Publications

@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 = {2024-05-08},

journal = {International Journal of Primatology},

volume = {45},

pages = {951-971},

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 = {2024-04-01},

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{JAGIELLO2024168959,

title = {The plastic homes of hermit crabs in the Anthropocene},

author = {Zuzanna Jagiello and Łukasz Dylewski and Marta Szulkin},

url = {https://www.sciencedirect.com/science/article/pii/S0048969723075885},

doi = {https://doi.org/10.1016/j.scitotenv.2023.168959},

issn = {0048-9697},

year  = {2024},

date = {2024-02-25},

urldate = {2024-01-01},

journal = {Science of The Total Environment},

volume = {913},

pages = {168959},

abstract = {Plastic is the most pervasive element of marine waste, with harmful impact on wildlife. By using iEcology (i.e., internet Ecology, use of online data sources as a new tool in ecological research), we report on the emergence of a novel behaviour in hermit crabs related to the use of plastic or other anthropogenic materials as protective shells. We analysed images posted on social media to identify 386 individuals with artificial shells — mainly plastic caps (85 %). We report that 10 of the world's 16 terrestrial hermit crabs use artificial shells, a behaviour observed on all of the Earth's tropical coasts. Four non-exclusive mechanisms may drive individual choice for artificial shells: sexual signaling, lightness of artificial shells, odour cues, and camouflage in a polluted environment. Further research is needed to determine the impact of this behaviour on hermit crab evolutionary trajectories.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{laska2024new,

title = {New insights into endolithic palaeocommunity development in mobile hard substrate using CT imaging of bioeroded clasts from the Pliocene (Almería, SE Spain)},

author = {Weronika Łaska and Francisco J Rodríguez-Tovar and Alfred Uchman},

year  = {2024},

date = {2024-02-08},

urldate = {2024-01-01},

journal = {The Science of Nature},

volume = {111},

number = {1},

pages = {1–25},

publisher = {Springer},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{skawina2024tracking,

title = {Tracking the micro-and nanoplastics in the terrestrial-freshwater food webs. Bivalves as sentinel species},

author = {Aleksandra Skawina and Agnieszka Dąbrowska and Agata Bonk and Bohdan Paterczyk and Julita Nowakowska},

doi = {10.1016/j.scitotenv.2024.170468},

year  = {2024},

date = {2024-02-05},

urldate = {2024-02-05},

journal = {Science of The Total Environment},

volume = {917},

pages = {170468},

publisher = {Elsevier},

abstract = {Micro- (MPs) and nanoplastics (NPs) are currently ubiquitous in the ecosystems, and freshwater biota is still insufficiently studied to understand the global fate, transport paths, and consequences of their presence. Thus, in this study, we investigated the role of bivalves and a trophic transfer of MPs and NPs in an experimental food chain. The food chain consisted of terrestrial non-selective detritivore Dendrobaena (Eisenia) sp., freshwater benthic filter feeder Unio tumidus, and freshwater benthic detritivore-collectors Asellus aquaticus or Gammarus sp. Animals were exposed to different fluorescently labeled micro- and nanoplastics (PMMA 20 μm, nanoPS 15–18 nm, and 100 nm, PS 1 μm and 20 μm, PE from cosmetics) as well as to the faeces of animals exposed to plastics to assess their influence on the environmental transportation, availability to biota, and bioaccumulation of supplied particles. Damaged and intact fluorescent particles were observed in the faeces of terrestrial detritivores and in the droppings of aquatic filter feeders, respectively. They were also present in the guts of bivalves and of crustaceans which were fed with bivalve droppings. Bivalves (Unio tumidus, and additionally Unio pictorum, and Sphaerium corneum) produced droppings containing micro- and nanoparticles filtered from suspension and deposited them onto the tank bottom, making them available for broader feeding guilds of animals (e.g. collectors, like crustaceans). Finally, the natural ageing of PS and its morphological changes, leakage of the fluorescent labelling, and agglomeration of particles were demonstrated. That supports our hypothesis of the crucial role of the characterization of physical and chemical materials in adequately understanding the mechanisms of their interaction with biota. Microscopical methods (confocal, fluorescent, scanning electron) and Raman and FT-IR spectroscopy were used to track the particles' passage in a food web and monitor structural changes of the MPs' and NPs' surface.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1002/pro.4846,

title = {AlphaFold2 captures the conformational landscape of the HAMP signaling domain},

author = {Aleksander Winski and Jan Ludwiczak and Malgorzata Orlowska and Rafal Madaj and Kamil Kaminski and Stanislaw Dunin-Horkawicz},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4846},

doi = {https://doi.org/10.1002/pro.4846},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Protein Science},

volume = {33},

number = {1},

pages = {e4846},

abstract = {Abstract In this study, we present a conformational landscape of 5000 AlphaFold2 models of the Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases (HAMP) domain, a short helical bundle that transduces signals from sensors to effectors in two-component signaling proteins such as sensory histidine kinases and chemoreceptors. The landscape reveals the conformational variability of the HAMP domain, including rotations, shifts, displacements, and tilts of helices, many combinations of which have not been observed in experimental structures. HAMP domains belonging to a single family tend to occupy a defined region of the landscape, even when their sequence similarity is low, suggesting that individual HAMP families have evolved to operate in a specific conformational range. The functional importance of this structural conservation is illustrated by poly-HAMP arrays, in which HAMP domains from families with opposite conformational preferences alternate, consistent with the rotational model of signal transduction. The only poly-HAMP arrays that violate this rule are predicted to be of recent evolutionary origin and structurally unstable. Finally, we identify a family of HAMP domains that are likely to be dynamic due to the presence of a conserved pi-helical bulge. All code associated with this work, including a tool for rapid sequence-based prediction of the rotational state in HAMP domains, is deposited at https://github.com/labstructbioinf/HAMPpred.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{molecules29020338,

title = {Novichok Nerve Agents as Inhibitors of Acetylcholinesterase - In Silico Study of Their Non-Covalent Binding Affinity},

author = {Rafal Madaj and Bartłomiej Gostyński and Arkadiusz Chworos and Marek Cypryk},

url = {https://www.mdpi.com/1420-3049/29/2/338},

doi = {10.3390/molecules29020338},

issn = {1420-3049},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Molecules},

volume = {29},

number = {2},

abstract = {In silico studies were performed to assess the binding affinity of selected organophosphorus compounds toward the acetylcholinesterase enzyme (AChE). Quantum mechanical calculations, molecular docking, and molecular dynamics (MD) with molecular mechanics Generalized-Born surface area (MM/GBSA) were applied to assess quantitatively differences between the binding energies of acetylcholine (ACh; the natural agonist of AChE) and neurotoxic, synthetic correlatives (so-called “Novichoks”, and selected compounds from the G- and V-series). Several additional quantitative descriptors like root-mean-square fluctuation (RMSF) and the solvent accessible surface area (SASA) were briefly discussed to give—to the best of our knowledge—the first quantitative in silico description of AChE—Novichok non-covalent binding process and thus facilitate the search for an efficient and effective treatment for Novichok intoxication and in a broader sense—intoxication with other warfare nerve agents as well.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1021/acsmedchemlett.3c00263b,

title = {Lysophosphatidylcholines Enriched with cis and trans Palmitoleic Acid Regulate Insulin Secretion via GPR119 Receptor},

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

url = {https://doi.org/10.1021/acsmedchemlett.3c00263},

doi = {10.1021/acsmedchemlett.3c00263},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {ACS Medicinal Chemistry Letters},

volume = {15},

number = {2},

pages = {197-204},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{scott2023new,

title = {New paromomyids (Mammalia, Primates) from the Paleocene of southwestern Alberta, Canada, and an analysis of paromomyid interrelationships},

author = {Craig S Scott and Sergi López-Torres and Mary T Silcox and Richard C Fox},

url = {https://www.cambridge.org/core/journals/journal-of-paleontology/article/new-paromomyids-mammalia-primates-from-the-paleocene-of-southwestern-alberta-canada-and-an-analysis-of-paromomyid-interrelationships/85328AE223A9AE66A2948F6FB06712CD},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Journal of Paleontology},

pages = {1--22},

publisher = {Cambridge University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1093/bioinformatics/btad579b,

title = {pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models},

author = {Kamil Kaminski and Jan Ludwiczak and Kamil Pawlicki and Vikram Alva and Stanislaw Dunin-Horkawicz},

url = {https://doi.org/10.1093/bioinformatics/btad579},

doi = {10.1093/bioinformatics/btad579},

issn = {1367-4811},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Bioinformatics},

volume = {39},

number = {10},

pages = {btad579},

abstract = {The detection of homology through sequence comparison is a typical first step in the study of protein function and evolution. In this work, we explore the applicability of protein language models to this task.We introduce pLM-BLAST, a tool inspired by BLAST, that detects distant homology by comparing single-sequence representations (embeddings) derived from a protein language model, ProtT5. Our benchmarks reveal that pLM-BLAST maintains a level of accuracy on par with HHsearch for both highly similar sequences (with >50% identity) and markedly divergent sequences (with <30% identity), while being significantly faster. Additionally, pLM-BLAST stands out among other embedding-based tools due to its ability to compute local alignments. We show that these local alignments, produced by pLM-BLAST, often connect highly divergent proteins, thereby highlighting its potential to uncover previously undiscovered homologous relationships and improve protein annotation.pLM-BLAST is accessible via the MPI Bioinformatics Toolkit as a web server for searching precomputed databases (https://toolkit.tuebingen.mpg.de/tools/plmblast). It is also available as a standalone tool for building custom databases and performing batch searches (https://github.com/labstructbioinf/pLM-BLAST).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}