
author = {Tomasz Sulej and Grzegorz Niedźwiedzki and Mateusz Tałanda and Dawid Dróżdż and Ewa Hara},
url = {https://doi.org/10.1080/08912963.2018.1471477},
doi = {10.1080/08912963.2018.1471477},
year = {2020},
date = {2020-01-01},
journal = {Historical Biology},
volume = {32},
number = {1},
pages = {80-92},
publisher = {Taylor & Francis},
abstract = {ABSTRACTBicuspid, tricuspid and tetracuspid postcanine teeth of a new non-mammaliaform eucynodont, Polonodon woznikiensis gen. et sp. nov. from the mid-late Carnian (early Late Triassic) of Woźniki clay-pit, Silesia (southern Poland) show incipient root division. They are similar to teeth of Dromatheriidae from the Carnian (early Late Triassic) to the Rhaetian (late Late Triassic) of Europe, India, and USA and the dentition of brasilodontids from the early Norian (mid Late Triassic) of Brazil. The P. woznikiensis teeth differ from those of the latter group mostly in the absence of cingulum. Some of the new fossils from Silesia provide the oldest Laurasian record of eucynodont teeth with the main cusp (a) anterior edge very long as the mesial cusp b is placed much lower than cusp c (distal). The contemporaneous Alemoatherium huebneri, from Gondwana, had similar postcanines. The findings from Poland indicate that this postcanine morphology was present in non-mammaliaform cynodonts from both hemispheres as early as the mid-late Carnian. The distal end of the humerus from the same locality is also described.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
ABSTRACTBicuspid, tricuspid and tetracuspid postcanine teeth of a new non-mammaliaform eucynodont, Polonodon woznikiensis gen. et sp. nov. from the mid-late Carnian (early Late Triassic) of Woźniki clay-pit, Silesia (southern Poland) show incipient root division. They are similar to teeth of Dromatheriidae from the Carnian (early Late Triassic) to the Rhaetian (late Late Triassic) of Europe, India, and USA and the dentition of brasilodontids from the early Norian (mid Late Triassic) of Brazil. The P. woznikiensis teeth differ from those of the latter group mostly in the absence of cingulum. Some of the new fossils from Silesia provide the oldest Laurasian record of eucynodont teeth with the main cusp (a) anterior edge very long as the mesial cusp b is placed much lower than cusp c (distal). The contemporaneous Alemoatherium huebneri, from Gondwana, had similar postcanines. The findings from Poland indicate that this postcanine morphology was present in non-mammaliaform cynodonts from both hemispheres as early as the mid-late Carnian. The distal end of the humerus from the same locality is also described.
Lukešová, Soňa; Karlicki, Michał; Hadariová, Lucia Tomečková; Szabová, Jana; Karnkowska, Anna; Hampl, Vladimír
In: Environmental Microbiology Reports, vol. 12, no. 1, pp. 78-91, 2020.
@article{https://doi.org/10.1111/1758-2229.12817,
title = {Analyses of environmental sequences and two regions of chloroplast genomes revealed the presence of new clades of photosynthetic euglenids in marine environments},
author = {Soňa Lukešová and Michał Karlicki and Lucia Tomečková Hadariová and Jana Szabová and Anna Karnkowska and Vladimír Hampl},
url = {https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1758-2229.12817},
doi = {https://doi.org/10.1111/1758-2229.12817},
year = {2020},
date = {2020-01-01},
journal = {Environmental Microbiology Reports},
volume = {12},
number = {1},
pages = {78-91},
abstract = {Euglenophyceae are unicellular algae with the majority of their diversity known from small freshwater reservoirs. Only two dozen species have been described to occur in marine habitats, but their abundance and diversity remain unexplored. Phylogenetic studies revealed marine prasinophyte green alga, Pyramimonas parkeae, as the closest extant relative of the euglenophytes' plastid, but similarly to euglenophytes, our knowledge about the diversity of Pyramimonadales is limited. Here we explored Euglenophyceae and Pyramimonadales phylogenetic diversity in marine environmental samples. We yielded 18S rDNA and plastid 16S rDNA sequences deposited in public repositories and reconstructed Euglenophyceae reference trees. We searched high-throughput environmental sequences from the TARA Oceans expedition and Ocean Sampling Day initiative for 18S rDNA and 16S rDNA, placed them in the phylogenetic context and estimated their relative abundances. To avoid polymerase chain reaction (PCR) bias, we also exploited metagenomic data from the TARA Oceans expedition for the presence of rRNA sequences from these groups. Finally, we targeted these protists in coastal samples by specific PCR amplification of two parts of the plastid genome uniquely shared between euglenids and Pyramimonadales. All approaches revealed previously undetected, but relatively low-abundant lineages of marine Euglenophyceae. Surprisingly, some of those lineages are branching within the freshwater or brackish genera.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Euglenophyceae are unicellular algae with the majority of their diversity known from small freshwater reservoirs. Only two dozen species have been described to occur in marine habitats, but their abundance and diversity remain unexplored. Phylogenetic studies revealed marine prasinophyte green alga, Pyramimonas parkeae, as the closest extant relative of the euglenophytes' plastid, but similarly to euglenophytes, our knowledge about the diversity of Pyramimonadales is limited. Here we explored Euglenophyceae and Pyramimonadales phylogenetic diversity in marine environmental samples. We yielded 18S rDNA and plastid 16S rDNA sequences deposited in public repositories and reconstructed Euglenophyceae reference trees. We searched high-throughput environmental sequences from the TARA Oceans expedition and Ocean Sampling Day initiative for 18S rDNA and 16S rDNA, placed them in the phylogenetic context and estimated their relative abundances. To avoid polymerase chain reaction (PCR) bias, we also exploited metagenomic data from the TARA Oceans expedition for the presence of rRNA sequences from these groups. Finally, we targeted these protists in coastal samples by specific PCR amplification of two parts of the plastid genome uniquely shared between euglenids and Pyramimonadales. All approaches revealed previously undetected, but relatively low-abundant lineages of marine Euglenophyceae. Surprisingly, some of those lineages are branching within the freshwater or brackish genera.
Dzik, Jerzy
Decline in diversity of early Palaeozoic loosely coiled gastropod protoconchs Journal Article
In: Lethaia, vol. 53, no. 1, pp. 32–46, 2020.
@article{dzik_decline_2020,
title = {Decline in diversity of early Palaeozoic loosely coiled gastropod protoconchs},
author = {Jerzy Dzik},
year = {2020},
date = {2020-01-01},
journal = {Lethaia},
volume = {53},
number = {1},
pages = {32--46},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pawlak, Wojciech; Tałanda, Mateusz; Sulej, Tomasz; Niedźwiedzki, Grzegorz
Dipnoan from the Upper Triassic of East Greenland and remarks about palaeobiogeography of Ptychoceratodus Journal Article
In: Acta Palaeontologica Polonica, vol. 65, pp. 561-574, 2020.
@article{Pawlak2020DipnoanFT,
title = {Dipnoan from the Upper Triassic of East Greenland and remarks about palaeobiogeography of Ptychoceratodus},
author = {Wojciech Pawlak and Mateusz Tałanda and Tomasz Sulej and Grzegorz Niedźwiedzki},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Acta Palaeontologica Polonica},
volume = {65},
pages = {561-574},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Haelewaters, Danny; Okrasińska, Alicja; Gorczak, Michał; Pfister, Donald H.
Draft Genome Sequence of the Globally Distributed Cockroach-Infecting Fungus Herpomyces periplanetae Strain D. Haelew. 1187d Journal Article
In: Microbiology Resource Announcements, vol. 9, no. 6, 2020.
@article{Haelewaterse01458-19,
title = {Draft Genome Sequence of the Globally Distributed Cockroach-Infecting Fungus Herpomyces periplanetae Strain D. Haelew. 1187d},
author = {Danny Haelewaters and Alicja Okrasińska and Michał Gorczak and Donald H. Pfister},
editor = {Antonis Rokas},
url = {https://mra.asm.org/content/9/6/e01458-19},
doi = {10.1128/MRA.01458-19},
year = {2020},
date = {2020-01-01},
journal = {Microbiology Resource Announcements},
volume = {9},
number = {6},
publisher = {American Society for Microbiology Journals},
abstract = {Herpomyces periplanetae is an obligate biotroph of Periplaneta americana, the American cockroach. Its nearly cosmopolitan distribution is shaped by its globally invasive host and the international pet trade. Here, we report the draft genome sequence of H. periplanetae, based on a thallus from P. americana collected in Cambridge, Massachusetts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Herpomyces periplanetae is an obligate biotroph of Periplaneta americana, the American cockroach. Its nearly cosmopolitan distribution is shaped by its globally invasive host and the international pet trade. Here, we report the draft genome sequence of H. periplanetae, based on a thallus from P. americana collected in Cambridge, Massachusetts.
Dzik, Jerzy
Ewolucja. Twórcza moc selekcji Book
Wydawnictwa Uniwersytetu Warszawskiego, Warszawa, 2020, ISBN: 978-83-235-4105-9, (Publication Title: Wydawnictwa Uniwersytetu Warszawskiego).
@book{dzik_ewolucja_2020,
title = {Ewolucja. Twórcza moc selekcji},
author = {Jerzy Dzik},
isbn = {978-83-235-4105-9},
year = {2020},
date = {2020-01-01},
publisher = {Wydawnictwa Uniwersytetu Warszawskiego},
address = {Warszawa},
note = {Publication Title: Wydawnictwa Uniwersytetu Warszawskiego},
keywords = {},
pubstate = {published},
tppubtype = {book}
}
Pindakiewicz, Maciej; Tałanda, Mateusz; Sulej, Tomasz; Niedźwiedzki, Grzegorz; Sennikov, A G; Bakayev, A; Bulanov, V V; Golubev, V; Minikh, A V
Feeding convergence among ray-finned fishes: teeth of the herbivorous actinopterygians from the latest Permian of East European Platform, Russia Journal Article
In: Acta Palaeontologica Polonica, vol. 65, no. 1, pp. 71–79, 2020.
@article{Pindakiewicz2020FeedingCA,
title = {Feeding convergence among ray-finned fishes: teeth of the herbivorous actinopterygians from the latest Permian of East European Platform, Russia},
author = {Maciej Pindakiewicz and Mateusz Tałanda and Tomasz Sulej and Grzegorz Niedźwiedzki and A G Sennikov and A Bakayev and V V Bulanov and V Golubev and A V Minikh},
year = {2020},
date = {2020-01-01},
journal = {Acta Palaeontologica Polonica},
volume = {65},
number = {1},
pages = {71--79},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kovač, Marta; Gorczak, Michał; Wrzosek, Marta; Tkaczuk, Cezary; Pernek, Milan
In: Insects, vol. 11, no. 10, 2020, ISSN: 2075-4450.
@article{insects11100679,
title = {Identification of Entomopathogenic Fungi as Naturally Occurring Enemies of the Invasive Oak Lace Bug, Corythucha arcuata (Say) (Hemiptera: Tingidae)},
author = {Marta Kovač and Michał Gorczak and Marta Wrzosek and Cezary Tkaczuk and Milan Pernek},
url = {https://www.mdpi.com/2075-4450/11/10/679},
doi = {https://doi.org/10.3390/insects11100679},
issn = {2075-4450},
year = {2020},
date = {2020-01-01},
journal = {Insects},
volume = {11},
number = {10},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Łukomska-Kowalczyk, Maja; Chaber, Katarzyna; Fells, Alicja; Milanowski, Rafał; Zakryś, Bożena
Molecular and Morphological Delimitation of Species in the Group of Lepocinclis Ovum-like taxa (Euglenida) Journal Article
In: Journal of Phycology, vol. 56, no. 2, pp. 283-299, 2020.
@article{https://doi.org/10.1111/jpy.12949,
title = {Molecular and Morphological Delimitation of Species in the Group of Lepocinclis Ovum-like taxa (Euglenida)},
author = {Maja Łukomska-Kowalczyk and Katarzyna Chaber and Alicja Fells and Rafał Milanowski and Bożena Zakryś},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.12949},
doi = {https://doi.org/10.1111/jpy.12949},
year = {2020},
date = {2020-01-01},
journal = {Journal of Phycology},
volume = {56},
number = {2},
pages = {283-299},
abstract = {Although Lepocinclis ovum is recognized as a cosmopolitan and common species, and Lepocinclis globulus is the type species of the genus Lepocinclis, their correct identification is nearly impossible. The reason is that over 30 morphologically similar taxa appear in the literature, but no good diagnostic features exist to distinguish amongst them. Using environmental sampling and nuclear SSU rDNA sequencing, we delimited species within the group of Lepocinclis ovum-like taxa. Morphological and molecular features were analyzed for taxa isolated from Poland and six cultured strains from algal collections. In the case of environmental sampling, DNA was obtained from a small number of cells (20–400) isolated with a micropipette without setting up laboratory cultures (52 isolates), and phylogenetic analyses were based on the variation in nSSU rDNA. Apart from L. ovum and L. globulus, 13 other species were distinguished and four taxa (Lepocinclis conica comb. nov., L. fominii comb. nov., L. gracilicauda comb. nov., and L. pseudofominii nom. nov.) had their taxonomic ranks changed. For all verified species, diagnostic descriptions were emended and epitypes designated. The only exception was L. ovum, for which the epitype was questioned and thus, a new candidate for the epitype was suggested for future adoption.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Although Lepocinclis ovum is recognized as a cosmopolitan and common species, and Lepocinclis globulus is the type species of the genus Lepocinclis, their correct identification is nearly impossible. The reason is that over 30 morphologically similar taxa appear in the literature, but no good diagnostic features exist to distinguish amongst them. Using environmental sampling and nuclear SSU rDNA sequencing, we delimited species within the group of Lepocinclis ovum-like taxa. Morphological and molecular features were analyzed for taxa isolated from Poland and six cultured strains from algal collections. In the case of environmental sampling, DNA was obtained from a small number of cells (20–400) isolated with a micropipette without setting up laboratory cultures (52 isolates), and phylogenetic analyses were based on the variation in nSSU rDNA. Apart from L. ovum and L. globulus, 13 other species were distinguished and four taxa (Lepocinclis conica comb. nov., L. fominii comb. nov., L. gracilicauda comb. nov., and L. pseudofominii nom. nov.) had their taxonomic ranks changed. For all verified species, diagnostic descriptions were emended and epitypes designated. The only exception was L. ovum, for which the epitype was questioned and thus, a new candidate for the epitype was suggested for future adoption.
Czepiński, Łukasz
New protoceratopsid specimens improve the age correlation of the Upper Cretaceous Gobi Desert strata Journal Article
In: Acta Palaeontologica Polonica, vol. 65, 2020.
@article{Czepiski2020NewPS,
title = {New protoceratopsid specimens improve the age correlation of the Upper Cretaceous Gobi Desert strata},
author = {Łukasz Czepiński},
year = {2020},
date = {2020-01-01},
journal = {Acta Palaeontologica Polonica},
volume = {65},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Czepiński, Łukasz
Ontogeny and variation of a protoceratopsid dinosaur Bagaceratops rozhdestvenskyi from the Late Cretaceous of the Gobi Desert Journal Article
In: Historical Biology, vol. 32, no. 10, pp. 1394–1421, 2020.
@article{doi:10.1080/08912963.2019.1593404,
title = {Ontogeny and variation of a protoceratopsid dinosaur Bagaceratops rozhdestvenskyi from the Late Cretaceous of the Gobi Desert},
author = {Łukasz Czepiński},
url = {https://doi.org/10.1080/08912963.2019.1593404},
doi = {10.1080/08912963.2019.1593404},
year = {2020},
date = {2020-01-01},
journal = {Historical Biology},
volume = {32},
number = {10},
pages = {1394--1421},
publisher = {Taylor & Francis},
abstract = {Bagaceratops rozhdestvenskyi is a ceratopsian dinosaur from the Late Cretaceous Baruungoyot Formation of the Gobi Desert, closely related to Protoceratops spp. Several Bag. rozhdestvenskyi skulls demonstrate a wide range of variation in their morphology and size. Here I argue that the observed variability is most likely of intraspecific nature. Specimens classified in a few allegedly distinct species from the same or near-contemporary sediments, namely Gobiceratops minutus, Lamaceratops tereschenkoi and Platyceratops tatarinovi from Baruungoyot Formation, and Magnirostris dodsoni from Bayan Mandahu, are younger subjective synonyms of Bag. rozhdestvenskyi. They plausibly represent an ontogenetic series within the latter. Breviceratops kozlowskiiis a distinct taxon. The evolutionary relationships within Protoceratopsidae are complicated by the mosaic distribution of plesiomorphic and derived features in distinct species. I suggest that taxa distribution and observed changes in morphology are an evidence for the ancestral position of Protoceratops andrewsi among protoceratopsids. It implies possible temporary separation between the geological formations of the Gobi Desert yielding distinct protoceratopsid species. The novel evolutionary scenario suggests number of convergences that occurred in Protoceratopsidae and Ceratopsoidea (reduction of the premaxillary dentition, fusion of nasals, development of the accessory antorbital fenestra). Present study reveals the significance of the intraspecific and ontogenetic variation in the study of the neoceratopsian taxonomy.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bagaceratops rozhdestvenskyi is a ceratopsian dinosaur from the Late Cretaceous Baruungoyot Formation of the Gobi Desert, closely related to Protoceratops spp. Several Bag. rozhdestvenskyi skulls demonstrate a wide range of variation in their morphology and size. Here I argue that the observed variability is most likely of intraspecific nature. Specimens classified in a few allegedly distinct species from the same or near-contemporary sediments, namely Gobiceratops minutus, Lamaceratops tereschenkoi and Platyceratops tatarinovi from Baruungoyot Formation, and Magnirostris dodsoni from Bayan Mandahu, are younger subjective synonyms of Bag. rozhdestvenskyi. They plausibly represent an ontogenetic series within the latter. Breviceratops kozlowskiiis a distinct taxon. The evolutionary relationships within Protoceratopsidae are complicated by the mosaic distribution of plesiomorphic and derived features in distinct species. I suggest that taxa distribution and observed changes in morphology are an evidence for the ancestral position of Protoceratops andrewsi among protoceratopsids. It implies possible temporary separation between the geological formations of the Gobi Desert yielding distinct protoceratopsid species. The novel evolutionary scenario suggests number of convergences that occurred in Protoceratopsidae and Ceratopsoidea (reduction of the premaxillary dentition, fusion of nasals, development of the accessory antorbital fenestra). Present study reveals the significance of the intraspecific and ontogenetic variation in the study of the neoceratopsian taxonomy.
Dzik, Jerzy
Ordovician conodonts and the Tornquist Lineament Journal Article
In: Palaeogeography, Palaeoclimatology, Palaeoecology, vol. 549, 2020.
@article{dzik_ordovician_2020,
title = {Ordovician conodonts and the Tornquist Lineament},
author = {Jerzy Dzik},
year = {2020},
date = {2020-01-01},
journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
volume = {549},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wijayawardene, N N; Hyde, K D; Al-Ani, L K T; Tedersoo, L; Haelewaters, Danny; Rajeshkumar, K C; Zhao, R L; Aptroot, A; D., V Leontyev; Saxena, R K; Tokarev, Y S; Dai, D Q; Letcher, P M; Stephenson, S L; Ertz, D; Lumbsch, H T; Kukwa, M; I., V Issi; Madrid, H; Phillips, A J L; Selbmann, L; Pfliegler, W P; Horvath, E; Bensch, K; Kirk, P M; Kolarikova, K; Raja, H A; Radek, R; Papp, V; Dima, B; Ma, J; Malosso, E; Takamatsu, S; Rambold, G; Gannibal, P B; Triebel, D; Gautam, A K; Avasthi, S; Suetrong, S; Timdal, E; Fryar, S C; Delgado, G; Reblova, M; Doilom, M; Dolatabadi, S; Pawłowska, Julia Z.; Humber, R A; Kodsueb, R; Sanchez-Castro, I; Goto, B T; Silva, D K A; de Souza, F A; Oehl, F R; da Silva, G A; Silva, I R; Blaszkowski, J; Jobim, K; Maia, L C; Barbosa, F R; Fiuza, P O; Divakar, P K; Shenoy, B D; Castaneda-Ruiz, R F; Somrithipol, S; Lateef, A A; Karunarathna, S C; Tibpromma, S; Mortimer, P E; Wanasinghe, D N; Phookamsak, R; Xu, J; Wang, Y; Tian, F; Alvarado, P; Li, D W; Kusan, I; Matocec, N; Masic, A; Tkalcec, Z; Maharachchikumbura, S S N; Papizadeh, M; Heredia, G; Wartchow, F; Bakhshi, M; Boehm, E; Youssef, N; Hustad, V P; Lawrey, J D; Santiago, A L C M A; Bezerra, J D P; Souza-Motta, C M; Firmino, A L; Tian, Q; Houbraken, J; Hongsanan, S; Tanaka, K; Dissanayake, A J; Monteiro, J S; Grossart, H P; Suija, A; Weerakoon, G; Etayo, J; Tsurykau, A; Vazquez, V; Mungai, P; Damm, U; Li, Q R; Zhang, H; Boonmee, S; Lu, Y Z; Becerra, A G; Kendrick, B; Brearley, F Q; Motiejunaite, J; Sharma, B; Khare, R; Gaikwad, S; Wijesundara, D S A; Tang, L Z; He, M Q; Flakus, A; Rodriguez-Flakus, P; Zhurbenko, M P; McKenzie, E H C; Stadler, M; Bhat, D J; Liu, J K; Raza, M; Jeewon, R; Nassonova, E S; Prieto, M; Jayalal, R G U; Erdogdu, M; Yurkov, A; Schnittler, M; Shchepin, O N; Novozhilov, Y K; Silva-Filho, A G S; Gentekaki, E; Liu, P; Cavender, J C; Kang, Y; Mohammad, S; Zhang, L F; Xu, R F; Li, Y M; Dayarathne, M C; Ekanayaka, A H; Wen, T C; Deng, C Y; Pereira, O L; Navathe, S; Hawksworth, D L; Fan, X L; Dissanayake, L S; Kuhnert, E; Thines, M
Outline of Fungi and fungus-like taxa Journal Article
In: Mycosphere, vol. 11, no. 1, pp. 1060–1456, 2020, ISSN: 2077-7000.
@article{8660838,
title = {Outline of Fungi and fungus-like taxa},
author = {N N Wijayawardene and K D Hyde and L K T Al-Ani and L Tedersoo and Danny Haelewaters and K C Rajeshkumar and R L Zhao and A Aptroot and V Leontyev D. and R K Saxena and Y S Tokarev and D Q Dai and P M Letcher and S L Stephenson and D Ertz and H T Lumbsch and M Kukwa and V Issi I. and H Madrid and A J L Phillips and L Selbmann and W P Pfliegler and E Horvath and K Bensch and P M Kirk and K Kolarikova and H A Raja and R Radek and V Papp and B Dima and J Ma and E Malosso and S Takamatsu and G Rambold and P B Gannibal and D Triebel and A K Gautam and S Avasthi and S Suetrong and E Timdal and S C Fryar and G Delgado and M Reblova and M Doilom and S Dolatabadi and Julia Z. Pawłowska and R A Humber and R Kodsueb and I Sanchez-Castro and B T Goto and D K A Silva and F A de Souza and F R Oehl and G A da Silva and I R Silva and J Blaszkowski and K Jobim and L C Maia and F R Barbosa and P O Fiuza and P K Divakar and B D Shenoy and R F Castaneda-Ruiz and S Somrithipol and A A Lateef and S C Karunarathna and S Tibpromma and P E Mortimer and D N Wanasinghe and R Phookamsak and J Xu and Y Wang and F Tian and P Alvarado and D W Li and I Kusan and N Matocec and A Masic and Z Tkalcec and S S N Maharachchikumbura and M Papizadeh and G Heredia and F Wartchow and M Bakhshi and E Boehm and N Youssef and V P Hustad and J D Lawrey and A L C M A Santiago and J D P Bezerra and C M Souza-Motta and A L Firmino and Q Tian and J Houbraken and S Hongsanan and K Tanaka and A J Dissanayake and J S Monteiro and H P Grossart and A Suija and G Weerakoon and J Etayo and A Tsurykau and V Vazquez and P Mungai and U Damm and Q R Li and H Zhang and S Boonmee and Y Z Lu and A G Becerra and B Kendrick and F Q Brearley and J Motiejunaite and B Sharma and R Khare and S Gaikwad and D S A Wijesundara and L Z Tang and M Q He and A Flakus and P Rodriguez-Flakus and M P Zhurbenko and E H C McKenzie and M Stadler and D J Bhat and J K Liu and M Raza and R Jeewon and E S Nassonova and M Prieto and R G U Jayalal and M Erdogdu and A Yurkov and M Schnittler and O N Shchepin and Y K Novozhilov and A G S Silva-Filho and E Gentekaki and P Liu and J C Cavender and Y Kang and S Mohammad and L F Zhang and R F Xu and Y M Li and M C Dayarathne and A H Ekanayaka and T C Wen and C Y Deng and O L Pereira and S Navathe and D L Hawksworth and X L Fan and L S Dissanayake and E Kuhnert and M Thines},
url = {http://dx.doi.org/10.5943/mycosphere/11/1/8},
doi = {http://dx.doi.org/10.5943/mycosphere/11/1/8},
issn = {2077-7000},
year = {2020},
date = {2020-01-01},
journal = {Mycosphere},
volume = {11},
number = {1},
pages = {1060--1456},
publisher = {Mycosphere Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Frankiewicz, Kamil E; Oskolski, Alexei; Banasiak, Łukasz; Fernandes, Francisco; Reduron, Jean-Pierre; Reyes-Betancort, Jorge-Alfredo; Szczeparska, Liliana; Alsarraf, Mohammed; Baczyński, Jakub; Spalik, Krzysztof
Parallel evolution of arborescent carrots (Daucus) in Macaronesia Journal Article
In: American Journal of Botany, vol. 107, no. 3, pp. 394-412, 2020.
@article{https://doi.org/10.1002/ajb2.1444,
title = {Parallel evolution of arborescent carrots (Daucus) in Macaronesia},
author = {Kamil E Frankiewicz and Alexei Oskolski and Łukasz Banasiak and Francisco Fernandes and Jean-Pierre Reduron and Jorge-Alfredo Reyes-Betancort and Liliana Szczeparska and Mohammed Alsarraf and Jakub Baczyński and Krzysztof Spalik},
url = {https://bsapubs.onlinelibrary.wiley.com/doi/abs/10.1002/ajb2.1444},
doi = {https://doi.org/10.1002/ajb2.1444},
year = {2020},
date = {2020-01-01},
journal = {American Journal of Botany},
volume = {107},
number = {3},
pages = {394-412},
abstract = {Premise Despite intensive research, the pathways and driving forces behind the evolution of derived woodiness on oceanic islands remain obscure. The genus Daucus comprises mostly herbs (therophytes, hemicryptophytes) with few rosette treelets (chamaephytes) endemic to various Macaronesian archipelagos, suggesting their independent evolution. To elucidate the evolutionary pathways to derived woodiness, we examined phylogenetic relationships and the habit and secondary xylem evolution in Daucus and related taxa. Methods Sixty taxa were surveyed for molecular markers, life history, and habit traits. Twenty-one species were considered for wood anatomical characters. A dated phylogeny was estimated using Bayesian methods. The evolution of selected traits was reconstructed using parsimony and maximum likelihood. Results Daucus dispersed independently to the Canary Islands (and subsequently to Madeira), Cape Verde, and the Azores in the late Miocene and Pleistocene. Life span, reproductive strategy, and life form were highly homoplastic; the ancestor of Daucus was probably a monocarpic, biennial hemicryptophyte. Rosette treelets evolved independently in the Canarian-Madeiran lineage and in Cape Verde, the latter within the last 0.13 Myr. Treelets and hemicryptophytes did not differ in wood anatomy. Pervasive axial parenchyma in wood occurred more often in polycarpic rather than monocarpic species. Conclusions Life span and life form in Daucus are evolutionarily labile and may change independently of wood anatomy, which is related to plant reproductive strategy rather than to life form. Insular woodiness may evolve rapidly (as demonstrated in D. bischoffii), and in Daucus, it does not seem to be an adaptation to lower the risk of xylem embolism.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Premise Despite intensive research, the pathways and driving forces behind the evolution of derived woodiness on oceanic islands remain obscure. The genus Daucus comprises mostly herbs (therophytes, hemicryptophytes) with few rosette treelets (chamaephytes) endemic to various Macaronesian archipelagos, suggesting their independent evolution. To elucidate the evolutionary pathways to derived woodiness, we examined phylogenetic relationships and the habit and secondary xylem evolution in Daucus and related taxa. Methods Sixty taxa were surveyed for molecular markers, life history, and habit traits. Twenty-one species were considered for wood anatomical characters. A dated phylogeny was estimated using Bayesian methods. The evolution of selected traits was reconstructed using parsimony and maximum likelihood. Results Daucus dispersed independently to the Canary Islands (and subsequently to Madeira), Cape Verde, and the Azores in the late Miocene and Pleistocene. Life span, reproductive strategy, and life form were highly homoplastic; the ancestor of Daucus was probably a monocarpic, biennial hemicryptophyte. Rosette treelets evolved independently in the Canarian-Madeiran lineage and in Cape Verde, the latter within the last 0.13 Myr. Treelets and hemicryptophytes did not differ in wood anatomy. Pervasive axial parenchyma in wood occurred more often in polycarpic rather than monocarpic species. Conclusions Life span and life form in Daucus are evolutionarily labile and may change independently of wood anatomy, which is related to plant reproductive strategy rather than to life form. Insular woodiness may evolve rapidly (as demonstrated in D. bischoffii), and in Daucus, it does not seem to be an adaptation to lower the risk of xylem embolism.
Świś, Przemysław; Broda, Krzysztof; Duda, Piotr; Dróżdż, Dawid; Łazuka, Anna
The early Famennian (Late Devonian) conodonts natural assemblages from Holy Cross Mountains (Poland) Journal Article
In: Historical Biology, vol. 0, no. 0, pp. 1-8, 2020.
@article{doi:10.1080/08912963.2020.1719085,
title = {The early Famennian (Late Devonian) conodonts natural assemblages from Holy Cross Mountains (Poland)},
author = {Przemysław Świś and Krzysztof Broda and Piotr Duda and Dawid Dróżdż and Anna Łazuka},
url = {https://doi.org/10.1080/08912963.2020.1719085},
doi = {10.1080/08912963.2020.1719085},
year = {2020},
date = {2020-01-01},
journal = {Historical Biology},
volume = {0},
number = {0},
pages = {1-8},
publisher = {Taylor & Francis},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Piechowski, Rafał; Tałanda, Mateusz
The locomotor musculature and posture of the early dinosauriform Silesaurus opolensis provides a new look into the evolution of Dinosauromorpha Journal Article
In: Journal of Anatomy, vol. 236, no. 6, pp. 1044-1100, 2020.
@article{https://doi.org/10.1111/joa.13155,
title = {The locomotor musculature and posture of the early dinosauriform Silesaurus opolensis provides a new look into the evolution of Dinosauromorpha},
author = {Rafał Piechowski and Mateusz Tałanda},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/joa.13155},
doi = {https://doi.org/10.1111/joa.13155},
year = {2020},
date = {2020-01-01},
journal = {Journal of Anatomy},
volume = {236},
number = {6},
pages = {1044-1100},
abstract = {Abstract It is widely accepted that ornithodirans (bird lineage) and some pseudosuchians (crocodilian lineage) achieved fully erect limb posture in different ways. Ornithodirans have buttress-erected hindlimbs, while some advanced pseudosuchians have pillar-erected hindlimbs. Analysis of the musculoskeletal apparatus of the early dinosauriform Silesaurus opolensis challenges this view. This ornithodiran had pillar-erected hindlimbs like some pseudosuchians. This condition could be autapomorphic or represents a transitional state between adductor-controlled limb posture of early dinosauromorphs and the buttress-erected hindlimbs of dinosaurs. This sequence of changes is supported by Triassic tracks left by animals of the dinosaurian lineage. It was associated with the strong development of knee flexors and extensors. Furthermore, the forelimbs of Silesaurus were fully erect, analogously to those of early sauropods. Members of both lineages reduced the muscles related to the protraction, retraction and bending of the limb. They used forelimbs more as a body support and less for propulsion. A similar scapula and humerus construction can be found in the Lagerpetidae and Lewisuchus, suggesting that long, slender, fully erected forelimbs are primitive for all Dinosauromorpha, not just Silesauridae. Early dinosaurs redeveloped several muscle attachments on the forelimb, probably in relation to bipedality.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract It is widely accepted that ornithodirans (bird lineage) and some pseudosuchians (crocodilian lineage) achieved fully erect limb posture in different ways. Ornithodirans have buttress-erected hindlimbs, while some advanced pseudosuchians have pillar-erected hindlimbs. Analysis of the musculoskeletal apparatus of the early dinosauriform Silesaurus opolensis challenges this view. This ornithodiran had pillar-erected hindlimbs like some pseudosuchians. This condition could be autapomorphic or represents a transitional state between adductor-controlled limb posture of early dinosauromorphs and the buttress-erected hindlimbs of dinosaurs. This sequence of changes is supported by Triassic tracks left by animals of the dinosaurian lineage. It was associated with the strong development of knee flexors and extensors. Furthermore, the forelimbs of Silesaurus were fully erect, analogously to those of early sauropods. Members of both lineages reduced the muscles related to the protraction, retraction and bending of the limb. They used forelimbs more as a body support and less for propulsion. A similar scapula and humerus construction can be found in the Lagerpetidae and Lewisuchus, suggesting that long, slender, fully erected forelimbs are primitive for all Dinosauromorpha, not just Silesauridae. Early dinosaurs redeveloped several muscle attachments on the forelimb, probably in relation to bipedality.
Świś, Przemysław; Dzik, Jerzy
The oral apparatus composition of the Early Carboniferous elictognathid conodont 'Siphonodella' Journal Article
In: Lethaia, 2020, (Publisher: Wiley).
@article{swis_oral_2020,
title = {The oral apparatus composition of the Early Carboniferous elictognathid conodont 'Siphonodella'},
author = {Przemysław Świś and Jerzy Dzik},
url = {https://doi.org/10.1111%2Flet.12406},
doi = {10.1111/let.12406},
year = {2020},
date = {2020-01-01},
journal = {Lethaia},
note = {Publisher: Wiley},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dzik, Jerzy
Variability of conch morphology in a cephalopod species from the Cambrian to Ordovician transition strata of Siberia Journal Article
In: Acta Palaeontologica Polonica, vol. 65, pp. 149–165, 2020, (Publisher: Polska Akademia Nauk Instytut Paleobiologii (Institute of Paleobiology, Polish Academy of Sciences)).
@article{dzik_variability_2020,
title = {Variability of conch morphology in a cephalopod species from the Cambrian to Ordovician transition strata of Siberia},
author = {Jerzy Dzik},
url = {https://doi.org/10.4202%2Fapp.00674.2019},
doi = {10.4202/app.00674.2019},
year = {2020},
date = {2020-01-01},
journal = {Acta Palaeontologica Polonica},
volume = {65},
pages = {149--165},
note = {Publisher: Polska Akademia Nauk Instytut Paleobiologii (Institute of Paleobiology, Polish Academy of Sciences)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2019
Haelewaters, Danny; Kesel, André De; Gorczak, Michał; Bao, Kevin; Gort, Gerrit; Zhao, Serena Y.; Pfister, Donald H.
In: Northeastern Naturalist, vol. 25, no. sp9, pp. 110–149, 2019, ISSN: 1092-6194.
@article{Haelewaters2019Dec,
title = {Laboulbeniales (Ascomycota) of the Boston Harbor Islands II (and Other Localities): Species Parasitizing Carabidae, and the Laboulbenia flagellata Species Complex},
author = {Danny Haelewaters and André De Kesel and Michał Gorczak and Kevin Bao and Gerrit Gort and Serena Y. Zhao and Donald H. Pfister},
url = {https://bioone.org/journals/northeastern-naturalist/volume-25/issue-sp9/045.025.s906/Laboulbeniales-Ascomycota-of-the-Boston-Harbor-Islands-II-and-Other/10.1656/045.025.s906.short},
doi = {10.1656/045.025.s906},
issn = {1092-6194},
year = {2019},
date = {2019-12-01},
journal = {Northeastern Naturalist},
volume = {25},
number = {sp9},
pages = {110--149},
publisher = {Eagle Hill Institute},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Tischer, Marta; Gorczak, Michał; Bojarski, Błażej; Pawłowska, Julia; Hoffeins, Christel; Hoffeins, Hans Werner; Wrzosek, Marta
New fossils of ascomycetous anamorphic fungi from Baltic amber Journal Article
In: Fungal Biology, vol. 123, no. 11, pp. 804–810, 2019, ISSN: 1878-6146.
@article{Tischer2019Nov,
title = {New fossils of ascomycetous anamorphic fungi from Baltic amber},
author = {Marta Tischer and Michał Gorczak and Błażej Bojarski and Julia Pawłowska and Christel Hoffeins and Hans Werner Hoffeins and Marta Wrzosek},
doi = {10.1016/j.funbio.2019.08.003},
issn = {1878-6146},
year = {2019},
date = {2019-11-01},
journal = {Fungal Biology},
volume = {123},
number = {11},
pages = {804--810},
publisher = {British Mycological SocietyElsevier Ltd},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pawłowska, Julia; Okrasińska, Alicja; Kisło, Kamil; Aleksandrzak-Piekarczyk, Tamara; Szatraj, Katarzyna; Dolatabadi, Somayeh; Muszewska, Anna
Carbon assimilation profiles of mucoralean fungi show their metabolic versatility Journal Article
In: Scientific Reports, vol. 9, pp. 11864, 2019.
@article{pawlowska2019,
title = {Carbon assimilation profiles of mucoralean fungi show their metabolic versatility},
author = {Julia Pawłowska and Alicja Okrasińska and Kamil Kisło and Tamara Aleksandrzak-Piekarczyk and Katarzyna Szatraj and Somayeh Dolatabadi and Anna Muszewska },
url = {https://www.nature.com/articles/s41598-019-48296-w#citeas},
doi = {https://doi.org/10.1038/s41598-019-48296-w},
year = {2019},
date = {2019-08-14},
journal = {Scientific Reports},
volume = {9},
pages = {11864},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Grond, Joost; Płecha, Magdalena; Hahn, Christoph; Wiig, Øystein; Bachmann, Lutz
Mitochondrial genomes of ancient bowhead whales (Balaena mysticetus) from Svalbard Journal Article
In: Mitochondrial DNA Part B, vol. 4, no. 2, pp. 4152–4154, 2019, ISSN: 2380-2359.
@article{Grond2019,
title = {Mitochondrial genomes of ancient bowhead whales (Balaena mysticetus) from Svalbard},
author = {Joost Grond and Magdalena Płecha and Christoph Hahn and Øystein Wiig and Lutz Bachmann},
url = {https://www.tandfonline.com/doi/full/10.1080/23802359.2019.1693284},
doi = {10.1080/23802359.2019.1693284},
issn = {2380-2359},
year = {2019},
date = {2019-07-01},
journal = {Mitochondrial DNA Part B},
volume = {4},
number = {2},
pages = {4152--4154},
abstract = {The endangered Spitsbergen stock of bowhead whales (Balaena mysticetus) has once been large with up to estimated 100,000 individuals. Genetic diversity of the extant Spitsbergen stock is unknown. We present 10 complete mitochondrial genomes of heterochronous ancient bowhead whale samples from Svalbard (14C age estimate range: 215–8885 years) obtained via NGS of total genomic DNA extracts. The ten mitogenomes differed by nucleotide substitutions and/or indels, and there was a total of 160 variable positions. The average nucleotide diversity was π = 0.0029. There was no statistically significant correlation between genetic divergence and time.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The endangered Spitsbergen stock of bowhead whales (Balaena mysticetus) has once been large with up to estimated 100,000 individuals. Genetic diversity of the extant Spitsbergen stock is unknown. We present 10 complete mitochondrial genomes of heterochronous ancient bowhead whale samples from Svalbard (14C age estimate range: 215–8885 years) obtained via NGS of total genomic DNA extracts. The ten mitogenomes differed by nucleotide substitutions and/or indels, and there was a total of 160 variable positions. The average nucleotide diversity was π = 0.0029. There was no statistically significant correlation between genetic divergence and time.
PW, Crous; AJ, Carnegie; MJ, Wingfield; R, Sharma; G, Mughini; ME, Noordeloos; A, Santini; YS, Shouche; JDP, Bezerra; B, Dima; V, Guarnaccia; I, Imrefi; Ž, Jurjević; DG, Knapp; GM, Kovács; D, Magistà; G, Perrone; T, Rämä; YA, Rebriev; RG, Shivas; SM, Singh; CM, Souza-Motta; R, Thangavel; NN, Adhapure; AV, Alexandrova; AC, Alfenas; RF, Alfenas; P, Alvarado; AL, Alves; DA, Andrade; JP, Andrade; RN, Barbosa; A, Barili; CW, Barnes; IG, Baseia; JM, Bellanger; C, Berlanas; AE, Bessette; AR, Bessette; AY, Biketova; FS, Bomfim; TE, Brandrud; K, Bransgrove; ACQ, Brito; JF, Cano-Lira; T, Cantillo; AD, Cavalcanti; R, Cheewangkoon; RS, Chikowski; C, Conforto; TRL, Cordeiro; JD, Craine; R, Cruz; U, Damm; de RJV, Oliveira; de JT, Souza; de HG, Souza; JDW, Dearnaley; RA, Dimitrov; F, Dovana; A, Erhard; F, Esteve-Raventós; CR, Félix; G, Ferisin; RA, Fernandes; RJ, Ferreira; LO, Ferro; CN, Figueiredo; JL, Frank; KTLS, Freire; D, García; J, Gené; A, Gêsiorska; TB, Gibertoni; RAG, Gondra; DE, Gouliamova; D, Gramaje; F, Guard; LFP, Gusmão; S, Haitook; Y, Hirooka; J, Houbraken; V, Hubka; A, Inamdar; T, Iturriaga; I, Iturrieta-González; M, Jadan; N, Jiang; A, Justo; AV, Kachalkin; VI, Kapitonov; M, Karadelev; J, Karakehian; T, Kasuya; I, Kautmanová; J, Kruse; I, Kušan; TA, Kuznetsova; MF, Landell; KH, Larsson; HB, Lee; DX, Lima; CRS, Lira; AR, Machado; H, Madrid; OMC, Magalhães; H, Majerova; EF, Malysheva; RR, Mapperson; PAS, Marbach; MP, Martín; A, Martín-Sanz; N, Matočec; AR, McTaggart; JF, Mello; RFR, Melo; A, Mešić; SJ, Michereff; AN, Miller; A, Minoshima; L, Molinero-Ruiz; OV, Morozova; D, Mosoh; M, Nabe; R, Naik; K, Nara; SS, Nascimento; RP, Neves; I, Olariaga; RL, Oliveira; TGL, Oliveira; T, Ono; ME, Ordoñez; AM, Ottoni; LM, Paiva; F, Pancorbo; B, Pant; J, Pawłowska; SW, Peterson; DB, Raudabaugh; E, Rodríguez-Andrade; E, Rubio; K, Rusevska; ALCMA, Santiago; ACS, Santos; C, Santos; NA, Sazanova; S, Shah; J, Sharma; BDB, Silva; JL, Siquier; MS, Sonawane; AM, Stchigel; T, Svetasheva; N, Tamakeaw; MT, Telleria; PV, Tiago; CM, Tian; Z, Tkalčec; MA, Tomashevskaya; HH, Truong; MV, Vecherskii; CM, Visagie; A, Vizzini; N, Yilmaz; IV, Zmitrovich; EA, Zvyagina; T, Boekhout; T, Kehlet; T, Læssøe; JZ., Groenewald
Fungal Planet description sheets: 868-950 Journal Article
In: Persoonia, vol. 42, pp. 291, 2019.
@article{Crous2019Jun,
title = {Fungal Planet description sheets: 868-950},
author = {Crous PW and Carnegie AJ and Wingfield MJ and Sharma R and Mughini G and Noordeloos ME and Santini A and Shouche YS and Bezerra JDP and Dima B and Guarnaccia V and Imrefi I and Jurjević Ž and Knapp DG and Kovács GM and Magistà D and Perrone G and Rämä T and Rebriev YA and Shivas RG and Singh SM and Souza-Motta CM and Thangavel R and Adhapure NN and Alexandrova AV and Alfenas AC and Alfenas RF and Alvarado P and Alves AL and Andrade DA and Andrade JP and Barbosa RN and Barili A and Barnes CW and Baseia IG and Bellanger JM and Berlanas C and Bessette AE and Bessette AR and Biketova AY and Bomfim FS and Brandrud TE and Bransgrove K and Brito ACQ and Cano-Lira JF and Cantillo T and Cavalcanti AD and Cheewangkoon R and Chikowski RS and Conforto C and Cordeiro TRL and Craine JD and Cruz R and Damm U and Oliveira de RJV and Souza de JT and Souza de HG and Dearnaley JDW and Dimitrov RA and Dovana F and Erhard A and Esteve-Raventós F and Félix CR and Ferisin G and Fernandes RA and Ferreira RJ and Ferro LO and Figueiredo CN and Frank JL and Freire KTLS and García D and Gené J and Gêsiorska A and Gibertoni TB and Gondra RAG and Gouliamova DE and Gramaje D and Guard F and Gusmão LFP and Haitook S and Hirooka Y and Houbraken J and Hubka V and Inamdar A and Iturriaga T and Iturrieta-González I and Jadan M and Jiang N and Justo A and Kachalkin AV and Kapitonov VI and Karadelev M and Karakehian J and Kasuya T and Kautmanová I and Kruse J and Kušan I and Kuznetsova TA and Landell MF and Larsson KH and Lee HB and Lima DX and Lira CRS and Machado AR and Madrid H and Magalhães OMC and Majerova H and Malysheva EF and Mapperson RR and Marbach PAS and Martín MP and Martín-Sanz A and Matočec N and McTaggart AR and Mello JF and Melo RFR and Mešić A and Michereff SJ and Miller AN and Minoshima A and Molinero-Ruiz L and Morozova OV and Mosoh D and Nabe M and Naik R and Nara K and Nascimento SS and Neves RP and Olariaga I and Oliveira RL and Oliveira TGL and Ono T and Ordoñez ME and Ottoni AM and Paiva LM and Pancorbo F and Pant B and Pawłowska J and Peterson SW and Raudabaugh DB and Rodríguez-Andrade E and Rubio E and Rusevska K and Santiago ALCMA and Santos ACS and Santos C and Sazanova NA and Shah S and Sharma J and Silva BDB and Siquier JL and Sonawane MS and Stchigel AM and Svetasheva T and Tamakeaw N and Telleria MT and Tiago PV and Tian CM and Tkalčec Z and Tomashevskaya MA and Truong HH and Vecherskii MV and Visagie CM and Vizzini A and Yilmaz N and Zmitrovich IV and Zvyagina EA and Boekhout T and Kehlet T and Læssøe T and Groenewald JZ.},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6712538/},
doi = {10.3767/persoonia.2019.42.11},
year = {2019},
date = {2019-06-01},
journal = {Persoonia},
volume = {42},
pages = {291},
publisher = {Westerdijk Fungal Biodiversity Institute},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Płecha, Magdalena; Panagiotopoulou, Hanna; Popović, Danijela; Michalska-Parda, Aleksandra; Gromadka, Robert; Węgleński, Piotr; Stanković, Anna
Microsatellite multiplexes for the genetic analyses of northern pike (Esox lucius) populations Journal Article
In: Fisheries & Aquatic Life, vol. 27, no. 1, pp. 33–40, 2019, ISSN: 2545-059X.
@article{Pecha2019,
title = {Microsatellite multiplexes for the genetic analyses of northern pike (Esox lucius) populations},
author = {Magdalena Płecha and Hanna Panagiotopoulou and Danijela Popović and Aleksandra Michalska-Parda and Robert Gromadka and Piotr Węgleński and Anna Stanković},
url = {https://content.sciendo.com/doi/10.2478/aopf-2019-0004},
doi = {10.2478/aopf-2019-0004},
issn = {2545-059X},
year = {2019},
date = {2019-03-01},
journal = {Fisheries & Aquatic Life},
volume = {27},
number = {1},
pages = {33--40},
abstract = {The northern pike (Esox lucius L.) is a commercially important fish that forms freshwater and brackish populations. While the first ecotype is still quite abundant, the second has suffered rapid declines in recent years. Populations inhabiting the Baltic coastal waters of Poland have been supported by stocking programs since the late 1990s. This study describes a multiplex microsatellite (msDNA) assay consisting of 12 loci divided conveniently into two amplification sets (Elu78, Elu87, B451, Elu37, B457, B16, B25, and Elu19, Elu76, B422, Elu2, Elu7). The assay was optimized for genetic analyses of freshwater and brackish populations. These multiplexes were successfully executed to obtain the genetic profiles of 668 individuals from 16 populations (Poland and Germany). The average number of alleles was equal to 10.4, whereas the observed heterozygosity per locus ranged from 0.18 to 0.89, with the average value of 0.64. The probability of the identity of the marker sets indicated the high power of identification of unique genotypes. Therefore, this molecular tool can be used to describe the genetic variability of populations, select the proper source of breeding material, and monitor the progress of stocking efforts in genetic conservation projects of this species.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The northern pike (Esox lucius L.) is a commercially important fish that forms freshwater and brackish populations. While the first ecotype is still quite abundant, the second has suffered rapid declines in recent years. Populations inhabiting the Baltic coastal waters of Poland have been supported by stocking programs since the late 1990s. This study describes a multiplex microsatellite (msDNA) assay consisting of 12 loci divided conveniently into two amplification sets (Elu78, Elu87, B451, Elu37, B457, B16, B25, and Elu19, Elu76, B422, Elu2, Elu7). The assay was optimized for genetic analyses of freshwater and brackish populations. These multiplexes were successfully executed to obtain the genetic profiles of 668 individuals from 16 populations (Poland and Germany). The average number of alleles was equal to 10.4, whereas the observed heterozygosity per locus ranged from 0.18 to 0.89, with the average value of 0.64. The probability of the identity of the marker sets indicated the high power of identification of unique genotypes. Therefore, this molecular tool can be used to describe the genetic variability of populations, select the proper source of breeding material, and monitor the progress of stocking efforts in genetic conservation projects of this species.
Banasiak, Łukasz; Pietras, Marcin; Wrzosek, Marta; Okrasińska, Alicja; Gorczak, Michał; Kolanowska, Marta; Pawłowska, Julia
In: Fungal Ecology, vol. 39, pp. 94 - 99, 2019, ISSN: 1754-5048.
@article{BANASIAK201994,
title = {Aureoboletus projectellus (Fungi, Boletales) – An American bolete rapidly spreading in Europe as a new model species for studying expansion of macrofungi},
author = {Łukasz Banasiak and Marcin Pietras and Marta Wrzosek and Alicja Okrasińska and Michał Gorczak and Marta Kolanowska and Julia Pawłowska},
url = {http://www.sciencedirect.com/science/article/pii/S1754504818301491},
doi = {https://doi.org/10.1016/j.funeco.2018.12.006},
issn = {1754-5048},
year = {2019},
date = {2019-01-01},
journal = {Fungal Ecology},
volume = {39},
pages = {94 - 99},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Qvarnström, Martin; Wernström, Joel Vikberg; Piechowski, Rafał; Tałanda, Mateusz; Ahlberg, Per E; Niedźwiedzki, Grzegorz
Beetle-bearing coprolites possibly reveal the diet of a Late Triassic dinosauriform Journal Article
In: Royal Society Open Science, vol. 6, no. 3, pp. 181042, 2019, (Publisher: The Royal Society).
@article{qvarnstrom_beetle-bearing_2019,
title = {Beetle-bearing coprolites possibly reveal the diet of a Late Triassic dinosauriform},
author = {Martin Qvarnström and Joel Vikberg Wernström and Rafał Piechowski and Mateusz Tałanda and Per E Ahlberg and Grzegorz Niedźwiedzki},
url = {https://doi.org/10.1098%2Frsos.181042},
doi = {10.1098/rsos.181042},
year = {2019},
date = {2019-01-01},
journal = {Royal Society Open Science},
volume = {6},
number = {3},
pages = {181042},
note = {Publisher: The Royal Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Haelewaters, Danny; Pfliegler, Walter P; Gorczak, Michał; Pfister, Donald H
Birth of an order: Comprehensive molecular phylogenetic study excludes Herpomyces (Fungi, Laboulbeniomycetes) from Laboulbeniales Journal Article
In: Molecular Phylogenetics and Evolution, vol. 133, pp. 286 - 301, 2019, ISSN: 1055-7903.
@article{HAELEWATERS2019286,
title = {Birth of an order: Comprehensive molecular phylogenetic study excludes Herpomyces (Fungi, Laboulbeniomycetes) from Laboulbeniales},
author = {Danny Haelewaters and Walter P Pfliegler and Michał Gorczak and Donald H Pfister},
url = {http://www.sciencedirect.com/science/article/pii/S1055790317307984},
doi = {https://doi.org/10.1016/j.ympev.2019.01.007},
issn = {1055-7903},
year = {2019},
date = {2019-01-01},
journal = {Molecular Phylogenetics and Evolution},
volume = {133},
pages = {286 - 301},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dolatabadi, Somayeh; Rezaei-Matehkolaei, Ali; Pawlowska, Julia; Hosseini, Seyyed Abolfazl; Najafzadeh, Mohammad Javad; Madrid, Hugo
Chaetothyrialean fungi from aromatic hydrocarbon-polluted environments of Iran Journal Article
In: Nova Hedwigia, vol. 108, no. 3-4, pp. 405-426, 2019.
@article{dolatabadi2019,
title = {Chaetothyrialean fungi from aromatic hydrocarbon-polluted environments of Iran},
author = {Somayeh Dolatabadi and Ali Rezaei-Matehkolaei and Julia Pawlowska and Seyyed Abolfazl Hosseini and Mohammad Javad Najafzadeh and Hugo Madrid},
url = {http://dx.doi.org/10.1127/nova_hedwigia/2018/0509},
doi = {10.1127/nova_hedwigia/2018/0509},
year = {2019},
date = {2019-01-01},
journal = {Nova Hedwigia},
volume = {108},
number = {3-4},
pages = {405-426},
publisher = {Schweizerbart Science Publishers},
address = {Stuttgart, Germany},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Han, Kwi Young; Maciszewski, Kacper; Graf, Louis; Yang, Ji Hyun; Andersen, Robert A; Karnkowska, Anna; Yoon, Hwan Su
Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization Journal Article
In: Journal of Phycology, vol. 55, no. 5, pp. 1166-1180, 2019.
@article{https://doi.org/10.1111/jpy.12904,
title = {Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization},
author = {Kwi Young Han and Kacper Maciszewski and Louis Graf and Ji Hyun Yang and Robert A Andersen and Anna Karnkowska and Hwan Su Yoon},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.12904},
doi = {https://doi.org/10.1111/jpy.12904},
year = {2019},
date = {2019-01-01},
journal = {Journal of Phycology},
volume = {55},
number = {5},
pages = {1166-1180},
abstract = {Dictyochophyceae (silicoflagellates) are unicellular freshwater and marine algae (Heterokontophyta, stramenopiles). Despite their abundance in global oceans and potential ecological significance, discovered in recent years, neither nuclear nor organellar genomes of representatives of this group were sequenced until now. Here, we present the first complete plastid genome sequences of Dictyochophyceae, obtained from four species: Dictyocha speculum, Rhizochromulina marina, Florenciella parvula and Pseudopedinella elastica. Despite their comparable size and genetic content, these four plastid genomes exhibit variability in their organization: plastid genomes of F. parvula and P. elastica possess conventional quadripartite structure with a pair of inverted repeats, R. marina instead possesses two direct repeats with the same orientation and D. speculum possesses no repeats at all. We also observed a number of unusual traits in the plastid genome of D. speculum, including expansion of the intergenic regions, presence of an intron in the otherwise non-intron-bearing psaA gene, and an additional copy of the large subunit of RuBisCO gene (rbcL), the last of which has never been observed in any plastid genome. We conclude that despite noticeable gene content similarities between the plastid genomes of Dictyochophyceae and their relatives (pelagophytes, diatoms), the number of distinctive features observed in this lineage strongly suggests that additional taxa require further investigation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dictyochophyceae (silicoflagellates) are unicellular freshwater and marine algae (Heterokontophyta, stramenopiles). Despite their abundance in global oceans and potential ecological significance, discovered in recent years, neither nuclear nor organellar genomes of representatives of this group were sequenced until now. Here, we present the first complete plastid genome sequences of Dictyochophyceae, obtained from four species: Dictyocha speculum, Rhizochromulina marina, Florenciella parvula and Pseudopedinella elastica. Despite their comparable size and genetic content, these four plastid genomes exhibit variability in their organization: plastid genomes of F. parvula and P. elastica possess conventional quadripartite structure with a pair of inverted repeats, R. marina instead possesses two direct repeats with the same orientation and D. speculum possesses no repeats at all. We also observed a number of unusual traits in the plastid genome of D. speculum, including expansion of the intergenic regions, presence of an intron in the otherwise non-intron-bearing psaA gene, and an additional copy of the large subunit of RuBisCO gene (rbcL), the last of which has never been observed in any plastid genome. We conclude that despite noticeable gene content similarities between the plastid genomes of Dictyochophyceae and their relatives (pelagophytes, diatoms), the number of distinctive features observed in this lineage strongly suggests that additional taxa require further investigation.
Wojewódzka, Aneta; Baczyński, Jakub; Banasiak, Łukasz; Downie, Stephen R; Czarnocka-Cieciura, Agnieszka; Gierek, Michał; Frankiewicz, Kamil; Spalik, Krzysztof
Evolutionary shifts in fruit dispersal syndromes in Apiaceae tribe Scandiceae Journal Article
In: Plant Systematics and Evolution, vol. 305, no. 5, pp. 401–414, 2019, ISSN: 0378-2697, 2199-6881.
@article{wojewodzka_evolutionary_2019,
title = {Evolutionary shifts in fruit dispersal syndromes in Apiaceae tribe Scandiceae},
author = {Aneta Wojewódzka and Jakub Baczyński and Łukasz Banasiak and Stephen R Downie and Agnieszka Czarnocka-Cieciura and Michał Gierek and Kamil Frankiewicz and Krzysztof Spalik},
url = {http://link.springer.com/10.1007/s00606-019-01579-1},
doi = {10.1007/s00606-019-01579-1},
issn = {0378-2697, 2199-6881},
year = {2019},
date = {2019-01-01},
urldate = {2021-02-03},
journal = {Plant Systematics and Evolution},
volume = {305},
number = {5},
pages = {401--414},
abstract = {Apiaceae tribe Scandiceae includes species with diverse fruits that depending upon their morphology are dispersed by gravity, carried away by wind, or transported attached to animal fur or feathers. This diversity is particularly evident in Scandiceae subtribe Daucinae, a group encompassing species with wings or spines developing on fruit secondary ribs. In this paper, we explore fruit evolution in 86 representatives of Scandiceae and outgroups to assess adaptive shifts related to the evolutionary switch between anemochory and epizoochory and to identify possible dispersal syndromes, i.e., patterns of covariation of morphological and life-history traits that are associated with a particular vector. We also assess the phylogenetic signal in fruit traits. Principal component analysis of 16 quantitative fruit characters and of plant height did not clearly separate species having different dispersal strategies as estimated based on fruit appendages. Only presumed anemochory was weakly associated with plant height and the flattening of mericarps with their accompanying anatomical changes. We conclude that in Scandiceae, there are no distinct dispersal syndromes, but a continuum of fruit morphologies relying on different dispersal vectors. Phylogenetic mapping of ten discrete fruit characters on trees inferred by nrDNA ITS and cpDNA sequence data revealed that all are homoplastic and of limited use for the delimitation of genera. Spines evolved from wings developing on secondary ribs. We hypothesize that spines cannot form on primary ribs because these contain vascular bundles that may constrain such a transformation. We describe a new subtribe for Artedia and propose three new combinations in Daucus.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Apiaceae tribe Scandiceae includes species with diverse fruits that depending upon their morphology are dispersed by gravity, carried away by wind, or transported attached to animal fur or feathers. This diversity is particularly evident in Scandiceae subtribe Daucinae, a group encompassing species with wings or spines developing on fruit secondary ribs. In this paper, we explore fruit evolution in 86 representatives of Scandiceae and outgroups to assess adaptive shifts related to the evolutionary switch between anemochory and epizoochory and to identify possible dispersal syndromes, i.e., patterns of covariation of morphological and life-history traits that are associated with a particular vector. We also assess the phylogenetic signal in fruit traits. Principal component analysis of 16 quantitative fruit characters and of plant height did not clearly separate species having different dispersal strategies as estimated based on fruit appendages. Only presumed anemochory was weakly associated with plant height and the flattening of mericarps with their accompanying anatomical changes. We conclude that in Scandiceae, there are no distinct dispersal syndromes, but a continuum of fruit morphologies relying on different dispersal vectors. Phylogenetic mapping of ten discrete fruit characters on trees inferred by nrDNA ITS and cpDNA sequence data revealed that all are homoplastic and of limited use for the delimitation of genera. Spines evolved from wings developing on secondary ribs. We hypothesize that spines cannot form on primary ribs because these contain vascular bundles that may constrain such a transformation. We describe a new subtribe for Artedia and propose three new combinations in Daucus.
Uhlik, Marcin Edward
In: Journal of Crustacean Biology, vol. 40, no. 1, pp. 37-44, 2019, ISSN: 0278-0372.
@article{10.1093/jcbiol/ruz084,
title = {Evolutionary significance of the embryological development of the daphniid cladocerans Ceriodaphnia Dana, 1853 and Scapholeberis Schoedler, 1858 (Branchiopoda: Cladocera: Daphniidae)},
author = {Marcin Edward Uhlik},
url = {https://doi.org/10.1093/jcbiol/ruz084},
doi = {10.1093/jcbiol/ruz084},
issn = {0278-0372},
year = {2019},
date = {2019-01-01},
journal = {Journal of Crustacean Biology},
volume = {40},
number = {1},
pages = {37-44},
abstract = {The embryological development of Ceriodaphnia reticulataDumont & Pensaert, 1983 and Scapholeberis rammneriJurine, 1820 were investigated using scanning electron microscopy. A carapace spine did not develop and there was no fusion of the first antennae. These are apparent apomorphies of DaphniaMüller, 1785, which suggests that the common ancestor of Daphniidae Straus, 1820 did not have a carapace spine during its embryological development, and its first antennae were short and separated during embryogenesis. Morphological evidence thus appears congruent with molecular interpretations showing that ScapholeberisSchoedler, 1858 is basal to other genera of Daphniidae, Ceriodaphnia being a sister taxon to Daphnia.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The embryological development of Ceriodaphnia reticulataDumont & Pensaert, 1983 and Scapholeberis rammneriJurine, 1820 were investigated using scanning electron microscopy. A carapace spine did not develop and there was no fusion of the first antennae. These are apparent apomorphies of DaphniaMüller, 1785, which suggests that the common ancestor of Daphniidae Straus, 1820 did not have a carapace spine during its embryological development, and its first antennae were short and separated during embryogenesis. Morphological evidence thus appears congruent with molecular interpretations showing that ScapholeberisSchoedler, 1858 is basal to other genera of Daphniidae, Ceriodaphnia being a sister taxon to Daphnia.
Spalik, Krzysztof; Wojewódzka, Aneta; Constantinidis, Theophanis; Downie, Stephen R; Gierek, Michał; Banasiak, Łukasz
Laserocarpum, a new genus of Apiaceae endemic to Greece Journal Article
In: Acta Soc Bot Pol, pp. 9, 2019.
@article{spalik_laserocarpum_2019,
title = {Laserocarpum, a new genus of Apiaceae endemic to Greece},
author = {Krzysztof Spalik and Aneta Wojewódzka and Theophanis Constantinidis and Stephen R Downie and Michał Gierek and Łukasz Banasiak},
year = {2019},
date = {2019-01-01},
journal = {Acta Soc Bot Pol},
pages = {9},
abstract = {Laserpitium pseudomeum is an endemic umbellifer of Greece occurring in the mountains of Sterea Ellas and northern Peloponnese. Molecular data indicate that it is not related to its putative congeners, but instead constitutes an isolated lineage. The nuclear ribosomal DNA ITS tree places it as a weakly supported sister group to Portenschlagiella ramosissima, the sole species in its genus, whereas the tree inferred from three noncoding cpDNA loci does not confirm this relationship. Portenschlagiella ramosissima is sometimes placed in Athamanta, an affinity supported neither by molecular data nor by fruit morphology. Laserpitium pseudomeum notably differs from P. ramosissima in vegetative, flower, and fruit characteristics, and no obvious morphological synapomorphies indicate their close relationship. Therefore, we place L. pseudomeum in the newly described genus Laserocarpum and lectotypify the species with the specimen Orphanides 2019 (G00766460) at G-Boiss.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Laserpitium pseudomeum is an endemic umbellifer of Greece occurring in the mountains of Sterea Ellas and northern Peloponnese. Molecular data indicate that it is not related to its putative congeners, but instead constitutes an isolated lineage. The nuclear ribosomal DNA ITS tree places it as a weakly supported sister group to Portenschlagiella ramosissima, the sole species in its genus, whereas the tree inferred from three noncoding cpDNA loci does not confirm this relationship. Portenschlagiella ramosissima is sometimes placed in Athamanta, an affinity supported neither by molecular data nor by fruit morphology. Laserpitium pseudomeum notably differs from P. ramosissima in vegetative, flower, and fruit characteristics, and no obvious morphological synapomorphies indicate their close relationship. Therefore, we place L. pseudomeum in the newly described genus Laserocarpum and lectotypify the species with the specimen Orphanides 2019 (G00766460) at G-Boiss.
Ignatenko, Antonina; Gumińska, Natalia; Milanowski, Rafał
Mechanizmy utraty i nabywania intronów spliceosomalnych Journal Article
In: Postepy biochemii, vol. 65, no. 4, pp. 289–298, 2019, ISSN: 00325422.
@article{Ignatenko2019,
title = {Mechanizmy utraty i nabywania intronów spliceosomalnych},
author = {Antonina Ignatenko and Natalia Gumińska and Rafał Milanowski},
url = {https://postepybiochemii.ptbioch.edu.pl/index.php/PB/article/view/292},
doi = {10.18388/pb.2019_292},
issn = {00325422},
year = {2019},
date = {2019-01-01},
journal = {Postepy biochemii},
volume = {65},
number = {4},
pages = {289--298},
abstract = {Introny to wewnątrzgenowe sekwencje niekodujące. Dawniej były uznawane za „śmieciowy” DNA, jednak obecnie uważa się, że są ważnymi elementami wpływającymi na funkcjonowanie genomu. Udowodniono, że introny zwiększają różnorodność transkryptomu i proteomu, spełniają w komórce role regulatorowe, wpływają na ekspresję genów oraz obróbkę, translację i degradację mRNA. Ze względu na sposób powstawania dzielą się na trzy główne kategorie: spliceosomalne, samowycinające się oraz introny tRNA. Introny spliceosomalne są charakterystyczne dla organizmów eukariotycznych. Analizy sekwencji genów ortologicznych w rożnych grupach eukariontów pozwoliły zidentyfikować wiele przypadków nabywania oraz utraty intronów. Niektóre z tych zdarzeń miały miejsce w dalekiej przeszłości, do innych doszło stosunkowo niedawno. Uważa się, że procesy te mogą działać jako jedna z sił napędowych w ewolucji genów eukariotycznych.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Introny to wewnątrzgenowe sekwencje niekodujące. Dawniej były uznawane za „śmieciowy” DNA, jednak obecnie uważa się, że są ważnymi elementami wpływającymi na funkcjonowanie genomu. Udowodniono, że introny zwiększają różnorodność transkryptomu i proteomu, spełniają w komórce role regulatorowe, wpływają na ekspresję genów oraz obróbkę, translację i degradację mRNA. Ze względu na sposób powstawania dzielą się na trzy główne kategorie: spliceosomalne, samowycinające się oraz introny tRNA. Introny spliceosomalne są charakterystyczne dla organizmów eukariotycznych. Analizy sekwencji genów ortologicznych w rożnych grupach eukariontów pozwoliły zidentyfikować wiele przypadków nabywania oraz utraty intronów. Niektóre z tych zdarzeń miały miejsce w dalekiej przeszłości, do innych doszło stosunkowo niedawno. Uważa się, że procesy te mogą działać jako jedna z sił napędowych w ewolucji genów eukariotycznych.
Świś, Przemysław
Population dynamics of the Late Devonian conodont Alternognathus calibrated in days Journal Article
In: Historical Biology, vol. 31, no. 9, pp. 1161-1169, 2019.
@article{doi:10.1080/08912963.2018.1427088,
title = {Population dynamics of the Late Devonian conodont Alternognathus calibrated in days},
author = {Przemysław Świś},
url = {https://doi.org/10.1080/08912963.2018.1427088},
doi = {10.1080/08912963.2018.1427088},
year = {2019},
date = {2019-01-01},
journal = {Historical Biology},
volume = {31},
number = {9},
pages = {1161-1169},
publisher = {Taylor & Francis},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pawlak, Wojciech; Czepiński, Łukasz; Majchrzyk, Aleksander; Duk, Katarzyna
Przegląd skamieniałości krcegowców i flory z terenów dzisiejszej Polski zgromadzonych w Muzeum Historii Naturalnej w Wiedniu Journal Article
In: Przegląd Geologiczny, vol. 67, no. 1, pp. 48, 2019, ISSN: 0033-2151.
@article{Pawlak2019,
title = {Przegląd skamieniałości krcegowców i flory z terenów dzisiejszej Polski zgromadzonych w Muzeum Historii Naturalnej w Wiedniu},
author = {Wojciech Pawlak and Łukasz Czepiński and Aleksander Majchrzyk and Katarzyna Duk},
url = {https://geojournals.pgi.gov.pl/pg/article/view/26781},
issn = {0033-2151},
year = {2019},
date = {2019-01-01},
journal = {Przegląd Geologiczny},
volume = {67},
number = {1},
pages = {48},
abstract = {Current territory of Poland was an exploration area for paleontologists from other European countries throughout the almost entire nineteenth century. A considerable part of findings were stored in institutions located beyond current borders of Poland. We have examined, documented and identified above
350 fossils housed in the Natural History Museum in Vienna (Naturhistorisches Museum Wien). The collection includes paleobotanical and paleozoological specimens from the Little Poland and the Upper Silesia. Some of these specimens are a unique material from the localities which are no longer available.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Current territory of Poland was an exploration area for paleontologists from other European countries throughout the almost entire nineteenth century. A considerable part of findings were stored in institutions located beyond current borders of Poland. We have examined, documented and identified above
350 fossils housed in the Natural History Museum in Vienna (Naturhistorisches Museum Wien). The collection includes paleobotanical and paleozoological specimens from the Little Poland and the Upper Silesia. Some of these specimens are a unique material from the localities which are no longer available.
350 fossils housed in the Natural History Museum in Vienna (Naturhistorisches Museum Wien). The collection includes paleobotanical and paleozoological specimens from the Little Poland and the Upper Silesia. Some of these specimens are a unique material from the localities which are no longer available.
Adl, Sina M; Bass, David; Lane, Christopher E; Lukeš, Julius; Schoch, Conrad L; Smirnov, Alexey; Agatha, Sabine; Berney, Cedric; Brown, Matthew W; Burki, Fabien; Cárdenas, Paco; Čepička, Ivan; Chistyakova, Lyudmila; Campo, Javier; Dunthorn, Micah; Edvardsen, Bente; Eglit, Yana; Guillou, Laure; Hampl, Vladimír; Heiss, Aaron A; Hoppenrath, Mona; James, Timothy Y; Karnkowska, Anna; Karpov, Sergey; Kim, Eunsoo; Kolisko, Martin; Kudryavtsev, Alexander; Lahr, Daniel J G; Lara, Enrique; Gall, Line Le; Lynn, Denis H; Mann, David G; Massana, Ramon; Mitchell, Edward A D; Morrow, Christine; Park, Jong Soo; Pawlowski, Jan W; Powell, Martha J; Richter, Daniel J; Rueckert, Sonja; Shadwick, Lora; Shimano, Satoshi; Spiegel, Frederick W; Torruella, Guifré; Youssef, Noha; Zlatogursky, Vasily; Zhang, Qianqian
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes Journal Article
In: Journal of Eukaryotic Microbiology, vol. 66, no. 1, pp. 4–119, 2019, ISSN: 1066-5234.
@article{Adl20194,
title = {Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes},
author = {Sina M Adl and David Bass and Christopher E Lane and Julius Lukeš and Conrad L Schoch and Alexey Smirnov and Sabine Agatha and Cedric Berney and Matthew W Brown and Fabien Burki and Paco Cárdenas and Ivan {Č}epi{č}ka and Lyudmila Chistyakova and Javier Campo and Micah Dunthorn and Bente Edvardsen and Yana Eglit and Laure Guillou and Vladimír Hampl and Aaron A Heiss and Mona Hoppenrath and Timothy Y James and Anna Karnkowska and Sergey Karpov and Eunsoo Kim and Martin Kolisko and Alexander Kudryavtsev and Daniel J G Lahr and Enrique Lara and Line {Le Gall} and Denis H Lynn and David G Mann and Ramon Massana and Edward A D Mitchell and Christine Morrow and Jong Soo Park and Jan W Pawlowski and Martha J Powell and Daniel J Richter and Sonja Rueckert and Lora Shadwick and Satoshi Shimano and Frederick W Spiegel and Guifré Torruella and Noha Youssef and Vasily Zlatogursky and Qianqian Zhang},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85060143843&doi=10.1111%2Fjeu.12691&partnerID=40&md5=956ade828edfb6373cb9ca412704d137 https://onlinelibrary.wiley.com/doi/10.1111/jeu.12691},
doi = {10.1111/jeu.12691},
issn = {1066-5234},
year = {2019},
date = {2019-01-01},
journal = {Journal of Eukaryotic Microbiology},
volume = {66},
number = {1},
pages = {4--119},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Maciszewski, Kacper; Karnkowska, Anna
Should I stay or should I go? Retention and loss of components in vestigial endosymbiotic organelles Journal Article
In: Current Opinion in Genetics & Development, vol. 58-59, pp. 33-39, 2019, ISSN: 0959-437X, (Evolutionary genetics).
@article{MACISZEWSKI201933,
title = {Should I stay or should I go? Retention and loss of components in vestigial endosymbiotic organelles},
author = {Kacper Maciszewski and Anna Karnkowska},
url = {https://www.sciencedirect.com/science/article/pii/S0959437X19300425},
doi = {https://doi.org/10.1016/j.gde.2019.07.013},
issn = {0959-437X},
year = {2019},
date = {2019-01-01},
journal = {Current Opinion in Genetics & Development},
volume = {58-59},
pages = {33-39},
abstract = {Our knowledge on the variability of the reduced forms of endosymbiotic organelles – mitochondria and plastids – is expanding rapidly, thanks to growing interest in peculiar microbial eukaryotes, along with the availability of the methods used in modern genomics and transcriptomics. The aim of this work is to highlight the most recent advances in understanding these organelles’ diversity, physiology and evolution. We also outline the known mechanisms behind the convergence of traits between organelles which have undergone reduction independently, the importance of the earliest evolutionary events in determining the vestigial organelles’ eventual fate, and a proposed classification of nonphotosynthetic plastids.},
note = {Evolutionary genetics},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Our knowledge on the variability of the reduced forms of endosymbiotic organelles – mitochondria and plastids – is expanding rapidly, thanks to growing interest in peculiar microbial eukaryotes, along with the availability of the methods used in modern genomics and transcriptomics. The aim of this work is to highlight the most recent advances in understanding these organelles’ diversity, physiology and evolution. We also outline the known mechanisms behind the convergence of traits between organelles which have undergone reduction independently, the importance of the earliest evolutionary events in determining the vestigial organelles’ eventual fate, and a proposed classification of nonphotosynthetic plastids.
Jagielski, Tomasz; Bakuła, Zofia; Gawor, Jan; Maciszewski, Kacper; Kusber, Wolf-Henning; Dyląg, Mariusz; Nowakowska, Julita; Gromadka, Robert; Karnkowska, Anna
The genus Prototheca (Trebouxiophyceae, Chlorophyta) revisited: Implications from molecular taxonomic studies Journal Article
In: Algal Research, vol. 43, pp. 101639, 2019, ISSN: 2211-9264.
@article{JAGIELSKI2019101639,
title = {The genus Prototheca (Trebouxiophyceae, Chlorophyta) revisited: Implications from molecular taxonomic studies},
author = {Tomasz Jagielski and Zofia Bakuła and Jan Gawor and Kacper Maciszewski and Wolf-Henning Kusber and Mariusz Dyląg and Julita Nowakowska and Robert Gromadka and Anna Karnkowska},
url = {https://www.sciencedirect.com/science/article/pii/S2211926419303509},
doi = {https://doi.org/10.1016/j.algal.2019.101639},
issn = {2211-9264},
year = {2019},
date = {2019-01-01},
journal = {Algal Research},
volume = {43},
pages = {101639},
abstract = {The only algae which are able to inflict disease on humans and other mammals through active invasion and spread within the host tissues belong to either of two genera: Chlorella and Prototheca. Whereas Chlorella infections are extremely rare, with only two human cases reported in the literature, protothecosis is an emerging disease of humans and domestic animals, especially dairy cows. The genus Prototheca, erected by Krüger in 1894, has undergone several significant revisions, as more phenotypic, chemotaxonomic, and molecular data have become available. Due to this, a large number of Prototheca strains have been accumulated in public culture collections, over the years, where they still exist under outdated or invalid infraspecific or species names. In this study, the partial cytb gene was used as a marker to revise the taxonomy and nomenclature of a set of Prototheca strains, preserved in major algae culture repositories worldwide. Within the genus, two main lineages were observed, with a dominance of typically dairy cattle-associated (i.e. P. ciferrii, formerly P. zopfii gen. 1, the here validated P. blaschkeae, and one newly erected species, namely P. bovis, formerly P. zopfii gen. 2) and human-associated (i.e. P. wickerhamii, P. cutis, P. miyajii) species, respectively. In the former lineage, three newly described species were allocated, namely P. cookei sp. nov., P. cerasi sp. nov., and P. pringsheimii sp. nov., and the lecto- and epitypified P. zopfii species. The second, or so-called P. wickerhamii lineage, incorporated a newly proposed species of P. xanthoriae sp. nov. These protothecans were shown as the closest relatives of the photosynthetic genera, Chlorella and Auxenochlorella. The environmental species P. ulmea was synonymized with the lecto- and epitypified P. moriformis species. For circumscription and differentiation of Prototheca spp., the use of phenotypic characters, and morphology in particular, is of limited value and should rather be auxiliary to molecular marker-based approaches. As demonstrated in our previous study and corroborated in the present one, the cytb gene provides higher resolution than the conventional rDNA markers, and currently represents the most efficient barcode for the Prototheca algae.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The only algae which are able to inflict disease on humans and other mammals through active invasion and spread within the host tissues belong to either of two genera: Chlorella and Prototheca. Whereas Chlorella infections are extremely rare, with only two human cases reported in the literature, protothecosis is an emerging disease of humans and domestic animals, especially dairy cows. The genus Prototheca, erected by Krüger in 1894, has undergone several significant revisions, as more phenotypic, chemotaxonomic, and molecular data have become available. Due to this, a large number of Prototheca strains have been accumulated in public culture collections, over the years, where they still exist under outdated or invalid infraspecific or species names. In this study, the partial cytb gene was used as a marker to revise the taxonomy and nomenclature of a set of Prototheca strains, preserved in major algae culture repositories worldwide. Within the genus, two main lineages were observed, with a dominance of typically dairy cattle-associated (i.e. P. ciferrii, formerly P. zopfii gen. 1, the here validated P. blaschkeae, and one newly erected species, namely P. bovis, formerly P. zopfii gen. 2) and human-associated (i.e. P. wickerhamii, P. cutis, P. miyajii) species, respectively. In the former lineage, three newly described species were allocated, namely P. cookei sp. nov., P. cerasi sp. nov., and P. pringsheimii sp. nov., and the lecto- and epitypified P. zopfii species. The second, or so-called P. wickerhamii lineage, incorporated a newly proposed species of P. xanthoriae sp. nov. These protothecans were shown as the closest relatives of the photosynthetic genera, Chlorella and Auxenochlorella. The environmental species P. ulmea was synonymized with the lecto- and epitypified P. moriformis species. For circumscription and differentiation of Prototheca spp., the use of phenotypic characters, and morphology in particular, is of limited value and should rather be auxiliary to molecular marker-based approaches. As demonstrated in our previous study and corroborated in the present one, the cytb gene provides higher resolution than the conventional rDNA markers, and currently represents the most efficient barcode for the Prototheca algae.
Karnkowska, Anna; Treitli, Sebastian C; Brzoň, Ondřej; Novák, Lukáš; Vacek, Vojtěch; Soukal, Petr; Barlow, Lael D; Herman, Emily K; Pipaliya, Shweta V; Pánek, Tomáš; Žihala, David; Petrželková, Romana; Butenko, Anzhelika; Eme, Laura; Stairs, Courtney W; Roger, Andrew J; Eliáš, Marek; Dacks, Joel B; Hampl, Vladimír
The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion Journal Article
In: Molecular Biology and Evolution, vol. 36, no. 10, pp. 2292-2312, 2019, ISSN: 0737-4038.
@article{10.1093/molbev/msz147,
title = {The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion},
author = {Anna Karnkowska and Sebastian C Treitli and Ondřej Brzoň and Lukáš Novák and Vojtěch Vacek and Petr Soukal and Lael D Barlow and Emily K Herman and Shweta V Pipaliya and Tomáš Pánek and David Žihala and Romana Petrželková and Anzhelika Butenko and Laura Eme and Courtney W Stairs and Andrew J Roger and Marek Eliáš and Joel B Dacks and Vladimír Hampl},
url = {https://doi.org/10.1093/molbev/msz147},
doi = {10.1093/molbev/msz147},
issn = {0737-4038},
year = {2019},
date = {2019-01-01},
journal = {Molecular Biology and Evolution},
volume = {36},
number = {10},
pages = {2292-2312},
abstract = {The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here, we report an extensive analysis of the M. exilis genome to address this question. Unexpectedly, we find that M. exilis genome structure and content is similar in complexity to other eukaryotes and less “reduced” than genomes of some other protists from the Metamonada group to which it belongs. Furthermore, the predicted cytoskeletal systems, the organization of endomembrane systems, and biosynthetic pathways also display canonical eukaryotic complexity. The only apparent preadaptation that permitted the loss of mitochondria was the acquisition of the SUF system for Fe–S cluster assembly and the loss of glycine cleavage system. Changes in other systems, including in amino acid metabolism and oxidative stress response, were coincident with the loss of mitochondria but are likely adaptations to the microaerophilic and endobiotic niche rather than the mitochondrial loss per se. Apart from the lack of mitochondria and peroxisomes, we show that M. exilis is a fully elaborated eukaryotic cell that is a promising model system in which eukaryotic cell biology can be investigated in the absence of mitochondria.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here, we report an extensive analysis of the M. exilis genome to address this question. Unexpectedly, we find that M. exilis genome structure and content is similar in complexity to other eukaryotes and less “reduced” than genomes of some other protists from the Metamonada group to which it belongs. Furthermore, the predicted cytoskeletal systems, the organization of endomembrane systems, and biosynthetic pathways also display canonical eukaryotic complexity. The only apparent preadaptation that permitted the loss of mitochondria was the acquisition of the SUF system for Fe–S cluster assembly and the loss of glycine cleavage system. Changes in other systems, including in amino acid metabolism and oxidative stress response, were coincident with the loss of mitochondria but are likely adaptations to the microaerophilic and endobiotic niche rather than the mitochondrial loss per se. Apart from the lack of mitochondria and peroxisomes, we show that M. exilis is a fully elaborated eukaryotic cell that is a promising model system in which eukaryotic cell biology can be investigated in the absence of mitochondria.
Pawłowska, Julia; Frąc, Magdalena; Kałucka, Izabela; Ruszkiewicz-Michalska, Małgorzata; Różalska, Sylwia; Wrzosek, Marta
The XVIII Congress of European Mycologists: Conference Report Journal Article
In: Journal of Fungi, vol. 5, no. 4, 2019, ISSN: 2309-608X.
@article{jof5040110,
title = {The XVIII Congress of European Mycologists: Conference Report},
author = {Julia Pawłowska and Magdalena Frąc and Izabela Kałucka and Małgorzata Ruszkiewicz-Michalska and Sylwia Różalska and Marta Wrzosek},
url = {https://www.mdpi.com/2309-608X/5/4/110},
doi = {10.3390/jof5040110},
issn = {2309-608X},
year = {2019},
date = {2019-01-01},
journal = {Journal of Fungi},
volume = {5},
number = {4},
abstract = {The 18th Congress of European Mycologists took place from 16 to 21 September 2019 in Warsaw and Białowieża, Poland (Figure 1) [...]},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The 18th Congress of European Mycologists took place from 16 to 21 September 2019 in Warsaw and Białowieża, Poland (Figure 1) [...]
Piechowski, Rafał; Niedźwiedzki, Grzegorz; Tałanda, Mateusz
Unexpected bird-like features and high intraspecific variation in the braincase of the Triassic relative of dinosaurs Journal Article
In: Historical Biology, vol. 31, no. 8, pp. 1065–1081, 2019, (Publisher: Taylor & Francis _eprint: https://doi.org/10.1080/08912963.2017.1418339).
@article{piechowski_unexpected_2019,
title = {Unexpected bird-like features and high intraspecific variation in the braincase of the Triassic relative of dinosaurs},
author = {Rafał Piechowski and Grzegorz Niedźwiedzki and Mateusz Tałanda},
url = {https://doi.org/10.1080/08912963.2017.1418339},
doi = {10.1080/08912963.2017.1418339},
year = {2019},
date = {2019-01-01},
journal = {Historical Biology},
volume = {31},
number = {8},
pages = {1065--1081},
abstract = {Abstract Silesaurus opolensis Dzik, 2003 from the Late Triassic (late Carnian) of Poland is a key taxon for understanding the evolution of early dinosaurs. High intraspecific variation observed in the S. opolensis braincase brings caution in taxonomic and diversity studies of early dinosauromorphs. The external and internal osteology of three almost complete braincases of S. opolensis show that this taxon shares several similarities with other early dinosauriforms, which supports a close relationship among these forms. However, the paroccipital processes of S. opolensis are directed ventrally like in birds, reaching the level of the ventral margin of the basioccipital condyle. In dinosauromorphs, these processes usually have an almost horizontal orientation (presumed to be the plesiomorphic condition). Modifications observed in birds and S. opolensis have resulted in the dorsoventral expansion of M. complexus and M. depressor mandibulae, which occupy the dorsolateral part of the posterior side of the skull. In adult birds, these muscles act strongly on the initial upstroke of the head during drinking. Therefore, the inferred condition of these muscles in S. opolensis may imply that Silesauridae evolved toward bird-like feeding behaviour.},
note = {Publisher: Taylor & Francis
_eprint: https://doi.org/10.1080/08912963.2017.1418339},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract Silesaurus opolensis Dzik, 2003 from the Late Triassic (late Carnian) of Poland is a key taxon for understanding the evolution of early dinosaurs. High intraspecific variation observed in the S. opolensis braincase brings caution in taxonomic and diversity studies of early dinosauromorphs. The external and internal osteology of three almost complete braincases of S. opolensis show that this taxon shares several similarities with other early dinosauriforms, which supports a close relationship among these forms. However, the paroccipital processes of S. opolensis are directed ventrally like in birds, reaching the level of the ventral margin of the basioccipital condyle. In dinosauromorphs, these processes usually have an almost horizontal orientation (presumed to be the plesiomorphic condition). Modifications observed in birds and S. opolensis have resulted in the dorsoventral expansion of M. complexus and M. depressor mandibulae, which occupy the dorsolateral part of the posterior side of the skull. In adult birds, these muscles act strongly on the initial upstroke of the head during drinking. Therefore, the inferred condition of these muscles in S. opolensis may imply that Silesauridae evolved toward bird-like feeding behaviour.