Molecular biology and evolution最新文献

{"title":"Accessible, realistic genome simulation with selection using stdpopsim.","authors":"Graham Gower, Nathaniel S Pope, Murillo F Rodrigues, Silas Tittes, Linh N Tran, Ornob Alam, Maria Izabel A Cavassim, Peter D Fields, Benjamin C Haller, Xin Huang, Ben Jeffrey, Kevin Korfmann, Christopher C Kyriazis, Jiseon Min, Inés Rebollo, Clara T Rehmann, Scott T Small, Chris C R Smith, Georgia Tsambos, Yan Wong, Yu Zhang, Christian D Huber, Gregor Gorjanc, Aaron P Ragsdale, Ilan Gronau, Ryan N Gutenkunst, Jerome Kelleher, Kirk E Lohmueller, Daniel R Schrider, Peter L Ralph, Andrew D Kern","doi":"10.1093/molbev/msaf236","DOIUrl":"10.1093/molbev/msaf236","url":null,"abstract":"<p><p>Selection is a fundamental evolutionary force that shapes patterns of genetic variation across species. However, simulations incorporating realistic selection along heterogeneous genomes in complex demographic histories are challenging, limiting our ability to benchmark statistical methods aimed at detecting selection and to explore theoretical predictions. stdpopsim is a community-maintained simulation library that already provides an extensive catalog of species-specific population genetic models. Here we present a major extension to the stdpopsim framework that enables simulation of various modes of selection, including background selection, selective sweeps, and arbitrary distributions of fitness effects (DFE) acting on annotated subsets of the genome (for instance, exons). This extension maintains stdpopsim's core principles of reproducibility and accessibility while adding support for species-specific genomic annotations and published DFE estimates. We demonstrate the utility of this framework by comparing methods for demographic inference, DFE estimation, and selective sweep detection across several species and scenarios. Our results demonstrate the robustness of demographic inference methods to selection on linked sites, reveal the sensitivity of DFE-inference methods to model assumptions, and show how genomic features, like recombination rate and functional sequence density, influence power to detect selective sweeps. This extension to stdpopsim provides a powerful new resource for the population genetics community to explore the interplay between selection and other evolutionary forces in a reproducible, user-friendly framework.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145137919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of sex-biased gene expression during transitions to separate sexes in the Silene genus.","authors":"Djivan Prentout, Aline Muyle, Niklaus Zemp, Adil El Filali, Bastien Boussau, Pascal Touze, Jos Käfer, Gabriel A B Marais","doi":"10.1093/molbev/msaf229","DOIUrl":"https://doi.org/10.1093/molbev/msaf229","url":null,"abstract":"<p><p>Sexual dimorphism is widespread among species with separate sexes, and its extent is thought to be governed by the differential expression of thousands of genes between males and females (known as Sex-Biased Genes, hereafter SBGs). SBGs have been studied in numerous species, but rarely through comparative approaches, which limits our understanding of their evolution, especially during multiple, independent transitions to separate sexes. We sequenced the transcriptomes of nine dioecious species (with separate males and females), two gynodioecious species (with separate females and hermaphrodites) and two hermaphrodite species from the Silene genus. Our dataset encompasses three independent transitions to dioecy, ranging from less than 1 million years ago (Mya) to about 11 Mya. We found that the number of both female and male-biased genes positively correlates with the age of separate sexes, with species with older sex separation exhibiting the most numerous sex-biased genes. More specifically, male-biased expression tends to emerge early, as soon as females coexist with hermaphrodites (gynodioecy). Numbers of female-biased genes are rare at first, and their numbers only increase after a transition to separate males and females (dioecy). Additionally, we found that both positive selection and genetic drift contribute to the evolution of SBGs. Overall, this study provides new insights into the mechanisms underlying sex-biased gene evolution during transitions to separate sexes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145137902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive annotation of olfactory and gustatory receptor genes and transposable elements revealed their evolutionary dynamics in aphids.","authors":"Sergio Gabriel Olvera-Vazquez, Xilong Chen, Aurélie Mesnil, Camille Meslin, Fabricio Almeida-Silva, Johann Confais, Yann Bourgeois, Gianluca Lombardi, Célia Lougmani, Karine Alix, Nicolas Francillonne, Nathalie Choisne, Stephane Cauet, Jean-Christophe Simon, Christelle Buchard, Nathalie Rodde, David Ogereau, Claire Mottet, Alexandre Degrave, Elorri Segura, Alessandra Carbone, Barrès Benoît, Emmanuelle Jacquin-Joly, William Marande, Dominique Lavenier, Fabrice Legeai, Amandine Cornille","doi":"10.1093/molbev/msaf238","DOIUrl":"https://doi.org/10.1093/molbev/msaf238","url":null,"abstract":"<p><p>Gene duplication and transposable elements (TEs) are major drivers of genomic innovation that can fuel adaptation. While the roles of duplication and TE-driven diversification are documented in plant pathogens, they remain insufficiently explored in insect pests such as aphids, where olfactory (OR) and gustatory receptor (GR) genes are key to host recognition. We analyzed 521 OR and 399 GR genes, alongside TEs, across 12 aphid genomes with varying host ranges. Aphid lineages with broader host ranges exhibited higher evolutionary rates, driven by gene family expansions linked to host interaction, including lipid metabolism, immune function, and transposase activity. OR and GR genes evolved through proximal and tandem duplications and were shaped by diversifying selection, with bursts of positive selection followed by prolonged purifying selection, consistent with adaptation to novel hosts. Younger TEs were significantly enriched near OR genes compared to GRs and other genomic regions, suggesting a catalytic role of TEs in their diversification. However, OR proteins encoded by TE-associated ORs exhibited reduced functional potential. In contrast, GR proteins encoded by TE-associated GRs retained signatures of adaptation, as inferred from deep learning models predicting functionally important protein regions. These findings suggest that TE activity may facilitate functional innovation in GRs while alleviating constraints or pseudogenization in ORs. This study reveals how duplication, selection, and TE dynamics shape gene evolution in insect pests. It also provides the first chromosome-scale genome assembly of Dysaphis plantaginea, with comprehensive annotations and functional predictions of OR/GR genes, bridging adaptive evolution with mechanistic insights.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145130772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary refinement of mitochondrial and plastid targeting sequences coincides with the late diversification of land plants.","authors":"Parth K Raval, Carolina García García, Maria-Darline Somoano Sanchez, Sven B Gould","doi":"10.1093/molbev/msaf240","DOIUrl":"https://doi.org/10.1093/molbev/msaf240","url":null,"abstract":"<p><p>Plastids and mitochondria are key to plant survival and adaptation. The evolutionary progress of land plants (embryophytes) witnessed gene and genome duplications, and the expansion of organelle-localised proteins. To deal with the increase of nuclear-encoded proteins, targeting to and import by the mitochondrion and plastid are known to have adapted in multiple ways. It included the addition of entire new import channels and lineage-specific import receptors. Through comparative genomics and experimental biology, we uncover further changes of the organelle import machineries. Their evolution likely served to enhance the rate of protein import and improved its physiological regulation, e.g. via interactions between the import channel and respiratory complex. On the cargo side, nuclear-encoded N-terminal targeting sequences of mitochondrial (mTPs) and plastidal (pTPs) proteins diverged in their charge via a preference for phosphorylatable amino acids (adding negative charges after phosphorylation) and an avoidance of positive charges in the pTPs, which is most evident in eudicots. Using Chlamydomonas and Marchantia, we experimentally underscore that the evolved TP divergence prevents mis-sorting between mitochondria and plastids. In line with the increase of phosphorylatable amino acids in the pTPs, we pinpoint the embryophytic origin of a membrane-anchored phosphatase, PAP2, that is associated with targeting sequence processing. On the whole, we propose a revised model for plant organelle protein import evolution from algae to angiosperms, which facilitated flourishing of this lineage on the land.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145130818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of SL-RNA Genes and Their Splicing Targets in Parasitic Flatworms.","authors":"Javier Calvelo, Héctor Musto, Uriel Koziol, Andrés Iriarte","doi":"10.1093/molbev/msaf228","DOIUrl":"https://doi.org/10.1093/molbev/msaf228","url":null,"abstract":"<p><p>Spliced Leader (SL) trans-splicing is a key step in the processing of many mRNAs in different eukaryotic lineages, including in parasitic flatworms. Despite its importance, efforts for its characterization in this phylum have remained a collection of single-species studies with little exploration at a wider phylogenetic context. In this work, we present a comprehensive analysis of this process, based on the available genomic and transcriptomic data of 24 cestode and trematode species, including the identification of the SL-RNA sequences and their splicing acceptor transcripts and sites. We identified a main pattern of concerted evolution of SL-RNA loci in most flatworm species, as well as divergence of SL-RNA loci in selected species. However, even in species with several divergent SL-RNAs, there was no specialization in their targets. This, along with low SL trans-splicing levels, is in stark contrast with the global patterns of SL trans-splicing usage in nematodes. SL trans-splicing could be detected for a limited number of mRNAs in all species (< 31%), and we found extensive use of the same splice acceptor sites for cis-splicing, especially for monocistronic transcripts. Ancestral SL trans-splicing sites are found in many conserved genes, including in putative ancestral operons that are shared between cestodes and trematodes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145125124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From Rabl-like architecture to chromosome territories: a conserved developmental transition in animal genomes.","authors":"Jing Liu","doi":"10.1093/molbev/msaf235","DOIUrl":"https://doi.org/10.1093/molbev/msaf235","url":null,"abstract":"<p><p>In eukaryotes, chromosomes can be arranged with centromeres and/or telomeres clustered at opposite poles of the nucleus (Rabl-like, RBL) or as discrete spatial domains (Chromosome territory, CT). These patterns were thought to be species-specific, possibly linked to the presence or absence of condensin II subunits. Time-series embryonic chromatin maps from three distantly related animals reveal that RBL and CT reflect cell state rather than species identity, and a conserved RBL-to-CT transition has occurred during development. This shift is not significantly correlated with condensin II gene expression, but may be influenced by the genomic distribution of repetitive sequences. In late developmental stages, long-range cis- and trans-interactions between active A1 sub-compartments progressively intensify, ultimately establishing CT as the dominant architecture. These results uncover a conserved, developmentally regulated reorganization of 3D genome structure across animals.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wide diversity and complex evolution of M42 aminopeptidases with contrasted functional properties in Archaea.","authors":"Emilie Chagny, Najwa Taib, Daphna Fenel, Eric Girard, Simonetta Gribaldo, Didier Flament, Bruno Franzetti","doi":"10.1093/molbev/msaf233","DOIUrl":"https://doi.org/10.1093/molbev/msaf233","url":null,"abstract":"<p><p>M42 peptidases (TET) are ubiquitous, giant self-compartmentalized aminopeptidases forming unique tetrahedral structures. TETs may participate in protein homeostasis and amino acid recycling by processing peptides downstream of the proteasome and other related proteolytic complexes. Currently, only five TETs have been extensively studied in Archaea from the Thermococcales order, with a predominant focus on structural characterization. Therefore, a clear view of the diversity and biological activities of this large enzymatic family is lacking. In this study, we establish robust criteria for high-throughput identification of TET peptidases from sequence data and reveal their wide taxonomic distribution in Archaea. We functionally characterize six additional TETs, including four from Asgardarcheota. Our results identify two main functional classes, with generalist TETs displaying broad-spectrum activities, and specialized TETs with more selective activities. We also report the first description of methionyl- and isoleucyl-aminopeptidases in the TET family. In addition to their diverse substrate specificities, the characterized TETs exhibit distinct activation profiles, varying in optimal temperature, pH, and metal cofactor requirements. Combining functional and phylogenetic analyses, we propose a classification of TET peptidases into 11 groups. Notably, we identify generalist group 11 as the ancestral TET in Archaea, from which specialized TETs arose following gene duplication or horizontal transfer. Finally, we highlight the presence of multiple TETs with selective activities in heterotrophic and mixotrophic organisms, suggesting a metabolic role for these enzymes in the degradation of environmental peptides. Overall, our work illuminates an underexplored diversity of TET enzymes, uncovering a complex evolutionary history that shaped their functional diversification.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional determinants and evolutionary consequences of pleiotropy in complex and Mendelian traits.","authors":"Yury A Barbitoff, Polina M Bogaichuk, Nadezhda S Pavlova, Polina V Malysheva, Alexander V Predeus","doi":"10.1093/molbev/msaf232","DOIUrl":"https://doi.org/10.1093/molbev/msaf232","url":null,"abstract":"<p><p>Pleiotropy, a phenomenon of multiple phenotypic effects of the same genetic alteration, is one of the most important features of genotype-to-phenotype networks. Over the last century, biologists have actively debated the prevalence, mechanisms, and consequences of pleiotropy. In this work, we employed data on genotype-to-phenotype associations from the Human Phenotype Ontology and Mouse Genome Database, as well as genome-wide associations from the UK Biobank and FinnGen cohorts to investigate the similarities and dissimilarities in the patterns of pleiotropy between species and different trait types (i.e., Mendelian traits and complex traits). We found that the pleiotropic effects of genes correlate well between species, but have a much weaker correlation when comparing different types of traits for the same species. In all cases, however, highly pleiotropic genes possessed a common set of features, such as the broad expression across tissues, involvement in many biological processes, or a high number of protein-protein interactions of the respective gene products. Furthermore, we observed a universal tendency of highly pleiotropic genes to be under greater negative selection pressure compared to other groups of genes, including genes essential for cell growth and development. Besides, highly pleiotropic genes also show a significant enrichment of recent positive selection signals at pleiotropic loci. Taken together, our results pinpoint a common mechanism underlying pleiotropic effects in different trait domains, and suggest that high degree of pleiotropy plays a role in adaptation, despite imposing additional constraint on genetic variation.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A General Principle of Neuronal Evolution Reveals a Human-Accelerated Neuron Type Potentially Underlying the High Prevalence of Autism in Humans.","authors":"Alexander L Starr, Hunter B Fraser","doi":"10.1093/molbev/msaf189","DOIUrl":"10.1093/molbev/msaf189","url":null,"abstract":"<p><p>The remarkable ability of a single genome sequence to encode a diverse collection of distinct cell types, including the thousands of cell types found in the mammalian brain, is a key characteristic of multicellular life. While it has been observed that some cell types are far more evolutionarily conserved than others, the factors driving these differences in the evolutionary rate remain unknown. Here, we hypothesized that highly abundant neuronal cell types may be under greater selective constraint than rarer neuronal types, leading to variation in their rates of evolution. To test this, we leveraged recently published cross-species single-nucleus RNA-sequencing datasets from three distinct regions of the mammalian neocortex. We found a strikingly consistent relationship where more abundant neuronal subtypes show greater gene expression conservation between species, which replicated across three independent datasets covering >106 neurons from six species. Based on this principle, we discovered that the most abundant type of neocortical neurons-layer 2/3 intratelencephalic excitatory neurons-has evolved exceptionally quickly in the human lineage compared to other apes. Surprisingly, this accelerated evolution was accompanied by the dramatic down-regulation of autism-associated genes, which was likely driven by polygenic positive selection specific to the human lineage. In summary, we introduce a general principle governing neuronal evolution and suggest that the exceptionally high prevalence of autism in humans may be a direct result of natural selection for lower expression of a suite of genes that conferred a fitness benefit to our ancestors while also rendering an abundant class of neurons more sensitive to perturbation.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 9","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12410989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145000907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How Did Evolution Halve Genome Size During an Oceanic Island Colonization?","authors":"Vadim A Pisarenco, Adrià Boada-Figueras, Marta Olivé-Muñiz, Paula Escuer, Nuria Macías-Hernández, Miquel A Arnedo, Pablo Librado, Alejandro Sánchez-Gracia, Sara Guirao-Rico, Julio Rozas","doi":"10.1093/molbev/msaf206","DOIUrl":"10.1093/molbev/msaf206","url":null,"abstract":"<p><p>Red devil spiders of the genus Dysdera colonized the Canary Islands and underwent an extraordinary diversification. Notably, their genomes are nearly half the size of their mainland counterparts (∼1.7 vs. ∼3.3 Gb). This offers a unique model to solve long-standing debates regarding the roles of adaptive and nonadaptive forces on shaping genome size evolution. To address these, we conducted comprehensive genomic analyses based on three high-quality chromosome-level assemblies, including two newly generated ones. We find that insular species experienced a reduction in genome size, affecting all genomic elements, including intronic and intergenic regions, with transposable element (TE) loss accounting for most of this contraction. Additionally, autosomes experienced a disproportionate reduction compared to the X chromosome. Paradoxically, island species exhibit higher levels of nucleotide diversity and recombination, lower TE activity in recent times, and evidence of intensified natural selection, collectively pointing to larger long-term effective population sizes in species from the Canary Islands. Overall, our findings align with the nonadaptive mutational hazard hypothesis, supporting purifying selection against slightly deleterious DNA and TE insertions as the primary mechanism driving genome size reduction.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}