Genome Biology and Evolution最新文献

{"title":"Selective Regimes and Evolutionary Dynamics of Z and W Gametologs Across an Expanded Avian Neo-Sex Chromosome.","authors":"Simon J Ellerstrand, Bengt Hansson","doi":"10.1093/gbe/evag204","DOIUrl":"10.1093/gbe/evag204","url":null,"abstract":"<p><p>Sex chromosome evolution is characterized by Y/W degeneration and its consequences for selection on X/Z-linked recessive mutations in the heterogametic sex, yet how functional constraints modulate the evolutionary dynamics of Z-W gametologs remains poorly resolved. We addressed this question in larks (Alaudidae), a lineage carrying enlarged neo-sex chromosomes with multiple evolutionary strata formed through repeated translocations and successive recombination-suppression events. Using whole-genome sequences of males and females of two Alauda species, we analysed 1,759 Z-W gametologs. We found that W-gene degeneration was governed primarily by evolutionary time and intrinsic gene features: long genes were lost earliest, although this tendency was mitigated by gene essentiality, as indicated by high haploinsufficiency scores. Z-linked genes lacking a functional W counterpart exhibited higher nonsynonymous divergence than Z genes retaining a functional W, consistent with selection-driven faster-Z evolution. The strongest signature of purifying selection, comparable to that of pseudoautosomal genes, was observed in haploinsufficient Z-linked genes, which were also more likely to retain W gametologs. Although W genes generally diverged faster, their selection signatures covaried with those of Z and with haploinsufficiency, suggesting partially shared Z-W evolutionary dynamics. Notably, a small subset of W genes showed intensified or positive selection, including several genes associated with putative female-specific functions. Together, our results demonstrate that gene essentiality slows functional divergence on both Z and W, modulates faster-Z dynamics and enables key W genes to remain functional-and potentially advantageous for females-for millions of generations after recombination cessation.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13524101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148706343","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":"Beyond Invariable Sites: Using Evolutionary Stasis to Map Multilayered Constraints on the Evolution of Viral and Mammalian Genomes.","authors":"Sergei L Kosakovsky Pond, Hannah Verdonk, Steven Weaver, Gallean Brown, Danielle Callan, Anton Nekrutenko, Darren P Martin","doi":"10.1093/gbe/evag184","DOIUrl":"10.1093/gbe/evag184","url":null,"abstract":"<p><p>The quantification of genomic conservation has progressed from foundational statistical modeling of evolutionary rates to state-of-the-art deep learning architectures. However, a major resolution gap remains at the zero-rate origin, where standard selection inference tools fail to distinguish between sites that are invariant due to chance (stochastic invariance) or low substitution opportunity and those that are invariant due to extreme purifying selection. We present B-STILL (Bayesian Significance Test of Invariant Low Likelihoods), a hierarchical Bayesian framework designed to resolve the selective landscape of protein-coding genes near the zero-rate limit. By leveraging gene-level rate distributions (prior calibration) and modeling codon-site-specific substitution opportunities (determined by genetic-code degeneracy and nucleotide substitution biases), B-STILL quantifies the statistical significance of observed stasis. We define a rate-based stasis threshold to identify evolutionary stasis anchors (ESAs)-sites where the upper bound on the evolutionary rate is statistically constrained relative to the background rate of the gene due to extreme purifying selection. Validation against clinical and pathogen datasets confirms that ESAs are strong predictors of biological fitness and pathogenicity. Applying B-STILL across viral and mammalian genomes, we identify thousands of significantly clustered ESAs that map to known functional domains and uncharacterized structural motifs. These results establish B-STILL as a scalable, statistically rigorous framework for high-resolution genomic annotation, converting previously uninformative invariant sites into precise markers of extreme evolutionary constraint.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13427764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148602148","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":"NOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species Complex.","authors":"S Lorena Ament-Velásquez, Sven J Saupe","doi":"10.1093/gbe/evag185","DOIUrl":"10.1093/gbe/evag185","url":null,"abstract":"<p><p>Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria. Some fungal NLRs are known to control regulated cell death in the context of allorecognition, the capacity to recognize conspecific nonself. However, the function of most fungal NLR genes remains unknown. Here, we characterize the evolution of the NLRs repertoire in the Podospora anserina species complex. We show that the vast majority of the NLRs display effector domains known to be involved in regulated cell death execution. Moreover, NLRs undergo more rapid gene turnover than random genes, show higher dN/dS values, and faster evolutionary rates. A subgroup of NLRs, distinguished by superstructure-forming repeats with very high sequence identity (high internal conservation), evolved independently multiple times. We found that high internal conservation NLRs are more associated with transposable elements, exhibit higher nucleotide diversity partially driven by repeat-induced point mutation, and show elevated Tajima's D values indicative of balancing selection. Furthermore, high internal conservation NLR phylogenies do not recapitulate species relationships, which we determined is caused by both balancing selection and introgression. In addition, we identified cases of repeat exchange between distinct high internal conservation NLR genes, implying that novel binding specificities may evolve through repeat shuffling, thereby increasing allelic diversity. Finally, we determined that NLR genes with high internal conservation repeats exist outside of the fungal realm, arguing for similar dynamics in other taxa. Overall, these findings suggest that fungal NLRs evolve under diversity-enhancing mechanisms and display selective signatures consistent with a general immune function.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148561359","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":"CAPHEINE, or Everything and the Kitchen Sink: A Workflow for Automating Selection Analyses Using HyPhy.","authors":"Hannah Verdonk, Danielle Callan, Sergei Pond","doi":"10.1093/gbe/evag173","DOIUrl":"10.1093/gbe/evag173","url":null,"abstract":"<p><p>Here, we present CAPHEINE, a computational workflow that starts with a set of unaligned pathogen sequences and a reference genome and performs a comprehensive exploratory evolutionary analysis of the input data. CAPHEINE pairs nicely with studies of site-level selection dynamics, gene-level positive selection, and lineage-specific shifts in selective pressure. Our workflow is portable across Mac OS, Windows, and Linux, allowing researchers to focus on results. CAPHEINE is freely available at https://github.com/veg/CAPHEINE, along with a set of usage instructions.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13427765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148470168","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":"Lineage-Specific Retention of the Plastid tilS-trnI(CAU) Module and Its Variable Relationship With Codon Usage Evolution in Green Algae.","authors":"Nam Ju Lee, Jeongha So, Jehyun Jeon, Young Wook Ko, Hyunsik Chae, Sanghee Kim, Sung Mi Cho","doi":"10.1093/gbe/evag199","DOIUrl":"10.1093/gbe/evag199","url":null,"abstract":"<p><p>Plastid genomes retain a reduced but essential translation system inherited from cyanobacterial ancestors, but the evolutionary constraints shaping their diversification remain poorly resolved. One key component ensuring translational fidelity is the tRNAIle-lysidine system, mediated by tRNAIle-lysidine synthetase (TilS), which enables accurate decoding of the AUA isoleucine codon. Here, we characterized the complete plastid genome of the Antarctic green alga Micractinium simplicissimum and investigated the evolutionary distribution of the tilS-trnI(CAU) module across green algal plastomes. Phylogenomic analyses of 35 plastomes revealed consistent retention of this module in Chlorellales, whereas partial loss or structural fragmentation occurred in core Trebouxiophyceae lineages. Comparative analyses of codon usage showed that AUA frequencies varied widely among major green algal lineages but were not tightly associated with tilS retention, suggesting partial evolutionary decoupling between tRNA modification systems and synonymous codon usage. Structural comparisons further revealed lineage-specific insertions and domain rearrangements in plastid TilS proteins relative to their cyanobacterial homologs. Candidate nuclear-encoded TilS homologs were additionally identified in several plastid tilS-lacking taxa, suggesting possible intracellular relocation of decoding functions. Together, these findings suggest that plastid decoding systems evolve through modular, lineage-specific trajectories that allow structural plasticity while maintaining translational fidelity. This study provides new insights into the evolutionary dynamics of gene expression systems in endosymbiotic organelles.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13494906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148706355","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":"Viral Lifecycle Dynamics and Spatial Structure Explain Why Accessory Genes Are Associated With Temperate Phages.","authors":"Sultan Ahmed Nazir, Bram van Dijk","doi":"10.1093/gbe/evag181","DOIUrl":"10.1093/gbe/evag181","url":null,"abstract":"<p><p>Genes encoding for virulence factors are frequently found on prophages, yet the evolutionary forces driving this association remain unclear. The evolutionary association of mobile genetic elements with host-beneficial genes is known to be hindered by the stability of chromosomal loci and competition with mobile genetic elements lacking accessory genes. Using a mathematical model that incorporates these constraints, we identify two key mechanisms that help overcome them, resulting in the evolutionary linkage of accessory genes, like virulence genes, to prophages. First, we show that migration across bacterial populations favors the association of genes with prophages when the gene is beneficial in certain environments (e.g. virulence genes in the gut) that also trigger higher rates of prophage induction. Second, we show that within-population spatial dynamics also promotes the association of weakly selected genes and phages. Here, virion dispersal allows phage-encoded genes to spread into patches of bacteria lacking the gene, giving them a selective advantage over immobile chromosomal genes. We argue that these mechanisms are less applicable for plasmids and other mobile genetic elements, highlighting a potentially unique role for phages in shaping bacterial adaptation. By demonstrating how phage lifecycle dynamics and spatial heterogeneity drive mobile genetic element-gene associations, our work provides new insights into the evolution of phage-encoded virulence.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13427762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148445777","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":"A T2T Genome of the Lobed-Lip Iguazu Joana (Crenicichla tuca) Reveals Intrachromosomal Rearrangements and Trans-species Polymorphism in Cichlid Fishes.","authors":"Mylena Daiana Santander, Henrique Rosa Varella, Diego Baldo, Frederico Henning","doi":"10.1093/gbe/evag179","DOIUrl":"10.1093/gbe/evag179","url":null,"abstract":"<p><p>Genomic architecture is a key factor shaping the landscape of linkage disequilibrium between divergently selected traits. By facilitating the detection of intrachromosomal variants, long-read data fueled recent interest in the role of structural variants in adaptive radiation. The Neotropical cichlid genus Crenicichla provides a compelling system for replicated adaptive radiation in riverine environments in which at least two lineages show repeated ecomorphological evolution. The lack of South American cichlid reference genomes has thus far limited investigation of chromosomal evolution across cichlid radiations and precluded testing the role of structural variants in Crenicichla adaptive radiation. Here, we generated a complete assembly of Crenicichla tuca (iguassuensis group) collected from the type locality. To investigate structural variants within Crenicichla, we produced ultra-long reads for Crenicichla missioneira. We then conduct comparative genomics across cichlids using published chromosome-level genomes. Despite karyotypic stability in Crenicichla, intrachromosomal structural variants are abundant and enriched in repetitive genomic regions. Comparisons with other cichlid radiations indicate the predominance of intrachromosomal rearrangements. Chromosomes LG03, LG23, LG10, and LG11 show signatures of chromosomal instability, which seem to be associated with highly repetitive DNA composition and enrichment of immune-related genes. Structural variants polymorphic in both Crenicichla species are consistent with the maintenance of trans-species polymorphism through balancing selection on immune-related genes. Our results add to the growing evidence that structural variation is widespread, even when overall chromosomal morphology remains unchanged. Our approach combining field-based extractions with PacBio HiFi and ONT UL proved sufficient to generate a T2T assembly and holds great potential for evolutionary and conservation genomics in biodiversity hotspots.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"18 8","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13458148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148764604","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":"Sex-Specific Landscapes of Crossover and Noncrossover Recombination in Coppery Titi Monkeys (Plecturocebus cupreus).","authors":"Cyril J Versoza, Karen L Bales, Jeffrey D Jensen, Susanne P Pfeifer","doi":"10.1093/gbe/evag186","DOIUrl":"10.1093/gbe/evag186","url":null,"abstract":"<p><p>Along with germline mutations, meiotic recombination plays a fundamental role in shaping genetic diversity and thus directly influences a species' potential adaptive response to environmental change, amongst other features. Despite the recombination landscape being of central importance for a variety of questions in molecular evolution, the genome-wide distribution and frequency of recombination remains to be elucidated in many nonhuman primate species. Utilizing novel high-coverage genomic data from three multi-sibling families, we here provide the first estimates of the rates and patterns of crossover and noncrossover recombination in coppery titi monkeys (Plecturocebus cupreus)-a socially monogamous, pair-bonded primate that serves as an important model in behavioral research. Consistent with haplorrhines, crossover and noncrossover recombination in this platyrrhine are frequently localized at PRDM9-mediated hotspots, characterized by a 15-mer binding motif with substantial similarities to the degenerate 13-mer motif found in humans. The sex-averaged crossover rate in coppery titi monkeys is comparable with those of other primates; however, no significant difference in recombination rates was observed between the sexes, despite a pronounced maternal age effect in the species. Similarities also exist with regards to the sex-specific genomic distribution of noncrossover events, though the minimal conversion tract lengths of extended events was observed to be considerably longer in maternally inherited noncrossovers. Taken together, these similarities and differences in the recombination landscape relative to other primates highlight the importance of incorporating species-specific rates and patterns in evolutionary models, and the resources provided here will thus serve to aid future studies in this important primate model system.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13447096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148548734","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":"Molecular Evolution of a Sex-Linked Inversion Polymorphism in Zebra Finches.","authors":"Peter D Price, Jake Pepper, Thea F Rogers, Alison E Wright, Jon Slate","doi":"10.1093/gbe/evag056","DOIUrl":"10.1093/gbe/evag056","url":null,"abstract":"<p><p>Recent years have seen an explosion in examples of supergenes, where recombination is suppressed between haplotypes, often via inversion polymorphisms, to control complex traits. However, an enduring problem in evolutionary biology is understanding the molecular consequences of recombination suppression, especially when it has been present for long periods. Here, we explore the molecular evolution of the A and B haplotypes of a large, sex-linked inversion polymorphism in a passerine bird, the zebra finch (Taeniopygia guttata) responsible for most of the genetic variation in sperm morphology. We find evidence for reduced efficacy of purifying selection acting on the coding sequence of the Z-linked haplotypes and an increase in mutational load. However, we fail to find a positive association between expression and sequence divergence, consistent with an absence of any compensatory expression evolution for the accumulation of deleterious alleles.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13372037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147354716","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":"Evidence that Zymocin-Like Killer Plasmids Were Present in the Common Ancestor of Terrestrial Fungi.","authors":"Padraic G Heneghan, Letal I Salzberg, Kenneth H Wolfe","doi":"10.1093/gbe/evag157","DOIUrl":"10.1093/gbe/evag157","url":null,"abstract":"<p><p>Some budding yeasts secrete killer toxins made by linear dsDNA plasmids located in the cytosol. The best-known example is the Kluyveromyces lactis toxin zymocin, which is encoded by a 9-kb killer plasmid assisted by a 13-kb helper plasmid. These plasmids are distantly related to eukaryotic dsDNA viruses and have been called virus-like elements (VLEs) but they do not produce virus particles. Their evolutionary origin is unclear because VLEs have been found only in budding yeasts (subphylum Saccharomycotina of phylum Ascomycota) and not in any other fungi. Here, we show that similar VLEs are present in two other phyla of terrestrial fungi, Zoopagomycota and Mucoromycota. In Zoopagomycota, some isolates of Coemansia harbor more than 20 different linear dsDNA plasmids simultaneously, many of which encode their own DNA polymerases (DNAPs). The chitinase genes present on some of the newly discovered VLEs are orthologs of the chitinase subunits of killer toxins encoded by Saccharomycotina VLEs, suggesting that some of the new VLEs may be killer plasmids. Phylogenetic analysis of DNAPs shows that the diversity of VLEs in Zoopagomycota greatly exceeds that in Saccharomycotina, and that Saccharomycotina killer and helper plasmids are related to two lineages of VLEs present in Zoopagomycota. Our results suggest that VLEs were present in the common ancestor of all terrestrial fungi about 650 Mya, and that they were already subdivided into killer and helper types by this time.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13348850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148316988","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}