Molecular biology and evolution最新文献

{"title":"The genomic basis of the tristylous floral polymorphism - evidence for a role of gene duplications in a region of restricted recombination.","authors":"Haoran Xue, Yunchen Gong, Stephen I Wright, Spencer C H Barrett","doi":"10.1093/molbev/msaf170","DOIUrl":"https://doi.org/10.1093/molbev/msaf170","url":null,"abstract":"<p><p>Tristyly is an angiosperm sexual polymorphism characterized by three flower morphs maintained in populations by negative frequency-dependent selection resulting from disassortative mating among morphs. The floral morphs possess reciprocal stigma and anther heights controlled by two epistatically interacting diallelic loci (S and M). Although considerable progress has been made on determining the genetic architecture and genes governing the related heterostylous polymorphism distyly, our understanding of these aspects of the genetic basis of tristyly have not been examined. Here, we address this knowledge gap by investigating the genomic basis of tristyly in Eichhornia paniculata (Pontederiaceae), an annual bee-pollinated herb native to the Neotropics, primarily N.E. Brazil. Chromosome-level genome assemblies of E. paniculata identified the S- and M-loci on either side of a large region of low recombination on the same chromosome----. The S-locus consisted of two divergent haplotypes: the S-haplotype (2.51-Mb) with three S-haplotype specific genes and the s-haplotype (596-kb) with five s-haplotype specific genes. Two of the S-haplotype specific genes, LAZY1-S and HRGP-S, were specifically expressed in styles and stamens, respectively, making them candidate tristyly genes and providing evidence for this locus functioning as a hemizygous supergene. The M-locus contained one gene (LAZY1-M), homologous to LAZY1-S, present in the M-haplotype but absent from the m-haplotype. Estimates of gene ages and phylogenetic reconstruction were consistent with the theoretical prediction that the S-locus evolved before the M-locus. Evidence for re-use of the same gene highlights the potential role of gene duplication in the evolution of epistatic multilocus polymorphisms.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144667988","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":"ASTER: A Package for Large-scale Phylogenomic Reconstructions.","authors":"Chao Zhang, Rasmus Nielsen, Siavash Mirarab","doi":"10.1093/molbev/msaf172","DOIUrl":"https://doi.org/10.1093/molbev/msaf172","url":null,"abstract":"<p><p>Many algorithms are available for inferring species trees from various input types while accounting for gene tree discordance. Several quartet-based species tree inference methods, collectively known as the ASTRAL family, are based on similar ideas and are in wide use. Here, we integrate all ASTRAL-like methods into a single package called ASTER, comprising several tools, each designed for a different input type: (1) ASTRAL for single-copy gene tree topologies, (2) weighted ASTRAL (wASTRAL) for singlecopy gene tees with branch length and/or support, (3) ASTRAL-Pro for multi-copy gene tree topologies, (4) CASTER for multiple sequence alignments, including genome alignments, and (5)WASTER for shortreads and assembled genomes. These tools collectively enhance the scalability, accuracy, and versatility of species tree inference.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649898","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":"Molecular phylogeny of the SELMA translocation machinery recounts the evolution of complex photosynthetic eukaryotes.","authors":"Rafael I Ponce-Toledo, David Moreira, Purificación López-García, Philippe Deschamps","doi":"10.1093/molbev/msaf167","DOIUrl":"https://doi.org/10.1093/molbev/msaf167","url":null,"abstract":"<p><p>Photosynthetic eukaryotes and their relatives are the result of an intricate evolutionary history involving a series of plastid acquisitions through endosymbiosis, multiple reversions to heterotrophy, and sometimes total plastid losses. Among these events, one of the most debated is the emergence and diversification of the CASH lineages (Cryptophyta, Alveolata, Stramenopiles and Haptophyta). Although they all include species bearing a complex plastid that derived from the endosymbiosis of a red alga, their phylogenetic relationships remain controversial, and the timing and number of plastid acquisitions are still undetermined. The inner metabolism of all plastids is mostly supported by nuclear-encoded proteins, and consequently, mechanisms allowing the relocation of those proteins have evolved or were recycled at each endosymbiotic event. Thus, the study of the composition and origins of those translocation machineries provides important clues for understanding how photosynthetic lineages have emerged and might be related. In CASH species, the SELMA complex, composed of about 20 proteins, is dedicated to the transport of pre-proteins across the periplastidial membrane, the second outermost membrane of complex red plastids. In this work, we present a comprehensive genomic survey and phylogenetic analysis of the proteins composing the SELMA complex. We confirm the presence, homology and monophyletic origin of SELMA in the four CASH lineages and use these observations to infer a scenario for the serial transmission of secondary red plastids that differs from previous hypotheses and sheds new light on the evolution of photosynthetic eukaryotes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144612216","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":"Somatic evolution of stem cell mutations in long-lived plants.","authors":"Frank Johannes","doi":"10.1093/molbev/msaf165","DOIUrl":"https://doi.org/10.1093/molbev/msaf165","url":null,"abstract":"<p><p>Long-lived perennial plants accumulate numerous somatic mutations with age. Mutations originating in stem cells at the shoot apex often become fixed in large sectors of the plant body due to cell lineage drift during repeated branching. Understanding the somatic evolution of such mutations requires knowledge of the effective stem cell population size, the cellular bottleneck strength during branch initiation, and the mutation rate. Here we show that these parameters can be estimated directly from cell-layer-enriched DNA sequencing data, thus filling a gap where no other in vivo method exists.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564951","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":"Odorant receptors mediating avoidance of toxic mustard oils in Drosophila melanogaster are expanded in herbivorous relatives.","authors":"Teruyuki Matsunaga, Carolina E Reisenman, Benjamin Goldman-Huertas, Srivarsha Rajshekar, Hiromu C Suzuki, David Tadres, Joshua Wong, Matthieu Louis, Santiago R Ramírez, Noah K Whiteman","doi":"10.1093/molbev/msaf164","DOIUrl":"10.1093/molbev/msaf164","url":null,"abstract":"<p><p>Plants release defense volatile compounds that can deter herbivores. Among them are electrophilic toxins, such as isothiocyanates from mustard plants, that activate pain receptors by contact (i.e. taste) in many animals, including Drosophila melanogaster. While specialist insects have evolved strategies to tolerate toxicity and use mustard plants as hosts, it is unclear whether non-specialist insects detect and avoid electrophilic toxins via olfaction. To address this, and to understand if specialized insects co-opted these toxic compounds as host plant olfactory cues, we leveraged closely related drosophilid species, including the microbe-feeding D. melanogaster and Scaptomyza pallida, and the mustard-feeding specialist S. flava. In olfactory assays, D. melanogaster exposed to allyl isothiocyanate volatiles were rapidly immobilized, demonstrating the high toxicity of this wasabi-derived compound to non-specialists. Through single sensillum electrophysiological recordings from olfactory organs and behavioral assays, we identified an Olfactory receptor (Or) necessary for volatile detection and behavioral aversion to allyl isothiocyanate in D. melanogaster. RNA sequencing and heterologous expression revealed that S. flava possess lineage-specific, triplicated homologs of this Or, and that each paralog exhibited broadened and distinct sensitivity to isothiocyanate compounds. Using AlphaFold2 modeling, site-directed mutagenesis and electrophysiological recordings, we identified two critical amino acid substitutions that changed the sensitivity of these paralogs from fruit-derived odors to isothiocyanates in the mustard specialist S. flava. Our findings show that non-specialists can detect electrophiles via olfaction, and that their olfactory systems can rapidly adapt to toxic host plant niches through co-option and duplication of ancestral chemosensory genes with few amino acid changes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564950","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":"Divergence of Leptin Receptor and Interleukin-6 Receptor Subunit b in Early Vertebrate Evolution and Physiological Insights from the Sea Lamprey.","authors":"Ningping Gong, André Barany, Jessica L Norstog, Dan Larhammar, Björn Thrandur Björnsson, Amy M Regish, Stephen D McCormick, Mark A Sheridan","doi":"10.1093/molbev/msaf157","DOIUrl":"10.1093/molbev/msaf157","url":null,"abstract":"<p><p>Current knowledge of class-I cytokine receptors comes primarily from studies in jawed vertebrates (gnathostomes), and their origin and evolution remain unresolved. In this study, we identified a leptin receptor-like sequence (LepRL) and three interleukin-6 receptor subunit b-like sequences (IL6RBL) from a jawless vertebrate (cyclostome), the sea lamprey (Petromyzon marinus). Based on structural, phylogenetic, and syntenic analyses, we deduced that these lamprey receptors are likely distinct ohnologs to gnathostome LepR and IL6RB-related receptors, respectively, that arose in the two rounds of vertebrate whole-genome duplication (1R and 2R). Notably, lamprey LepRL likely originated from a different 1R progenitor than the one giving rise to gnathostome LepR during cyclostome hexaploidization. Differential patterns in mRNA expression of LepRL and IL6RBLs were observed among adult tissues, during larval metamorphosis, and in response to juvenile feeding. Feeding stimulated hepatic expression of LepRL and IL6RBL (namely, IL6RBL1) mRNAs in correlation with upregulation of insulin-like growth factor mRNA, whereas brain LepRL and IL6RBL1 mRNA expression was correlated positively with neuropeptide Y but inversely with intestinal content in fed juveniles. Notably, these observations along with immunolocalization of LepRL in the hypothalamus suggest a role of leptin signaling in regulating energy balance that is conserved among vertebrates. Additionally, seawater exposure stimulated branchial LepRL expression coincident with increased expression of ion transporters in ionocytes, indicating a role of leptin signaling in osmoregulation. These findings provide new insight into the early evolution of class-I cytokine receptors and reveal diverse functions of the leptin signaling system in jawless vertebrate.</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/PMC12284397/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540874","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":"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":"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}