Molecular biology and evolution最新文献_第2页

Regulatory activity and evolutionary co-option of cis-regulatory elements underlying bear hibernation. 熊冬眠背后的顺式调控元件的调控活动和进化选择。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag193

Blair W Perry, Kara Ryan, Kerry L McGowan, T Brock Wooldridge, Marina Savenkova, Sascha H Duttke, Heiko T Jansen, Charles T Robbins, Joanna L Kelley

{"title":"Regulatory activity and evolutionary co-option of cis-regulatory elements underlying bear hibernation.","authors":"Blair W Perry, Kara Ryan, Kerry L McGowan, T Brock Wooldridge, Marina Savenkova, Sascha H Duttke, Heiko T Jansen, Charles T Robbins, Joanna L Kelley","doi":"10.1093/molbev/msag193","DOIUrl":"10.1093/molbev/msag193","url":null,"abstract":"Uncovering the regulatory architectures that underlie complex phenotypes can provide insight into both the mechanisms and evolution of unique adaptations. In bears, thousands of genes are differentially expressed in a tissue-specific manner during hibernation, many of which are involved in major vertebrate metabolic signaling pathways. However, the precise regulatory mechanisms driving these gene expression changes, and the extent of their conservation in nonhibernating mammals, remain poorly understood. Using capped-small RNA-sequencing from brown bear adipose tissue, we identify putative enhancers that exhibit dynamic shifts in regulatory activity during hibernation. The majority of these enhancers share sequence homology with known human enhancers, yet many appear to target distinct genes, suggesting a role of regulatory co-option in the evolution of hibernation. Using these newly identified enhancers, we identify transcription factors putatively underlying hibernation gene expression, expanding our mechanistic understanding of hibernation physiology. Additionally, we find evidence for selection on cis-regulatory sequences associated with physiological adaptation across bears. Collectively, this study provides new perspectives on the mechanisms and evolution of mammalian hibernation and the roles of regulatory sequences in the evolution of complex physiological adaptations.","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/PMC13669786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148701850","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

No genome-wide correlations and little shared genetic architecture between reproductive life-history traits and estrogen receptor-positive breast cancer risk. 生殖生活史特征与雌激素受体阳性乳腺癌风险之间没有全基因组相关性，共享的遗传结构也很少。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag222

Euan A Young, E Yagmur Erten, Erik Postma, Virpi Lummaa, Bert van der Vegt, Geertruida H de Bock, Hannah L Dugdale

{"title":"No genome-wide correlations and little shared genetic architecture between reproductive life-history traits and estrogen receptor-positive breast cancer risk.","authors":"Euan A Young, E Yagmur Erten, Erik Postma, Virpi Lummaa, Bert van der Vegt, Geertruida H de Bock, Hannah L Dugdale","doi":"10.1093/molbev/msag222","DOIUrl":"10.1093/molbev/msag222","url":null,"abstract":"Estrogen receptor-positive breast cancer (ER + BC) is one of the most prevalent cancers, but the evolutionary processes shaping genetic variation in ER + BC risk are poorly understood. Both evolutionary life-history theory and evidence from studies of individual ER + BC risk variants suggest that increased genetic ER + BC risk is associated with faster maturation, earlier reproduction, and/or increased reproductive success (i.e. there is a trade-off), but it is unclear how well this pattern is replicated when considering the polygenic architecture of these traits after controlling for potential biases. Here, we estimate genome-wide genetic correlations between ER + BC risk and three reproductive traits (age at menarche, age at first birth, and the number of children) using genomic restricted maximum-likelihood analyses on Lifelines biobank data and linkage disequilibrium score regressions on population and family-based genome-wide association study data. Regardless of the data or method used, genetic correlations were low and not statistically significant. Further analyses decomposing genome-wide genetic variance into local regions detected only three loci exhibiting significant pleiotropy between ER + BC risk and age at menarche, suggesting little shared genetic architecture between ER + BC risk and reproductive traits. Thus, the role of life-history trade-offs in shaping ER + BC risk in European populations appears, at most, small, and the evolutionary processes giving rise to this life-threatening disease remain unclear. Future studies could examine the impact of evolutionary mismatches in shaping ER + BC risk, where conducting longitudinal studies on populations transitioning to reproductive patterns observed in contemporary European populations would be most useful.","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/PMC13637042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148865678","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

Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges. 揭示针叶树巨基因组的结构变异：进化见解和技术挑战。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag239

Hui Liu, Wei Zhao, Jing-Fang Guo, Xue-Mei Yan, Yan-Jing Liu, Qing-Yin Zeng, Xiao-Ru Wang

{"title":"Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges.","authors":"Hui Liu, Wei Zhao, Jing-Fang Guo, Xue-Mei Yan, Yan-Jing Liu, Qing-Yin Zeng, Xiao-Ru Wang","doi":"10.1093/molbev/msag239","DOIUrl":"10.1093/molbev/msag239","url":null,"abstract":"Structural variants (SVs) are a major yet understudied source of genomic variation in conifers, whose large, repeat-rich genomes have hindered systematic SV discovery. Here, we combined whole-genome long-read and short-read sequencing to characterize the genomic landscape, functional impact, and evolutionary significance of SVs in a complex of three closely related pine species (Pinus densata, Pinus tabuliformis, and Pinus yunnanensis) with a hybridization history. From 21 long-read-sequenced individuals, we identified 5.7 million SVs, comprising 52% insertions, 43% deletions, and 5% inversions, duplications, and translocations. Approximately 97% of SVs were located in intergenic and intronic regions, and 60% overlapped transposable elements, whose activity shapes SV abundance and size variation. The proportion of loss-of-function (LoF) mutations was hundreds-fold higher among SVs than SNPs, with longer SVs more likely to cause LoF effects across all SV classes. Estimates of population diversity based on SVs and SNPs were largely concordant. In P. densata, the retention of parental SVs highlights the genomic signature of its admixed ancestry. We conducted graph pangenome-based SV genotyping in 29 short-read-sequenced individuals, yielding 44% recall and 70% precision, underlining the challenge of accurately recovering long-read-derived SVs in highly repetitive conifer genomes. Population-level selection scans on SNPs and genotyped SVs identified only 19% of candidate gene loci in common, indicating that the two marker types capture complementary components of environmental adaptation. Our findings demonstrate the importance of SVs as a dimension of genomic diversity and provide a foundation for integrating structural variation into evolutionary studies, conservation genomics, and tree breeding.","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/PMC13637045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148990690","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

The shortest animal introns: insights from parasitic cnidarians. 最短的动物内含子：来自寄生刺胞动物的见解。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag244

Racheli Hadjez, Tal Pupko, Stephen D Atkinson, Dorothée Huchon

{"title":"The shortest animal introns: insights from parasitic cnidarians.","authors":"Racheli Hadjez, Tal Pupko, Stephen D Atkinson, Dorothée Huchon","doi":"10.1093/molbev/msag244","DOIUrl":"10.1093/molbev/msag244","url":null,"abstract":"Spliceosomal introns are nearly ubiquitous across eukaryotes, yet the constraints shaping their length remain poorly understood. Generally, introns shorter than ∼30 bp are considered absent from animals. Here, we show that such ultra-short introns evolved independently at least twice within Metazoa. Using long-read sequencing, we assembled and annotated the genome of the myxobolid myxozoan Henneguya salminicola and identified exceptionally short introns with a median length of 27 bp. Comparative analyses of 51 metazoan genomes revealed that extreme intron shortening characterizes myxobolids, with Thelohanellus kitauei and Myxobolus rasmusseni exhibiting the shortest median intron length (22 bp) among sequenced animals. Outside Myxozoa, similarly short introns were found only in the dicyemid Dicyema japonicum. Sequence-logo analyses showed reduced 5' and 3' splice-site motifs in myxobolids and D. japonicum relative to other animals. Together, these results demonstrate that introns shorter than 30 bp occur in animals, and that extreme intron shortening evolved convergently in at least two parasitic animal lineages.","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/PMC13644364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149040119","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

DNA methylation dynamics associated with seasonal wing plasticity of Bicyclus anynana butterflies. 双环蝶季节性翅膀可塑性与DNA甲基化动力学相关。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag251

Suriya Narayanan Murugesan, Shen Tian, You Chen Roy Quah, Antónia Monteiro

{"title":"DNA methylation dynamics associated with seasonal wing plasticity of Bicyclus anynana butterflies.","authors":"Suriya Narayanan Murugesan, Shen Tian, You Chen Roy Quah, Antónia Monteiro","doi":"10.1093/molbev/msag251","DOIUrl":"10.1093/molbev/msag251","url":null,"abstract":"Over the years, multiple studies have linked phenotypic plasticity to changes in gene expression and alternative splicing, but the role of epigenomic regulation, such as DNA methylation, in mediating plastic responses is still poorly understood. DNA methylation has been proposed as a promising regulatory mechanism because of its potential effects on transcriptional activity and pre-mRNA splicing, especially when present within gene bodies in insects. Here, we examined the role of DNA methylation in the developing wings of Bicyclus anynana butterflies by testing its association with differential gene expression and alternative splicing between the two seasonal forms. Methylation differences between the seasonal forms were largely enriched in housekeeping genes but were not present in transcription factors and developmental genes associated with wing or eyespot development or in components of the ecdysone signaling pathway. We found a copy of DNA methyltransferase (Dnmt1) expressed faintly across the whole wing, with no specific expression in eyespots or other specific wing patterns in either seasonal form. Overall, our study provides a comprehensive characterization of DNA methylation in wing development in two seasonal forms, while providing very little support for the role of DNA methylation in driving differences in transcriptional profiles of two seasonal wing forms and in wing metamorphosis.","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/PMC13655617/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149081485","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

Evolution and metabolite signaling of fumarases (class I and II): origin, function, and subcellular targeting. 富马酸酶（I类和II类）的进化和代谢物信号传导：起源、功能和亚细胞靶向。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag240

Ophir Miller, Dror Jacobi, Liran Carmel, Ophry Pines

{"title":"Evolution and metabolite signaling of fumarases (class I and II): origin, function, and subcellular targeting.","authors":"Ophir Miller, Dror Jacobi, Liran Carmel, Ophry Pines","doi":"10.1093/molbev/msag240","DOIUrl":"10.1093/molbev/msag240","url":null,"abstract":"This study explores the evolutionary origins of class I and II fumarases across the tree of life, focusing on the prevalence and phylogenetic patterns of their enzymes. Using a dataset of ∼21,000 complete proteomes and MMseqs2 easy-search against known fumarase sequences, we identified representative sequences for each class and constructed phylogenetic trees. Class I fumarases are found primarily in bacteria and in several eukaryotic groups, including Protozoa, SAR, and algae, with absence in fungi and archaea and low presence in plants and animals. Their patchy distribution and absence in archaea suggest horizontal gene transfer from bacteria to eukaryotes. Class II fumarases are ubiquitously distributed across bacteria, archaea, and eukaryotes. Phylogenetic and genetic analyzes suggest a closer relationship between eukaryotic class II fumarases and bacterial homologs (particularly Alphaproteobacteria) compared to archaea. These results support the hypothesis that class II fumarase originated early on in bacteria and was then inherited by vertical gene transfer by eukaryotes. Analysis of protein sequences and structures for both classes demonstrates high evolutionary conservation, consistent with their essential catalytic function. Fumarases, TCA cycle enzymes, have been implicated in DNA damage response in numerous organisms, in all domains of life. These enzymes have also been shown to be dual targeted to mitochondria and the cytosol/nucleus in eukaryotes. We have examined how these two functions are linked to the evolution of fumarases and concluded that the extramitochondrial functions and subcellular localization of fumarases were determined much later in evolution. We conclude that metabolic signaling and its specific metabolites may provide the driving force for the fumarases' dual function, dual targeting, and interaction with different entities in the cell.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"43 10","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13655608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149167257","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

Diversity and divergence of two sympatric, sibling octopus species. 两种同域的兄弟章鱼物种的多样性和分化。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag248

Gabrielle C Coffing, Silas Tittes, Scott T Small, Andrew D Kern

{"title":"Diversity and divergence of two sympatric, sibling octopus species.","authors":"Gabrielle C Coffing, Silas Tittes, Scott T Small, Andrew D Kern","doi":"10.1093/molbev/msag248","DOIUrl":"10.1093/molbev/msag248","url":null,"abstract":"Coleoid cephalopods have convergently evolved many traits shared with vertebrates, including camera-type eyes, large brain-to-body size ratios, and complex behaviors. Most evolutionary studies of cephalopods have compared individual genomes of taxa that diverged tens to hundreds of millions of years ago; yet, very few have examined more recent evolution from a population genetics perspective. Here, we present a comparative population genomic analysis of the sympatric sister species Octopus bimaculatus and Octopus bimaculoides using whole-genome resequencing. Despite similar morphologies, these species differ substantially in their life histories, ecologies, and geographic distributions. Using demographic inference, we estimated that the two species diverged on the order of one million years ago, with point estimates from independent methods spanning roughly 0.4 to 1.3 million years, and that O. bimaculatus has maintained a consistently larger effective population size since divergence. Consistent with these demographic histories, we found stronger signatures of positive selection in O. bimaculatus, including a positive correlation between recombination rate and nucleotide diversity, more selective sweeps, and a higher proportion of mutations fixed by adaptation-all consistent with more efficient natural selection in larger populations. Protein-coding genes overlapping with selective sweeps were enriched for various functions that included many related to brain and eye development, suggesting that traits characteristic of coleoid cephalopods continue to be shaped by positive selection on recent timescales in these species. Comparing coding-sequence divergence on the Z chromosome to the autosomes, we also find evidence for a female-biased mutation rate, consistent with an independent estimate from a deeper-timescale cephalopod comparison.","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/PMC13669787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149168548","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

Natural selection shapes the evolution of the metabolome in Saccharomyces cerevisiae. 自然选择塑造了酿酒酵母代谢组的进化。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag246

Haichao Li, Haoxuan Liu

{"title":"Natural selection shapes the evolution of the metabolome in Saccharomyces cerevisiae.","authors":"Haichao Li, Haoxuan Liu","doi":"10.1093/molbev/msag246","DOIUrl":"10.1093/molbev/msag246","url":null,"abstract":"Metabolite abundances represent the ultimate functional outputs of cellular processes and provide a direct link between genotype and phenotype. While the evolutionary dynamics of mRNA and protein abundances have been extensively studied, the evolutionary forces shaping metabolite abundances remain largely unexplored. Here, we present a comprehensive framework to quantify natural selection acting on metabolite abundance using Saccharomyces cerevisiae as a model system. We quantified 1,037 metabolites across 21 mutation accumulation (MA) lines, their ancestor BY4741, and 18 wild isolates using liquid chromatography-tandem mass spectrometry. Despite MA lines and wild strains differing by ∼40-fold in genomic divergence, metabolite abundances were significantly more conserved among wild isolates, indicating strong natural selection acting on the metabolome. Using comparisons of variance components (Vg/Vm) and directional bias analyses, we found that the vast majority of metabolites were subject to natural selection. Approximately 28.58% of metabolites were inferred to be potentially under directional selection, with most of the remainder likely constrained by stabilizing selection. Notably, directional selection preferentially increased the abundance of high-abundance metabolites while reducing that of low-abundance metabolites, thereby increasing abundance divergence among metabolites. The direction of directional selection showed no significant bias across metabolite classes, except for amino acids and their derivatives, in which directional selection significantly favored reduced abundance of these metabolites, potentially reflecting their relatively high biosynthetic energy costs. Together, our findings reveal the patterns of natural selection acting on the metabolome and provide new insights into the evolution of the molecular processes linking gene expression to organismal phenotypes.","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/PMC13637043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149031008","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

Comparative pangenomics unveils distinct host adaptation trends and conserved biosynthetic potential in microbiome Clostridia. 比较泛基因组学揭示了微生物组梭状芽胞杆菌中不同的宿主适应趋势和保守的生物合成潜力。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag247

Lucas De Vrieze, Jan Aerts, Joleen Masschelein

{"title":"Comparative pangenomics unveils distinct host adaptation trends and conserved biosynthetic potential in microbiome Clostridia.","authors":"Lucas De Vrieze, Jan Aerts, Joleen Masschelein","doi":"10.1093/molbev/msag247","DOIUrl":"10.1093/molbev/msag247","url":null,"abstract":"To thrive in diverse ecological niches, bacteria adopt various lifestyles that range from living freely in the soil to forming close associations with human and animal hosts. However, the impact of these adaptation processes on their genomes and metabolisms remains largely unexplored beyond the genus level. Investigating these evolutionary dynamics at higher taxonomic levels can enhance our understanding of the relationship between host adaptation and functional capabilities. Here, we examine the evolutionary trajectories and metabolic capabilities of the Clostridia class, which displays a wide variety of lifestyles and is of high importance for industry, medicine, and microbiome research. First, we uncover that the clostridial orders have significantly different genomic divergence rates. Second, we show contrasting host adaptation tendencies in Oscillospirales and Lachnospirales, the two clostridial orders dominated by host-associated species. Species of the former have often undergone extensive genomic and functional specialization toward a host-associated lifestyle, while species of the latter tend to show a lower level of host adaptation, retaining a remarkably high number of free-living trait genes and a high degree of metabolic versatility. Third, we reveal substantial differences in genomic architecture and metabolic versatility between the clostridial orders and link these to the progressing stages of host adaptation. Additionally, we identify widely conserved biosynthetic gene clusters, highlighting untapped biosynthetic potential of evolutionary significance. Hence, the beyond-genus level analyses in this study provide valuable new insights into bacterial adaptation with broad implications for evolutionary biology, microbiome research, and biotechnology.","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/PMC13673991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112280","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

Herd immunity underlies homologous recombination in stationary phase bacteria. 群体免疫是固定相细菌同源重组的基础。

IF 6.4 1区生物学

Molecular biology and evolution Pub Date : 2026-10-03 DOI: 10.1093/molbev/msag238

Pavel Payne, Pavel Plevka, Jonathan P Bollback, Călin C Guet

{"title":"Herd immunity underlies homologous recombination in stationary phase bacteria.","authors":"Pavel Payne, Pavel Plevka, Jonathan P Bollback, Călin C Guet","doi":"10.1093/molbev/msag238","DOIUrl":"https://doi.org/10.1093/molbev/msag238","url":null,"abstract":"Homologous recombination is ubiquitous across evolution, generating variation through genetic reshuffling. Although bacteria lack meiotic recombination, homologous recombination has been known to extensively shape their genomes. However, the mechanisms and ecological conditions sustaining frequent recombination in bacteria remain unclear. Using an Escherichia coli-P1 phage model system, we reveal how frequent recombination emerges from CRISPR-based herd immunity to a generalized transducing phage (DNA vector). Herd immunity maintains phage-susceptible donor bacteria, recipient immune bacteria, and transducing phage, which promotes chromosomal gene flow that exceeds spontaneous mutation by up to two orders of magnitude. Notably, recombination begins as bacterial cultures enter stationary phase, when canonical mutation supply through population growth and DNA replication is strongly reduced, and recombination can be reinitiated by brief fresh nutrient pulses. Genetic analysis showed that stationary-phase recombination requires recA, recB, and recG, connecting this process to a defined homologous recombination pathway, and suggests a plausible transcriptional regulatory link to transition to nutrient limitation. Bacterial herd immunity therefore has an unexpected evolutionary consequence: it can promote homologous recombination by turning phages into de facto pollinators. This mechanism can help explain how high rates of homologous recombination may be sustained across bacterial populations and suggests that bacterial immune systems can shape molecular evolution not only by blocking infection but also by regulating genetic exchange.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"43 10","pages":""},"PeriodicalIF":6.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13633115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149111849","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