Monika Hospodářská, Petr Koutecký, Simona Koutková, Roger Vila, Gerard Talavera, Michal Rindoš, Irena Provazníková, Martina Dalíková, Petr Nguyen
{"title":"Polyommatine Blue Butterflies Reveal Unexpected Integrity of the W Sex Chromosome Amid Extensive Chromosomal Fragmentation Linked to Telomere Restoration.","authors":"Monika Hospodářská, Petr Koutecký, Simona Koutková, Roger Vila, Gerard Talavera, Michal Rindoš, Irena Provazníková, Martina Dalíková, Petr Nguyen","doi":"10.1093/gbe/evaf157","DOIUrl":"10.1093/gbe/evaf157","url":null,"abstract":"<p><p>Chromosomal rearrangements act as barriers to gene flow and can thus promote speciation. In moths and butterflies (Lepidoptera), which possess holocentric chromosomes facilitating karyotype changes, chromosome fusions are more common than fissions. Yet, limited evidence suggests that when speciation involves chromosomal rearrangements, it is most often linked to fissions. Notable karyotypic variation is observed in three clades of the subfamily Polyommatinae (Lycaenidae), with chromosome numbers ranging from n = 10 to 225. We investigated genome sizes and karyotypes in several species of the genera Polyommatus and Lysandra with modal and derived high chromosome numbers. Our findings showed no support for polyploidy, confirming previous conclusions about karyotypic diversification via chromosome fragmentation in this butterfly family. Species with high chromosome numbers have slightly larger genomes, which indicate a potential role of repetitive sequences but contradict the hypothesis of holocentric drive. Ends of fragmented chromosomes were healed with telomeres synthesized de novo, which were significantly larger than those of species with modal karyotype. No interstitial telomeric sequences were detected on autosomes. Internal telomeric signals on sex chromosomes, however, revealed multiple sex chromosome systems in Polyommatus (Plebicula) dorylas and Polyommatus icarus, with two karyotype races differing in sex chromosome constitution in the latter. Notably, the W chromosome resisted fragmentation, presumably due to its epigenetic silencing.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144834931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
James France, Wiesław Babik, Milena Cvijanović, Katarzyna Dudek, Ana Ivanović, Tijana Vučić, Ben Wielstra
{"title":"Identification of Y-chromosome Turnover in Newts Fails to Support a Sex Chromosome Origin for the Triturus Balanced Lethal System.","authors":"James France, Wiesław Babik, Milena Cvijanović, Katarzyna Dudek, Ana Ivanović, Tijana Vučić, Ben Wielstra","doi":"10.1093/gbe/evaf155","DOIUrl":"10.1093/gbe/evaf155","url":null,"abstract":"<p><p>Non-recombining regions often have profound effects on genome evolution, resulting in structures such as sex chromosomes and supergenes. Amongst the strangest examples are balanced lethal systems, such as that found in newts of the genus Triturus. These systems halve reproductive output, and the evolution of such a deleterious trait is difficult to explain. For Triturus, an intriguing model proposes that the balanced lethal system evolved from an ancestral Y-chromosome. To test this hypothesis, we identify the Y-chromosome of Triturus and verify whether it, or the balanced lethal system, is homologous to the Y-chromosome of its sister genus Lissotriton, which does not possess the balanced lethal system. We identify a set of candidate Y-linked markers in Triturus ivanbureschi and validate the male specificity of the markers in all major clades of Triturus. We place the Y-linked markers on a high-density linkage map of T. ivanbureschi that we construct with 7,233 RADseq markers. We then place both the Triturus and Lissotriton Y-linked regions within previously constructed target capture linkage maps that include genes linked to the balanced lethal system. We observe that neither the Triturus balanced lethal system, nor the Triturus Y-chromosome are homologous to the Lissotriton Y-chromosome. This is the first molecular evidence of a transition between Y-chromosome systems within salamanders. However, unless additional sex chromosome turnover events are involved, our data does not support a sex chromosome origin of the balanced lethal system.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12410432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144845586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Evolutionary Consequences of Unusually Large Pericentric TE-rich Regions in the Genome of a Neotropical Fig Wasp.","authors":"Zexuan Zhao, Kevin Quinteros, Carlos A Machado","doi":"10.1093/gbe/evaf158","DOIUrl":"10.1093/gbe/evaf158","url":null,"abstract":"<p><p>Transposable elements (TEs), despite generally being considered deleterious, represent a substantial portion of most eukaryotic genomes. Specific genomic regions, such as telomeres and pericentromeres, are often densely populated with TEs. In these regions, which tend to be gene-poor, reduced recombination shelters the genome from the deleterious effects of TEs. Here, we describe unusually large and continuous pericentromeric transposable element-rich regions in all chromosomes of the genome assembly of Pegoscapus hoffmeyeri sp. A (511.79 Mbp), a Neotropical fig wasp that is the obligate pollinator of Ficus obtusifolia. The identified pericentromeric transposable element-rich regions span nearly half (46%) of the genome, and harbor over 40% of all annotated genes, including 30% of conserved Benchmarking Universal Single-Copy Orthologs genes. We present evidence that low recombination in these transposable element-rich regions generates strong bimodal molecular evolution patterns genome-wide. Patterns of nucleotide diversity and protein-coding gene evolution in transposable element-rich regions are consistent with a reduced efficiency of selection and suggestive of strong Hill-Robertson effects. A significant reduction in third codon position GC content (GC3) in transposable element-rich regions emerged as the most distinctive gene feature differentiating genes in transposable element-rich regions from those in the rest of the genome, a pattern that likely results from the absence of GC-biased gene conversion. This remarkable bimodal compartmental genome organization in the genome of P. hoffmeyeri provides a unique example of how genome organization with compartmental transposable element distribution can lead to context-dependent gene evolution shaped by common evolutionary forces.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144951394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Correction to: Genetic Diversity in Chimpanzee Transcriptomics Does Not Represent Wild Populations.","authors":"","doi":"10.1093/gbe/evaf168","DOIUrl":"10.1093/gbe/evaf168","url":null,"abstract":"","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 9","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12409271/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144992349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nicolas Dussex, Vanessa C Bieker, Xin Sun, Mathilde Le Moullec, Erik Ersmark, Knut H Røed, John R Speakman, Leif Egil Loe, Love Dalén, Brage B Hansen, Michael D Martin
{"title":"The Genomic Basis of the Svalbard Reindeer's Adaptation to an Extreme Arctic Environment.","authors":"Nicolas Dussex, Vanessa C Bieker, Xin Sun, Mathilde Le Moullec, Erik Ersmark, Knut H Røed, John R Speakman, Leif Egil Loe, Love Dalén, Brage B Hansen, Michael D Martin","doi":"10.1093/gbe/evaf160","DOIUrl":"10.1093/gbe/evaf160","url":null,"abstract":"<p><p>Studying adaptation to extreme climates is essential for understanding evolutionary processes and how species evolve and persist under changing environmental conditions, such as climate warming. Here, we investigate the genomic basis of adaptations in the Svalbard reindeer (Rangifer tarandus platyrhynchus), an endemic subspecies that colonized the High Arctic approximately 7,000 years ago and developed a suite of adaptations for survival under conditions of extreme cold, changes in day length, and resource scarcity. Applying scans of selection, functional analysis of coding region variation, and characterization of copy number variation across reindeer populations from Svalbard, mainland Norway, mainland Russia, and Novaya Zemlya, our comparative genomics approach identified 150 genomic regions that are differentiated in Svalbard reindeer relative to mainland reindeer (R. tarandus). These genomic regions include genes linked to fat metabolism, energy conservation, cold tolerance, body size, fur morphology, and seasonal circadian rhythm. Our study highlights the advantages of using distinct approaches to uncover the genomic basis of adaptations and provides a path for future research into the evolution of species in similar environments.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12409278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144845587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Arlie R Macdonald, Maddie E James, Jonathan D Mitchell, Barbara R Holland
{"title":"From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.","authors":"Arlie R Macdonald, Maddie E James, Jonathan D Mitchell, Barbara R Holland","doi":"10.1093/gbe/evaf150","DOIUrl":"10.1093/gbe/evaf150","url":null,"abstract":"<p><p>Mapping genotypes to phenotypes is a fundamental goal in biology. Phylogenetic Genotype to Phenotype mapping methods are a relatively new set of tools that aim to identify genomic regions associated with trait variation between species. Here, we review recent developments in Phylogenetic Genotype to Phenotype mapping methods, focusing on three key areas: methods based on replicated substitutions at individual amino acid sites; methods detecting changes in evolutionary rates; and methods analyzing gene duplication and loss. We discuss how trait definition and measurement can impact these methods, as well as the genetic mechanisms that can give rise to trait variation between lineages. We examine the strengths and limitations of different approaches, highlighting the importance of explicit modeling of evolutionary processes. Finally, we outline promising future directions, including the integration of within-species variation, as well as epigenetic and environmental information. Since no single method is likely to identify all genomic regions of interest, we encourage users to apply a representative range of methods that are capable of detecting different types of associations. Overall, this review provides practitioners a roadmap for understanding and applying Phylogenetic Genotype to Phenotype mapping approaches.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 9","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12410988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145000409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Leveraging Weighted Quartet Distributions for Enhanced Species Tree Inference from Genome-Wide Data.","authors":"Navid Bin Hasan, Avijit Biswas, Zahin Wahab, Mahim Mahbub, Rezwana Reaz, Md Shamsuzzoha Bayzid","doi":"10.1093/gbe/evaf159","DOIUrl":"10.1093/gbe/evaf159","url":null,"abstract":"<p><p>Species tree estimation from genes sampled from throughout the whole genome is challenging because of gene tree discordance, often caused by incomplete lineage sorting (ILS). Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and theoretical guarantees of robustness to arbitrarily high amounts of ILS. ASTRAL, the most widely used quartet-based method, aims to infer species trees by maximizing the number of quartets in the gene trees consistent with the species tree. An alternative approach is inferring quartets for all subsets of four species and amalgamating them into a coherent species tree. While summary methods can be sensitive to gene tree estimation error, quartet amalgamation offers an advantage by potentially bypassing gene tree estimation. However, greatly understudied is the choice of weighted quartet inference method and downstream effects on species tree estimations under realistic model conditions. In this study, we investigated a wide array of methods for generating weighted quartets and critically assessed their impact on species tree inference. Our study provides evidence that the careful generation and amalgamation of weighted quartets, as implemented in methods like wQFM, can lead to significantly more accurate trees than popular methods like ASTRAL, especially in the face of gene tree estimation errors.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 9","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12401674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144951514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cyril J Versoza, Jeffrey D Jensen, Susanne P Pfeifer
{"title":"The landscape of structural variation in aye-ayes (Daubentonia madagascariensis).","authors":"Cyril J Versoza, Jeffrey D Jensen, Susanne P Pfeifer","doi":"10.1093/gbe/evaf167","DOIUrl":"10.1093/gbe/evaf167","url":null,"abstract":"<p><p>Aye-ayes (Daubentonia madagascariensis) are one of the 25 most critically endangered primate species in the world. Endemic to Madagascar, their small and highly fragmented populations make them particularly vulnerable to both genetic disease and anthropogenic environmental changes. Over the past decade, conservation genomic efforts have largely focused on inferring and monitoring population structure based on single nucleotide variants to identify and protect critical areas of genetic diversity. However, the recent release of a highly contiguous genome assembly allows, for the first time, for the study of structural genomic variation (deletions, duplications, insertions, and inversions) which are likely to impact a substantial proportion of the species' genome. Based on whole-genome data from 14 individuals, >1,000 autosomal structural variants were detected, affecting ∼240 kb of the aye-aye genome. The majority of these variants (>85%) were deletions shorter than 200 bp, consistent with the notion that longer structural mutations are often associated with strongly deleterious fitness effects. For example, two deletions longer than 850 bp located within disease-linked genes were predicted to impose substantial fitness deficits owing to a resulting frameshift and gene fusion, respectively; whereas several other major effect variants outside of coding regions are likely to impact gene regulatory landscapes. Taken together, this first glimpse into the landscape of structural variation in aye-ayes will enable future opportunities to advance our understanding of the traits impacting the fitness of this endangered species, as well as allow for enhanced evolutionary comparisons across the full primate clade.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144951556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Variation in genome architecture and epigenetic modification across the microsporidia phylogeny.","authors":"Pascal Angst, Dieter Ebert, Peter D Fields","doi":"10.1093/gbe/evaf166","DOIUrl":"https://doi.org/10.1093/gbe/evaf166","url":null,"abstract":"<p><p>Microsporidia are a model clade for studying intracellular parasitism, being well-known for their streamlined genomes and their extreme life history. Although microsporidia are highly diverse and ecologically important to a broad range of hosts, previous research on genome architecture has focused primarily on the mammal-infecting genus Encephalitozoon. Here, we expand that work, testing the universality of the patterns observed in Encephalitozoon by investigating and comparing variation in genetic and epigenetic architectures in the high-quality genome assemblies of several major microsporidia clades. Our comparison of nine genomes, including the first genome assemblies of Binucleata daphniae, Gurleya vavrai, and Conglomerata obtusa, and revised, improved assemblies of Glugoides intestinalis, Mitosporidium daphniae, and Ordospora colligata, found limited conservation of genetic and epigenetic architecture across all microsporidia, although many genomic characteristics, such as nucleotide composition and repeat content, were shared between genomes of the same or related clades. For example, rRNA genes were hypermethylated in most species, but their position close to chromosome ends was only found in the Encephalitozoon and its sister clade. GC-content varied widely, linked to genome size, phylogenetic position and activity of repeat elements. These findings enhance our insight into genome evolution and, consistent with findings from other systems, suggest epigenetic modification as a regulatory mechanism of gene expression and repeat element activity in microsporidia. Our comparative genome analysis reveals high variation in genetic and epigenetic architecture among microsporidia, despite all of them adapting to a parasitic lifestyle within host cells.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144951558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Petar Pajic, Luane Landau, Omer Gokcumen, Stefan Ruhl
{"title":"Saliva protein genes in humans were shaped during primate evolution.","authors":"Petar Pajic, Luane Landau, Omer Gokcumen, Stefan Ruhl","doi":"10.1093/gbe/evaf165","DOIUrl":"https://doi.org/10.1093/gbe/evaf165","url":null,"abstract":"<p><p>Genes within the secretory calcium-binding phosphoprotein (SCPP) locus diversified along with the formation of a calcified skeleton in vertebrates, the emergence of tooth enamel in fish, and the introduction of lactation in mammals, at each stage marking major transitions in life history. The SCPP locus also harbors genes expressed primarily and abundantly in the saliva of humans. Here, we explored the phylogeny and evolution of the saliva-related SCPP genes by harnessing available genomic and transcriptomic resources. We observe extensive diversification of SCPP genes within mammals, driven by gene duplications and losses, with the most pronounced changes occurring in the SCPP genes that are expressed in salivary glands. When comparing rodent and human SCPP genes, we concluded that regulatory shifts and gene turnover events likely facilitated the accelerated gain of salivary gland expression. In primate genomes, we found more recent duplication events that affected genes coding for proteins secreted in saliva. Several saliva-related SCPP genes in the primate lineage show signatures of positive selection, while the other genes in the SCPP locus remain conserved. Our results position saliva-related SCPP genes as highly malleable to evolutionary innovation. Variations shaped by dietary and pathogenic pressures likely influenced the functional properties of salivary proteins, impacting metabolic and immune-related traits in oral health among primates, including humans.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144951439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}