Publications

@article{Awdankiewicz2024,

title = {Timing of post-orogenic silicic volcanism in the eastern part of the European Variscides: constraints from SHRIMP U–Pb zircon study of the Permo-Carboniferous Góry Suche Rhyolitic Tuffs (the Intra-Sudetic Basin)},

author = {Marek Awdankiewicz and Magdalena Pańczyk and Izabela Ploch and Paweł Raczyński and Honorata Awdankiewicz and Anna Górecka-Nowak and Wojciech Pawlak and Tadeusz Peryt},

doi = {10.1007/s00531-024-02474-y},

issn = {1437-3262},

year  = {2024},

date = {2024-11-01},

urldate = {2024-11-01},

journal = {International Journal of Earth Sciences},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:p>The Góry Suche Rhyolitic Tuffs in the Intra-Sudetic Basin, in the eastern part of the Variscan Belt of Europe, represent a voluminous (ca. 100 km<jats:sup>3</jats:sup>), possibly caldera-related, ignimbrite-dominated complex and the Łomnica Rhyolites are associated, post-ignimbrite sills. Zircon separates from nine samples were dated using the U–Pb SHRIMP method. Well-defined concordia ages were determined in four ignimbrite samples (300.5 ± 2.0, 300.5 ± 1.4, 298.0 ± 1.6 and 297.2 ± 0.9 Ma) and in two rhyolite samples (298.4 ± 1.5 and 292.6 ± 1.9 Ma). Clustering of the ignimbrite sample ages between 300.5 ± 2.0 and 297.2 ± 0.9 Ma and geological evidence indicate the eruption and deposition of the tuffs close to the Carboniferous/Permian boundary, in a geologically rapid event at approximately 299 Ma. Zircon assemblages in three tuff specimens are strongly dominated by xenocrysts of various Palaeozoic and Precambrian ages that were incorporated during the eruption through the basin fill. The emplacement of the tuffs was followed (and partly overlapped?) by the emplacement of the Łomnica Rhyolites as sills in two episodes in the early Permian. The Góry Suche Rhyolitic Tuffs may be a few million years older than assumed so far, and this, as well as rather imprecise biostratigraphic constraints from the host sedimentary rocks, suggest a need for revision of the existing lithostratigraphic and evolutionary schemes for the Permo-Carboniferous of the Intra-Sudetic Basin. The studied tuffs and rhyolites together with coeval granitic plutons in vicinity can be linked to the onset of post-Carboniferous lithospheric thinning in Central Europe.</jats:p>

              <jats:p><jats:bold>Graphical abstract</jats:bold></jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jaworska2024,

title = {Dry-aged beef quality with the addition of Mucor flavus – Sensory, chemosensory and fatty acid analysis},

author = {Danuta Jaworska and Julia Pawłowska and Eliza Kostyra and Anna Piotrowska and Magdalena Płecha and Grzegorz Ostrowski and Edyta Symoniuk and David L. Hopkins and Krzysztof Sawicki and Wiesław Przybylski},

doi = {10.1016/j.meatsci.2024.109691},

issn = {0309-1740},

year  = {2024},

date = {2024-10-30},

urldate = {2024-10-00},

journal = {Meat Science},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Agiadi2024c,

title = {A revised marine fossil record of the Mediterranean before and after the Messinian salinity crisis},

author = {Konstantina Agiadi and Niklas Hohmann and Elsa Gliozzi and Danae Thivaiou and Francesca R. Bosellini and Marco Taviani and Giovanni Bianucci and Alberto Collareta and Laurent Londeix and Costanza Faranda and Francesca Bulian and Efterpi Koskeridou and Francesca Lozar and Alan Maria Mancini and Stefano Dominici and Pierre Moissette and Ildefonso Bajo Campos and Enrico Borghi and George Iliopoulos and Assimina Antonarakou and George Kontakiotis and Evangelia Besiou and Stergios D. Zarkogiannis and Mathias Harzhauser and Francisco Javier Sierro and Angelo Camerlenghi and Daniel García-Castellanos},

doi = {10.5194/essd-16-4767-2024},

issn = {1866-3516},

year  = {2024},

date = {2024-10-22},

urldate = {2024-00-00},

journal = {Earth System Science Data},

volume = {16},

number = {10},

pages = {4767--4775},

publisher = {Copernicus GmbH},

abstract = {<jats:p>Abstract. The Messinian salinity crisis and its precursor events have been the greatest environmental perturbation of the Mediterranean Sea to date, offering an opportunity to study the response of marine ecosystems to extreme hydrological change and a large-scale biological invasion. The restriction of the marine connection between the Mediterranean and the Atlantic Ocean resulted in stratification of the water column and high-amplitude variations in seawater temperature and salinity already from the early Messinian. Here, we present a unified and revised marine fossil record of the Mediterranean (https://doi.org/10.5281/zenodo.13358435, Agiadi et al., 2024) that covers the Tortonian stage, the pre-evaporitic Messinian stage, and the Zanclean stage and encompasses 23 032 occurrences of calcareous nannoplankton, dinoflagellates, foraminifera, corals, ostracods, bryozoans, echinoids, mollusks, fishes, and marine mammals. This record adheres to the FAIR principles, is updated in terms of taxonomy, and follows the currently accepted stratigraphic framework. Based on this record, knowledge gaps are identified, which are due to spatiotemporal inconsistencies in sampling effort and the distribution of sedimentary facies, as well as the inherent differences in the preservation potential between the groups. Additionally, sampling bias in old records may have distorted the record in favor of larger, more impressive taxa within groups. This record is now ready to be used to answer both geological and biological questions about the Mediterranean Sea and beyond and is amendable when new fossil data are brought to light.

                    </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wijayawardene2024,

title = {Classes and phyla of the kingdom Fungi},

author = {Nalin N. Wijayawardene and Kevin D. Hyde and Kirill V. Mikhailov and Gábor Péter and André Aptroot and Carmen L. A. Pires-Zottarelli and Bruno T. Goto and Yuri S. Tokarev and Danny Haelewaters and Samantha C. Karunarathna and Paul M. Kirk and André L. C. M. de A. Santiago and Ramesh K. Saxena and Nathan Schoutteten and Madhara K. Wimalasena and Vladimir V. Aleoshin and Abdullah M. S. Al-Hatmi and Kahandawa G. S. U. Ariyawansa and Amanda R. Assunção and Thushara C. Bamunuarachchige and Hans-Otto Baral and D. Jayarama Bhat and Janusz Błaszkowski and Teun Boekhout and Nattawut Boonyuen and Michael Brysch-Herzberg and Bin Cao and Jonathan Cazabonne and Xue-Mei Chen and Claudia Coleine and Dong-Qin Dai and Heide-Marie Daniel and Suzana B. G. da Silva and Francisco Adriano de Souza and Somayeh Dolatabadi and Manish K. Dubey and Arun K. Dutta and Aseni Ediriweera and Eleonora Egidi and Mostafa S. Elshahed and Xinlei Fan and Juliana R. B. Felix and Mahesh C. A. Galappaththi and Marizeth Groenewald and Li-Su Han and Bo Huang and Vedprakash G. Hurdeal and Anastasia N. Ignatieva and Gustavo H. Jerônimo and Ana L. de Jesus and Serhii Kondratyuk and Jaturong Kumla and Martin Kukwa and Qirui Li and Juliana L. R. Lima and Xiao-Yong Liu and Wenhua Lu and H. Thorsten Lumbsch and Hugo Madrid and Franco Magurno and Guy Marson and Eric H. C. McKenzie and Audrius Menkis and Armin Mešić and Elaine C. R. Nascimento and Elena S. Nassonova and Yong Nie and Naasson V. L. Oliveira and Emilia A. Ossowska and Julia Pawłowska and Ursula Peintner and Igor R. Pozdnyakov and Bhagya M. Premarathne and A. K. Hasith Priyashantha and C. Alisha Quandt and Mariana B. Queiroz and Kunhiraman C. Rajeshkumar and Mubashar Raza and Niranjan Roy and Milan C. Samarakoon and Alessandra A. Santos and Lidiane A. Santos and Felix Schumm and Laura Selbmann and Faruk Selçuk and D. Rabern Simmons and Anastasia V. Simakova and Maudy Th. Smith and Onden Paraparath Sruthi and Nakarin Suwannarach and Kazuaki Tanaka and Saowaluck Tibpromma and Elias O. Tomás and Merve Ulukapı and Nicolas Van Vooren and Dhanushka N. Wanasinghe and Evi Weber and Qianzhen Wu and Er Fu Yang and Ryuichi Yoshioka and Noha H. Youssef and Annemarie Zandijk and Gui-Qing Zhang and Jin-Yong Zhang and Heng Zhao and RuiLin Zhao and Oleg A. Zverkov and Marco Thines and Sergey A. Karpov},

doi = {10.1007/s13225-024-00540-z},

issn = {1878-9129},

year  = {2024},

date = {2024-10-15},

urldate = {2024-10-15},

journal = {Fungal Diversity},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:p>Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom <jats:italic>Fungi</jats:italic>, drawing upon a comprehensive phylogenomic analysis of <jats:italic>Holomycota</jats:italic>, with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of <jats:italic>Fungi,</jats:italic> viz<jats:italic>. Aphelidiomycota</jats:italic>, <jats:italic>Ascomycota</jats:italic>, <jats:italic>Basidiobolomycota</jats:italic>, <jats:italic>Basidiomycota</jats:italic>, <jats:italic>Blastocladiomycota</jats:italic>, <jats:italic>Calcarisporiellomycota</jats:italic>, <jats:italic>Chytridiomycota</jats:italic>, <jats:italic>Entomophthoromycota</jats:italic>, <jats:italic>Entorrhizomycota</jats:italic>, <jats:italic>Glomeromycota</jats:italic>, <jats:italic>Kickxellomycota</jats:italic>, <jats:italic>Monoblepharomycota</jats:italic>, <jats:italic>Mortierellomycota</jats:italic>, <jats:italic>Mucoromycota</jats:italic>, <jats:italic>Neocallimastigomycota</jats:italic>, <jats:italic>Olpidiomycota</jats:italic>, <jats:italic>Rozellomycota</jats:italic>, <jats:italic>Sanchytriomycota,</jats:italic> and <jats:italic>Zoopagomycota</jats:italic>. In the phylogenies, <jats:italic>Caulochytriomycota</jats:italic> resides in <jats:italic>Chytridiomycota</jats:italic>; thus, the former is regarded as a synonym of the latter, while <jats:italic>Caulochytriomycetes</jats:italic> is viewed as a class in <jats:italic>Chytridiomycota</jats:italic>. We provide a description of each phylum followed by its classes. A new subphylum, <jats:italic>Sanchytriomycotina</jats:italic> Karpov is introduced as the only subphylum in <jats:italic>Sanchytriomycota</jats:italic>. The subclass <jats:italic>Pneumocystomycetidae</jats:italic> Kirk et al. in <jats:italic>Pneumocystomycetes</jats:italic>, <jats:italic>Ascomycota</jats:italic> is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1002/ece3.70333,

title = {Ant's Nest as a microenvironment: Distinct Mucoromycota (Fungi) community of the red wood ants' (Formica polyctena) mounds},

author = {Igor Siedlecki and Michał Kochanowski and Julia Pawłowska and Gabriela Reszotnik and Alicja Okrasińska and Marta Wrzosek},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.70333},

doi = {https://doi.org/10.1002/ece3.70333},

year  = {2024},

date = {2024-10-09},

urldate = {2024-10-09},

journal = {Ecology and Evolution},

volume = {14},

number = {10},

pages = {e70333},

abstract = {Abstract Many social insect species build nests, which differ from the surrounding environment and are often occupied by specific organismal communities. These organisms may interact mutualistically or parasitically with the nest-builders, or simply co-occur, being able to survive in these microenvironments. In temperate forests, red wood ants (e.g. Formica polyctena) are known to create distinct, highly developed nests, which consist of large, above-ground mounds, built primarily out of plant matter collected from the forest litter. The microorganismal communities of such mounds remain understudied. As representatives of Mucoromycota fungi commonly engage in the decomposition process of the forest litter, they would be expected to occur in the mounds. However, it is still not known whether the Mucoromycota community of these ants' nests differ from the one of the surrounding forest litter. In order to distinguish mound-associated taxa, we characterized Mucoromycota communities of Formica polyctena mounds and the surrounding forest litter. We sampled four sites, twice in a season. Sampled material was plated on agar media and emerging Mucoromycota colonies were identified based on their morphology. Fungal identification was further confirmed using DNA barcoding. In order to compare described communities, PERMANOVA test and non-metric multidimensional scaling ordinations were used. To distinguish taxa associated with the mounds, multilevel pattern analysis was performed. Our results show that the Mucoromycota community of Formica polyctena's mound differs from the community of the surrounding forest litter. While representatives of Entomortierella lignicola and Absidia cylindrospora clade were found to be associated with the mound environment, representatives of Umbelopsis curvata and Podila verticillata-humilis clade were associated with forest litter, and were rarely present in the mounds. Our findings strongly suggest that the red wood ants' nest is a specific microenvironment in the temperate forest floor, which is a preferred microhabitat for the mound-associated Mucoromycota, possibly adapted to live in proximity to ants.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{app14199053,

title = {Fungal Biostarter and Bacterial Occurrence of Dry-Aged Beef: The Sensory Quality and Volatile Aroma Compounds after 21 Days of Aging},

author = {Wiesław Przybylski and Danuta Jaworska and Paweł Kresa and Grzegorz Ostrowski and Magdalena Płecha and Dorota Korsak and Dorota Derewiaka and Lech Adamczak and Urszula Siekierko and Julia Pawłowska},

url = {https://www.mdpi.com/2076-3417/14/19/9053},

doi = {10.3390/app14199053},

issn = {2076-3417},

year  = {2024},

date = {2024-10-08},

urldate = {2024-01-01},

journal = {Applied Sciences},

volume = {14},

number = {19},

abstract = {In this study, we decided to test the hypothesis that the fungal biostarter M. flavus used during a 21-day beef dry-aging process significantly impacts the composition of other microorganisms, the profile of volatile compounds, meat hardness characteristics, and, consequently, the sensory quality. The experiments were performed on samples derived from animals crossbred between Holstein–Fresian cows and meat breed bulls. Two groups of samples were studied, including the control group, without biostarter, and a group inoculated with the M. flavus biostarter. Both sample groups were seasoned for 21 days in the dry-aging fridge. The physicochemical parameters (pH, color parameters), the chemical composition of muscle, the determination of the shear force, the profile of volatile compounds (VOCs), and the sensory quality were evaluated after aging. During this study, classical microbiological methods were used to investigate the influence of fungal biostarters on the growth and survival of bacteria and other fungi (e.g., yeasts) during the dry-aging process of beef (DAB). The M. flavus biostarter improved the sensory quality of DAB, allowing high sensory quality to be achieved after just 21 days. This is likely due to the diverse VOCs produced by the fungus, including 1-tetradecanol, 2-nonenal, trans-2-undecenoic acid, and the following esters: formic acid hexyl ester, 10-undecenoic acid methyl ester, and 4-methylpentanoic acid methyl ester. The presence of the biostarter had no significant effect on the number of the bacteria or the survivability of the L. monocytogenes on the meat’s surface in laboratory conditions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Raza2024,

title = {New sivatheriine giraffid (Ruminantia, Mammalia) craniodental material from the Siwaliks of Pakistan},

author = {Tehreem Raza and Riffat Yasin and Sergi López-Torres and Natalie M. Warburton and Khizar Samiullah and Abdul Ghaffar and Muhammad N. Khan and Chaman Ara and Eisha Muzaffar},

doi = {10.1080/02724634.2024.2376241},

issn = {1937-2809},

year  = {2024},

date = {2024-10-01},

urldate = {2024-10-00},

journal = {Journal of Vertebrate Paleontology},

pages = {e2376241},

publisher = {Informa UK Limited},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Witasik2024,

title = {Modified laminar bone did not stop sauropods from achieving large body sizes},

author = {Marceli Witasik and Justyna Słowiak and Tomasz Szczygielski},

doi = {10.1080/02724634.2024.2396816},

issn = {1937-2809},

year  = {2024},

date = {2024-09-30},

urldate = {2024-09-30},

journal = {Journal of Vertebrate Paleontology},

publisher = {Informa UK Limited},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Agiadi2024b,

title = {Late Miocene transformation of Mediterranean Sea biodiversity},

author = {Konstantina Agiadi and Niklas Hohmann and Elsa Gliozzi and Danae Thivaiou and Francesca R. Bosellini and Marco Taviani and Giovanni Bianucci and Alberto Collareta and Laurent Londeix and Costanza Faranda and Francesca Bulian and Efterpi Koskeridou and Francesca Lozar and Alan Maria Mancini and Stefano Dominici and Pierre Moissette and Ildefonso Bajo Campos and Enrico Borghi and George Iliopoulos and Assimina Antonarakou and George Kontakiotis and Evangelia Besiou and Stergios D. Zarkogiannis and Mathias Harzhauser and Francisco Javier Sierro and Marta Coll and Iuliana Vasiliev and Angelo Camerlenghi and Daniel García-Castellanos},

doi = {10.1126/sciadv.adp1134},

issn = {2375-2548},

year  = {2024},

date = {2024-09-25},

urldate = {2024-09-25},

journal = {Science Advances},

volume = {10},

number = {39},

pages = {eadp1134},

publisher = {American Association for the Advancement of Science (AAAS)},

abstract = {<jats:p>Understanding deep-time marine biodiversity change under the combined effects of climate and connectivity changes is fundamental for predicting the impacts of modern climate change in semi-enclosed seas. We quantify the Late Miocene–Early Pliocene [11.63 to 3.6 million years (Ma)] taxonomic diversity of the Mediterranean Sea for calcareous nannoplankton, dinocysts, foraminifera, ostracods, corals, molluscs, bryozoans, echinoids, fishes, and marine mammals. During this time, marine biota was affected by global climate cooling and the restriction of the Mediterranean’s connection to the Atlantic Ocean that peaked with the Messinian salinity crisis. Although the net change in species richness from the Tortonian to the Zanclean varies by group, species turnover is greater than 30% in all cases, reflecting a high degree of reorganization of the marine ecosystem after the crisis. The results show a clear perturbation already in the pre-evaporitic Messinian (7.25 to 5.97 Ma), with patterns differing among groups and subbasins.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{McCartney2024,

title = {The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics},

author = {Ann M. Mc Cartney and Giulio Formenti and Alice Mouton and (...) and Julia Pawlowska and (...) and Camila J. Mazzoni},

doi = {https://doi.org/10.1038/s44185-024-00054-6},

year  = {2024},

date = {2024-09-16},

urldate = {2024-09-16},

journal = {NPJ Biodiversity},

volume = {3},

issue = {28},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Uhlik2024,

title = {Embryogeny of            \textit{Pleuroxus aduncus}            (Jurine, 1820) and            \textit{Chydorus sphaericus}            S. Lato (Müller, 1776) indicate on conservative instars development among family Chydoridae (Crustacea, Cladocera, Anomopoda)},

author = {Marcin E. Uhlik},

doi = {10.1080/24750263.2024.2393834},

issn = {2475-0263},

year  = {2024},

date = {2024-09-09},

urldate = {2024-07-02},

journal = {The European Zoological Journal},

volume = {91},

number = {2},

pages = {1035--1051},

publisher = {Informa UK Limited},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Agiadi2024,

title = {The marine biodiversity impact of the Late Miocene Mediterranean salinity crisis},

author = {Konstantina Agiadi and Niklas Hohmann and Elsa Gliozzi and Danae Thivaiou and Francesca R. Bosellini and Marco Taviani and Giovanni Bianucci and Alberto Collareta and Laurent Londeix and Costanza Faranda and Francesca Bulian and Efterpi Koskeridou and Francesca Lozar and Alan Maria Mancini and Stefano Dominici and Pierre Moissette and Ildefonso Bajo Campos and Enrico Borghi and George Iliopoulos and Assimina Antonarakou and George Kontakiotis and Evangelia Besiou and Stergios D. Zarkogiannis and Mathias Harzhauser and Francisco Javier Sierro and Marta Coll and Iuliana Vasiliev and Angelo Camerlenghi and Daniel García-Castellanos},

doi = {10.1126/science.adp3703},

year  = {2024},

date = {2024-08-29},

urldate = {2024-08-29},

journal = {Science},

volume = {385},

number = {6712},

pages = {986--991},

publisher = {American Association for the Advancement of Science (AAAS)},

abstract = {<jats:p>Massive salt accumulations, or salt giants, have formed in highly restricted marine basins throughout geological history, but their impact on biodiversity has been only patchily studied. The salt giant in the Mediterranean Sea formed as a result of the restriction of its gateway to the Atlantic during the Messinian Salinity Crisis (MSC) 5.97 to 5.33 million years ago. Here, we quantify the biodiversity changes associated with the MSC based on a compilation of the Mediterranean fossil record. We conclude that 86 endemic species of the 2006 pre-MSC marine species survived the crisis, and that the present eastward-decreasing richness gradient in the Mediterranean was established after the MSC.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tsuboi2024,

title = {The Paradox of Predictability Provides a Bridge Between Micro- and Macroevolution},

author = {Masahito Tsuboi and Jacqueline Sztepanacz and Stephen De Lisle and Kjetil L Voje and Mark Grabowski and Melanie J Hopkins and Arthur Porto and Meghan Balk and Mikael Pontarp and Daniela Rossoni and Laura S Hildesheim and Quentin J-B Horta-Lacueva and Niklas Hohmann and Agnes Holstad and Moritz Lürig and Lisandro Milocco and Sofie Nilén and Arianna Passarotto and Erik I Svensson and Cristina Villegas and Erica Winslott and Lee Hsiang Liow and Gene Hunt and Alan C Love and David Houle},

doi = {10.1093/jeb/voae103},

issn = {1420-9101},

year  = {2024},

date = {2024-08-29},

urldate = {2024-08-29},

journal = {Journal of Evolutionary Biology},

pages = {voae103},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

               <jats:p>The relationship between the evolutionary dynamics observed in contemporary populations (microevolution) and evolution on timescales of millions of years (macroevolution) has been a topic of considerable debate. Historically, this debate centers on inconsistencies between microevolutionary processes and macroevolutionary patterns. Here, we characterize a striking exception: emerging evidence indicates that standing variation in contemporary populations and macroevolutionary rates of phenotypic divergence are often positively correlated. This apparent consistency between micro- and macroevolution is paradoxical because it contradicts our previous understanding of phenotypic evolution and is so far unexplained. Here, we explore the prospects for bridging evolutionary timescales through an examination of this “paradox of predictability.” We begin by explaining why the divergence-variance correlation is a paradox, followed by data analysis to show that the correlation is a general phenomenon across a broad range of temporal scales, from a few generations to tens of millions of years. Then we review complementary approaches from quantitative-genetics, comparative morphology, evo-devo, and paleontology to argue that they can help to address the paradox from the shared vantage point of recent work on evolvability. In conclusion, we recommend a methodological orientation that combines different kinds of short-term and long-term data using multiple analytical frameworks in an interdisciplinary research program. Such a program will increase our general understanding about how evolution works within and across timescales.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vardi2024,

title = {Leveraging social media and other online data to study animal behavior},

author = {Reut Vardi and Andrea Soriano-Redondo and Jorge S. Gutiérrez and Łukasz Dylewski and Zuzanna Jagiello and Peter Mikula and Oded Berger-Tal and Daniel T. Blumstein and Ivan Jarić and Valerio Sbragaglia},

doi = {10.1371/journal.pbio.3002793},

issn = {1545-7885},

year  = {2024},

date = {2024-08-29},

urldate = {2024-08-29},

journal = {PLoS Biol},

volume = {22},

number = {e3002793},

issue = {8},

publisher = {Public Library of Science (PLoS)},

abstract = {The widespread sharing of information on the Internet has given rise to ecological studies that use data from digital sources including digitized museum records and social media posts. Most of these studies have focused on understanding species occurrences and distributions. In this essay, we argue that data from digital sources also offer many opportunities to study animal behavior including long-term and large-scale comparisons within and between species. Following Nikko Tinbergen’s classical roadmap for behavioral investigation, we show how using videos, photos, text, and audio posted on social media and other digital platforms can shed new light on known behaviors, particularly in a changing world, and lead to the discovery of new ones.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nithin2024,

title = {Exploring protein functions from structural flexibility using <scp>CABS</scp>‐flex modeling},

author = {Chandran Nithin and Rocco Peter Fornari and Smita P. Pilla and Karol Wroblewski and Mateusz Zalewski and Rafał Madaj and Andrzej Kolinski and Joanna M. Macnar and Sebastian Kmiecik},

doi = {10.1002/pro.5090},

issn = {1469-896X},

year  = {2024},

date = {2024-08-28},

urldate = {2024-09-00},

journal = {Protein Science},

volume = {33},

issue = {9},

pages = {e5090},

publisher = {Wiley},

abstract = {Understanding protein function often necessitates characterizing the flexibility of protein structures. However, simulating protein flexibility poses significant challenges due to the complex dynamics of protein systems, requiring extensive computational resources and accurate modeling techniques. In response to these challenges, the CABS‐flex method has been developed as an efficient modeling tool that combines coarse‐grained simulations with all‐atom detail. Available both as a web server and a standalone package, CABS‐flex is dedicated to a wide range of users. The web server version offers an accessible interface for straightforward tasks, while the standalone command‐line program is designed for advanced users, providing additional features, analytical tools, and support for handling large systems. This paper examines the application of CABS‐flex across various structure–function studies, facilitating investigations into the interplay among protein structure, dynamics, and function in diverse research fields. We present an overview of the current status of the CABS‐flex methodology, highlighting its recent advancements, practical applications, and forthcoming challenges.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hohmann2024,

title = {Identification of the mode of evolution in incomplete carbonate successions},

author = {Niklas Hohmann and Joël R. Koelewijn and Peter Burgess and Emilia Jarochowska},

doi = {10.1186/s12862-024-02287-2},

issn = {2730-7182},

year  = {2024},

date = {2024-08-23},

urldate = {2024-12-00},

journal = {BMC Ecology and Evolution},

volume = {24},

number = {113},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:sec>

                <jats:title>Background</jats:title>

                <jats:p>The fossil record provides the unique opportunity to observe evolution over millions of years, but is known to be incomplete. While incompleteness varies spatially and is hard to estimate for empirical sections, computer simulations of geological processes can be used to examine the effects of the incompleteness <jats:italic>in silico</jats:italic>.</jats:p>

                <jats:p>We combine simulations of different modes of evolution (stasis, (un)biased random walks) with deposition of carbonate platforms strata to examine how well the mode of evolution can be recovered from fossil time series, and how test results vary between different positions in the carbonate platform and multiple stratigraphic architectures generated by different sea level curves.</jats:p>

              </jats:sec><jats:sec>

                <jats:title>Results</jats:title>

                <jats:p>Stratigraphic architecture and position along an onshore-offshore gradient has only a small influence on the mode of evolution recovered by statistical tests. For simulations of random walks, support for the correct mode decreases with time series length.</jats:p>

                <jats:p>Visual examination of trait evolution in lineages shows that rather than stratigraphic incompleteness, maximum hiatus duration determines how much fossil time series differ from the original evolutionary process. Gradual directional evolution is more susceptible to stratigraphic effects, turning it into punctuated evolution. In contrast, stasis remains unaffected.</jats:p>

              </jats:sec><jats:sec>

                <jats:title>Conclusions</jats:title>

                <jats:p>• Fossil time series favor the recognition of both stasis and complex, punctuated modes of evolution.</jats:p>

                <jats:p>• Not stratigraphic incompleteness, but the presence of rare, prolonged gaps has the largest effect on trait evolution. This suggests that incomplete sections with regular hiatus frequency and durations can potentially preserve evolutionary history without major biases. Understanding external controls on stratigraphic architectures such as sea level fluctuations is crucial for distinguishing between stratigraphic effects and genuine evolutionary process.</jats:p>

              </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DZIK2024,

title = {A variety of meroms and affinity of receptaculitids},

author = {Jerzy Dzik},

doi = {10.18261/let.57.2.7},

issn = {1502-3931},

year  = {2024},

date = {2024-08-21},

urldate = {2024-06-20},

journal = {Lethaia},

volume = {57},

number = {2},

pages = {1-8},

publisher = {Scandinavian University Press / Universitetsforlaget AS},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{López-Torres2024,

title = {The allometry of brain size in Euarchontoglires: clade-specific patterns and their impact on encephalization quotients},

author = {Sergi López-Torres and Ornella C Bertrand and Łucja Fostowicz-Frelik and Madlen M Lang and Chris J Law and San Martin-Flores, Gabriela and Michael A Schillaci and Mary T Silcox},

editor = {Deyan Ge},

doi = {10.1093/jmammal/gyae084},

issn = {1545-1542},

year  = {2024},

date = {2024-08-16},

urldate = {2024-08-16},

journal = {Journal of Mammalogy},

volume = {XX},

pages = {1-16},

publisher = {Oxford University Press (OUP)},

abstract = {The timing and nature of evolutionary shifts in the relative brain size of Primates have been extensively studied. Less is known, however, about the scaling of the brain-to-body size in their closest living relatives, i.e., among other members of Euarchontoglires (Dermoptera, Scandentia, Lagomorpha, Rodentia). Ordinary least squares (OLS), reduced major axis (RMA), and phylogenetic generalized least squares (PGLS) regressions were fitted to the largest euarchontogliran data set of brain and body mass, comprising 715 species. Contrary to previous inferences, lagomorph brain sizes (PGLS slope = 0.465; OLS slope = 0.593) scale relative to body mass similarly to rodents (PGLS = 0.526; OLS = 0.638), and differently than primates (PGLS = 0.607; OLS = 0.794). There is a shift in the pattern of the scaling of the brain in Primates, with Strepsirrhini occupying an intermediate stage similar to Scandentia but different from Rodentia and Lagomorpha, while Haplorhini differ from all other groups in the OLS and RMA analyses. The unique brain–body scaling relationship of Primates among Euarchontoglires illustrates the need for clade-specific metrics for relative brain size (i.e., encephalization quotients; EQs) for more restricted taxonomic entities than Mammalia. We created clade-specific regular and phylogenetically adjusted EQ equations at superordinal, ordinal, and subordinal levels. When using fossils as test cases, our results show that generalized mammalian equations underestimate the encephalization of the stem lagomorph Megalagus turgidus in the context of lagomorphs, overestimate the encephalization of the stem primate Microsyops annectens and the early euprimate Necrolemur antiquus, but provide similar EQ values as our new strepsirrhine-specific EQ when applied to the early euprimate Adapis parisiensis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Stadnicki2024,

title = {Application of criminology in urban ecology and evolution: Routine Activity Theory and field equipment disappearance dynamics},

author = {Ignacy Stadnicki and Michela Corsini and Marta Szulkin},

doi = {10.1016/j.ecolind.2024.112095},

issn = {1470-160X},

year  = {2024},

date = {2024-08-01},

urldate = {2024-08-00},

journal = {Ecological Indicators},

volume = {165},

pages = {112095},

publisher = {Elsevier BV},

abstract = {Research in urban ecology and evolution relies on the use of deployable scientific equipment. If left unattended in the field, scientific equipment may be prone to vandalism and theft, especially in the urban space. Here, we empirically applied a theory derived from the field of criminology, specifically the Routine Activity Theory (RAT) framework, to predict disappearance rates of scientific equipment in an ongoing urban ecology research project. First, we tested a routinely applied method of equipment protection – labelling – and investigated whether equipment disappearance varied with label information content and message tone. Second, we examined whether equipment attributes (price, mass, volume, colour, and type of installation) and environmental variables (human presence, tree cover, distance to paths and distance to roads) covaried with the disappearance of two types of field equipment, and whether patterns of disappearance changed over time spent in the urban space (novelty effect). The disappearance of 474 nestboxes and 141 frassboxes was followed over four years and two field seasons, respectively. By using the RAT framework, we predicted that nestboxes would be less likely to disappear than frassboxes. In contrast to an earlier reporting, we did not find any association between label type and disappearance rates. Instead, environmental variables covaried with equipment disappearance: for both types of scientific equipment, there was an interaction between human presence and tree cover. Thus, in highly-frequented places with dense tree cover, people were more likely to remove scientific equipment, possibly because they felt less visible. We also detected an interaction between distance to roads and paths for frassboxes but not for nestboxes, revealing that equipment properties may interact with the environmental setting. Importantly, frassbox disappearance decreased over time in both study seasons, indicating the important role of novelty for scientific equipment disappearance rates. We encourage other researchers, site-managers and stakeholders working in cities and other frequently visited areas to apply the RAT framework, as it is a potentially universal, easily applicable and inexpensive method to gain insight into patterns of equipment disappearance in the public space, thereby enhancing the capacity for informed project planning and as a result, safer, and more effective studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gorczak2024,

title = {Mycological records by Fungal Diversity and Conservation Section of the Polish Mycological Society. Part 4.},

author = {Michał Gorczak and Grażyna Domian and Judyta Konik and Barbara Kudławiec and Anna Kujawa and Tomasz Leski and Marcin Lożek and Grażyna Naser and Julia Pawłowska and Małgorzata Stasińska and Natalia Stokłosa and Marta Wrzosek},

url = {https://kp.org.pl/images/pp/artykuły_od_2019/1_2024_XXXV_1/Gorczak%20i%20in_2024_Obserwacje%20mykologiczne%20cz.%20IV.pdf},

year  = {2024},

date = {2024-08-01},

urldate = {2024-08-01},

journal = {Przegląd Przyrodniczy},

volume = {XXXV},

issue = {1},

pages = {3-50},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mikina2024,

title = {Transposon-derived introns as an element shaping the structure of eukaryotic genomes},

author = {Weronika Mikina and Paweł Hałakuc and Rafał Milanowski},

doi = {10.1186/s13100-024-00325-w},

issn = {1759-8753},

year  = {2024},

date = {2024-07-27},

urldate = {2024-12-00},

journal = {Mobile DNA},

volume = {15},

pages = {15},

publisher = {Springer Science and Business Media LLC},

abstract = {The widely accepted hypothesis postulates that the first spliceosomal introns originated from group II self-splicing introns. However, it is evident that not all spliceosomal introns in the nuclear genes of modern eukaryotes are inherited through vertical transfer of intronic sequences. Several phenomena contribute to the formation of new introns but their most common origin seems to be the insertion of transposable elements. Recent analyses have highlighted instances of mass gains of new introns from transposable elements. These events often coincide with an increase or change in the spliceosome's tolerance to splicing signals, including the acceptance of noncanonical borders. Widespread acquisitions of transposon-derived introns occur across diverse evolutionary lineages, indicating convergent processes. These events, though independent, likely require a similar set of conditions. These conditions include the presence of transposon elements with features enabling their removal at the RNA level as introns and/or the existence of a splicing mechanism capable of excising unusual sequences that would otherwise not be recognized as introns by standard splicing machinery. Herein we summarize those mechanisms across different eukaryotic lineages.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Di Lecce2024,

title = {Extra‐pair paternity in two passerine birds breeding in a gradient of urbanisation},

author = {Irene Di Lecce and Joanna Sudyka and Charles Perrier and Marta Szulkin},

doi = {10.1111/mec.17481},

issn = {1365-294X},

year  = {2024},

date = {2024-07-23},

urldate = {2024-09-00},

journal = {Molecular Ecology},

volume = {33},

number = {e17481.},

issue = {17},

publisher = {Wiley},

abstract = {Abstract Urbanisation has been increasing worldwide in recent decades, driving environmental change and exerting novel selective pressures on wildlife. Phenotypic differences between urban and rural individuals have been widely documented in several taxa. However, the extent to which urbanisation impacts mating strategies is less known. Here, we investigated extra‐pair paternity variation in great tits (Parus major) and blue tits (Cyanistes caeruleus) breeding in nestboxes set in a gradient of urbanisation in Warsaw, Poland, over three breeding seasons. Urbanisation was quantified as the amount of light pollution, noise pollution, impervious surface area (ISA) and tree cover within a 100‐m radius around each nestbox. We obtained genotypes for 1213 great tits at 7344 SNP markers and for 1299 blue tits at 9366 SNP markers with a genotyping‐by‐sequencing method, and inferred extra‐pair paternity by computing a genomewide relatedness matrix. We report higher extra‐pair paternity in blue tits breeding in more urbanised areas, for example, with higher light pollution and ISA, and lower tree cover. However, no such trend was found in great tits. Late‐stage survival of individual nestlings in both species was not associated with paternity or urbanisation proxies, thus we were not able to detect fitness benefits or drawbacks of being an extra‐pair offspring in relation to urbanisation. Our results contribute to the growing body of knowledge reporting on the effects of urbanisation on avian ecology and behaviour, and confirm species‐specific and population‐specific patterns of extra‐pair paternity variation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Brady2024,

title = {The effects of ordered multistate morphological characters on phylogenetic analyses of eutherian mammals},

author = {Peggy L. Brady and Castellon Arteaga, Alejandro and Sergi López-Torres and Mark S. Springer},

url = {https://link.springer.com/article/10.1007/s10914-024-09727-2},

doi = {10.1007/s10914-024-09727-2},

year  = {2024},

date = {2024-07-18},

urldate = {2024-07-18},

journal = {Journal of Mammalian Evolution},

volume = {31},

pages = {28},

publisher = {Springer Link},

abstract = {Multistate morphological characters are routinely used in phylogenetic analyses. Individual multistate characters may be treated as linearly ordered, partially ordered, or unordered. Each option implies a hypothesis of character evolution, and significant debate surrounds the appropriateness of ordering multistate characters. Several previous analyses support ordering multistate morphological characters when the character states form a morphocline. Here, we explore the effects of ordering a subset of characters in the largest morphological character matrix that is available for placental mammals. All multistate characters were assessed and were ordered only if the character states were meristic or hypothesized to form a morphocline. We then performed parsimony analyses, with and without molecular scaffolds, to examine the effects of ordering on placental mammal phylogeny. We also performed pseudoextinction analyses, which treated designated extant taxa as extinct by eliminating them from the molecular scaffold and scoring soft-tissue characters as missing, to determine if ordered or unordered characters would more accurately reconstruct the relationships of pseudoextinct placental orders. Character ordering affected the placement of a variety of taxa in non-scaffolded analyses, but the effects were less evident in scaffolded analyses. Nevertheless, one of the islands of most parsimonious trees with the ordered data set and a scaffold for extant taxa supported the inclusion of Leptictida, including the Late Cretaceous Gypsonictops, inside of crown Placentalia. Our analyses rarely supported the monophyly of Tamirtheria, the Late Cretaceous-Paleogene stem-based clade that is hypothesized to be the sister to Placentalia. Pseudoextinction analyses using ordered and unordered characters both reconstructed 12 of 19 pseudoextinct orders in positions that are incongruent with a well-supported molecular scaffold. These results suggest that the use of ordered multistate characters does not increase the proportion of well-supported molecular clades that are reconstructed with the largest available phenomic data set for placental mammals.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{PAWLAK2024,

title = {A new early Permian actinopterygian assemblage shows environmental controls  on the distribution of Paramblypterus (Intra-Sudetic Basin, Poland)},

author = {Wojciech Pawlak and Izabela Ploch and Stanislav Štamberg and Paweł Raczyński and Hubert Kiersnowski},

doi = {10.7306/gq.1741},

issn = {1641-7291},

year  = {2024},

date = {2024-07-04},

urldate = {2024-07-04},

journal = {Geological  Quarterly},

volume = {68},

number = {2},

pages = {1-14},

publisher = {Polish Geological Institute - National Research Institute (PGI-NRI)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{AbramczykFUSE24,

title = {Fungal Planet description sheets: 1614–1696},

author = {Crous, PW and Juriević, Ż and Balashow, S and (...) and Abramczyk, B and Nowak, M and Wiktorowicz, D and Pawłowska, J and (...)},

url = {https://fuse-journal.org/images/Issues/Vol13Art11.pdf},

doi = {doi.org/10.3114/fuse.2024.13.11},

year  = {2024},

date = {2024-06-29},

urldate = {2024-06-29},

journal = {Fungal Systematics and Evolution},

volume = {13},

number = {11},

pages = {183-440},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Same-sex sexual behaviour among mammals is widely observed, yet seldomly reported: Evidence from an online expert survey},

author = {Karyn A. Anderson and Julie A. Teichroeb and Malcolm S. Ramsay and Iulia Bădescu and Sergi López-Torres and James K. Gibb},

url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0304885},

doi = {10.1371/journal.pone.0304885},

year  = {2024},

date = {2024-06-20},

journal = {PLoS ONE},

volume = {19},

issue = {6},

pages = {e0304885},

abstract = {Same-sex sexual behaviour (SSSB) occurs in most animal clades, but published reports are largely concentrated in a few taxa. Thus, there remains a paucity of published reports for most mammalian species. We conducted a cross-sectional expert survey to better understand the underlying reasons for the lack of publications on this topic. Most respondents researched Primates (83.6%, N = 61), while the rest studied Carnivora (6.9%, N = 5), Rodentia (4.1%, N = 3), Artiodactyla (2.7%, N = 2), and Proboscidea (2.7%, N = 2). Most respondents (76.7%, N = 56) had observed SSSB in their study species, but only 48.2% (N = 27) collected data on SSSB, and few (18.5%, N = 5) had published papers on SSSB. Of the unique species identified as engaging in SSSB in the survey, 38.6% (N = 17) have no existing reports of SSSB to the knowledge of the authors. In both the survey questions and freeform responses, most respondents indicated that their lack of data collection or publication on SSSB was because the behaviours were rare, or because it was not a research priority of their lab. No respondents reported discomfort or sociopolitical concerns at their university or field site as a reason for why they did not collect data or publish on SSSB. Multiple logistic regressions were performed to assess whether taxa studied, education level, or identification within the LGBTQ+ community predicted observing, collecting data on, or publishing on SSSB, but none of these variables were significant predictors. These results provide preliminary evidence that SSSB occurs more frequently than what is available in the published record and suggest that this may be due to a publishing bias against anecdotal evidence.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shirley2024,

title = {Increasing control over biomineralization in conodont evolution},

author = {Bryan Shirley and Isabella Leonhard and Duncan J. E. Murdock and John Repetski and Przemysław Świś and Michel Bestmann and Pat Trimby and Markus Ohl and Oliver Plümper and Helen E. King and Emilia Jarochowska},

url = {https://www.nature.com/articles/s41467-024-49526-0},

doi = {10.1038/s41467-024-49526-0},

issn = {2041-1723},

year  = {2024},

date = {2024-06-20},

urldate = {2024-01-01},

journal = {Nature Communications 2024 15:1},

volume = {15},

issue = {1},

pages = {1-13},

publisher = {Nature Publishing Group},

abstract = {Vertebrates use the phosphate mineral apatite in their skeletons, which allowed them to develop tissues such as enamel, characterized by an outstanding combination of hardness and elasticity. It has been hypothesized that the evolution of the earliest vertebrate skeletal tissues, found in the teeth of the extinct group of conodonts, was driven by adaptation to dental function. We test this hypothesis quantitatively and demonstrate that the crystallographic order increased throughout the early evolution of conodont teeth in parallel with morphological adaptation to food processing. With the c-axes of apatite crystals oriented perpendicular to the functional feeding surfaces, the strongest resistance to uniaxial compressional stress is conferred along the long axes of denticles. Our results support increasing control over biomineralization in the first skeletonized vertebrates and allow us to test models of functional morphology and material properties across conodont dental diversity. Conodonts, early vertebrates, are thought to have evolved complex tooth tissue as an adaptation for feeding. Here, the authors use Electron Backscatter Diffraction to show increasing dental crystallographic order through conodont evolution, in parallel with dietary adaptations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Protecting stable biological nomenclatural systems enables universal communication: A collective international appeal},

author = {Pedro Jiménez-Mejías and Saúl Manzano and Vinita Gowda and Frank-Thorsten Krell and Mei-Ying Lin and Santiago Martín-Bravo and Laura Martín-Torrijos and Nieto Feliner, Gonzalo and Sergei L Mosyakin and Robert F C Naczi and Carmen Acedo and Inés Álvarez and Jorge V Crisci and Luceño Garcés, Modesto and John Manning and Moreno Saiz, Juan Carlos and A Muthama Muasya and Ricarda Riina and Sánchez Meseguer, Andrea and Daniel Sánchez-Mata and additional 1543 coauthors},

url = {https://academic.oup.com/bioscience/advance-article/doi/10.1093/biosci/biae043/7696204},

doi = {10.1093/biosci/biae043},

year  = {2024},

date = {2024-06-19},

urldate = {2024-06-19},

journal = {BioScience},

pages = {biae043},

abstract = {The fundamental value of universal nomenclatural systems in biology is that they enable unambiguous scientific communication. However, the stability of these systems is threatened by recent discussions asking for a fairer nomenclature, raising the possibility of bulk revision processes for “inappropriate”names. It is evident that such proposals come from very deep feelings, but we show how they can irreparably damage the foundation of biological communication and, in turn, the sciences that depend on it. There are four essential consequences of objective codes of nomenclature: universality, stability, neutrality, and transculturality. These codes provide fair and impartial guides to the principles governing biological nomenclature and allow unambiguous universal communication in biology. Accordingly, no subjective proposals should be allowed to undermine them.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Savage2024,

title = {Online toolkits for collaborative and inclusive global research in urban evolutionary ecology},

author = {Amy M. Savage and Meredith J. Willmott and Pablo Moreno‐García and Zuzanna Jagiello and Daijiang Li and Anna Malesis and Lindsay S. Miles and Cristian Román‐Palacios and David Salazar‐Valenzuela and Brian C. Verrelli and Kristin M. Winchell and Marina Alberti and Santiago Bonilla‐Bedoya and Elizabeth Carlen and Cleo Falvey and Lauren Johnson and Ella Martin and Hanna Kuzyo and John Marzluff and Jason Munshi‐South and Megan Phifer‐Rixey and Ignacy Stadnicki and Marta Szulkin and Yuyu Zhou and Kiyoko M. Gotanda},

doi = {10.1002/ece3.11633},

issn = {2045-7758},

year  = {2024},

date = {2024-06-03},

urldate = {2024-06-00},

journal = {Ecology and Evolution},

volume = {14},

number = {6},

publisher = {Wiley},

abstract = {<jats:title>Abstract</jats:title><jats:p>Urban evolutionary ecology is inherently interdisciplinary. Moreover, it is a field with global significance. However, bringing researchers and resources together across fields and countries is challenging. Therefore, an online collaborative research hub, where common methods and best practices are shared among scientists from diverse geographic, ethnic, and career backgrounds would make research focused on urban evolutionary ecology more inclusive. Here, we describe a freely available online research hub for toolkits that facilitate global research in urban evolutionary ecology. We provide rationales and descriptions of toolkits for: (1) decolonizing urban evolutionary ecology; (2) identifying and fostering international collaborative partnerships; (3) common methods and freely‐available datasets for trait mapping across cities; (4) common methods and freely‐available datasets for cross‐city evolutionary ecology experiments; and (5) best practices and freely available resources for public outreach and communication of research findings in urban evolutionary ecology. We outline how the toolkits can be accessed, archived, and modified over time in order to sustain long‐term global research that will advance our understanding of urban evolutionary ecology.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Abramczyk24,

title = { Mucor thermorhizoides—A New Species from Post-mining Site in Sudety Mountains (Poland).},

author = {Beniamin Abramczyk and Dorota Wiktorowicz and Alicja Okrasińska and Julia Pawłowska},

url = {https://link.springer.com/article/10.1007/s00284-024-03708-7},

doi = {https://doi.org/10.1007/s00284-024-03708-7},

year  = {2024},

date = {2024-06-01},

urldate = {2024-06-01},

journal = {Current Microbiology},

volume = {81},

issue = {201},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Klug2024,

title = {Anatomy and size of Megateuthis, the largest belemnite},

author = {Christian Klug and Günter Schweigert and René Hoffmann and Dirk Fuchs and Alexander Pohle and Robert Weis and De Baets, Kenneth},

doi = {10.1186/s13358-024-00320-x},

issn = {1664-2384},

year  = {2024},

date = {2024-05-30},

urldate = {2024-05-30},

journal = {Swiss Journal of Palaeontology},

volume = {143},

number = {1},

pages = {1-19},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:p>Belemnite rostra are very abundant in Mesozoic marine deposits in many regions. Despite this abundance, soft-tissue specimens of belemnites informing about anatomy and proportions of these coleoid cephalopods are extremely rare and limited to a few moderately large genera like <jats:italic>Passaloteuthis</jats:italic> and <jats:italic>Hibolithes</jats:italic>. For all other genera, we can make inferences on their body proportions and body as well as mantle length by extrapolating from complete material. We collected data of the proportions of the hard parts of some Jurassic belemnites in order to learn about shared characteristics in their gross anatomy. This knowledge is then applied to the Bajocian genus <jats:italic>Megateuthis</jats:italic>, which is the largest known belemnite genus worldwide. Our results provide simple ratios that can be used to estimate belemnite body size, where only the rostrum is known.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1098/rsbl.2024.0041,

title = {A diadectid skin impression and its implications for the evolutionary origin of epidermal scales},

author = {Sebastian Voigt and Gabriela Calábková and Izabela Ploch and Vojtěch Nosek and Wojciech Pawlak and Paweł Raczyński and Frederik Spindler and Ralf Werneburg},

url = {https://royalsocietypublishing.org/doi/abs/10.1098/rsbl.2024.0041},

doi = {10.1098/rsbl.2024.0041},

year  = {2024},

date = {2024-05-22},

urldate = {2024-01-01},

journal = {Biology Letters},

volume = {20},

number = {5},

pages = {20240041},

abstract = {Corneous skin appendages are not only common and diverse in crown-group amniotes but also present in some modern amphibians. This raises the still unresolved question of whether the ability to form corneous skin appendages is an apomorphy of a common ancestor of amphibians and amniotes or evolved independently in both groups. So far, there is no palaeontological contribution to the issue owing to the lack of keratin soft tissue preservation in Palaeozoic anamniotes. New data are provided by a recently discovered ichnofossil specimen from the early Permian of Poland that shows monospecific tetrapod footprints associated with a partial scaly body impression. The traces can be unambiguously attributed to diadectids and are interpreted as the globally first evidence of horned scales in tetrapods close to the origin of amniotes. Taking hitherto little-noticed scaly skin impressions of lepospondyl stem amniotes from the early Permian of Germany into account, the possibility has to be considered that the evolutionary origin of epidermal scales deeply roots among anamniotes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1098/rsos.240233,

title = {Extreme neck elongation evolved despite strong developmental constraints in bizarre Triassic reptiles—implications for neck modularity in archosaurs},

author = {Adam Rytel and Christine Böhmer and Stephan N. F. Spiekman and Mateusz Tałanda},

url = {https://royalsocietypublishing.org/doi/abs/10.1098/rsos.240233},

doi = {10.1098/rsos.240233},

year  = {2024},

date = {2024-05-15},

urldate = {2024-01-01},

journal = {Royal Society Open Science},

volume = {11},

number = {5},

pages = {240233},

abstract = {The Triassic radiation of vertebrates saw the emergence of the modern vertebrate groups, as well as numerous extinct animals exhibiting conspicuous, unique anatomical characteristics. Among these, members of Tanystropheidae (Reptilia: Archosauromorpha) displayed cervical vertebral elongation to an extent unparalleled in any other vertebrate. Tanystropheids were exceptionally ecologically diverse and had a wide spatial and temporal distribution. This may have been related to their neck anatomy, yet its evolution and functional properties remain poorly understood. We used geometric morphometrics to capture the intraspecific variation between the vertebrae comprising the cervical column among early archosauromorphs, to trace the evolutionary history of neck elongation in these animals. Our results show that the cervical series of these reptiles can be divided into modules corresponding to those of extant animals. Tanystropheids achieved neck elongation through somite elongation and a shift between cervical and thoracic regions, without presacral vertebrae count increase—contrary to crown archosaurs. This suggests a peculiar developmental constraint that strongly affected the evolution of tanystropheids. The data obtained just at the base of the archosauromorph phylogenetic tree are crucial for further studies on the modularity of vertebral columns of not only Triassic reptile groups but extant and other extinct animals as well.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1007/s10764-024-00433-7,

title = {Dental Topographic Analysis of Living and Fossil Lorisoids: Investigations into Markers of Exudate Feeding in Lorises and Galagos},

author = {Keegan R. Selig and Sergi López-Torres and Anne M. Burrows and Mary T. Silcox},

url = {https://link.springer.com/article/10.1007/s10764-024-00433-7},

doi = {https://doi.org/10.1007/s10764-024-00433-7},

year  = {2024},

date = {2024-05-08},

urldate = {2024-01-01},

journal = {International Journal of Primatology},

volume = {0},

number = {0},

pages = {0-0},

abstract = {Abstract Studies integrating patterns of molar morphology and diet are particularly useful to address questions of evolutionary history and diet in extinct taxa. However, such studies are lacking among lorisoids compared with other primates. Lorisoidea is distinctive when considering diet as some taxa consume large quantities of gums or exudates, whereas others consume none. Although there has been previous study of the relationship between craniodental form and exudate feeding, little is known about how patterns of exudate feeding covary with variation in molar topography. We analyzed a sample (n = 52) of lorisoids representing 17 extant taxa and one extinct taxon (Karanisia clarki). We used dental topographic metrics to quantify functional aspects (i.e., curvature, complexity, and relief) of occlusal morphology. We also used ancestral state reconstruction to estimate topographic parameters for the last common ancestors (LCA) of Lorisoidea, Lorisidae, and Galagidae. As with previous studies, we found that higher topographic values characterize insectivores, whereas frugivores tend to have lower values. We reconstructed the LCA of Lorisoidea, Lorisidae, and Galagidae as insectivorous, with Lorisidae slightly more insectivorous, and potentially more exudativorous than Galagidae. Moreover, we identified a significant interaction between the primary dietary component (i.e., fruit or insects) and the level of exudate feeding in our sample, with exudate-feeding insectivores being associated with lower topographic values than exclusive insectivores. Finally, we reconstruct K. clarki as an insectivore, contrary to previous findings, although whether the animal fed on exudates remains ambiguous. Overall, our results provide a framework for testing ecological hypotheses about lorisoids and may point to a unique pattern of molar topography among exudativores.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1002/jmor.21700,

title = {Aplacophoran traits in the late Ordovician septemchitonid polyplacophorans},

author = {Jerzy Dzik},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jmor.21700},

doi = {https://doi.org/10.1002/jmor.21700},

year  = {2024},

date = {2024-05-08},

urldate = {2024-05-22},

journal = {Journal of Morphology},

volume = {285},

number = {5},

pages = {e21700},

abstract = {Abstract A sample of phosphatized, originally calcareous, mollusk shells from the Katian age uppermost Mójcza Limestone at its type locality yielded a few hundred polyplacophoran plates. The chelodids are very rare among them. Three septemchitonid species dominate. They represent a gradation from underived steep roof-like plates to almost cylindrical ones, leaving only a narrow ventral slit for the foot. Apparently, this represents the first step toward the extremely derived ‘segmented clam’ Bauplan of the Silurian Carnicoleus, with plates completely closed at the venter except for the mouth and anal openings. To enable growth, the plates became thinner and more flexible (or perhaps resorbed) along the dorsum. The tendency toward reduction of the ventral gap of the plates in the early Paleozoic septemchitonid polyplacophorans implies their lack of ability to cling to the substrate with a muscular foot. In compensation, their plates changed toward a more efficient protective function, covering the animal body sides more and more completely. This may explain the origin of the ventral furrow of extant solenogasters hiding the rudimentary foot. An opposite route was chosen by the coeval Acaenoplax lineage, in which the plates did not contact each other, exposing much of the soft body on the dorsum. In both cases the animals appeared to be worm-like, perhaps representing different ways of evolution from the Paleozoic chitons to the extant aplacophorans.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Peona2024,

title = {Teaching transposon classification as a means to crowd source the curation of repeat annotation – a tardigrade perspective},

author = {Valentina Peona and Jacopo Martelossi and Dareen Almojil and Julia Bocharkina and Ioana Brännström and Max Brown and Alice Cang and Tomàs Carrasco-Valenzuela and Jon DeVries and Meredith Doellman and Daniel Elsner and Pamela Espíndola-Hernández and Guillermo Friis Montoya and Bence Gaspar and Danijela Zagorski and Paweł Hałakuc and Beti Ivanovska and Christopher Laumer and Robert Lehmann and Ljudevit Luka Boštjančić and Rahia Mashoodh and Sofia Mazzoleni and Alice Mouton and Maria Anna Nilsson and Yifan Pei and Giacomo Potente and Panagiotis Provataris and José Ramón Pardos-Blas and Ravindra Raut and Tomasa Sbaffi and Florian Schwarz and Jessica Stapley and Lewis Stevens and Nusrat Sultana and Radka Symonova and Mohadeseh S. Tahami and Alice Urzì and Heidi Yang and Abdullah Yusuf and Carlo Pecoraro and Alexander Suh},

doi = {10.1186/s13100-024-00319-8},

issn = {1759-8753},

year  = {2024},

date = {2024-05-06},

urldate = {2024-12-00},

journal = {Mobile DNA},

volume = {15},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:sec>

                <jats:title>Background</jats:title>

                <jats:p>The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences.</jats:p>

              </jats:sec><jats:sec>

                <jats:title>Results</jats:title>

                <jats:p>Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries.</jats:p>

              </jats:sec><jats:sec>

                <jats:title>Conclusions</jats:title>

                <jats:p>The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.</jats:p>

              </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Leonard2024,

title = {A global initiative for ecological and evolutionary hologenomics},

author = {Aoife Leonard and (...) Marta Szulkin and (...) and Antton Alberdi},

doi = {10.1016/j.tree.2024.03.005},

issn = {0169-5347},

year  = {2024},

date = {2024-05-00},

urldate = {2024-05-00},

journal = {Trends in Ecology & Evolution},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Urban2024,

title = {Interactions between climate change and urbanization will shape the future of biodiversity},

author = {Mark C. Urban and Marina Alberti and Luc De Meester and Yuyu Zhou and Brian C. Verrelli and Marta Szulkin and Chloé Schmidt and Amy M. Savage and Patrick Roberts and L. Ruth Rivkin and Eric P. Palkovacs and Jason Munshi-South and Anna N. Malesis and Nyeema C. Harris and Kiyoko M. Gotanda and Colin J. Garroway and Sarah E. Diamond and Simone Des Roches and Anne Charmantier and Kristien I. Brans},

doi = {10.1038/s41558-024-01996-2},

issn = {1758-6798},

year  = {2024},

date = {2024-05-00},

urldate = {2024-05-00},

journal = {Nat. Clim. Chang.},

volume = {14},

number = {5},

pages = {436--447},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1093/zoolinnean/zlae048,

title = {Osteology, phylogenetic affinities, and palaeobiogeographic significance of the bizarre ornithischian dinosaur Ajkaceratops kozmai from the Late Cretaceous European archipelago},

author = {Łukasz Czepiński and Daniel Madzia},

url = {https://doi.org/10.1093/zoolinnean/zlae048},

doi = {10.1093/zoolinnean/zlae048},

issn = {0024-4082},

year  = {2024},

date = {2024-04-29},

urldate = {2024-01-01},

journal = {Zoological Journal of the Linnean Society},

pages = {zlae048},

abstract = {At the climax of their evolutionary history in the latest Cretaceous, ceratopsian dinosaurs were among the most dominant components of North American and Asian land ecosystems. In other continental landmasses, however, ceratopsians were extraordinarily rare and the affinities of their proposed representatives often turned out to be inconclusive. Arguably the most significant evidence of Ceratopsia from outside North America and Asia is represented by Ajkaceratops kozmai from the Santonian (Upper Cretaceous) of Hungary. We provide a detailed osteological description of Ajkaceratops and highlight its bizarre anatomy. Ajkaceratops has been ‘traditionally’ interpreted to represent a Bagaceratops-like coronosaur, and its occurrence on the European islands was hypothesized to probably result from an early Late Cretaceous dispersal event from Asia. However, while the snout of Ajkaceratops may resemble that of some ceratopsians, closer inspection of the preserved elements indicates that these similarities are largely superficial. While it cannot be ruled out that Ajkaceratops represents a highly peculiar member of the clade, its placement is far from certain. Still, the discovery of Ajkaceratops exemplifies the importance and uniqueness of European dinosaur faunas.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Johnson2024,

title = {Effects of urban-induced mutations on ecology, evolution and health},

author = {Marc T. J. Johnson and Irtaqa Arif and Francesco Marchetti and Jason Munshi-South and Rob W. Ness and Marta Szulkin and Brian C. Verrelli and Carole L. Yauk and Daniel N. Anstett and Warren Booth and Aude E. Caizergues and Elizabeth J. Carlen and Anthony Dant and Josefa González and César González Lagos and Madeleine Oman and Megan Phifer-Rixey and Diana J. Rennison and Michael S. Rosenberg and Kristin M. Winchell},

doi = {10.1038/s41559-024-02401-z},

issn = {2397-334X},

year  = {2024},

date = {2024-04-19},

urldate = {2024-04-19},

journal = {Nat Ecol Evol},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{GUMINSKA2024126033,

title = {Circular extrachromosomal DNA in Euglena gracilis under normal and stress conditions},

author = {Natalia Gumińska and Paweł Hałakuc and Bożena Zakryś and Rafał Milanowski},

url = {https://www.sciencedirect.com/science/article/pii/S1434461024000257},

doi = {https://doi.org/10.1016/j.protis.2024.126033},

issn = {1434-4610},

year  = {2024},

date = {2024-04-03},

urldate = {2024-01-01},

journal = {Protist},

volume = {175},

number = {3},

pages = {126033},

abstract = {Extrachromosomal circular DNA (eccDNA) enhances genomic plasticity, augmenting its coding and regulatory potential. Advances in high-throughput sequencing have enabled the investigation of these structural variants. Although eccDNAs have been investigated in numerous taxa, they remained understudied in euglenids. Therefore, we examined eccDNAs predicted from Illumina sequencing data of Euglena gracilis Z SAG 1224–5/25, grown under optimal photoperiod and exposed to UV irradiation. We identified approximately 1000 unique eccDNA candidates, about 20% of which were shared across conditions. We also observed a significant enrichment of mitochondrially encoded eccDNA in the UV-irradiated sample. Furthermore, we found that the heterogeneity of eccDNA was reduced in UV-exposed samples compared to cells that were grown in optimal conditions. Hence, eccDNA appears to play a role in the response to oxidative stress in Euglena, as it does in other studied organisms. In addition to contributing to the understanding of Euglena genomes, our results contribute to the validation of bioinformatics pipelines on a large, non-model genome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Janas2024,

title = {Plumage coloration differs between offspring raised in natural cavities and nestboxes},

author = {Katarzyna Janas and Irene Di Lecce and Marta Szulkin and Joanna Sudyka},

doi = {10.1093/ornithology/ukae002},

issn = {2732-4613},

year  = {2024},

date = {2024-04-02},

urldate = {2024-04-02},

journal = {Ornithology},

volume = {141},

number = {2},

pages = {ukae002},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

               <jats:p>Most of our knowledge of secondary hole-nesting birds comes from populations breeding in human-provided nestboxes, yet these might differ from natural cavities in a number of parameters, including internal dimensions or microclimate, leading to differences in reproductive ecology. Here, we demonstrate differences in plumage coloration, an important visual signal of individual quality, in Blue Tit (Cyanistes caeruleus) and Great Tit (Parus major) nestlings raised in natural cavities and nestboxes. For this study, we collected feather samples over two breeding seasons and applied reflectance spectrophotometry to calculate color metrics. Carotenoid chroma was higher in nestbox-reared Blue Tits, whereas brightness was higher in nestbox-reared Great Tits (with a similar tendency for Blue Tits). The latter result might be explained by the better nutritional condition of Great Tit nestlings raised in nestboxes. Furthermore, we found no evidence for preference of adults expressing more elaborate plumage towards a specific cavity type in either species. Consequently, we assume that differences in nestling plumage reported here are driven by rearing conditions (nestboxes vs. natural cavities) and not by differences in plumage-based parental quality. Our study adds to the growing body of evidence confirming that anthropogenic environmental modifiers, such as nestboxes, might influence avian physiology and the resulting phenotype.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zakryś2024,

title = {Discovery of a new photosynthetic euglenoid in Poland: Euglena mazurica sp. nov. (Euglenales, Euglenaceae)},

author = {Bożena Zakryś and Katarzyna Jankowska and Anna Majerowicz and Alicja Fells and Maja Łukomska-Kowalczyk},

doi = {10.1016/j.protis.2024.126015},

issn = {1434-4610},

year  = {2024},

date = {2024-04-01},

urldate = {2024-04-00},

journal = {Protist},

volume = {175},

number = {2},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hollender2024,

title = {Single-cell genomics revealed Candidatus Grellia alia sp. nov. as an endosymbiont of Eutreptiella sp. (Euglenophyceae)},

author = {Metody Hollender and Marta Sałek and Michał Karlicki and Anna Karnkowska},

doi = {10.1016/j.protis.2024.126018},

issn = {1434-4610},

year  = {2024},

date = {2024-04-01},

urldate = {2024-04-00},

journal = {Protist},

volume = {175},

number = {2},

publisher = {Elsevier BV},

abstract = {Though endosymbioses between protists and prokaryotes are widespread, certain host lineages have received disproportionate attention what may indicate either a predisposition to such interactions or limited studies on certain protist groups due to lack of cultures. The euglenids represent one such group in spite of microscopic observations showing intracellular bacteria in some strains. Here, we perform a comprehensive molecular analysis of a previously identified endosymbiont in the Eutreptiella sp. CCMP3347 using a single cell approach and bulk culture sequencing. The genome reconstruction of this endosymbiont allowed the description of a new endosymbiont Candidatus Grellia alia sp. nov. from the family Midichloriaceae. Comparative genomics revealed a remarkably complete conjugative type IV secretion system present in three copies on the plasmid sequences of the studied endosymbiont, a feature missing in the closely related Grellia incantans. This study addresses the challenge of limited host cultures with endosymbionts by showing that the genomes of endosymbionts reconstructed from single host cells have the completeness and contiguity that matches or exceeds those coming from bulk cultures. This paves the way for further studies of endosymbionts in euglenids and other protist groups. The research also provides the opportunity to study the diversity of endosymbionts in natural populations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1111/1462-2920.16606,

title = {How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation},

author = {Fernando Useros and Iván García-Cunchillos and Nicolas Henry and Cédric Berney and Enrique Lara},

url = {https://enviromicro-journals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.16606},

doi = {https://doi.org/10.1111/1462-2920.16606},

year  = {2024},

date = {2024-03-20},

urldate = {2024-01-01},

journal = {Environmental Microbiology},

volume = {26},

number = {3},

pages = {e16606},

abstract = {Abstract Metabarcoding approaches targeting microeukaryotes have deeply changed our vision of protist environmental diversity. The public repository EukBank consists of 18S v4 metabarcodes from 12,672 samples worldwide. To estimate how far this database provides a reasonable overview of all eukaryotic diversity, we used Arcellinida (lobose testate amoebae) as a case study. We hypothesised that (1) this approach would allow the discovery of unexpected diversity, but also that (2) some groups would be underrepresented because of primer/sequencing biases. Most of the Arcellinida sequences appeared in freshwater and soil, but their abundance and diversity appeared underrepresented. Moreover, 84% of ASVs belonged to the suborder Phryganellina, a supposedly species-poor clade, whereas the best-documented suborder (Glutinoconcha, 600 described species) was only marginally represented. We explored some possible causes of these biases. Mismatches in the primer-binding site seem to play a minor role. Excessive length of the target region could explain some of these biases, but not all. There must be some other unknown factors involved. Altogether, while metabarcoding based on ribosomal genes remains a good first approach to document microbial eukaryotic clades, alternative approaches based on other genes or sequencing techniques must be considered for an unbiased picture of the diversity of some groups.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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},

urldate = {2024-03-11},

journal = {The Anatomical Record},

volume = {307},

issue = {6},

pages = {1995-2006},

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}

}

@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}

}

@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}

}

@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}

}

@article{Bartoszek2024,

title = {Analytical advances alleviate model misspecification in non-Brownian multivariate comparative methods},

author = {Krzysztof Bartoszek and Jesualdo Fuentes-González and Venelin Mitov and Jason Pienaar and Marcin Piwczyński and Radosław Puchałka and Krzysztof Spalik and Kjetil Lysne Voje},

doi = {https://doi.org/10.1093/evolut/qpad185},

year  = {2024},

date = {2024-03-01},

urldate = {2024-03-01},

journal = {Evolution},

volume = {78},

issue = {3},

pages = {389-400},

abstract = {Adams and Collyer argue that contemporary multivariate (Gaussian) phylogenetic comparative methods are prone to favouring more complex models of evolution and sometimes rotation invariance can be an issue. Here we dissect the concept of rotation invariance and point out that, depending on the understanding, this can be an issue with any method that relies on numerical instead of analytical estimation approaches. We relate this to the ongoing discussion concerning phylogenetic principal component analysis. Contrary to what Adams and Collyer found, we do not observe a bias against the simpler Brownian motion process in simulations when we use the new, improved, likelihood evaluation algorithm employed by mvSLOUCH, which allows for studying much larger phylogenies and more complex model setups.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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 = {2023-12-15},

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}

}

@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}

}

@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}

}

@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}

}

@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 = {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}

}

@article{Smug2023,

title = {Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts},

author = {Bogna J. Smug and Krzysztof Szczepaniak and Eduardo P. C. Rocha and Stanislaw Dunin-Horkawicz and Rafał J. Mostowy},

url = {https://doi.org/10.1038/s41467-023-43236-9},

doi = {10.1038/s41467-023-43236-9},

issn = {2041-1723},

year  = {2023},

date = {2023-11-28},

urldate = {2023-11-28},

journal = {Nature Communications},

volume = {14},

number = {1},

pages = {7460},

abstract = {Biological modularity enhances evolutionary adaptability. This principle is vividly exemplified by bacterial viruses (phages), which display extensive genomic modularity. Phage genomes are composed of independent functional modules that evolve separately and recombine in various configurations. While genomic modularity in phages has been extensively studied, less attention has been paid to protein modularity—proteins consisting of distinct building blocks that can evolve and recombine, enhancing functional and genetic diversity. Here, we use a set of 133,574 representative phage proteins and highly sensitive homology detection to capture instances of domain mosaicism, defined as fragment sharing between two otherwise unrelated proteins, and to understand its relationship with functional diversity in phage genomes. We discover that unrelated proteins from diverse functional classes frequently share homologous domains. This phenomenon is particularly pronounced within receptor-binding proteins, endolysins, and DNA polymerases. We also identify multiple instances of recent diversification via domain shuffling in receptor-binding proteins, neck passage structures, endolysins and some members of the core replication machinery, often transcending distant taxonomic and ecological boundaries. Our findings suggest that ongoing diversification via domain shuffling is reflective of a co-evolutionary arms race, driven by the need to overcome various bacterial resistance mechanisms against phages.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@article{Orłowska2023,

title = {Fucose as a nutrient ligand for Dikarya and a building block of early diverging lineages},

author = {Małgorzata Orłowska and Drishtee Barua and Sebastian Piłsyk and Anna Muszewska},

doi = {10.1186/s43008-023-00123-8},

issn = {2210-6359},

year  = {2023},

date = {2023-09-05},

urldate = {2023-12-00},

journal = {IMA Fungus},

volume = {14},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:sec>

                <jats:title>Abstract</jats:title>

                <jats:p>Fucose is a deoxyhexose sugar present and studied in mammals. The process of fucosylation has been the primary focus in studies relating to fucose in animals due to the presence of fucose in Lewis antigens. Very few studies have reported its presence in Fungi, mostly in <jats:italic>Mucoromycotina</jats:italic>. The constitution of 25% and 12% of this sugar in the carbohydrates of cell wall in the respective <jats:italic>Umbelopsis</jats:italic> and <jats:italic>Mucorales</jats:italic> strains boosts the need to bridge the gap of knowledge on fucose metabolism across the fungal tree of life. In the absence of a network map involving fucose proteins, we carried out an <jats:italic>in-silico</jats:italic> approach to construct the fucose metabolic map in <jats:italic>Fungi</jats:italic>. We analyzed the taxonomic distribution of 85 protein families in <jats:italic>Fungi</jats:italic> including diverse early diverging fungal lineages. The expression of fucose-related protein-coding genes proteins was validated with the help of transcriptomic data originating from representatives of early diverging fungi. We found proteins involved in several metabolic activities apart from fucosylation such as synthesis, transport and binding. Most of the identified protein families are shared with <jats:italic>Metazoa</jats:italic> suggesting an ancestral origin in <jats:italic>Opisthokonta</jats:italic>. However, the overall complexity of fucose metabolism is greater in Metazoa than in <jats:italic>Fungi</jats:italic>. Massive gene loss has shaped the evolutionary history of these metabolic pathways, leading to a repeated reduction of these pathways in most yeast-forming lineages. Our results point to a distinctive mode of utilization of fucose among fungi belonging to <jats:italic>Dikarya</jats:italic> and the early diverging lineages. We speculate that, while <jats:italic>Dikarya</jats:italic> used fucose as a source of nutrients for metabolism, the early diverging group of fungi depended on fucose as a building block and signaling compound.</jats:p>

              </jats:sec><jats:sec>

                <jats:title>Graphical abstract</jats:title>

                

              </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@article{Panagiotopoulou2023,

title = {Extensive search of genetic sex markers in Siberian (Acipenser baerii) and Atlantic (A. oxyrinchus) sturgeons},

author = {Hanna Panagiotopoulou and Kacper Marzecki and Jan Gawor and Heiner Kuhl and Michał Koper and Piotr Weglenski and Magdalena Fajkowska and Mirosław Szczepkowski and Mateusz Baca and Joern Gessner and Magdalena Płecha and Małgorzata Rzepkowska},

doi = {10.1016/j.aquaculture.2023.739517},

issn = {0044-8486},

year  = {2023},

date = {2023-08-00},

urldate = {2023-08-00},

journal = {Aquaculture},

volume = {573},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{10.1093/aob/mcad103,

title = {Pseudanthia in angiosperms: a review},

author = {Baczyński, Jakub and Claßen-Bockhoff, Regine},

url = {https://academic.oup.com/aob/article-pdf/132/2/179/52210840/mcad103.pdf},

doi = {10.1093/aob/mcad103},

year  = {2023},

date = {2023-07-25},

urldate = {2023-07-25},

journal = {Annals of Botany},

volume = {132},

number = {2},

pages = {179-202},

abstract = {Pseudanthia or ‘false flowers’ are multiflowered units that resemble solitary flowers in form and function. Over the last century the term ‘pseudanthium’ has been applied to a wide array of morphologically divergent blossoms, ranging from those with easily noticeable florets to derived, reduced units in which individual flowers become almost indistinguishable. Although initially admired mostly by botanists, the diversity and widespread distribution of pseudanthia across angiosperms has already made them a fascinating topic for evolutionary and developmental comparative studies.This review synthesizes historical and current concepts on the biology of pseudanthia. Our first aim is to establish a clear, operational definition of pseudanthium and disentangle common terminological misconceptions surrounding that term. Our second aim is to summarize knowledge of the morphological and developmental diversity of pseudanthia and embed it within a modern phylogenetic framework. Lastly, we want to provide a comprehensive overview on the evolution and ecological importance of pseudanthia and outline perspectives for future studies.The understanding of pseudanthia has changed multiple times and reflects three different interpretations of their ‘flower-like’ qualities: developmental (similarity in structure), figural (similarity in form and function) and phylogenetic (homology between angiosperm flowers and monoecious reproductive shoots in gymnosperms). Here, we propose to narrow the term pseudanthium to multiflowered blossoms resembling zoophilous flowers in form, i.e. in being structurally subdivided in a showy periphery and a reproductive centre. According to this definition, pseudanthia sensu stricto evolved independently in at least 41 angiosperm families. The recurrent acquisition of pseudanthia sensu stricto in all major lineages of flowering plants indicates repeated interactions between developmental constraints (smallness of flowers, meristematic conditions) and selective pressures, such as demands of pollinators and/or environmental conditions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Puchałka2023,

title = {Phylogenetic position of Dorema within Ferula (Apiaceae)},

author = {Radosław Puchałka and Krzysztof Spalik and Paulina Trzeciak and Łukasz Banasiak and Marcin Piwczyński},

doi = {https://doi.org/10.1007/s00606-023-01857-z},

year  = {2023},

date = {2023-07-21},

urldate = {2023-07-21},

journal = {Plant Systematics and Evolution},

volume = {309},

number = {28},

abstract = {Dorema (Apiaceae) includes 12 species distributed in the Irano-Turanian region. The genus differs from other genera of subfamily Apioideae in having paniculate inflorescences with simple umbels. Recently, molecular phylogenetic analyses placed six species of Dorema, including the generitype, in Ferula, thus subsuming the former into the synonymy of the latter. The remaining six congeners have not been yet included in molecular analyses. Here, we fill this gap by determining the phylogenetic position of these species. Because of a low resolution in some parts of the Ferula tree in earlier studies, alongside standard set of markers—nuclear nrDNA ITS and plastid rps16 and rpoC1 introns and the rpoB-trnC intergenic spacer—we additionally assessed the utility of nrDNA ETS sequences in resolving infrageneric relationships in the genus. We included 43 ingroup species representing major infrageneric divisions recognised in the most recent taxonomic revision. Although we were not successful in obtaining all markers for all newly studied species, they were placed with high support in one clade within section Peucedanoides together with formerly studied congeners in all maximum likelihood and Bayesian analyses of nuclear, plastid, and combined data sets. The addition of the ETS marker to the combined phylogenetic analyses confirmed the most recent classification of Ferula with increased branch support in some parts of the tree. However, many branches still remained unresolved. In particular, the monophyly of former Dorema within section Peucedanoides as suggested by morphology has not been definitely confirmed. A new combination and two nomina nova are proposed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{Korkus2023,

title = {\textit{Trans}-palmitoleic acid, a dairy fat biomarker, stimulates insulin secretion and activates G protein-coupled receptors with a different mechanism from the \textit{cis} isomer},

author = {Eliza Korkus and Marcin Szustak and Rafal Madaj and Arkadiusz Chworos and Anna Drzazga and Maria Koziołkiewicz and Grzegorz Dąbrowski and Sylwester Czaplicki and Iwona Konopka and Edyta Gendaszewska-Darmach},

doi = {10.1039/d2fo03412c},

issn = {2042-650X},

year  = {2023},

date = {2023-07-17},

urldate = {2023-07-17},

journal = {Food Funct.},

volume = {14},

number = {14},

pages = {6496--6512},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {<jats:p>

            <jats:italic>Trans</jats:italic>- and <jats:italic>cis</jats:italic> palmitoleic acids stimulate insulin secretion from pancreatic β cells with a similar potency. Both isomers activate GPR40, GPR55, GPR119, and GPR120 receptors with similar potency but with activation of different signaling pathways.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@article{Nawrocka2023,

title = {Abdominal aortic aneurysm influences the indices of arterial stiffness recorded by pulse wave analysis},

author = {Izabela Nawrocka and Izabella Krzykwa and Łukasz Artyszuk and Beniamin Abramczyk and Cezary Szmigielski and Maciej Siński and Piotr Abramczyk},

doi = {10.5603/ah.a2023.0014},

issn = {2449-6162},

year  = {2023},

date = {2023-06-30},

urldate = {2023-06-30},

journal = {Arterial Hypertension},

volume = {27},

number = {2},

pages = {99--106},

publisher = {VM Media Group sp. z o.o},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@article{Di Lecce2023,

title = {Extra‐pair paternity, breeding density, and synchrony in natural cavities versus nestboxes in two passerine birds},

author = {Irene Di Lecce and Charles Perrier and Marta Szulkin and Joanna Sudyka},

doi = {10.1002/ece3.10163},

issn = {2045-7758},

year  = {2023},

date = {2023-06-00},

urldate = {2023-06-00},

journal = {Ecology and Evolution},

volume = {13},

number = {6},

publisher = {Wiley},

abstract = {<jats:title>Abstract</jats:title><jats:p>Most of what is known about extra‐pair paternity in hole‐nesting birds derives from studies using artificial nesting sites, such as nestboxes. However, it has rarely been investigated whether inference drawn from breeding events taking place in nestboxes matches what would be observed under natural conditions, that is, in natural cavities. We here report on a variation in promiscuity in blue tits and great tits nesting in natural cavities and nestboxes in an urban forest in Warsaw, Poland. Specifically, we tested whether local breeding density, local breeding synchrony, and extra‐pair paternity (inferred from SNP data generated with a high‐throughput genotyping by sequencing method) differed between birds nesting in natural cavities and nestboxes. In both blue tits and great tits, the frequency of extra‐pair paternity was similar between the two cavity types. In blue tits, we observed shorter nearest neighbor distance, higher neighbor density, and higher synchronous neighbor density (i.e., density of fertile females) in nestboxes relative to natural cavities. No such pattern was found in great tits. Moreover, we detected a positive relationship between the proportion of extra‐pair offspring in the nest and neighbor density around the nest in blue tits. Our results revealed that the provisioning of nestboxes did not change rates of extra‐pair paternity, suggesting that conclusions drawn from nestbox studies might adequately represent the natural variation in extra‐pair matings in some species or sites. However, the observed differences in spatiotemporal components of breeding dynamics highlight the fact that these parameters should be carefully considered when comparing mating behavior across studies and/or sites.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@article{hsieh2023intermittent,

title = {Intermittent and temporally variable bioturbation by some terrestrial invertebrates: implications for ichnology},

author = {Shannon Hsieh and Weronika Łaska and Alfred Uchman},

doi = {10.1007/s00114-023-01833-0},

year  = {2023},

date = {2023-03-07},

urldate = {2023-03-07},

journal = {The Science of Nature},

volume = {110},

number = {2},

pages = {11},

publisher = {Springer},

abstract = {Bedding planes and vertical sections of many sedimentary rock formations reveal bioturbation structures, including burrows, produced by diverse animal taxa at different rates and durations. These variables are not directly measurable in the fossil record, but neoichnological observations and experiments provide informative analogues. Comparable to marine invertebrates from many phyla, a captive beetle larva burrowing over 2 weeks showed high rates of sediment disturbance within the first 100 h but slower rates afterwards. Tunnelling by earthworms and adult dung beetles is also inconstant—displacement of lithic material alternates with organic matter displacement, often driven by food availability with more locomotion when hungry. High rates of bioturbation, as with locomotion generally, result from internal and external drives, slowing down or stopping when needs are filled. Like other processes affecting sediment deposition and erosion, rates can drastically differ based on measured timescale, with short bursts of activity followed by hiatuses, concentrated in various seasons and ontogenetic stages for particular species. Assumptions of constant velocities within movement paths, left as traces afterward, may not apply in many cases. Arguments about energetic efficiency or optimal foraging based on ichnofossils have often overlooked these and related issues. Single bioturbation rates from short-term experiments in captivity may not be comparable to rates measured at an ecosystem level over a year or generalized across multiple time scales where conditions differ even for the same species. Neoichnological work, with an understanding of lifetime variabilities in bioturbation and their drivers, helps connect ichnology with behavioural biology and movement ecology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bartoszek2023b,

title = {Model selection performance in phylogenetic comparative methods under multivariate Ornstein–Uhlenbeck models of trait evolution},

author = {Krzysztof Bartoszek and Jesualdo Fuentes-González and Venelin Mitov and Jason Pienaar and Marcin Piwczyński and Radosław Puchałka and Krzysztof Spalik and Kjetil Lysne Voje},

doi = {https://doi.org/10.1093/sysbio/syac079},

year  = {2023},

date = {2023-03-01},

urldate = {2023-03-01},

journal = {Systematic Biology},

volume = {72},

issue = {2},

pages = {275-293},

abstract = {The advent of fast computational algorithms for phylogenetic comparative methods allows for considering multiple hypotheses concerning the co-adaptation of traits and also for studying if it is possible to distinguish between such models based on contemporary species measurements. Here we demonstrate how one can perform a study with multiple competing hypotheses using mvSLOUCH by analyzing two data sets, one concerning feeding styles and oral morphology in ungulates, and the other concerning fruit evolution in Ferula (Apiaceae). We also perform simulations to determine if it is possible to distinguish between various adaptive hypotheses. We find that Akaike’s information criterion corrected for small sample size has the ability to distinguish between most pairs of considered models. However, in some cases there seems to be bias towards Brownian motion or simpler Ornstein–Uhlenbeck models. We also find that measurement error and forcing the sign of the diagonal of the drift matrix for an Ornstein–Uhlenbeck process influences identifiability capabilities. It is a cliché that some models, despite being imperfect, are more useful than others. Nonetheless, having a much larger repertoire of models will surely lead to a better understanding of the natural world, as it will allow for dissecting in what ways they are wrong.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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 = {2023-02-16},

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}

}

@article{Frankiewicz2023,

title = {Wood and bark structure in Buddleja: anatomical background of stem morphology},

author = {K E Frankiewicz and J H Chau and J Baczyński and A Wdowiak and A Oskolski},

doi = {https://doi.org/10.1093/aobpla/plad003},

year  = {2023},

date = {2023-02-01},

urldate = {2023-02-01},

journal = {AoB Plants},

volume = {15},

issue = {2},

pages = {plad003},

abstract = {Bark (all tissues outside of the vascular cambium) has been extensively studied in recent years, especially its anatomy and physiology. Macromorphological bark characters can be important taxonomically for many plant groups, including the genus Buddleja (Scrophulariaceae). However, the relationship between macroscopic bark appearance and its microscopic structure remains obscure, hampering the use and interpretation of bark traits in plant taxonomy and phylogenetics as well as in other fields of botany. We studied micro- and macrostructure of bark in the species of Buddleja representing wide taxonomic and geographic diversity to identify general relationships between bark anatomy and morphology. We also examined Buddleja xylem and discussed the importance of anatomical traits for understanding the relationships between clades in this genus. The smooth bark surface in sect. Gomphostigma and the outgroup (Freylinia spp.) relates to the small number of periderms of superficial origin and limited sclerification. This allows for the retention of visible lenticels. In the rest of Buddleja, bark sloughs off and division of labour is present: collapsed phloem undergoes sclerification and acts as a protective layer, while thin-walled phellem forms the separation layers. A similar pattern is found in some groups (e.g. Lonicera), but in others (e.g. Vitis and the species of Eucalyptus with stringy bark), the pattern is inversed. Wood and bark anatomy supports a sister relationship between the southern African section Gomphostigma and the rest of Buddleja but is taxonomically uninformative among remaining clades. Limited development of periderms and sclerification allows for the retention of a smooth bark surface and conspicuous lenticels. Sloughing off of bark requires division of labour into a lignified protective layer and a thin-walled separation layer. These two functions are never served by a single tissue but are rather divided between phloem and periderm. How more subtle features (e.g. size and shape of fissures) are determined requires further study. Simultaneously, bark anatomy could be a useful source of data to complement molecular phylogenetic studies in a total evidence approach for systematics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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},

urldate = {2023-01-15},

journal = {Science of The Total Environment},

volume = {856},

number = {2},

pages = {159072},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@article{Abramczyk_2022,

title = {Effects of trigeminal nerve stimulation on parameters derived from pulse wave analysis in young healthy subjects},

author = {A. Janczak and B. Abramczyk and P Abramczyk

},

doi = {10.26402/jpp.2022.3.13},

year  = {2022},

date = {2022-10-03},

journal = {Journal of Physiology and Pharmacology},

volume = {73},

issue = {3},

pages = {451-457},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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},

urldate = {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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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},

urldate = {2021-02-25},

journal = {Acta Mycologica},

volume = {55},

number = {2},

pages = {55211},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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},

urldate = {2021-01-01},

journal = {Insects},

volume = {12},

number = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}