Molecular biology and evolution最新文献

{"title":"Phylogenomics supports monophyly of marsupial crustaceans: a journey to direct development.","authors":"Anna-Chiara Barta, Markus Grams, Heather Bracken-Grissom, Saskia Brix, Lívia M Cordeiro, Brittany Cummings, Stormie Collins, William J Farris, Sarah Gerken, Christoph G Höpel, Anne-Nina Lörz, Siena McKim, Kenneth Meland, Luise Kruckenhauser, Jørgen Olesen, Pedro A Peres, Stefan Richter, Regina Wetzer, Jason Williams, Kevin M Kocot, Martin Schwentner","doi":"10.1093/molbev/msag178","DOIUrl":"https://doi.org/10.1093/molbev/msag178","url":null,"abstract":"<p><p>Peracarida (marsupial crustaceans) represent one of the most diverse and ecologically important crustacean groups, yet their evolutionary relationships have long been debated. Here, we present the most comprehensive phylogenomic analysis of Peracarida to date, incorporating the relict taxa Thermosbaenacea, Mictacea, Ingolfiellida, and Spelaeogriphacea in a phylogenomic framework. Our results robustly confirm peracarid monophyly and recover a well-supported clade uniting Mancoida (Isopoda, Tanaidaca, Cumacea, Spelaeogriphacea) and Mictacea. We propose for Mictacea to be classified as part of the Mancoida, which is defined by shared developmental and morphological traits. Thermosbaenacea is suggested as sister group to all other Peracarida, although this position was not recovered in all analyses. The inferred phylogeny further suggests that evolution of Peracarida involved a transition from an intermediate \"pseudodirect\" developmental mode to the direct development seen in most lineages. We further show that the shift to extensive brood care within the marsupium, accompanied by the loss of a free-swimming larval stage, may have accelerated rates of molecular evolution across lineages. Together, these findings provide a robust evolutionary framework for this major malacostracan lineage and highlight how key reproductive innovations reshaped the genomic and life-history trajectories of the marsupial crustaceans.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"43 8","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13472170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148761522","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":"Evolutionary adaptation proceeds through a small number of phenotypic modules.","authors":"Mohammad Hossein Donyavi, Reza Ghelich, Kara Schmidlin, Grant Kinsler, Kerry Geiler-Samerotte","doi":"10.1093/molbev/msag183","DOIUrl":"https://doi.org/10.1093/molbev/msag183","url":null,"abstract":"<p><p>Understanding how the myriad molecular impacts of mutation percolate to influence higher-order traits and ultimately fitness requires compressing a many-to-many mapping into something tractable. Decades of theoretical work suggest this may be possible because biological systems are modular: effects of perturbation are often funneled through particular pathways or subsystems rather than propagating freely through the organism. Yet, few empirical systems have been able to demonstrate such modularity at scale. Here, we show that, even across 774 diverse yeast lineages, fitness variation across 12 drug environments is organized by a strikingly low-dimensional structure defined by only a few inferred phenotypic axes that capture the main patterns of variation. Lineages drawn from multiple evolutionary histories reveal more of these phenotypic axes than those derived from a single selection pressure. Consistent with many of these lineages having evolved under strong selection pressure, their mutations often exhibit broad pleiotropy, affecting nearly all inferred phenotypic axes. However, fitness in any given drug depends on a much sparser subset of the phenotypic modules these axes reflect. By compressing many-to-many relationships, this low-dimensional framework exposes the modular phenotypic space, as well as the context-dependent contribution of each phenotypic module to fitness that can constrain the pleiotropic effects of adaptive mutations. It also highlights that the apparent complexity of genotype-phenotype-fitness maps depends not only on environmental context but also on the diversity of mutations through which they are observed, laying the groundwork for identifying the key phenotypic modules that matter for fitness.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"43 8","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13487634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795441","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":"Convergent elevation of mitochondrial proton leakage improves thermogenesis in honeybees.","authors":"Ye Xiao, Lifei Qiu, Hao Wang, Yuanchan Fan, Zhunan Zhao, Dan-Yang Wu, Zhengwei Wang, Junzheng Zhang, Misbah A Malik, Sajad H Parey, Min Tang, Baojun Sun, Weiguo Du, Xin Zhou, Shanlin Liu","doi":"10.1093/molbev/msag174","DOIUrl":"10.1093/molbev/msag174","url":null,"abstract":"<p><p>The independent range expansions of the honeybees Apis cerana and A. mellifera from tropical origins into temperate environments have had profound ecological and agricultural impacts. Both species have convergently evolved enhanced thermogenic capacity relative to closely related taxa restricted to tropical and subtropical regions. However, the intrinsic physiological and molecular mechanisms enabling enhanced thermogenesis remain unclear. Here, we first show that A. cerana and A. mellifera exhibit increased proton leak, as evidenced by mitochondrial oxygen consumption assays, directly contributing to elevated heat production. Using a comparative framework supported by newly assembled high-quality genomes, we further identify accelerated evolution in mitochondrial metabolic pathways in both wide-ranged species. At the gene level, we identify Ptcd1 as a key candidate, showing signatures of positive selection and convergent amino acid substitution in both A. cerana and A. mellifera. Functional validation in Drosophila demonstrates that Ptcd1 promotes insect thermogenesis by modulating mitochondrial metabolism and ultrastructure. Moreover, knock-in Drosophila lines expressing Ptcd1 isoforms derived from A. cerana, the tropical species A. dorsata, and a targeted reversion mutation reveal that the Q208K substitution, unique to A. cerana and A. mellifera, increases proton leak and enhances heat generation. Together, these findings demonstrate that the independent fixation of a single amino acid change in PTCD1 has contributed to convergent enhancement of thermogenesis in both A. cerana and A. mellifera. This molecular innovation likely facilitated their expansion into temperate climates and highlights mitochondrial regulation as a fundamental axis of thermal adaptation shared across diverse animal lineages.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13451093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148471643","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":"Pig Matrix: a matched multiomics 3D regulatory genomics database for evolutionary and comparative analyses in pigs.","authors":"Chao Guo, Dezhi Hua, Shuang Gan, Yue-Dong Zhang, Hang Liu, Mengting Ding, Minghao Cao, Qiuhan Wen, Chen Yan, Jing-Sheng Lu, Lei Liu, Yi-Fan Jiang, Guoqiang Yi, Zhonglin Tang, Xiang-Dong Ding, Hai-Bing Xie, Zhong-Yin Zhou, Min-Sheng Peng, Ya-Nan Wang, Xuemei Lu, Ya-Ping Zhang","doi":"10.1093/molbev/msag190","DOIUrl":"10.1093/molbev/msag190","url":null,"abstract":"<p><p>The pig (Sus scrofa) is an important model for evolutionary, comparative, and translational research; however, current functional genomic resources in pigs remain largely limited to one-dimensional genomic annotation and are therefore insufficient for systematically resolving regulatory region-gene relationships, particularly distal ones. Here, we present the Pig Matrix database, a comprehensive 3D regulatory genomics database for pigs, available at https://pigmatrix.kiz.ac.cn/. Built on a standardized experimental framework, Pig Matrix integrates matched multiomics datasets across tissues, developmental stages, and porcine cell lines, including genomic, transcriptomic, epigenomic, and 3D genome information. In total, it contains 16 library types across 7 omics layers and 7,959 processed files from 1,170 libraries. By integrating epigenomic and 3D genome information, Pig Matrix links cis-regulatory elements (CREs) to putative proximal and distal target genes, thereby facilitating interpretation of noncoding variants and genomic signals. This database provides modules for genes, candidate CREs, 3D genome architecture, genome browsing, and single-cell transcriptomics, together with dedicated evolution and comparative resources and user-oriented Genome Annotation and LiftOver tools. A representative use case illustrates how 3D regulatory annotation extends interpretation beyond linear annotation alone, recovering additional candidate genes in domestication-related signals, notably including the classical domestication gene KIT. Pig Matrix also incorporates xenotransplantation-related resources and may support benchmarking of AI models for regulatory genomics. Together, Pig Matrix provides an integrated platform for regulatory interpretation, evolutionary analysis, and comparative genomics in pigs.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148630938","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":"Genetic background shapes the transcriptional activity and phenotypic contribution of a horizontally acquired region in yeast.","authors":"Andrés Romero, Camila Bastías, Matteo De Chiara, Xanita Saayman, Hajar Cherkaoui, Benjamin Barré, Francisco A Cubillos, Claudio Martínez, Eduardo I Kessi-Pérez, Gianni Liti, Francisco Salinas","doi":"10.1093/molbev/msag187","DOIUrl":"10.1093/molbev/msag187","url":null,"abstract":"<p><p>Horizontal gene transfer is the movement of genetic material across species. In Saccharomyces cerevisiae, a DNA segment known as Region B was acquired horizontally from a distant yeast species. This region (∼17 Kb) encodes five genes and is present in the genomes of yeast strains from different phylogenetic clades. Interestingly, the presence of Region B is not restricted to yeast strains isolated from fermentative environments, leaving its contribution to yeast niche-specific adaptation unclear. In this work, the genomic structure of Region B was analyzed in yeast strains from the ScRAP (S. cerevisiae Reference Assembly Panel) collection, identifying ten structural variants that maintain a circular continuity. To assess the role of Region B in yeast adaptation, we performed a high-throughput phenotyping of the ScRAP collection under different growth conditions, identifying that Region B is associated with higher tolerance to oxidative stress. Then, we characterized the transcriptional activity of each gene within Region B using a fluorescent reporter. The results revealed that gene expression depends on the host's genetic background and transcription factors encoded within Region B. To identify the genetic determinants involved in Region B expression within different genetic backgrounds, three expression quantitative trait loci were mapped and validated. Finally, by performing the deletion of Region B in two different strains, we determined a background-dependent contribution of this region to various fermentative phenotypes. Altogether, our results suggest a complex regulatory interaction between the horizontally acquired genes and the host genome that contributes to yeast adaptation under fermentation conditions.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13447093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148562584","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":"Retraction of: Epistatic Effects Between Amino Acid Insertions and Substitutions Mediate Toxin resistance of Vertebrate Na+,K+-ATPases.","authors":"","doi":"10.1093/molbev/msag201","DOIUrl":"10.1093/molbev/msag201","url":null,"abstract":"","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"43 8","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13522922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148840756","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":"ESL-PSC Toolkit: a graphical software environment for linking shared genetic changes to convergent phenotypes.","authors":"John B Allard, Sudhir Kumar","doi":"10.1093/molbev/msag205","DOIUrl":"10.1093/molbev/msag205","url":null,"abstract":"<p><p>Convergent evolution provides a useful framework for testing whether independent origins of similar traits share common genetic mechanisms. Evolutionary Sparse Learning with Paired Species Contrast (ESL-PSC) is an approach to identify genes and sites associated with convergent traits from aligned sequences by fitting sparse predictive models to phylogenetically informed species contrasts. However, practical use of ESL-PSC currently requires substantial command-line fluency and expertise for data assembly, species-pair design, and output interpretation. Here, we present an integrated ESL-PSC analysis environment (ESL-PSC Toolkit) centered on a graphical user interface (GUI). ESL-PSC Toolkit is designed to assist users from experimental design through data interpretation without requiring extensive technical expertise. It supports guided input validation, interactive tree-based pair selection, live execution, post-run exploration of ranked genes and aligned sites, a complementary substitution-counting method, and analysis of continuous quantitative convergent traits. The computational backend has been reimplemented in Rust with many performance optimizations and parallelism, greatly reducing runtime for most analyses and enabling cross-platform packaged distributions. Downloadable GUI and CLI toolkit software packages for Mac, Windows, and Linux are available at https://github.com/kumarlabgit/ESL-PSC/releases/latest.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13511134/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148720781","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":"Parasites constrain within-population diversification while accelerating between-population divergence in an RNA replication system.","authors":"Yuki Kanai, Norikazu Ichihashi","doi":"10.1093/molbev/msag184","DOIUrl":"10.1093/molbev/msag184","url":null,"abstract":"<p><p>Diversification of replicators from simple self-replicating RNA molecules is a major challenge in prebiotic evolution. In our previous evolution experiment using an RNA replication system derived from the Qβ phage, a single RNA species spontaneously diversified into multiple coexisting host and parasite RNA lineages through arms race dynamics, suggesting that host-parasite interactions may promote diversification in molecular replicator ecosystems. To test this idea more directly, we evolved six independent RNA populations under high-parasite and low-parasite conditions. High-parasite populations showed accelerated mutation fixation and greater sequence divergence between populations. However, contrary to expectation, host diversification within populations was limited under high-parasite conditions, whereas transient diversification into at most three host lineages occurred under low-parasite conditions. Sequence and biochemical analyses indicate that this diversification was consistent with relaxed selection among host RNAs that achieved similar replication yields under compartmentalized replication. In contrast, coexistence with parasites helped maintain high replication capacities by continuously imposing selection for improved replication. These results suggest that antagonistic host-parasite interactions help maintain functional activity and promote divergence between populations while constraining diversification within populations. Such opposing effects may have shaped the balance between functional optimization and diversification during early molecular evolution.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148562537","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":"Emergence and stabilization of a neo-Y chromosome in nematode species with rare males.","authors":"Brice Letcher, Lewis Stevens, Nathanaëlle Saclier, Andrew Hsiao, Manuela Kieninger, Eva Wenger, Caroline Launay, Mark Blaxter, Marie Delattre","doi":"10.1093/molbev/msag177","DOIUrl":"10.1093/molbev/msag177","url":null,"abstract":"<p><p>How do sex chromosomes evolve in the transition to asexuality? So far, species that depart from canonical sexual reproduction-for example, parthenogens with rare sex or species where the paternal genome is set aside-have been found to carry either no sex chromosomes or sex chromosomes but no male-specific sex chromosome (i.e. no Y). Here we reveal that, in Mesorhabditis nematodes, a new Y chromosome evolved once, from sexual ancestors, in species that have transitioned into an unconventional mode of reproduction called autopseudogamy. In this reproductive system, females produce clonal females plus rare (∼10%) males that are needed for fertilization but that do not contribute to the female genome. Analyzing the Y chromosomes of two autopseudogamous species, we found high levels of degeneration, most likely due to loss of recombination, and two additional conserved features: (i) they accumulated male-beneficial genes, and (ii) they display a strong fertilization drive, in that mainly Y-bearing sperm fertilize female oocytes. Both features are likely evolutionarily favorable in the context of autopseudogamy. Our results suggest that male-specific chromosomes can still be maintained in systems with rare, and possibly \"genetically useless,\" males.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13511141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148549610","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":"Epistatic impacts of cis- and trans-regulatory mutations on the distribution of mutational effects for gene expression in Saccharomyces cerevisiae.","authors":"Eden McQueen, Bing Yang, Patricia J Wittkopp","doi":"10.1093/molbev/msag172","DOIUrl":"10.1093/molbev/msag172","url":null,"abstract":"<p><p>Epistasis can influence evolution by causing the distribution of phenotypic effects for new mutations to vary among genotypes. Here, we investigate how epistatic interactions between new mutations and an existing regulatory mutation might impact the evolution of gene expression using Saccharomyces cerevisiae. We do so by estimating the distribution of mutational effects for expression of a fluorescent reporter protein driven by the S. cerevisiae TDH3 promoter in a reference strain as well as in eight mutant strains. Each of the mutant strains differed from the reference strain by a single mutation affecting expression of the focal gene. We found that two of these regulatory mutations changed the degree of mutational robustness, as measured by the variance of the distribution of mutational effects, with one initial regulatory mutation increasing mutational robustness while another decreased it. We also found that four of our initial regulatory mutants caused a change in the relative frequency and/or effect size of mutations increasing or decreasing expression, as measured by a change in skewness relative to the reference. Strikingly, in all four of these cases, the change in skewness increased the likelihood that new mutations would at least partially compensate for the effects of the initial regulatory mutation. If this form of epistatic impact on the distribution of mutational effects is common, it should increase the fixation probability of compensatory mutations affecting traits under stabilizing selection and could help explain the prevalence of alleles with compensatory effects in natural populations of S. cerevisiae.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13447094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148471679","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}