Molecular biology and evolution最新文献

{"title":"Expression Divergence in Response to Sex-biased Selection.","authors":"Karl Grieshop, Michelle J Liu, Ryan S Frost, Matthew P Lindsay, Malak Bayoumi, Martin I Brengdahl, Ruxandra I Molnar, Aneil F Agrawal","doi":"10.1093/molbev/msaf099","DOIUrl":"10.1093/molbev/msaf099","url":null,"abstract":"<p><p>It remains debated whether greater degrees of sexual dimorphism would evolve if not for intersexual genetic constraints. Here, we used experimental evolution to partially break the intersexual genetic constraint in Drosophila melanogaster to investigate the effects of a shared gene pool on the evolution of sexual dimorphism in gene expression. In six replicate populations of 1,000 flies, a dominant marker (DsRed) was used to force a \"Red\" pool of genetically variable Chromosome 2 copies through exclusive father-to-son inheritance, while a complimentary pool of \"NonRed\" chromosomes was inherited primarily from mothers to daughters. After 100 generations, we demonstrated the effect of Red male-limited chromosomes in increasing male mating success. Differentially expressed genes between flies with and without Red chromosomes had on average higher intersexual genetic correlations (rMF), as expected if such correlations represent a constraint to sex-specific adaptation under normal inheritance. If conflict hinders the evolution of further dimorphism, the transcriptomes of male-selected Red chromosomes were predicted to evolve to be \"masculinized\" relative to female-selected NonRed chromosomes. Consistent with this, splicing patterns in Red males (but not Red females) were masculinized relative to NonRed males. Contrastingly, gene expression levels were largely feminized in Red flies of both sexes compared with NonRed. We discuss alternative forms of intralocus sexual conflict that may explain these patterns.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 7","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12238715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144591791","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":"The Heterogametic Transition in European Bufo Toads Switches the Sex Linkage of Key Vertebrate Sex Determination Genes and Associates with a Large Sex Chromosome Effect.","authors":"Christophe Dufresnes, Pierre-André Crochet, Beata Rozenblut-Kościsty, Spartak N Litvinchuk, Nicolas Rodrigues, Nicolas Perrin, Daniel L Jeffries","doi":"10.1093/molbev/msaf142","DOIUrl":"10.1093/molbev/msaf142","url":null,"abstract":"<p><p>Characterizing the diversity and lability of the amphibian sex chromosomes holds key to understand what drives sex chromosome turnovers and assess the role of sex-linked genes in reproductive isolation and speciation. Here, we show that the heterogametic transition previously reported between the hybridizing toads Bufo bufo (ZW) and Bufo spinosus (XY) is nonhomologous, potentially implicates key genes of the vertebrate sex determination cascade (SOX9, DMRT1, and AMH), and is characterized by a much shorter ZW than XY segment. Integrating this information with published hybrid zone data suggests that both sex chromosomes resist interspecific introgression more than autosomes. These observations substantiate that sex chromosome turnovers preferentially involve chromosomes that host conserved sex-determining genes, imply heterochiasmy as a key factor of sex chromosome differentiation, and are consistent with a large sex chromosome effect, an empirical rule of speciation that is not expected with homomorphic sex chromosomes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12214457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144302492","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":"Widespread Genetic Signals of Visual System Adaptation in Deepwater Cichlid Fishes.","authors":"Julia I Camacho García, Milan Malinsky, Domino A Joyce, M Emília Santos, Grégoire Vernaz, Maxon J Ngochera, Hannes Svardal","doi":"10.1093/molbev/msaf147","DOIUrl":"10.1093/molbev/msaf147","url":null,"abstract":"<p><p>The light environment exerts a profound selection pressure on the visual system, driving morphological and molecular adaptations that may also contribute to species diversification. Here, we investigate the evolution and genetic basis of visual system diversification in deepwater cichlid fishes of the genus Diplotaxodon. We find that Diplotaxodon exhibit the greatest eye size variation among Lake Malawi cichlids and that this variation is largely uncoupled from phylogeny, with various nonsister species sharing similar eye sizes. Using a combination of genome-wide association analysis across nine Diplotaxodon species, haplotype-based selection scans, and transcriptome analysis, we uncover consistent and widespread signatures of evolution in visual pathways, centered on green-sensitive opsins and throughout the phototransduction cascade, suggesting coordinated evolution of eye size and visual molecular pathways. Our findings underscore the role of visual system diversification in niche specialization within deepwater habitats and offer new insights into visual system evolution within this extraordinary cichlid radiation.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248709","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":"PHACE: Phylogeny-Aware Detection of Molecular Coevolution.","authors":"Nurdan Kuru, Ogün Adebali","doi":"10.1093/molbev/msaf150","DOIUrl":"10.1093/molbev/msaf150","url":null,"abstract":"<p><p>The coevolution trends of amino acids within or between genes offer key insights into protein structure and function. Existing tools for uncovering coevolutionary signals primarily rely on multiple sequence alignments, often overlooking phylogenetic relatedness and shared evolutionary history. Here, we introduce PHACE, a phylogeny-aware coevolution algorithm that maps amino acid substitutions onto a phylogenetic tree to detect molecular coevolution. PHACE categorizes amino acids at each position into \"tolerable\" and \"intolerable\" groups, based on their independent recurrence across the tree, reflecting a position's tolerance to specific substitutions. Gaps are treated as a third character type, with only phylogenetically independent gap changes considered. The method computes substitution scores per branch by traversing the tree and quantifying probability differences across adjacent nodes for each group. To avoid artifacts from alignment errors, we apply a multiple sequence alignment-masking procedure. Compared to phylogeny-based methods (CAPS, CoMap) and state-of-the-art multiple sequence alignment-based approaches (DCA, GaussDCA, PSICOV, mutual information), PHACE shows significantly superior accuracy in identifying coevolving residue pairs, as measured by statistical metrics including Matthews correlation coefficient, area under the ROC curve, and F1 score. This performance stems from PHACE's explicit modeling of phylogenetic dependencies, often ignored in coevolution analyses.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12264334/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144608831","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":"Pervasive Divergence in Protein Thermostability is Mediated by Both Structural Changes and Cellular Environments.","authors":"Nilima Walunjkar, Timothy Y Lai, Nasima Akhter, James H Miller, John Q Bettinger, Erin Marcus, Eric M Phizicky, Sina Ghaemmaghami, Justin C Fay","doi":"10.1093/molbev/msaf137","DOIUrl":"10.1093/molbev/msaf137","url":null,"abstract":"<p><p>Temperature is a universal environmental constraint and organisms have evolved diverse mechanisms of thermotolerance. A central feature of thermophiles relative to mesophiles is a universal shift in protein stability, implying that it is a major constituent of thermotolerance. However, organisms have also evolved extensive buffering systems, such as those that disaggregate and refold denatured proteins and enable survival of heat shock. Here, we show that both cellular and protein structural changes contribute to divergence in protein thermostability between two closely related Saccharomyces species that differ by 8 °C in their thermotolerance. Using thermal proteomic profiling we find that 85% of S. cerevisiae proteins are more stable than their S. uvarum homologs and there is a 1.6 °C shift in average protein melting temperature. In an interspecific hybrid of the two species, S. cerevisiae proteins retain their thermostability, while the thermostability of their S. uvarum homologs is enhanced, indicating that cellular context contributes to protein stability differences. By purifying orthologous proteins, we show that amino acid substitutions underlie melting temperature differences for two proteins, Guk1 and Aha1. Amino acid substitutions are also computationally predicted to contribute to stability differences for most of the proteome. Our results imply that widespread changes in protein thermostability accompany the evolution of thermotolerance between closely related species.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12227239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234552","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":"Newly Developed Structure-Based Methods Do Not Outperform Standard Sequence-Based Methods for Large-Scale Phylogenomics.","authors":"Giacomo Mutti, Eduard Ocaña-Pallarès, Toni Gabaldón","doi":"10.1093/molbev/msaf149","DOIUrl":"10.1093/molbev/msaf149","url":null,"abstract":"<p><p>Recent developments in protein structure prediction have allowed the use of this previously limited source of information at genome-wide scales. It has been proposed that the use of structural information may offer advantages over sequences in phylogenetic reconstruction, due to their slower rate of evolution and direct correlation to function. Here, we examined how recently developed methods for structure-based homology search and tree reconstruction compare with current state-of-the-art sequence-based methods in reconstructing genome-wide collections of gene phylogenies (i.e. phylomes). While structure-based methods can be useful in specific scenarios, we found that their current performance does not justify using the newly developed structure-based methods as a default choice in large-scale phylogenetic studies. On the one hand, the best performing sequence-based tree reconstruction methods still outperform structure-based methods for this task. On the other hand, structure-based homology detection methods provide larger lists of candidate homologs, as previously reported. However, this comes at the expense of missing hits identified by sequence-based methods, as well as providing sets of homolog candidates with higher fractions of false positives. These insights help to guide the use of structural data in comparative genomics and highlight the need to continue improving structure-based approaches. Our pipeline is fully reproducible and has been implemented in a Snakemake workflow. This will facilitate a continuous assessment of future improvements of structure-based tools in the AlphaFold era.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12290511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144528922","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":"Genome-wide Parallelism Underlies Rapid Freshwater Adaptation Fueled by Standing Genetic Variation in a Wild Fish.","authors":"Hao Yang, Yu-Long Li, Teng-Fei Xing, Jian-Hui Wu, Ting Wang, Ming-Sheng Zhu, Jin-Xian Liu","doi":"10.1093/molbev/msaf160","DOIUrl":"10.1093/molbev/msaf160","url":null,"abstract":"<p><p>A fundamental focus of ecological and evolutionary biology is determining how natural populations adapt to environmental changes. Rapid parallel phenotypic evolution can be leveraged to uncover the genetics of adaptation. Using population genomic approaches, we investigated the genetic architecture underlying rapid parallel freshwater adaptation of Neosalanx brevirostris by comparing four freshwater-resident populations with their common ancestral anadromous population. We demonstrated that the rapid parallel adaptation to freshwater followed a complex polygenic architecture and was characterized by genomic-level parallelism, which proceeded predominantly through repeated selection on the preexisting standing genetic variations. Frequencies of the genome-wide adaptive standing variations were moderate in the ancestral anadromous population, which had pre-adapted to fluctuating salinities. Relatively large allele frequency shifts were observed at some adaptive single-nucleotide polymorphisms (SNPs) during parallel adaptation to freshwater environments, with a large fraction of freshwater-favored alleles being fixed or nearly fixed. These adaptive SNPs were involved in multiple biological functions associated with osmoregulation, immunoregulation, locomotion, metabolism, etc., which were highly consistent with the polygenic architecture of adaptive divergence between the two ecotypes involving multiple complex physiological and behavioral traits. This work provides insight into the mechanisms by which natural populations rapidly evolve to changes in the environment and highlights the importance of standing genetic variation for the evolutionary potential of populations facing global environmental changes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12279437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560457","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":"A Trade-Off between Body Mass and Cancer Resistance in Cetaceans Is Mediated by Cell Cycle-Related Gene Evolution.","authors":"Linxia Sun, Yi Li, Huijie Zhang, Xinrui Chen, Guang Yang, Shixia Xu","doi":"10.1093/molbev/msaf159","DOIUrl":"10.1093/molbev/msaf159","url":null,"abstract":"<p><p>Cetaceans, well-known for their exceptionally long lifespans and substantial body masses, demonstrate a lower risk of cancer mortality compared to other mammals, consistent with Peto's paradox. Yet, the underlying mechanisms of cancer resistance, possibly evolved due to large body size, remain largely unclear. Here, we conducted an evolutionary analysis of 50 cell cycle-related genes, which play crucial role in both cancer progression and organismal body mass modulation, to investigate the mechanisms underlying the trade-off between body size and cancer resistance in cetaceans. We found that 66.7% (4/6) rapidly evolving genes (i.e. CDK2, CDT1, ORC3, and DBF4) and 50% (2/4) positively selected genes (ORC2 and ORC3) identified in cetaceans are involved in regulating cell cycle checkpoints, which halt the cell cycle in response to damage to allow repair and prevent cancer induction. Additionally, we identified four-body mass-associated genes (CCNE1, ORC5, E2F3, and DBF4) known to regulate cell growth; mutations or dysregulation of these genes can drive uncontrolled proliferation and cancer development. Interestingly, convergent evolution was observed in the African elephant and the bowhead whale at the tumor suppressor gene MYT1, potentially revealing a convergent mechanism of cancer resistance in large-bodied species. Notably, in vitro assays revealed that a cetacean-specific mutation M155T in the rapidly evolving gene CCND1 more effectively suppressed tumor cell proliferation and migration. Overall, our study has provided new insights into how the evolution of cell cycle-related genes balances body mass and cancer resistance in cetaceans, offering molecular support for Peto's paradox.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12279436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144637646","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":"Connectivity and Adaptation Patterns of the Deep-Sea Ground-Forming Sponge Geodia hentscheli Across Its Entire Distribution.","authors":"Sergi Taboada, Cristina Díez-Vives, Marta Turon, María Belén Arias, Carles Galià-Camps, Paco Cárdenas, Vasiliki Koutsouveli, Francisca Correia de Carvalho, Ellen Kenchington, Andrew J Davies, Shuangqiang Wang, Marta Martín-Huete, Emyr Martyn Roberts, Joana R Xavier, David Combosch, Ana Riesgo","doi":"10.1093/molbev/msaf145","DOIUrl":"10.1093/molbev/msaf145","url":null,"abstract":"<p><p>Geodia hentscheli, a species forming sponge grounds in the North Atlantic and Arctic Oceans, is a common deep-sea organism, that plays a fundamental role in forming biogenic habitats. However, there is little information about gene flow and adaptation patterns of this species, which is crucial to develop effective management/conservation plans under current global change scenarios. Here, we generated ddRADseq data from 110 specimens of G. hentscheli, together with microbial profiling, transcriptomics, and metatranscriptomics for a selection of specimens to investigate their genetic diversity, molecular connectivity, and local adaptations. Sampling covered the species' entire distribution within a wide bathymetric range. We obtained 1,115 neutral SNPs and identified long-distance genetic connectivity among regions separated 1,000s of km, but strong genetic structure segregating populations by depth at ca. 1,300 m, in line with our microbial analyses. Coalescent analyses inferred the split of these depth-related genetic entities ∼10 KYA, coincident with the last postglacial maximum. Analyses of SNPs under selection, combined with transcriptomic and metatranscriptomic data highlight the presence of several sponge genes and microbial metabolic pathways involved in adaptation to depth, including heat shock proteins and fatty acids, among others. The physiological plasticity of the sponge and its microbiome as a function of depth suggest the existence of a host-microbiome metabolic compensation for G. hentscheli. This study provides a multiscale paradigmatic example of the depth-differentiation hypothesis, a phenomenon mainly caused by changes in environmental conditions at different depths, mainly related to the presence of water masses with different characteristics that drive local adaptations.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12240736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234550","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":"Dynamics of Deleterious Mutations and Purifying Selection in Small Population Isolates.","authors":"Ying Chen, Xueyun Feng, Kerry Reid, Chaowei Zhang, Ari Löytynoja, Juha Merilä","doi":"10.1093/molbev/msaf110","DOIUrl":"10.1093/molbev/msaf110","url":null,"abstract":"<p><p>The genomic consequences of prolonged population decline and isolation are increasingly recognized, but quantitative assessments of mutation loads have been limited by low population-level replication in individual studies. Moreover, how inbreeding and purifying selection shape the genomic landscape of deleterious variation remains poorly understood. We evaluated the abundance and frequency of putative deleterious mutations, characterized the landscape of deleterious variation, and measured the efficacy of purifying selection in 17 wild nine-spined stickleback (Pungitius pungitius) populations covering varying levels of inbreeding (FROH = 0.015 to 0.912) and histories of isolation. We found significantly more deleterious homozygous mutations and a greater frequency of mildly deleterious variants in long-term small, isolated, and inbred populations than in larger outbred populations. Deleterious homozygotes were enriched in runs of homozygosity regions across all study populations, but the extent of enrichment was more pronounced in larger outbred populations than in small inbred populations. Historical effective population sizes serve as an indicator of the strength of purifying selection for mildly deleterious alleles but not for strongly deleterious alleles. The results demonstrate that the accumulation and purging of deleterious variants can occur simultaneously and that a large fraction of segregating strongly deleterious variants are recessive lethals. These findings, which are based on analyses of highly replicated samples of populations, suggest that the level of inbreeding is a good predictor of realized loads of deleterious mutations and that the genomic consequences of prolonged isolation in small populations are predictable.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 7","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12278730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144675291","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}