Molecular biology and evolution最新文献

{"title":"Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes.","authors":"Samuel N Bogan, Nathan Surendran, Scott Hotaling, Thomas Desvignes, Iliana Bista, Luana S F Lins, Mari H Eilertsen, Nathalie R Le François, Tait Algayer, Scott L Hamilton, Paul B Frandsen, Federico G Hoffmann, Joanna L Kelley","doi":"10.1093/molbev/msaf219","DOIUrl":"https://doi.org/10.1093/molbev/msaf219","url":null,"abstract":"<p><p>Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower tissue freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes' tandem array structure and consequently poor resolution of these repetitive regions. Here, we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B. We also show that AFP copy number increased under low temperature but decreased with depth, potentially because pressure lowers freezing point. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which AFP III arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 10","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251815","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":"eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA.","authors":"Jin-Hao Zhang, Chang-Lin Yang, Chang-Yuan Ren, Ji Shi, Han-Xiao Zhou, Ying Zhang, Zhi-Yan Sun, Tao Jiang, Zheng Zhao","doi":"10.1093/molbev/msaf223","DOIUrl":"10.1093/molbev/msaf223","url":null,"abstract":"<p><p>Extrachromosomal circular DNA (eccDNA) refers to small, circular DNA molecules that originate from chromosomal sequences and are prevalent across nearly all eukaryotic organisms. In humans, eccDNAs are widely distributed in normal tissues, cancerous tissues, and body fluids, where they play important roles in tumorigenesis and are often associated with poor clinical outcomes. Given their biological and clinical significance, a well-integrated and high-quality database is essential for advancing eccDNA-related research. To address this need, we developed eccDNABase, a comprehensive and curated resource for browsing, searching, and analyzing eccDNAs across multiple species. The database systematically catalogs eccDNA-disease associations from diverse tissues and organisms. Currently, eccDNABase contains 1,875,452 eccDNA-disease associations, encompassing 8,398 ecDNA entries across nine species, 63 diseases, and healthy individuals. Each entry provides detailed information, including eccDNA ID, type, chromosomal localization, species, tissue or cell line source, disease name and Disease Ontology ID, overlap length and percentage with genes, oncogene overlap, detection method, and links to literature and source databases. Given its extensive and curated datasets, eccDNABase serves as a valuable resource for both basic and translational research, offering deeper insights into the role of eccDNA in health and disease. The database is publicly accessible at http://cgga.org.cn/eccDNABase/.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12485997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145092001","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":"Deciphering the Impact of Temperature on Pleiotropic Consequences of RNA Polymerase Mutations.","authors":"Deniz Ozbilek, Jake K Soley, Danna R Gifford, Christopher G Knight, Simon C Lovell, Mato Lagator","doi":"10.1093/molbev/msaf226","DOIUrl":"10.1093/molbev/msaf226","url":null,"abstract":"<p><p>Despite occurring in an essential molecule, mutations in RNA polymerase readily emerge and elicit complex pleiotropic effects across different levels of biological organization, which are all modulated by environment. We investigated the impact of temperature on the effects of six mutations on sequence, structure, transcriptome, and organismal traits. We found temperature altered the transcriptomic response and key organismal traits such as growth rate and biofilm formation in a genotype-specific manner. Critically, mechanistic insights into the possible drivers of mutational effects emerged only when examining the relationships between different levels of organization: location of mutations in the tertiary structure and distance to key interacting molecules partly explained the observed transcriptomic differences, which in turn drove the impact of mutations on organismal traits. While falling short of capturing the full complexity of the system, our findings underscore the benefits of integrating insights across multiple biological levels to understand the relationship between environment and mutational effects in molecules with extensive pleiotropic effects.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12503110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091935","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":"Large-scale Genome Analyses Provide Insights into Hymenoptera Evolution.","authors":"Chun He, Yi Yang, Xianxin Zhao, Junjie Li, Yuting Cai, Lijia Peng, Yuanyuan Liu, Shijiao Xiong, Yang Mei, Zhichao Yan, Jiale Wang, Shan Xiao, Ziwen Teng, Xueke Gao, Hui Xue, Qi Fang, Gongyin Ye, Xinhai Ye","doi":"10.1093/molbev/msaf221","DOIUrl":"10.1093/molbev/msaf221","url":null,"abstract":"<p><p>The order Hymenoptera includes a large number of species with diverse lifestyles and is known for its significant contributions to natural ecosystems. To better understand the evolution of this diverse order, we performed large-scale comparative genomics on 131 species from 13 superfamilies, covering most representative groups. We used these genomes to reveal an overall pattern of genomic change in terms of gene content and evolutionary rate throughout hymenopteran history. We identified genes that possibly contributed to the evolution of several key innovations, such as parasitoidism, wasp-waist, stinger, and secondary phytophagy. We also discovered the distinct genomic trajectories between the clade containing major parasitoid wasps (Parasitoida) and stinging species (Aculeata) since their divergence, which are involved in many aspects of genomic change, such as rapidly evolving gene families, gene gain and loss, and metabolic pathway evolution. In addition, we explored the genomic features accompanying the three independent evolution of secondary phytophagy. Our work provides insights for understanding genome evolution and the genomic basis of diversification in Hymenoptera.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086448","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":"MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics.","authors":"Maxwell Sanderford, Sudip Sharma, Glen Stecher, Michael Suleski, Jun Liu, Jieping Ye, Sudhir Kumar","doi":"10.1093/molbev/msaf224","DOIUrl":"10.1093/molbev/msaf224","url":null,"abstract":"<p><p>Evolutionary sparse learning uses supervised machine learning to build evolutionary models where genomic sites loci are parameters. It uses the Least Absolute Shrinkage and Selection Operator with bi-level sparsity to connect a specific phylogenetic hypothesis with sequence variation across genomic loci. The MyESL software addresses the need for open-source tools to perform evolutionary sparse learning analyses, offering features to preprocess input phylogenomic alignments, post-process output models to generate molecular evolutionary metrics, and make Least Absolute Shrinkage and Selection Operator regression adaptable and efficient for phylogenetic trees and alignments. The core of MyESL, which constructs models with logistic regressions using bi-level sparsity, is written in C++. Its input data preprocessing and result post-processing tools are developed in Python. Compared to other tools, MyESL is more computationally efficient and provides evolution-friendly inputs and outputs. These features have already enabled the use of MyESL in two phylogenomic applications, one to identify outlier sequences and fragile clades in inferred phylogenies and another to build genetic models of convergent traits. In addition to the use in a Python environment, MyESL is available as a standalone executable compatible across multiple platforms, which can be directly integrated into scripts and third-party software. The source code, executable, and documentation for MyESL are openly accessible at https://github.com/kumarlabgit/MyESL.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12498521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091968","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":"Rapid radiations outweigh reticulations during the evolution of a 750-million-year-old lineage of cyanobacteria.","authors":"Carlos J Pardo-De la Hoz, Diane L Haughland, Darcie Thauvette, Sydney Toni, Spencer Goyette, William White, Ian D Medeiros, Luc Cornet, Petr Dvořák, Diego Garfias-Gallegos, Jolanta Miadlikowska, Nicolas Magain, François Lutzoni","doi":"10.1093/molbev/msaf244","DOIUrl":"https://doi.org/10.1093/molbev/msaf244","url":null,"abstract":"<p><p>Species are a fundamental unit of biodiversity. Yet, the existence of clear species boundaries among bacteria has long been a subject of debate. Here, we studied species boundaries in the context of the phylogenetic history of Nostoc, a widespread genus of photoautotrophic and nitrogen-fixing cyanobacteria that includes many lineages that form symbiotic associations with plants (e.g., cycads and bryophytes) and fungi (e.g., cyanolichens). We found that the evolution of Nostoc was characterized by eight rapid radiations, many of which were associated with major events in the evolution of plants. In addition, incomplete lineage sorting associated with these rapid radiations outweighed reticulations during Nostoc evolution. We then show that the pattern of diversification of Nostoc shapes the distribution of average nucleotide identities (ANIs) into a complex mosaic, wherein some closely related clades are clearly isolated from each other by gaps in genomic similarity, while others form a continuum where genomic species boundaries are expected. Nevertheless, recently diverged Nostoc lineages often form cohesive clades that are maintained by within-clade gene flow. Boundaries to homologous recombination between these cohesive clades persist even when the potential for gene flow is high, i.e., when closely related clades of Nostoc cooccur or are locally found in symbiotic associations with the same lichen-forming fungal species. Our results demonstrate that rapid radiations are major contributors to the complex speciation history of Nostoc. This underscores the need to consider evolutionary information beyond thresholds of genomic similarity to delimit biologically meaningful units of biodiversity for bacteria.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145213185","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":"Introducing the Y-chromosomal Ancestral-like Reference Sequence-Improving the Capture of Human Evolutionary Information.","authors":"Zehra Köksal, Annina Preussner, Jaakko Leinonen, Taru Tukiainen","doi":"10.1093/molbev/msaf222","DOIUrl":"10.1093/molbev/msaf222","url":null,"abstract":"<p><p>Reference sequences are essential for reproducible genetic analyses but are often chosen without regard to evolutionary relevance within the analyzed species. The human Y chromosome is widely used in evolutionary studies, yet current references represent evolutionarily young sequences, which can cause misleading variant calling. To address this issue, we constructed a Y-chromosomal ancestral-like reference sequence to improve the detection of evolutionarily informative variants on the Y chromosome. The Y-chromosomal ancestral-like reference sequence was constructed by applying a weighted maximum parsimony approach to human and primate Y chromosome sequences. To benchmark the performance of the Y-chromosomal ancestral-like reference sequence, 40 Y chromosome short-read sequences from diverse haplogroups were aligned to Y-chromosomal ancestral-like reference sequence and existing references (GRCh37, GRCh38, and T2T-CHM13). Overall, the Y-chromosomal ancestral-like reference sequence yielded the highest and most consistent number of SNPs per sample (mean = 1,400; SD = 77), while other references yielded on average fewer variants (mean = 866 to 968) and showed greater variability across samples (SD = 457 to 531) depending on their phylogenetic distance from the reference. Additionally, alignments to the Y-chromosomal ancestral-like reference sequence resulted in calling solely SNPs with evolutionarily derived alleles, while alignments to other references resulted in calling on average 46% SNPs with ancestral alleles. This study demonstrates how the existing reference sequences fail to capture the full range of evolutionary information on the Y chromosome. The Y-chromosomal ancestral-like reference sequence improves capturing evolutionary information on the Y chromosome, making it a valuable resource for various evolutionary applications, such as TMRCA estimations and phylogenetic analyses. Finally, alongside the Y-chromosomal ancestral-like reference sequence, we provide a publicly available tool, polaryzer, to annotate variants as ancestral or derived in pre-aligned Y chromosome data.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12485614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086415","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":"Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors.","authors":"Xiao-Xu Pang, Jianquan Liu, Da-Yong Zhang","doi":"10.1093/molbev/msaf216","DOIUrl":"10.1093/molbev/msaf216","url":null,"abstract":"<p><p>Recent theoretical and algorithmic advances in introgression detection, coupled with the growing availability of genome-scale data, have highlighted the widespread occurrence of interspecific gene flow across the tree of life. However, current methods largely depend on the molecular clock assumption-a questionable premise given empirical evidence of substitution rate variation across lineages. While such rate heterogeneity is known to compromise gene flow detection among divergent lineages, its impact on closely related taxa at shallow evolutionary timescales remains poorly understood, likely because these taxa are often assumed to adhere to a molecular clock. To address this gap, we combine theoretical analyses and simulations to evaluate the robustness of widely used site pattern methods (D-statistic and HyDe) to rate variation across phylogenetic timescales. Our results demonstrate that both methods exhibit high sensitivity to even minor deviations from the molecular clock at shallow timescales, complementing previous findings at deeper scales. Specifically, in young phylogenies (with an age of 3 × 105 generations) with small population sizes, weak (17% difference) and moderate (33% difference) rate variation can inflate false-positive rates up to 35% and 100%, respectively, using site pattern counts from a 500 Mb genome. Employing a more distant outgroup intensifies these spurious signals. Our study demonstrates that summary tests for introgression are pervasively vulnerable to minor rate variations and underscores the critical need for advanced methodologies to disentangle genuine introgression from false signals generated by rate heterogeneity.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12485364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145030107","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":"Flexibility in Gene Coexpression at Developmental and Evolutionary Timescales.","authors":"Eva K Fischer, Youngseok Song, Wen Zhou, Kim L Hoke","doi":"10.1093/molbev/msaf194","DOIUrl":"10.1093/molbev/msaf194","url":null,"abstract":"<p><p>The explosion of next-generation sequencing technologies has allowed researchers to move from studying single genes to studying thousands of genes, and thereby to also consider the relationships within gene networks. Like others, we are interested in understanding how developmental and evolutionary forces shape the expression of individual genes, as well as the interactions among genes. In pursuing these questions, we confronted the central challenge that standard approaches fail to control the Type I error and/or have low power in the presence of high dimensionality (i.e. large number of genes) and small sample size, as in many gene expression studies. To overcome these challenges, we used random projection tests and correlation network comparisons to characterize differences in network connectivity and density. We detail central challenges, discuss sample size guidelines, and provide rigorous statistical approaches for exploring coexpression differences with small sample sizes. We apply these approaches in a species known for rapid adaptation-the Trinidadian guppy (Poecilia reticulata)-and find evidence for coexpression network differences at developmental and evolutionary timescales. Our findings suggest that flexibility in gene coexpression relationships could promote evolvability.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12486243/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835717","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":"Tandem Gene Clusters as Phylogenetic Anchors Reveal the Hidden History of Vertebrate Visual Opsins.","authors":"David Lagman, Christina A Bergqvist, Shigehiro Kuraku","doi":"10.1093/molbev/msaf231","DOIUrl":"10.1093/molbev/msaf231","url":null,"abstract":"<p><p>The expansion of the visual opsin gene family was a crucial event in the diversification of vertebrate vision in evolution. Additional expansions in phototransduction-related genes facilitated the development of dim-light (rods) and color vision (cones). Sequence-based phylogeny and gene positions from extant jawed vertebrate genomes are insufficient to untangle the visual opsin duplications in early vertebrates. Additionally, jawless vertebrates share a visual opsin gene repertoire with jawed vertebrates which conflicts with recent findings of distinct whole-genome duplications in each lineage. To resolve these questions, we analyzed jawless vertebrate genomes, focusing on visual opsin genes. Our findings, based on chromosomal arrangements and relationships, confirm tandem duplications of visual opsins before the vertebrate radiation.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 10","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12486383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200440","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}