Molecular biology and evolution最新文献

{"title":"Pseudogene revival drives repeated adaptation in fission yeast.","authors":"Zhiwei Wu, Xuke Liu, Hao Xu, Guan-Zhu Han","doi":"10.1093/molbev/msag120","DOIUrl":"https://doi.org/10.1093/molbev/msag120","url":null,"abstract":"<p><p>Repeated (parallel or convergent) evolution is often taken as evidence of adaptation and is relevant to the predictability of evolution. However, much remains unknown about the genetic basis of repeated evolution. Here, we use genome editing to progressively knock out all the complete transposable elements (TEs), a rich source of mutations, in the fission yeast Schizosaccharomyces pombe. While progressive knockout has no apparent effect on the biology or fitness of S. pombe under normal conditions, certain TE knockout strains exhibit growth arrest under acid challenge. We next perform parallel replay experiments by evolving S. pombe strains with a single TE and without TE under acid stress. Adaptation occurs rapidly and repeatedly. We do not detect any new TE insertions at appreciable frequencies, indicating that the observed repeated adaptation is not driven by TE insertions. Instead, revival mutations in SPBC409.08, a pseudogene that encodes a putative transporter of the major facilitator superfamily, repeatedly undergo hard or soft selective sweeps and drive adaptation in all the replicates. Although the revival mutations exhibit a trend of diminishing returns, they also repeatedly become fixed in all evolved wild type populations. This work unveils the significance of pseudogene revival on repeated evolution and thus evolutionary predictability.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856764","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":"Sequential origin of an alternative colony founding strategy driven by two supergenes in Temnothorax ants.","authors":"H Darras, C Yu, M Kever, M Stoldt, B Feldmeyer, S Foitzik","doi":"10.1093/molbev/msag115","DOIUrl":"https://doi.org/10.1093/molbev/msag115","url":null,"abstract":"<p><p>Recent discoveries reveal that many complex intraspecific polymorphisms are shaped by a single supergene that maintains coadapted genetic variants through suppressed recombination. Here we show that in the ant Temnothorax rugatulus, an extreme reproductive polymorphism is instead governed by two independent genomic rearrangements that arose sequentially on different chromosomes. Colonies of this species contain either a single large dispersing queen or multiple queens, including extremely miniaturized microgynes that cannot establish new colonies on their own and reproduce only by joining established multiple-queen colonies. Using chromosome-scale assemblies and population genomic data, we identify two genomic rearrangements, 9.3 Mb and 7.0 Mb in size, that jointly determine these strategies. Divergence dating shows that the supergene underlying colony social structure arose first, creating the conditions for the subsequent emergence of a miniaturization supergene. These findings demonstrate that complex adaptive strategies can be assembled stepwise through the sequential origin of multiple supergenes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840095","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":"Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster.","authors":"Prajal H Patel, Lars A Eicholt, Andreas Lange, Kerry L McDermott, Erich Bornberg-Bauer, Geoffrey D Findlay","doi":"10.1093/molbev/msag119","DOIUrl":"https://doi.org/10.1093/molbev/msag119","url":null,"abstract":"<p><p>Orphan genes evolve rapidly, raising questions about whether their functions remain conserved or diverge across species. To address this, we investigated goddard (gdrd), an orphan gene essential for spermatogenesis in Drosophila melanogaster. Within the Drosophila genus, Gdrd proteins retain a conserved core structure but display substantial variation in length and primary sequence. Here we perform cross-species gene-swap assays in D. melanogaster testes to examine how these lineage-specific changes affect Gdrd function. Strikingly, the highly divergent D. mojavensis ortholog fully rescues fertility in gdrd null flies, suggesting that ancestral Gdrd acted within a conserved spermatogenesis pathway. By contrast, several orthologs, including one from a more closely related species, cannot substitute for the melanogaster gene. Cytological analysis shows that all divergent Gdrd orthologs retain some ability to interact with axonemes and ring centrioles, consistent with the protein's structural conservation, but many non-complementing orthologs display weaker axonemal binding. Furthermore, all tested orthologs exhibit divergent localizations to organellar structures. Using computational analyses and molecular dynamics simulations, we identified intrinsic protein qualities that may account for several observations made in the gene swap assays. Rescuing orthologs bear motifs with shared physicochemical properties in their intrinsically disordered regions, while non-rescuing variants exhibit structural instabilities. Taken together, these findings show that while Gdrd's ancestral structure and interactions are conserved, several orthologs have undergone lineage-specific evolutionary changes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840121","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":"Using drift coefficients as a basis for inferring times, effective population sizes, and genetic adaptations.","authors":"Reiichiro Nakamichi, Jeffrey L Thorne, Hirohisa Kishino","doi":"10.1093/molbev/msag118","DOIUrl":"https://doi.org/10.1093/molbev/msag118","url":null,"abstract":"<p><p>Genetic drift and gene flow can give rise to a complex population genetic structure. The inverse problem of estimating the genetic drift and gene flow in the past, based on the present-day genomic population structure, can be solved using an admixture graph. This describes differentiated local populations in terms of population splits and migrations between populations. The history and associated levels of genetic drift and admixture can be estimated based on the genome-wide SNP allele frequency data. Here, we present a set of statistical methods based on the admixture graph. Applying a prior on the stochastic variation of the effective population size decomposes the genetic drift values that are associated with the non-migration edges into the timings of the population splits and the effective population sizes at those times. This decomposition facilitates downstream analyses such as reconstruction of ancestral allele frequencies via a Brownian motion model with admixture. To trace changes in allele frequencies on a world map, we estimated the geographic locations of the ancestral populations using Brownian motion, the rate of which depends on the genetic drift values. Mapping the history of putative adaptations onto a world map can illuminate factors responsible for regional population heterogeneity. We investigated the effectiveness of detecting adaptations with a numerical simulation that mimics human population history, and by analyzing the eQTLs of the MC1R gene, which is involved in regulation of skin and hair pigmentation.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840159","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":"The Genomic Basis of Independent Marine Transitions in Turtles: Convergent Episodic Adaptation and Demographic Shifts.","authors":"Elisa Ramos, Leon Hilgers, Tomás Carrasco-Valenzuela, Diego De Panis, Agnello Picorelli, James Sullivan, Marcela Uliano-Silva, Blair P Bentley, Peter A Scott, Michael Hiller, Mariana F Nery, H Bradley Shaffer, Lisa Komoroske, Camila J Mazzoni","doi":"10.1093/molbev/msag114","DOIUrl":"https://doi.org/10.1093/molbev/msag114","url":null,"abstract":"<p><p>The transition from terrestrial to marine environments represents one of the most fundamental evolutionary shifts in vertebrate history, requiring radical physiological and genomic remodeling. We investigated the genomic signatures of saltwater adaptation in the green sea turtle (Chelonia mydas), the leatherback turtle (Dermochelys coriacea), and the independently evolved estuarine diamondback terrapin (Malaclemys terrapin). Our analyses reveal that the marine transition is characterized by rapid evolution and expansion in gene families linked to iron metabolism, organ morphogenesis, and sensory perception-patterns that mirror those seen in other secondarily marine tetrapods. Notably, while we identified shared targets of positive selection across these independent lineages, we found no evidence of repeated evolution at the nucleotide level, reinforcing that functional convergence often arises through distinct molecular trajectories. Furthermore, demographic reconstructions reveal that saltwater-adapted turtles share a history of deep-time population declines; however, the delayed recovery of M. terrapin underscores the specific susceptibility of estuarine specialists to Pleistocene sea-level volatility. By bridging comparative genomics and historical demography, this study provides new insights into the genomic basis of marine adaptations in turtles and a comprehensive framework for understanding the molecular and ecological mechanisms that facilitate major vertebrate transitions into the marine realm.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840066","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":"IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models.","authors":"Thomas K F Wong, Nhan Ly-Trong, Huaiyan Ren, Piyumal Demotte, Hector Baños, Andrew J Roger, Edward Susko, Chris Bielow, Nicola De Maio, Nick Goldman, Matthew W Hahn, Mario Dos Reis, Le Sy Vinh, Gavin Huttley, Robert Lanfear, Bui Quang Minh","doi":"10.1093/molbev/msag117","DOIUrl":"https://doi.org/10.1093/molbev/msag117","url":null,"abstract":"<p><p>IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelihood. Here, we present IQ-TREE version 3, the third major release of the software. IQ-TREE 3 significantly extends version 2 with new features, including mixture models as an alternative to partitioned models, gene and site concordance factors to quantify discordance between genomic regions, integration with phylogenomic divergence time estimation, and a fully-featured sequence simulator. The IQ-TREE 3 source code is available at https://github.com/iqtree/iqtree3.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840101","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":"Climate-associated natural selection in the human mitochondrial genome.","authors":"Finley Grover-Thomas, Lucy van Dorp, Francois Balloux, Aida M Andrés, M Florencia Camus","doi":"10.1093/molbev/msag044","DOIUrl":"10.1093/molbev/msag044","url":null,"abstract":"<p><p>Mitochondria are essential for cellular energy production and biosynthesis, thermogenesis, and cell signaling, and thus help coordinate physiological responses to changing environments. Humans (Homo sapiens) have adapted to cope with a wide range of climatic conditions, however the role of the mitochondrial genome (mtDNA) in mediating this process remains poorly understood. Here, we curated a dataset of 19,570 publicly available full human mitochondrial genomes, an approximate 40-fold increase on earlier studies, paired with modern climate and reconstructed paleoclimate variables. Using a Generalized Linear Model approach, we identify 18 independent candidate variants significantly associated with climatic conditions, suggesting local adaptation in human mitochondrial genomes. Candidate variants are distributed across multiple loci in regulatory, tRNA, rRNA and protein-coding regions-including prominently in ND2 and ND4 complex I subunits. Specific variants are predicted to impact mtDNA transcription, ribosome or protein structure, and multiple have been associated with disease pathologies. We further show that candidate variant genotype distributions are each best modeled by different paleo-bioclimatic variables, consistent with environmental stressors linked to our measured variables exerting subtly distinct selective effects. These stressors may reflect dietary changes or different thermogenic demands at lower temperatures. Our results provide genetic evidence to support the accumulating body of work from functional studies that mitochondria can modulate adaptation to diverse environments. This work underscores the importance of mtDNA in evolutionary biology and its relevance for understanding both disease and physiological variation in global populations.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146213091","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":"Evolution in metazoans of the TRPM channel family involves multiple gains and losses of genes and domains.","authors":"Marina Morini, Christina Bergqvist, Juan F Asturiano, Sylvie Dufour, Dan Larhammar","doi":"10.1093/molbev/msag098","DOIUrl":"10.1093/molbev/msag098","url":null,"abstract":"<p><p>Transient receptor potential (TRP) ion channels of the melastatin family (TRPM) have eight members in mammals with a broad spectrum of functions. We investigated the evolution of this complex gene family across metazoans. The characteristic aminoterminal melastatin domain and the carboxyterminal NUDT9 homology domain with similarity to ADP-ribose pyrophosphatase were added to the common ancestor of TRPM and its sister channel TRPS. Gene duplications before the origin of bilaterians resulted in four TRPM genes: α, β, βlike, and γ. The two latter were discovered in this study. All four and TRPS are present in extant mollusks, while differential losses occurred in the other animal lineages. TRPS, TRPMβlike, and TRPMγ were lost in early chordates, meaning that the vertebrate ancestor started with TRPMα and β, both of which were duplicated before the first vertebrate tetraploidization 1R. The ancestor of the micro-RNA genes mir-211 and mir-204 was inserted in an intron of the ancestor of TRPM1/TRPM3. The TRPM6/TRPM7 ancestor acquired a kinase domain, probably a copy of the syntenic alpha protein kinase ALPK2/3 ancestor gene. Vertebrate 1R and gnathostome 2R together with local gene duplication and losses resulted in eight TRPM (TRPM1 to 8) in the gnathostome ancestor. In cyclostomes, extensive gene losses after the hexaploidization led to four TRPM. The teleost-specific tetraploidization 3R generated further TRPM ohnologs. The NUDT9 homology domain is retained in TRPM2 and TRPS but was lost repeatedly during TRPM evolution. Thus, the TRPM family displays considerable evolutionary variation with regard to gene and domain gains and losses.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13143021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147675245","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":"Pangolin museum genomics reveal the dynamic genetic consequences and extinction risk of the critically endangered Chinese pangolin.","authors":"Jing Yang Hu, Yu Jiang, Song Li, Ting Ting Ying, Li Yu","doi":"10.1093/molbev/msag099","DOIUrl":"10.1093/molbev/msag099","url":null,"abstract":"<p><p>Human-driven biodiversity loss, intensified by illegal hunting and trafficking, has caused severe wildlife population declines and extinctions, necessitating studies on long-term genomic erosion to inform conservation strategies. While temporal genomic analyses using ancient and historical/museum DNA reveal generational impacts, sparse sampling often limits insights into prolonged declines, highlighting the need for time-resolved studies to understand sequential population decline and species persistence under sustained pressures. The Chinese pangolin (Manis pentadactyla), critically endangered as a result of historical overexploitation, has experienced severe continuous population decline pre-1979, 1980-1999, and post-2000. However, the temporal genetic consequences and associated extinction risks remain poorly understood. We analyzed 228 pangolin genomes (133 newly sequenced), spanning continuous population decline, to assess the dynamics of genomic erosion. Our results demonstrate that persistent population decline drives long-term genetic decline within populations, with the severity of population decline correlating directly with the degree of negative genetic impact (e.g. reduced diversity, increased inbreeding and genetic load) and extinction risk. Counterintuitively, however, between populations, those experiencing the most severe population decline (e.g. southwest China) exhibited less extreme relative genetic consequences compared to less severe population decline (e.g. south China), suggesting a stronger dependence on the history of effective population size before population decline. Critically, the contemporary South China population shows significantly lower genetic diversity, higher inbreeding, elevated genetic load, and consequently higher extinction risk, demanding urgent prioritization for conservation. This study provides novel insights into the complex genomic legacy of continuous population decline, elucidating anthropogenic impacts on genetic erosion and offering a scientific framework for targeted conservation strategies.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13137990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147675248","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":"Experimental evolution toward extinction in a molecular host-parasite system.","authors":"Kohtoh Yukawa, Tomoaki Yoshiyama, Ryo Mizuuchi, Norikazu Ichihashi","doi":"10.1093/molbev/msag084","DOIUrl":"https://doi.org/10.1093/molbev/msag084","url":null,"abstract":"<p><p>Theoretical studies have proposed that coevolution with parasitic replicators plays a critical role in the evolution of primitive life; however, experimental verification of the potential outcomes of such coevolutionary dynamics remains limited. We previously conducted a coevolutionary experiment using an RNA-protein replication system that resulted in the spontaneous diversification of host and parasitic RNAs into five distinct lineages with robust coreplication. Here, we report contrasting evolutionary outcomes from a second long-term coevolutionary experiment. Using a droplet flow reactor (FR) system with increased dilution frequency over 5,000 h (1,600 generations), we observed reduced diversity and frequent extinctions in later experimental stages. Coreplication assays of RNA clones revealed that the primary cause of this diversity loss was the shortened reaction time resulting from frequent dilution. Further analysis of RNA clones that emerged during evolution suggested that the frequent extinctions resulted from the appearance of highly competitive parasite species and the dominance of host species that exhibited reduced replication ability. These findings demonstrate that coevolution between host and parasitic replicators can result in diversity loss and frequent extinctions depending on dilution conditions, highlighting the critical role of environmental parameters, such as dilution ratio and frequency, in enabling primitive replicators to evolve sustainably toward the emergence of life.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"43 5","pages":""},"PeriodicalIF":5.3,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840194","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}