Molecular biology and evolution最新文献_第7页

The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model. 多物种聚结模型下测序和基因分型错误对基因组数据贝叶斯分析的影响。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-07-30 DOI: 10.1093/molbev/msaf184

Jiayi Ji, Paschalia Kapli, Tomáš Flouri, Ziheng Yang

{"title":"The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model.","authors":"Jiayi Ji, Paschalia Kapli, Tomáš Flouri, Ziheng Yang","doi":"10.1093/molbev/msaf184","DOIUrl":"10.1093/molbev/msaf184","url":null,"abstract":"The multispecies coalescent (MSC) model accounts for genealogical fluctuations across the genome and provides a framework for analyzing genomic data from closely related species to estimate species phylogenies and divergence times, infer interspecific gene flow, and delineate species boundaries. As the MSC model assumes correct sequences, sequencing and genotyping errors at low read depths may be a serious concern. Here, we use computer simulation to assess the impact of genotyping errors in phylogenomic data on Bayesian inference of the species tree and population parameters such as species split times, population sizes, and the rate of gene flow. The base-calling error rate is extremely influential. At the low rate of e = 0.001 (Phred score of 30), estimation of species trees and population parameters are little affected by genotyping errors even at the low depth of ∼3×. At high error rates (e = 0.005 or 0.01) and low depths (less than 10×), genotyping errors can reduce the power of species tree estimation, and introduce biases in estimates of population sizes, species divergence times, and the rate of gene flow. Treating heterozygotes in the sequences as missing data (ambiguities) may reduce the impact of genotyping errors. Our simulation suggests that it is preferable in terms of inference precision and accuracy to sequence a few samples at high depths rather than many samples at low depths.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 8","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12359030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874171","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

Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation. 用于改进跨站点进化变异建模的无限混合模型。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-07-30 DOI: 10.1093/molbev/msaf199

Mandev S Gill, Guy Baele, Marc A Suchard, Philippe Lemey

{"title":"Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation.","authors":"Mandev S Gill, Guy Baele, Marc A Suchard, Philippe Lemey","doi":"10.1093/molbev/msaf199","DOIUrl":"10.1093/molbev/msaf199","url":null,"abstract":"Scientific studies in many areas of biology routinely employ evolutionary analyses based on inference of phylogenetic trees from molecular sequence data. Evolutionary processes that act at the molecular level are highly variable, and properly accounting for heterogeneity is crucial for more accurate phylogenetic inference. Nucleotide substitution rates and patterns are known to vary among sites in multiple sequence alignments, and such variation can be modeled by partitioning alignments into categories corresponding to different substitution models. Determining a priori appropriate partitions can be difficult, however, and better model fit can be achieved through flexible Bayesian infinite mixture models that simultaneously infer the number of partitions, the partition that each site belongs to, and the evolutionary parameters corresponding to each partition. Here, we consider several different types of infinite mixture models, including classic Dirichlet process mixtures, as well as novel approaches for modeling across-site evolutionary variation: hierarchical models for data with a natural group structure, and infinite hidden Markov models that account for spatial patterns in alignments. In analyses of several viral data sets, we find that different types of models perform best in different scenarios, but infinite hidden Markov models emerge as particularly promising for larger data sets and complex evolutionary patterns characterized by multiple genes and overlapping reading frames. To enable these models to scale to large data sets, we adapt efficient Markov chain Monte Carlo algorithms and exploit opportunities for parallel computing. We implement this infinite mixture modeling framework in BEAST X, a widely-used software package for phylogenetic inference.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835719","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

A Splicing Mutation in mitfa is Involved in the Depigmentation of Cavefish Triplophysa rosa. 一个mitfa剪接突变参与了洞穴鱼的色素脱色。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-07-30 DOI: 10.1093/molbev/msaf175

Mingming Zhang, Qingshuo Zhao, Jinqing Huang, Ming Zou, Baocheng Guo, Yahui Zhao, Fanwei Meng

{"title":"A Splicing Mutation in mitfa is Involved in the Depigmentation of Cavefish Triplophysa rosa.","authors":"Mingming Zhang, Qingshuo Zhao, Jinqing Huang, Ming Zou, Baocheng Guo, Yahui Zhao, Fanwei Meng","doi":"10.1093/molbev/msaf175","DOIUrl":"10.1093/molbev/msaf175","url":null,"abstract":"Regression traits such as pigmentation loss in cave-dwelling species offer powerful models for understanding evolutionary mechanisms under extreme environments. In this study, we investigated the genetic and evolutionary mechanisms underlying pigmentation loss in the cavefish Triplophysa rosa, a depigmented, eyeless species endemic to subterranean habitats. Compared with its surface-dwelling relative T. stenura, T. rosa exhibited significantly reduced expression of melanogenesis genes, indicating transcriptional repression of pigmentation pathways. Further analysis revealed a novel splicing site mutation in melanocyte inducing transcription factor a (mitfa), which results in a 63-nt deletion and loss of 21 amino acids in the activation domain. Functional rescue assays in zebrafish confirmed that the loss of 21 amino acids in Mitfa severely compromises melanin synthesis. Additionally, a premature stop codon in tyrosinase-related protein 1a (tyrp1a) was detected, which may also contribute to the depigmented phenotype. Evolutionary analyses indicated that pigmentation-specific genes in the T. rosa lineage are under relaxed purifying selection, consistent with weakened selective constraints on pigmentation in cave environments. Collectively, our findings indicate that a splice-site mutation in mitfa, acting against a background of relaxed selection on pigmentation genes, contributes to pigmentation loss in T. rosa, offering integrated proximate (molecular) and evolutionary insights into the troglomorphic traits in cavefish.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12343024/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144708170","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

Convergent Evolution in Amblyopsid Cavefishes and the Age of Eastern North American Subterranean Ecosystems. 弱视类洞穴鱼的趋同进化与北美东部地下生态系统的时代。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-07-30 DOI: 10.1093/molbev/msaf185

Chase D Brownstein, Maxime Policarpo, Richard C Harrington, Eva A Hoffman, Maya F Stokes, Didier Casane, Thomas J Near

{"title":"Convergent Evolution in Amblyopsid Cavefishes and the Age of Eastern North American Subterranean Ecosystems.","authors":"Chase D Brownstein, Maxime Policarpo, Richard C Harrington, Eva A Hoffman, Maya F Stokes, Didier Casane, Thomas J Near","doi":"10.1093/molbev/msaf185","DOIUrl":"https://doi.org/10.1093/molbev/msaf185","url":null,"abstract":"Genomes provide tools for reconstructing organismal evolution and larger Earth system processes. Although genome sequences have been jointly analyzed with geological data to understand links between biological evolution and geological phenomena such as erosion and uplift, genomic and natural history observations have seldom been leveraged to reconstruct the timescale of landscape change in cases where traditional methods from the Earth sciences cannot. Here, we reconstruct the genomic evolution of cave-adapted amblyopsid fishes. Although high-resolution computed tomography reveals the strikingly similar skeletons of cave-adapted lineages, our analyses of the genomes of all species in this clade suggest that amblyopsids independently colonized caves and degenerated their eyes at least four times after descending from populations that already possessed adaptations to low-light environments. By examining pseudogenization through loss-of-function mutations in amblyopsids, we infer that the genomic bases of their vision degenerated over millions of years. We leverage these data to infer the ages of subterranean karstic ecosystems in eastern North America, which are difficult to date using standard geochronologic techniques. Our results support ancient ages for imperiled North American cave biotas and show how genomes can be used to inform the timescale of landscape evolution.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 8","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12375919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961605","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

Impact of Natural Transformation on the Acquisition of Novel Genes in Bacteria. 自然转化对细菌新基因获取的影响。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-07-30 DOI: 10.1093/molbev/msaf192

Fanny Mazzamurro, Marie Touchon, Xavier Charpentier, Eduardo P C Rocha

{"title":"Impact of Natural Transformation on the Acquisition of Novel Genes in Bacteria.","authors":"Fanny Mazzamurro, Marie Touchon, Xavier Charpentier, Eduardo P C Rocha","doi":"10.1093/molbev/msaf192","DOIUrl":"10.1093/molbev/msaf192","url":null,"abstract":"Natural transformation is the only process of gene exchange under the exclusive control of the recipient bacteria. It has often been considered as a source of novel genes, but quantitative assessments of this claim are lacking. To investigate the potential role of natural transformation in gene acquisition, we analyzed a large collection of genomes of Acinetobacter baumannii (Ab) and Legionella pneumophila (Lp) for which transformation rates were experimentally determined. Natural transformation rates are weakly correlated with genome size. But they are negatively associated with gene turnover in both species. This might result from a negative balance between the transformation's ability to cure the chromosome from mobile genetic elements (MGEs), resulting in gene loss, and its facilitation of gene acquisition. By comparing gene gains by transformation and MGEs, we found that transformation was associated with the acquisition of small sets of genes per event, which were also spread more evenly in the chromosome. We estimated the contribution of natural transformation to gene gains by comparing recombination-driven gene acquisition rates between transformable and non-transformable strains, finding that it facilitated the acquisition of ca. 6.4% (Ab) and 1.1% (Lp) of the novel genes. This moderate contribution of natural transformation to gene acquisition implies that most novel genes are acquired by other means. Yet, 15% of the recently acquired antibiotic resistance genes in A. baumannii may have been acquired by transformation. Hence, natural transformation may drive the acquisition of relatively few novel genes, but these may have a high fitness impact.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12359135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835718","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

ASTER: A Package for Large-Scale Phylogenomic Reconstructions. ASTER：一个用于大规模系统基因组重建的软件包。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-07-30 DOI: 10.1093/molbev/msaf172

Chao Zhang, Rasmus Nielsen, Siavash Mirarab

引用次数: 0

Somatic Evolution of Stem Cell Mutations in Long-Lived Plants. 长寿植物干细胞突变的体细胞进化。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-07-30 DOI: 10.1093/molbev/msaf165

Frank Johannes

引用次数: 0

Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales. 精确的，可扩展的结构变异基因分型在复杂的基因组在群体规模。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-07-30 DOI: 10.1093/molbev/msaf180

Ming Hu, Penglong Wan, Chengjie Chen, Shuyuan Tang, Jiahao Chen, Liang Wang, Mahul Chakraborty, Yongfeng Zhou, Jinfeng Chen, Brandon S Gaut, J J Emerson, Yi Liao

{"title":"Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.","authors":"Ming Hu, Penglong Wan, Chengjie Chen, Shuyuan Tang, Jiahao Chen, Liang Wang, Mahul Chakraborty, Yongfeng Zhou, Jinfeng Chen, Brandon S Gaut, J J Emerson, Yi Liao","doi":"10.1093/molbev/msaf180","DOIUrl":"10.1093/molbev/msaf180","url":null,"abstract":"Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce Structural Variants Genotyping of Assemblies on Population scales (SVGAP), a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level. Through extensive benchmarks using simulated SV datasets at individual, population, and phylogenetic contexts, we demonstrate that SVGAP performs favorably relative to existing tools in SV discovery. Additionally, SVGAP is one of the few tools to address the challenge of genotyping SVs within large assembled genome samples, and it generates fully genotyped VCF files. Applying SVGAP to 26 maize genomes revealed hidden genomic diversity in centromeres, driven by abundant insertions of centromere-specific LTR-retrotransposons. The output of SVGAP is well-suited for pangenome construction and facilitates the interpretation of previously unexplored genomic regions.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12362251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732312","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

Multiple Autopolyploid Arabidopsis lyrata Populations Stabilized by Long-Range Adaptive Introgression Across Eurasia. 欧亚大陆上的多个自多倍体拟南芥（Arabidopsis lyrata）群体通过长期适应性渗入稳定下来。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-07-30 DOI: 10.1093/molbev/msaf153

Alison D Scott, Uliana K Kolesnikova, Anna Glushkevich, Laura Steinmann, Nikita P Tikhomirov, Ursula Pfordt, Magdalena Bohutínská, Robin Burns, Alexey P Seregin, Filip Kolar, Roswitha Schmickl, Polina Yu Novikova

{"title":"Multiple Autopolyploid Arabidopsis lyrata Populations Stabilized by Long-Range Adaptive Introgression Across Eurasia.","authors":"Alison D Scott, Uliana K Kolesnikova, Anna Glushkevich, Laura Steinmann, Nikita P Tikhomirov, Ursula Pfordt, Magdalena Bohutínská, Robin Burns, Alexey P Seregin, Filip Kolar, Roswitha Schmickl, Polina Yu Novikova","doi":"10.1093/molbev/msaf153","DOIUrl":"10.1093/molbev/msaf153","url":null,"abstract":"Abundance of established polyploid lineages varies across lineages, evolutionary time, and geography, suggesting both genetics and environment play a role in polyploid persistence. We show Arabidopsis lyrata is the most polyploid-rich species complex in the Arabidopsis genus, with multiple origins of autotetraploidy. This is revealed by genomic data from over 400 A. lyrata samples across Eurasia. We found over 30 previously undescribed autotetraploid populations in Siberia with a minimum of two separate origins, independent of those previously reported in Central Europe. The establishment of Siberian tetraploids is mediated by meiotic adaptation at the same genes as in European tetraploid A. lyrata and Arabidopsis arenosa, despite their genomic divergence and geographical separation. Haplotype analysis based on synthetic long-read assemblies supports the long-range introgression of adaptive alleles from the tetraploid interspecific pool of European A. lyrata and A. arenosa to tetraploid Siberian A. lyrata. Once adaptations to polyploidy emerge, they promote the establishment of new polyploid lineages through adaptive inter- and intraspecific introgression.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12342985/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699021","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

An Extension of Muller's Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content. 性染色体基因内容进化的Muller遮蔽假说的延伸。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-07-30 DOI: 10.1093/molbev/msaf177

Andrea Mrnjavac, Beatriz Vicoso, Tim Connallon

{"title":"An Extension of Muller's Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.","authors":"Andrea Mrnjavac, Beatriz Vicoso, Tim Connallon","doi":"10.1093/molbev/msaf177","DOIUrl":"10.1093/molbev/msaf177","url":null,"abstract":"The first influential hypothesis for sex chromosome evolution was proposed in 1914 by H. J. Muller, who argued that once recombination was suppressed between the X and Y chromosomes, Y-linked genes become \"sheltered\" from selection, leading to accumulation of recessive loss-of-function (LOF) mutations and decay of Y-linked genes. The hypothesis fell out of favor in the 1970s because early mathematical models failed to support it and data on the dominance of lethal mutations were viewed as incompatible with the hypothesis. We reevaluate the main arguments against Muller's hypothesis and find that they do not conclusively exclude a role for sheltering in sex chromosome evolution. By relaxing restrictive assumptions of earlier models, we show that sheltering promotes fixation of LOF mutations with sexually dimorphic fitness effects, resulting in decay of X-linked genes that are exclusively expressed by males and Y-linked genes that are primarily, though not necessarily exclusively, expressed by females. We further show that drift and other processes contributing to Y degeneration (i.e. selective interference and regulatory evolution) expand conditions of Y-linked gene loss by sheltering. The actual contribution of sheltering to sex chromosome evolution hinges upon the distribution of dominance and sex-specific fitness effects of LOF mutations, which we discuss.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12342767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718190","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