Molecular biology and evolution最新文献

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A deep learning-based score to evaluate multiple sequence alignments. 基于深度学习的评分,用于评估多个序列比对。
IF 6.4 1区 生物学
Molecular biology and evolution Pub Date : 2026-08-01 DOI: 10.1093/molbev/msag173
Nimrod Serok, Ksenia Polonsky, Haim Ashkenazy, Itay Mayrose, Jeffrey L Thorne, Tal Pupko
{"title":"A deep learning-based score to evaluate multiple sequence alignments.","authors":"Nimrod Serok, Ksenia Polonsky, Haim Ashkenazy, Itay Mayrose, Jeffrey L Thorne, Tal Pupko","doi":"10.1093/molbev/msag173","DOIUrl":"10.1093/molbev/msag173","url":null,"abstract":"<p><p>Multiple sequence alignment (MSA) inference is a central task in molecular evolution and comparative genomics, and the reliability of downstream analyses, including phylogenetic inference, depends critically on alignment quality. Despite this importance, most widely used MSA methods optimize the sum-of-pairs (SoP) score, and relatively little attention has been paid to whether this objective function accurately reflects alignment accuracy. Here, we evaluate the performance of the SoP score using simulated and empirical benchmark alignments. For each dataset, we compare alternative MSAs derived from the same unaligned sequences and quantify the relationship between their SoP scores and their distances from a reference alignment. We show that the alignment with the optimal SoP score often does not correspond to the most accurate alignment. To address this limitation, we develop deep learning-based scoring functions that integrate a collection of MSA features. We first introduce Model 1, a regression model that predicts the distance of a given MSA from the reference alignment. Across simulated and empirical datasets, this learned score correlates more strongly with true alignment accuracy than the SoP score. However, Model 1 is less effective at identifying the best alignment among alternatives. We therefore develop Model 2, which takes as input a set of alternative MSAs generated from the same sequences and predicts their relative ranking. Model 2 more accurately identifies the top-ranking MSA than the SoP score, Model 1, and several widely used alignment programs. Using simulations, we show that selecting MSAs based on our approach leads to more accurate phylogenetic reconstructions.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13428293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148549661","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}
引用次数: 0
Bacterial Persistence Modulates the Speed, Magnitude, and Onset of Antibiotic Resistance Evolution. 细菌的持久性调节了抗生素耐药性进化的速度、幅度和开始。
IF 6.4 1区 生物学
Molecular biology and evolution Pub Date : 2026-08-01 DOI: 10.1093/molbev/msag180
Giorgio Boccarella, Philip Ruelens, Ernesto Berríos-Caro, Bram Van den Bergh, Lloyd Cool, Jan Michiels, Pieter van den Berg
{"title":"Bacterial Persistence Modulates the Speed, Magnitude, and Onset of Antibiotic Resistance Evolution.","authors":"Giorgio Boccarella, Philip Ruelens, Ernesto Berríos-Caro, Bram Van den Bergh, Lloyd Cool, Jan Michiels, Pieter van den Berg","doi":"10.1093/molbev/msag180","DOIUrl":"10.1093/molbev/msag180","url":null,"abstract":"<p><p>Bacterial persistence, a phenomenon where a subpopulation of cells can exhibit increased survival to antibiotic stress, allows part of the population to withstand antibiotic treatment. This can have far-reaching implications for the evolution of antibiotic resistance, yet its evolutionary consequences remain insufficiently understood. Here, using a combination of evolutionary modeling and experimental evolution data on Escherichia coli, we show that persistence impacts the speed, onset, and magnitude of antibiotic resistance evolution. Specifically, high persistence facilitates the slow establishment of small-effect mutations by protecting them from antibiotic killing, while low persistence boosts the rapid yet unpredictable emergence of rare large-effect resistance mutations by amplifying their competitive advantage. Our results show that persistence level has a critical impact on the trade-off between short-term population survival and the evolution of high-level resistance, with distinct outcomes depending on the severity of the antibiotic treatment regimen. These findings provide key insights for designing antibiotic treatment strategies that minimize the risk of antibiotic resistance evolution while maintaining treatment efficacy.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13475807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148549669","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}
引用次数: 0
Reconstructing the evolutionary origin of β-catenin recognition in the Wnt destruction complex. 重建Wnt破坏复合体中β-连环蛋白识别的进化起源。
IF 6.4 1区 生物学
Molecular biology and evolution Pub Date : 2026-08-01 DOI: 10.1093/molbev/msag185
Hongyan Sun, Brian M Walters, Radim Zidek, Mark Q Martindale, Athula H Wikramanayake
{"title":"Reconstructing the evolutionary origin of β-catenin recognition in the Wnt destruction complex.","authors":"Hongyan Sun, Brian M Walters, Radim Zidek, Mark Q Martindale, Athula H Wikramanayake","doi":"10.1093/molbev/msag185","DOIUrl":"10.1093/molbev/msag185","url":null,"abstract":"<p><p>Emergence of Wnt/β-catenin signaling was a major metazoan innovation, yet how its core molecular interactions evolved remains unresolved. Here, we investigated evolution of the Wnt/β-catenin destruction complex (BDC), a conserved regulatory module that represses Wnt/β-catenin signaling by targeting cytoplasmic β-catenin for degradation. In bilaterians, BDC activity depends on interactions between Axin, adenomatous polyposis coli (APC), and β-catenin. However, bioinformatic analyses suggested that early-diverging metazoans lack the canonical β-catenin-binding motifs required for these interactions raising questions about the origin of BDC function. Using functional assays in Nematostella vectensis, a representative of the Cnidaria, the outgroup to bilaterians, we demonstrate that both NvAxin and NvAPC regulate Wnt/β-catenin signaling, indicating the presence of a BDC despite the lack of canonical bilaterian binding motifs. In vitro experiments revealed that NvAxin binds Nvβ-catenin through previously unrecognized low-affinity interactions. Guided by AlphaFold3 predictions, we identified two β-catenin-binding motif-like sequences in cnidarian Axin including one within the Axin-RGS domain, and a single motif in the Axin-RGS domain of placozoans, sponges, and ctenophores. Functional analyses showed that a conserved residue within these motifs is required for Axin-β-catenin interaction. Our results support a model where an ancestral β-catenin-binding motif-like sequence in Axin-RGS acquired weak β-catenin-binding capacity in early-emerging metazoans followed by motif duplication in the cnidarian-bilaterian last common ancestor. In bilaterians, the duplicated β-catenin-binding motif evolved higher affinity for β-catenin, while the ancestral sequence was lost. By integrating phylogenetics, AI-based structural prediction, and experimental validation, we have revealed for the first time the molecular steps underlying functional evolution of a complex signaling pathway.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148562611","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}
引用次数: 0
Evaluating the adaptive hypothesis of A-to-I RNA editing in filamentous ascomycete fungi. 评价A-to-I RNA编辑在丝状子囊菌真菌中的适应性假说。
IF 6.4 1区 生物学
Molecular biology and evolution Pub Date : 2026-08-01 DOI: 10.1093/molbev/msag179
Jiachen Li, Daohan Jiang, Jianzhi Zhang
{"title":"Evaluating the adaptive hypothesis of A-to-I RNA editing in filamentous ascomycete fungi.","authors":"Jiachen Li, Daohan Jiang, Jianzhi Zhang","doi":"10.1093/molbev/msag179","DOIUrl":"10.1093/molbev/msag179","url":null,"abstract":"<p><p>A-to-I RNA editing enzymatically converts adenosine (A) to inosine (I) in RNA molecules. During sexual reproduction in several filamentous ascomycete fungi, hundreds to tens of thousands of protein-coding sites are edited from A to I, mostly read as guanine (G) by ribosomes. A previous study reported a higher frequency of nonsynonymous than synonymous editing and inferred that A-to-I editing is adaptive in these fungi. However, this inference was based on ∼1% of all editing sites due to methodological limitations, and an alternative nonadaptive explanation-the harm-permitting model-was not considered. Here, we develop a method to test the adaptive hypothesis of RNA editing while accounting for sequence motifs associated with editing, thereby enabling the inclusion of all detected editing events. We apply this method to genomic and transcriptomic data from Fusarium graminearum, Neurospora crassa, and Neurospora tetrasperma. Our analyses suggest that nonsynonymous A-to-I RNA editing in these species is frequently adaptive and that, for at least some nonsynonymous editing events, the benefit primarily arises from the production of multiple distinct proteins from a single gene. Nonetheless, not all nonsynonymous editing is adaptive. Sequence motifs prone to nonsynonymous editing have been selectively depleted at specific genomic locations in genes expressed in sexual reproduction, and a subset of editing events exhibits patterns consistent with the harm-permitting model. In summary, both adaptive and nonadaptive nonsynonymous editing exist in filamentous ascomycetes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13431901/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148536370","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}
引用次数: 0
Phylo-Movies: animating phylogenetic trees from sliding-window analyses. 进化电影:从滑动窗口分析的系统发育树动画。
IF 6.4 1区 生物学
Molecular biology and evolution Pub Date : 2026-08-01 DOI: 10.1093/molbev/msag194
Enes Sakalli, Simon Haendeler, Arndt von Haeseler, Heiko A Schmidt
{"title":"Phylo-Movies: animating phylogenetic trees from sliding-window analyses.","authors":"Enes Sakalli, Simon Haendeler, Arndt von Haeseler, Heiko A Schmidt","doi":"10.1093/molbev/msag194","DOIUrl":"10.1093/molbev/msag194","url":null,"abstract":"<p><p>Sliding-window phylogenetic analyses of multiple sequence alignments generate sequences of phylogenetic trees that can reveal phylogenetic conflict along genomes, as can be caused by recombination and other sources; yet, comparing trees across genomic windows remains challenging. Phylo-Movies is a browser-based tool-also available as a standalone desktop application-that decomposes topological differences between consecutive phylogenetic trees into interpretable rooted subtree prune-and-regraft moves and animates these transformations. We illustrate its use in two contexts: localizing candidate recombination breakpoints in norovirus genomes, where taxa change from polymerase-genotype-associated to capsid-genotype-associated placements at the ORF1/ORF2 junction, and exploring candidate rogue taxa that change position across bootstrap replicates. Phylo-Movies complements quantitative measures such as Robinson-Foulds distances, split-frequency support values, and rogue-taxon scores by showing which subtrees move and how their source and target placements differ. The animations also provide an intuitive educational tool for teaching and workshops. Phylo-Movies is freely available at https://enesberksakalli.github.io/phylo-movies/, with source code at https://github.com/enesBerkSakalli/phylo-movies, and demonstration videos at https://vimeo.com/1199476378, https://vimeo.com/1199476382, https://vimeo.com/1199476534, https://vimeo.com/1199487394, and https://vimeo.com/1199495473.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13501920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148713278","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}
引用次数: 0
EZmito2: a tool suite for mitochondrial genome dataset preparation, population genetics, and visualization. EZmito2:用于线粒体基因组数据集准备,群体遗传学和可视化的工具套件。
IF 6.4 1区 生物学
Molecular biology and evolution Pub Date : 2026-08-01 DOI: 10.1093/molbev/msag210
Claudio Cucini, Joan Pons, Rebecca Funari, Antonio Carapelli, Francesco Frati, Francesco Nardi
{"title":"EZmito2: a tool suite for mitochondrial genome dataset preparation, population genetics, and visualization.","authors":"Claudio Cucini, Joan Pons, Rebecca Funari, Antonio Carapelli, Francesco Frati, Francesco Nardi","doi":"10.1093/molbev/msag210","DOIUrl":"10.1093/molbev/msag210","url":null,"abstract":"<p><p>Mitogenomic datasets are central to molecular evolution and phylogenetics, yet preparatory workflows remain labor-intensive and prone to errors introduced during manual data preparation. EZmito2 is a re-implementation of the widely used EZmito pipeline that offers a fully reproducible and user-accessible solution for mitogenomic dataset curation and result visualization. It is accessible via a public web server for rapid analyses and through local installation, enabling reproducible workflows on personal computers or computational clusters. The pipeline consolidates the core modules-EZpipe, EZskew, and EZcodon-and extends functionality through newly developed tools for genome visualization (EZcircular, EZmap), chimeric region detection (EZmix), gene extraction from NCBI-deposited genomes (EZsplit), structural annotation of transmembrane domains in mitochondrial protein-coding genes (EZtrampo), and population genetic studies (EZdist, EZpcoa, EZpopstat). All tools accept standard input formats and generate ready-to-publish outputs. By providing a user-friendly platform for mitogenomic exploration and quality control, EZmito2 facilitates reproducible analyses for evolutionary and molecular research communities.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13524090/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795468","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}
引用次数: 0
Beyond fixation: persistent genetic variation under intense selection. 超越固定:强烈选择下的持续遗传变异。
IF 6.4 1区 生物学
Molecular biology and evolution Pub Date : 2026-08-01 DOI: 10.1093/molbev/msag188
Kenneth R Arnold, Zachary S Greenspan, Ryan D Robinson, Anastasia Pupo, Valeria V Chavarin, Kevin S Chang, Corrina O Cannell, Miao Qi, Laurence D Mueller, Michael R Rose, Mark A Phillips
{"title":"Beyond fixation: persistent genetic variation under intense selection.","authors":"Kenneth R Arnold, Zachary S Greenspan, Ryan D Robinson, Anastasia Pupo, Valeria V Chavarin, Kevin S Chang, Corrina O Cannell, Miao Qi, Laurence D Mueller, Michael R Rose, Mark A Phillips","doi":"10.1093/molbev/msag188","DOIUrl":"10.1093/molbev/msag188","url":null,"abstract":"<p><p>Understanding how and why genetic variation is maintained under sustained selection remains a central question in evolutionary genetics. Experimental evolution shows that adaptation in sexually reproducing populations is often highly polygenic, proceeding through coordinated, genome-wide allele frequency shifts from standing variation rather than classic hard sweeps. Recent explanations emphasize highly polygenic architectures, optimizing-selection, and genetic redundancy, which can slow fixation by distributing selection across many loci during adaptation. However, observations from long-term selection experiments reveal a pattern these frameworks do not fully explain: substantial genetic variation persists after hundreds of generations of intense directional selection in constant environments. Here, we use long-term experimental evolution in Drosophila melanogaster to test whether balancing-selection actively maintains genetic variation under strong life-history selection and preserves evolutionary reversibility. Longstanding populations selected for accelerated or delayed reproduction were shifted to the opposing regime, imposing age-structured fitness trade-offs. Notably, selection for early reproduction is associated with substantial loss of genetic variation, providing a stringent test of whether standing variation is truly depleted. Following reciprocal shifts, populations showed rapid phenotypic convergence toward the target regime. At the genomic level, allele-frequency trajectories were strongly antiparallel and highly repeatable across replicates, revealing coordinated polygenic responses. Reversing long-standing early-life selection produced a pronounced rebound in genome-wide heterozygosity. Deep sequencing uncovered ultra-rare alleles at sites appearing fixed under standard coverage, indicating low-frequency functional variation persists below detection thresholds. These results suggest that substantial genetic variation can persist under intense directional selection and be rapidly redeployed when selection reverses, consistent with widespread balancing-selection.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455604/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148604904","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}
引用次数: 0
Temperature-sensitive cytoplasmic incompatibility across divergent Wolbachia partly reflects cifB transcription, not endosymbiont density. 不同沃尔巴克氏体之间的温度敏感细胞质不相容性部分反映了cifB转录,而不是内共生体密度。
IF 6.4 1区 生物学
Molecular biology and evolution Pub Date : 2026-08-01 DOI: 10.1093/molbev/msag186
Basabi Bagchi, Lore Van Vlaenderen, Tim Wheeler, Elena Provencal, William R Conner, Kyle McGuire, Brandon S Cooper, J Dylan Shropshire
{"title":"Temperature-sensitive cytoplasmic incompatibility across divergent Wolbachia partly reflects cifB transcription, not endosymbiont density.","authors":"Basabi Bagchi, Lore Van Vlaenderen, Tim Wheeler, Elena Provencal, William R Conner, Kyle McGuire, Brandon S Cooper, J Dylan Shropshire","doi":"10.1093/molbev/msag186","DOIUrl":"10.1093/molbev/msag186","url":null,"abstract":"<p><p>Maternally transmitted Wolbachia bacteria are common in insects, with many strains altering host reproduction through cytoplasmic incompatibility (CI). Cytoplasmic incompatibility kills embryos fertilized by Wolbachia-bearing males unless those embryos also carry Wolbachia, which favors females with Wolbachia and drives the endosymbiont to higher frequencies in host populations. Strong CI now underpins successful applications that rely on maintaining pathogen-blocking Wolbachia transinfections in vector populations to reduce arboviral disease transmission. Temperature modulates CI strength (the proportion of embryos killed), with consequences for Wolbachia prevalence in natural and transinfected populations. Yet the mechanisms regulating temperature-sensitive CI-strength variation are poorly understood. We quantified CI strength across eight divergent Drosophila-associated Wolbachia strains at four temperatures (18 to 26 °C), while characterizing development time, Wolbachia and Wovirus densities, and transcription of the CI-inducing gene cifB. Four of eight Wolbachia strains exhibited temperature-sensitive CI, three of which induced CI at multiple temperatures. Of these three, two expressed significantly more cifB at the temperature yielding stronger CI, whereas testes Wolbachia density did not predict CI strength. Notably, cifB-transcript levels were consistently decoupled from Wolbachia and Wovirus densities, suggesting that cifB transcription is not regulated solely by symbiont abundance. We also report temperature-sensitive rescue of CI, Wolbachia-associated developmental acceleration, and strain-specific Wovirus-Wolbachia covariance. Our findings reveal temperature as a pervasive modulator of Wolbachia-host interactions at multiple levels and extend evidence that cifB transcription partly predicts variable CI strength across strain identities, male ages, and now temperatures. Cytoplasmic incompatibility variation unaccounted for by cifB transcription points toward additional regulatory or posttranscriptional mechanisms that we discuss.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148562619","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}
引用次数: 0
Plasticity-first evolution via CYP405 loss shaped chemical defenses in butterflies. 通过CYP405缺失的可塑性优先进化形成了蝴蝶的化学防御。
IF 6.4 1区 生物学
Molecular biology and evolution Pub Date : 2026-08-01 DOI: 10.1093/molbev/msag197
Erika C Pinheiro de Castro, Francesco Cicconardi, Ian A Warren, Nicol Rueda-M, Camilo Salazar, Søren Bak, Stephen H Montgomery, Chris D Jiggins
{"title":"Plasticity-first evolution via CYP405 loss shaped chemical defenses in butterflies.","authors":"Erika C Pinheiro de Castro, Francesco Cicconardi, Ian A Warren, Nicol Rueda-M, Camilo Salazar, Søren Bak, Stephen H Montgomery, Chris D Jiggins","doi":"10.1093/molbev/msag197","DOIUrl":"10.1093/molbev/msag197","url":null,"abstract":"<p><p>Phenotypic plasticity allows a single genotype to maintain its fitness across different environments. This facilitates colonization of new niches but can be further refined or even lost as lineages diversify. The toxic Heliconiini butterflies have biochemical plasticity: they either sequester their cyanogenic glucosides (CGs) from their larval host plant or biosynthesize them when compounds for sequestration are not available. Here, we trace the evolution of CG biosynthesis in Heliconiini butterflies, a fundamental component of this biochemical plasticity. We first reconstructed the evolutionary history of biochemical plasticity in Heliconiini using chemical data from over 700 individuals, demonstrating that plasticity was ancestral in the tribe but subsequently lost in a few clades, such as the Sapho clade specialized in CG sequestration. In lepidopterans, CG biosynthesis has previously been characterized in the moth Zygaena filipendulae, as the genes CYP405A2, CYP332A3, and UGT33A1. Thus, we CRISPR-edited CYP405 in Heliconius erato and confirmed that CYP405-knockout caterpillars do not biosynthesize CGs. We identified the CYP405As and CYP332As in other lepidopterans and found that both genes were independently co-opted into CG biosynthesis in the Heliconiinae butterflies and Zygaena moths. While most lepidopterans have a CYP332A, CYP405A is mostly restricted to butterflies and has been duplicated in all Heliconius species. Although several CYP405A copies were found in the Sapho clade, most of them lack structurally important P450 domains, which explains the loss of biochemical plasticity via specialization in CG sequestration. This is one of the few examples of plasticity-first evolution in which the genetic mechanisms associated with its refinement are known.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13494554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148701861","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}
引用次数: 0
Estimating the evolutionary fitness of specific synonymous codon changes. 估计特定同义密码子变化的进化适应度。
IF 6.4 1区 生物学
Molecular biology and evolution Pub Date : 2026-08-01 DOI: 10.1093/molbev/msag199
Vitor A C Pavinato, Jody Hey
{"title":"Estimating the evolutionary fitness of specific synonymous codon changes.","authors":"Vitor A C Pavinato, Jody Hey","doi":"10.1093/molbev/msag199","DOIUrl":"10.1093/molbev/msag199","url":null,"abstract":"<p><p>Synonymous mutations do not alter proteins but undergo natural selection in many species. For Drosophila melanogaster, reports on selection strength vary from undetectable to surprisingly strong. Here we apply a new method to estimate the population selection coefficient (2Ns) for all 134 ordered pairs of synonymous codon changes. The method uses ratios of site frequency spectra for synonymous codon changes and matched neutral changes, avoiding reliance on divergence data or codon frequencies and remaining relatively insensitive to demographic history. Results indicate that natural selection on synonymous codons is weak, with |2Ns|<2.30 for all pairs of codons and |2Ns|<1 for 49% of codon changes. Despite being derived solely from polymorphism data, codon fitness estimates are strongly correlated with observed codon frequencies. A selection-mutation-drift model based on these estimates accurately predicts codon usage, while a model based on mutation alone fails. Codon fitness estimates also predict expression-associated codon usage, with higher-fitness codons used more often in highly expressed genes. However, the effect of expression on selection strength is modest, with a 10-fold increase in expression predicted to increase the average strength of selection on synonymous codons by only 14%. Finally, we detect clear signs that selection favors codon changes that stabilize mRNA secondary structure. The convergence of multiple independent lines of evidence validates this polymorphism-based approach and provides a coherent framework for understanding selection on synonymous site evolution.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13494555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148707030","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}
引用次数: 0
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