Molecular biology and evolution最新文献

{"title":"Identifying adaptive variation in spatially structured populations using low-coverage whole-genome sequencing data.","authors":"Nikunj Goel, Christen M Bossu, Seorim Yi, Timothy M Brown, Erica C N Robertson, Peri E Bolton, Ben J Vernasco, Reza Goljani Amirkhiz, Erika S Zavaleta, Kristen C Ruegg, Mevin B Hooten","doi":"10.1093/molbev/msag255","DOIUrl":"10.1093/molbev/msag255","url":null,"abstract":"<p><p>Successful implementation of evolutionary programs to rescue climatically threatened species requires identification of adaptive variation. Although many genotype-environment association methods have been successful in identifying adaptive variation, current approaches can be improved in two important aspects. First, most existing methods do not account for genotype uncertainty in widely available low-coverage whole-genome sequencing data. Researchers often restrict analysis to loci for which genotypes can be inferred reliably or call the most probable genotype, allowing the use of genotype-based methods. However, discarding data and false genotype calls increase the uncertainty in estimates of genetic variation and can introduce systematic biases. Second, most methods use phenomenological approaches, such as logistic regression, to partition estimated variation into adaptive and nonadaptive components. Consequently, current approaches may fail to account for evolutionary processes, such as migration-selection balance. Structured migration between climatically disparate locations can produce deviations from a smooth S-shaped response curve, which can be difficult to accommodate using generalized linear models. To overcome these challenges, we developed a method that accounts for genotype uncertainty in sequencing data and propagates this uncertainty to inform the parameters of an evolutionary model. A key feature of this model is that it describes mechanistically how genetic variation arises from joint interactions between local adaptation, structured migration, mutation, and drift. Our synthetic simulation tests reveal that accounting for genotype uncertainty and structured migration substantially reduces false negatives. We also applied our approach to analyze data on North American rosy-finches (3.7 million SNPs), a high-alpine, climatically threatened clade of bird species.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13669788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112285","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":"Mito-nuclear incompatibility disrupts acyl-CoA oxidase 1/acyl-CoA oxidase 3-mediated mitochondria-peroxisome metabolic coordination in black soldier flies.","authors":"Xue Wang, Shuyun Zhao, Guoxin Huang, Runjia Wang, Xinrui Ren, Jing Liu, Junkui Huang, Jinhua Xiao","doi":"10.1093/molbev/msag241","DOIUrl":"10.1093/molbev/msag241","url":null,"abstract":"<p><p>Mito-nuclear coadaptation is a fundamental evolutionary process linking genomic interactions to metabolic performance and organismal fitness. Although mito-nuclear incompatibility is known to impair mitochondrial function and contribute to hybrid breakdown, its effects on metabolic coordination between cellular organelles remain poorly understood, particularly in insects. Here, we used the black soldier fly (Hermetia illucens L.) as an experimental model and established a mito-nuclear incompatibility system by introducing heterologous mitochondrial genomes into a common nuclear background. Integrating genomic, transcriptomic, metabolomic, and functional analyses, we found that mito-nuclear mismatch disrupted not only mitochondrial oxidative phosphorylation but also peroxisome biogenesis and fatty acid metabolism. We identified the peroxisomal acyl-CoA oxidases ACOX1 and ACOX3 as important components associated with mito-nuclear incompatibility-induced disruption of mitochondria-peroxisome metabolic coordination. Functional knockdown of acyl-CoA oxidase (ACOX) genes recapitulated major metabolic and fitness-related phenotypes associated with mito-nuclear mismatch, including energy deficiency, oxidative stress, delayed larval development, and reduced adult reproductive performance. Moreover, restoration of redox and energetic homeostasis partially rescued ACOX expression, whereas reinstating ACOX expression alleviated lipid metabolic defects in mismatched lines. Together, these findings support a model in which mito-nuclear incompatibility disrupts mitochondrial function and peroxisomal metabolic homeostasis, with reduced ACOX-dependent fatty acid metabolism representing an important component of broader mitochondria-peroxisome metabolic dysregulation. Our findings reveal a previously underappreciated role of mito-nuclear interactions in coordinating mitochondrial-peroxisomal metabolism and provide a mechanistic framework for understanding how genomic compatibility influences metabolic integration across cellular organelles.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149012545","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":"Contrasting modes of intron evolution in an evolutionarily distinct eukaryotic lineage revealed by comparative genomics of ciliated protists.","authors":"Zhaorui Zhou, Ruitao Gong, Yong Chi, Yurui Wang, Zhiqiang Ye, Ying Yan","doi":"10.1093/molbev/msag252","DOIUrl":"https://doi.org/10.1093/molbev/msag252","url":null,"abstract":"<p><p>Introns are widespread in eukaryotic genomes and play important roles in gene regulation, making intron evolution a long-standing focus of genome research. However, the patterns and mechanisms of intron evolution in evolutionarily ancient unicellular eukaryotes remain poorly understood. Here, we investigate intron evolution in ciliates, a morphologically and genetically diverse unicellular lineage, using a newly sequenced high-quality genome and comparative genomic data from derived and deep-branching lineages. Our analyses reveal that: 1) intron evolution in ciliates has been dominated by loss. While derived lineages experienced limited loss, the common ancestor of deep-branching groups, represented by heterotrich ciliates, underwent massive intron loss with almost no detectable gain. 2) Unlike derived ciliates, which display relatively uniform distributions of 3n, 3n+1, and 3n+2 introns or a low proportion of 3n introns, deep-branching ciliates show a striking dominance of tiny 3n introns. These are preferentially retained when generating in-frame premature termination codons (PTCs), likely allowing aberrant transcripts to be eliminated via nonsense-mediated mRNA decay, while introns incapable of forming PTCs tend to avoid insertion within protein domains, suggesting a strategy to reduce the metabolic cost of erroneous splicing. 3) Spliceosome analyses reveal conserved core catalytic components but lineage-specific variation in regulatory factors, suggesting differences in splicing regulation among ciliate lineages. Furthermore, the newly assembled 48.5 Mb Blepharisma genome encodes 27,571 protein-coding genes, and comparative analyses identified two rounds of whole-genome duplication in Blepharisma, one shared with Stentor. These findings provide new insights into intron evolution in unicellular eukaryotes and highlight ciliates as a powerful model for studying unconventional intron evolutionary strategies.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149081461","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":"An archaic reference-free method to jointly infer Neanderthal and Denisovan introgressed segments in modern human genomes.","authors":"Léo Planche, Anna Ilina, María C Ávila-Arcos, Flora Jay, Emilia Huerta-Sanchez, Vladimir Shchur","doi":"10.1093/molbev/msag235","DOIUrl":"https://doi.org/10.1093/molbev/msag235","url":null,"abstract":"<p><p>Admixture between populations is a common feature of human history. Admixture events introduce new genetic variation that can fuel evolution. Characterizing the significance of admixture events on the evolution of populations across various species is of great interest to evolutionary geneticists. Local Ancestry Inference (LAI) methods infer genetic ancestry of an individual at a particular chromosomal location. Certain methods specialize in detecting archaic introgression, which consists of interbreeding between modern and archaic humans like Neanderthals and Denisovans. Most current LAI methods allow the detection of a single archaic ancestry, and post-processing may distinguish between multiple waves of introgression. These methods vary in how they choose archaic or modern reference genomes for the inference. Here, we present a new HMM-based method (DAIseg), which has the advantage of simultaneously distinguishing between multiple waves of ancient and recent admixture, using only modern human reference genomes. Simulations demonstrate that DAIseg achieves higher overall performance than state-of-the-art methods. We also apply DAIseg to Papuan populations to jointly detect Denisovan and Neanderthal introgressed segments, and identify a higher number of archaic segments than previous methods. Analysis of inferred introgressed segments, shows that we can identify evidence for two Denisovan introgression events in Papuans. Overall, on top of being able to deal with both Archaic and recent admixture, DAIseg provides a more principled approach for detecting and classifying Denisovan and Neanderthal segments which will improve downstream analysis of introgressed segments to infer the impact of archaic introgression in humans.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148983166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From neuropeptides to toxins: illuminating the origins of venom complexity in cone snails.","authors":"Thomas Lund Koch, Giada Ferrari, Sunita B Sumanam, Paula Flórez Salcedo, Maren Watkins, Kevin Chase, Ave Tooming-Klunderud, Arturo O Lluisma, Angel Yanagihara, Neil D Young, Baldomero M Olivera, Eivind A B Undheim, Helena Safavi-Hemami","doi":"10.1093/molbev/msag206","DOIUrl":"10.1093/molbev/msag206","url":null,"abstract":"<p><p>New genes and gene functions are key drivers of evolutionary innovation. Venomous animals, such as cone snails, provide striking examples of gene innovation, yet the mechanisms by which toxins arise remain poorly understood. Using the Conus textile genome, we uncover how neuropeptide genes were recruited into the venom and neofunctionalized as doppelgänger toxins. We identify over 20 independent recruitment events that evolved dynamically across the Conus lineage. Rather than arising from ohnologs of a whole-genome duplication event ∼200 mya, these toxins evolved through diverse mechanisms, including exon shuffling, alternative splicing, and ectopic recombination, often facilitated by lineage-specific transposable elements. Our findings reveal a dynamic interplay between genome architecture and molecular innovation, offering broad insight into the evolution of complex gene repertoires in venoms and beyond.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13542836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148766246","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":"Ambrosia beetle invasions are structured by inbreeding, intraspecific hybridization, and bridgeheads.","authors":"Thomas L Schmidt, Anandi Bierman, Elizabeth J Huisamen, John S Terblanche, Ary A Hoffmann","doi":"10.1093/molbev/msag231","DOIUrl":"10.1093/molbev/msag231","url":null,"abstract":"<p><p>When invasive populations establish in regions far from their origin, they may accumulate deleterious mutations that limit population viability and later expansion. Invasions stemming from such bridgehead populations may experience further sequential bottlenecks. However, deleterious mutations can be masked or eliminated when populations outbreed with other lineages. Here, we analyze global invasions of a species complex of persistently inbreeding ambrosia beetles, using genomic data (n = 247) from invasive populations in Africa, North America, and Australia, and from native populations in Asia. We mostly focus on one species of this complex (Euwallacea fornicatus), which poses a severe threat to tree species worldwide and is rapidly expanding its global range. We uncover a single lineage of this species across California, South Africa, and Western Australia, involving an invasive bridgehead and containing almost no nuclear genetic variation. In South Africa, we identify a second lineage that has repeatedly hybridized with the first lineage. Genetic patterns in the native range indicate that such opportunistic outbreeding may be common. Despite lacking nuclear variation, the first lineage contained two CO1 haplotypes that were also observed in every hybrid lineage, pointing to heteroplasmy and possible hybrid origins of this lineage. Native populations had fewer missense mutations than invasive populations, indicating that opportunistic outbreeding may help purge fixed deleterious mutations when local lineage diversity is high. These findings highlight the importance of outbreeding even when inbreeding is common, and they demonstrate the biosecurity threat posed by subsequent gene flow into invasive populations.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13584198/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148912857","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":"Questioning the evidence for host-symbiont codiversification in mycorrhizal symbioses.","authors":"Fantine Bodin, Hélène Morlon, Benoît Perez-Lamarque","doi":"10.1093/molbev/msag207","DOIUrl":"10.1093/molbev/msag207","url":null,"abstract":"<p><p>The vast majority of plants form mycorrhizal symbioses. The ecological importance of these mutualistic interactions has sparked interest in their long evolutionary history. By examining interaction networks and phylogenetic trees, several studies have suggested that plants codiversify with their associated mycorrhizal fungi. However, recent research has demonstrated that phylogenetic congruence (interpreted as codiversification when divergence times match) is often conflated with another pattern called cophylogenetic signal (ie closely related plants interacting with closely related fungi and vice versa), which may arise from different biological processes. We performed cophylogenetic analyses on 29 diverse mycorrhizal networks to reevaluate the evidence for codiversification in mycorrhizal symbioses. We found a significant cophylogenetic signal but no phylogenetic congruence: Closely related plants often interact with closely related fungi, but their phylogenies do not match. Instead of codiversification, this finding is consistent with trait matching between plants and mycorrhizal fungi, where compatible, evolutionarily conserved plant and fungal traits govern their interactions. Our work highlights the importance of appropriately interpreting the cophylogenetic methods used to study the macroevolution of plants and their mycorrhizal fungi. It suggests that previous evidence of codiversification in mycorrhizal symbioses actually detected cophylogenetic signal, since, across the multiple and diverse networks analyzed here, there is no evidence that codiversification occurred during the evolution of mycorrhizal symbioses.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13533336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148759794","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":"Gene-level complexity explains genome-wide variation in the distribution of fitness effects.","authors":"Burçin Yıldırım, Jennifer E James","doi":"10.1093/molbev/msag216","DOIUrl":"10.1093/molbev/msag216","url":null,"abstract":"<p><p>The distribution of fitness effects (DFE)-describing how harmful, neutral, or beneficial new mutations are-is central to understanding how populations evolve. Although the DFE varies across genomes and species, it remains unclear which aspects of genomic organization drive this variation. Here, we inferred gene-level selective constraints across the genomes of Mus musculus castaneus, Drosophila melanogaster and Saccharomyces cerevisiae using a combination of population genetics and machine learning trained on diverse gene features. Many gene features were predictive of selective constraint, with conservation, gene structure, and expression being the most informative. These selective constraints delineated gene classes with distinct DFEs. Genes with higher connectivity and expression-features reflecting how many traits a gene influences-experienced stronger and less dispersed deleterious effects with increasing selective constraint. Between species, the rate of adaptation decreased with increasing organismal complexity, whereas across the genome it did not decrease monotonically with selective constraint, but tended to be higher at intermediate levels. While between-species comparisons of DFE parameters were less consistent with predictions of Fisher's geometric model (FGM) based on organismal complexity, variation in DFE parameters across the genome aligned more closely with FGM when complexity was considered at the gene level. Our results suggest that gene-level complexity, captured by genomic feature proxies, provides a more informative definition of complexity for DFE variation than organism-level labels, and highlight the value of using gene features collectively to link genomic architecture, fitness landscapes, and patterns of molecular evolution.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13537021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148851327","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 diversification of invertase paralogs couples carbon metabolism and sexual reproduction in fission yeasts.","authors":"Ambre Noly, Céline Faux, Maria Shaldaeva, Louison Bois-Naegelin, Philippe Fort, Dominique Helmlinger","doi":"10.1093/molbev/msag233","DOIUrl":"10.1093/molbev/msag233","url":null,"abstract":"<p><p>Dynamic patterns of gene gain and loss play a major role in the diversification of eukaryotes, reflecting adaptation to a broad range of ecological contexts. Reconstructing the evolutionary history of genes provides a powerful framework for understanding how functional innovation shapes life-history traits. Here, we report a comprehensive analysis of gene gain and loss across the fission yeast clade, whose evolutionary trajectory remains elusive. Reductive evolution of metabolic genes is a major contributor to species diversification, as observed in other fungal taxa. Notably, we uncovered an evolutionary scenario in which an ancestral gene duplication was followed by lineage-specific loss of one or the other paralog, except in Schizosaccharomyces pombe, which retained both. We demonstrate that these paralogs encode catalytically active invertases, named Inv1 and Inv2, with distinct enzymatic properties, localization, regulation, and physiological roles. Inv1 is a secreted enzyme subject to glucose-catabolite repression and is the sole invertase required for sucrose assimilation, resembling canonical yeast invertases. In contrast, Inv2 is intracellular, constitutively expressed, and required for inducing sexual differentiation in response to nutrient availability. Overall, these findings reveal an unexpected role for carbon metabolism in modulating the haploid-diploid cycle of fission yeasts, suggesting that diversification of core metabolic functions may contribute to adaptation to environments with distinct sugar compositions.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148912935","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":"Correction to: Deep learning reveals genomic regions introgressed between two recurrently hybridizing lynx species.","authors":"","doi":"10.1093/molbev/msag234","DOIUrl":"10.1093/molbev/msag234","url":null,"abstract":"","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"43 9","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13575817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148970270","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}