Genome Biology and Evolution最新文献

Genetic Predisposition Toward Multicellularity in Chlamydomonas reinhardtii. 莱茵衣藻多细胞遗传易感性。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-30 DOI: 10.1093/gbe/evaf090

I Chen Kimberly Chen, Shania Khatri, Matthew D Herron, Frank Rosenzweig

{"title":"Genetic Predisposition Toward Multicellularity in Chlamydomonas reinhardtii.","authors":"I Chen Kimberly Chen, Shania Khatri, Matthew D Herron, Frank Rosenzweig","doi":"10.1093/gbe/evaf090","DOIUrl":"10.1093/gbe/evaf090","url":null,"abstract":"The evolution from unicellular to multicellular organisms facilitates further phenotypic innovations, notably cellular differentiation. Multiple research groups have shown that, in the laboratory, simple, obligate multicellularity can evolve from a unicellular ancestor under appropriate selection. However, little is known about the extent to which deterministic factors such as ancestral genotype and environmental context influence the likelihood of this evolutionary transition. To test whether certain genotypes are predisposed to evolve multicellularity in different environments, we carried out a set of 24 evolution experiments, each founded by a population consisting of 10 different strains of the unicellular green alga Chlamydomonas reinhardtii, all in equal proportions. Twelve of the initially identical replicate populations were subjected to predation by the protist Paramecium tetraurelia, while the other 12 were subjected to settling selection by slow centrifugation. Population subsamples were transferred to fresh media on a weekly basis for a total of 40 transfers (∼600 generations). Heritable multicellular structures arose in 4 of 12 predation-selected populations (6 multicellular isolates in total), but never in the settling selection populations. By comparing whole genome sequences of the founder and evolved strains, we discovered that every multicellular isolate arose from one of two founders. Cell cluster size varied not only among evolved strains derived from different ancestors but also among strains derived from the same ancestor. These findings show that both deterministic and stochastic factors influence whether initially unicellular populations can evolve simple multicellular structures.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144085966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Discovering Intron Gain Events in Humans Through Large-Scale Evolutionary Comparisons. 通过大规模进化比较发现人类内含子获得事件。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-30 DOI: 10.1093/gbe/evaf091

Celine Hoh, Steven L Salzberg

引用次数: 0

The Role of Alternative Splicing in Marine-freshwater Divergence in Threespine Stickleback. 选择性剪接在三刺棘鱼海洋-淡水分化中的作用。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-28 DOI: 10.1093/gbe/evaf105

Carlos E Rodríguez-Ramírez, Catherine L Peichel

{"title":"The Role of Alternative Splicing in Marine-freshwater Divergence in Threespine Stickleback.","authors":"Carlos E Rodríguez-Ramírez, Catherine L Peichel","doi":"10.1093/gbe/evaf105","DOIUrl":"https://doi.org/10.1093/gbe/evaf105","url":null,"abstract":"Alternative splicing regulates which parts of a gene are kept in the messenger RNA and has long been appreciated as a mechanism to increase the diversity of the proteome within eukaryotic species. There is a growing body of evidence that alternative splicing might also play an important role in adaptive evolution. However, the relative contribution of differential alternative splicing (DS) to phenotypic evolution and adaptation is still unknown. In this study we asked whether DS played a role in adaptation to divergent marine and freshwater habitats in threespine stickleback (Gasterosteus aculeatus). Using two published gill RNAseq datasets, we identified differentially expressed and differentially spliced genes (DEGs and DSGs) between population pairs of marine-freshwater stickleback in the Northeast Pacific and tested whether they are preferentially found in regions of the genome involved in freshwater-marine divergence. We found over one hundred DSGs, which were found more often than expected in peaks of genetic divergence and quantitative trait loci (QTL) that underlie phenotypic divergence between ecotypes. DSGs and DEGs are similarly enriched in these regions. Among the different types of DS, mutually exclusive exon splicing is most strongly correlated with genetic divergence between ecotypes. Taken together, our results add support to the growing evidence that natural selection might have acted on DS and might have specifically played a role in the adaptive divergence of marine and freshwater sticklebacks. Our results also suggest that some types of DS events might contribute more than others to adaptation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144157958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Temporal Dynamics of Gene Expression During Metamorphosis in Two Distant Drosophila Species. 两个远缘果蝇物种变态过程中基因表达的时间动态。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-27 DOI: 10.1093/gbe/evaf100

A M Ozerova, D A Kulikova, M B Evgen'ev, M S Gelfand

引用次数: 0

Methylomes reveal recent evolutionary changes in populations of two plant species. 甲基组揭示了两种植物种群最近的进化变化。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-23 DOI: 10.1093/gbe/evaf101

Kevin Korfmann, Andreas Zauchner, Bing Huo, Corinna Grünke, Yitong Wang, Aurélien Tellier, Ramesh Arunkumar

{"title":"Methylomes reveal recent evolutionary changes in populations of two plant species.","authors":"Kevin Korfmann, Andreas Zauchner, Bing Huo, Corinna Grünke, Yitong Wang, Aurélien Tellier, Ramesh Arunkumar","doi":"10.1093/gbe/evaf101","DOIUrl":"https://doi.org/10.1093/gbe/evaf101","url":null,"abstract":"Plant DNA methylation changes occur hundreds to thousands of times faster than DNA mutations and can be transmitted transgenerationally, making them useful for studying population-scale patterns in clonal or selfing species. However, a state-of-the-art approach to use them for inferring population genetic processes and demographic histories is lacking. To address this, we compare evolutionary signatures extracted from CG methylomes and genomes in Arabidopsis thaliana and Brachypodium distachyon. While methylation variants (SMPs) are less effective than single nucleotide polymorphisms (SNPs) for identifying population differentiation in A. thaliana, they can classify phenotypically divergent B. distachyon subgroups that are otherwise genetically indistinguishable. The site frequency spectra generated using methylation sites from varied genomic locations and evolutionary conservation exhibit an excess of rare alleles. Nucleotide diversity estimates were three orders of magnitude higher for methylation variants than for SNPs in both species, driven by the higher epimutation rate. Correlations between SNPs and SMPs in nucleotide diversity and allele frequencies at gene exons are weak or absent in A. thaliana, possibly because the two sources of variation reflect evolutionary forces acting at different timescales. Linkage disequilibrium quickly decays within 100 bp for methylation variants in both plant species. Finally, we have developed a novel deep learning-based approach that infers demographic histories using methylation variation data alone. We identified recent population expansions in A. thaliana and B. distachyon using methylation variants that were not identified when using SNPs. Our study demonstrates the unique evolutionary insights methylomes provide that SNPs alone cannot reveal.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Parameter Scaling in Population Genetics Simulations May Introduce Unintended Background Selection: Considerations for Scaled Simulation Design. 群体遗传学模拟中的参数缩放可能引入意想不到的背景选择：缩放模拟设计的考虑。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-23 DOI: 10.1093/gbe/evaf097

Tessa Ferrari, Siyuan Feng, Xinjun Zhang, Jazlyn Mooney

{"title":"Parameter Scaling in Population Genetics Simulations May Introduce Unintended Background Selection: Considerations for Scaled Simulation Design.","authors":"Tessa Ferrari, Siyuan Feng, Xinjun Zhang, Jazlyn Mooney","doi":"10.1093/gbe/evaf097","DOIUrl":"https://doi.org/10.1093/gbe/evaf097","url":null,"abstract":"Scaling is a common practice in population genetic simulations to increase computational efficiency. However, few studies systematically examine the effects of scaling on diversity estimates and the comparability of scaled results to unscaled simulations and empirical data. We investigate the effects of scaling in two species, modern humans and Drosophila melanogaster. These species have stark differences in population size and generation time, necessitating moderate-to-no scaling for humans and dramatic scaling for Drosophila. We determine how coalescence, runtime, memory, estimates of diversity, the site frequency spectra, and linkage disequilibrium are influenced by scaling. We also examine the impact of simulated segment length and burn-in time on these metrics. Our results demonstrate that while computational efficiency improves with scaling, large scaling factors distort genetic diversity and dynamics between genetic variants, resulting in deviations from the intended model and empirical observations. Specifically, strongly scaled simulations may experience stronger negative selection on deleterious mutations, which amplifies background selection and purges linked mutations, leaving only rare strongly deleterious variants in the final population. We additionally show that a heuristic burn-in length of 10N generations is often insufficient for full coalescence in both models and alters expected linkage disequilibrium patterns. Finally, we provide considerations for conducting scaled simulations and offer potential strategies for the mitigation of scaling effects. For most non-model species simulations, we advocate for a bespoke scaling strategy drawn from these use-cases.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alternative mutational architectures producing identical M-matrices can lead to different patterns of evolutionary divergence. 产生相同m矩阵的不同突变结构可能导致不同的进化分化模式。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-23 DOI: 10.1093/gbe/evaf099

Daohan Jiang, Matt Pennell

{"title":"Alternative mutational architectures producing identical M-matrices can lead to different patterns of evolutionary divergence.","authors":"Daohan Jiang, Matt Pennell","doi":"10.1093/gbe/evaf099","DOIUrl":"10.1093/gbe/evaf099","url":null,"abstract":"Explaining macroevolutionary divergence in light of population genetics requires understanding the extent to which the patterns of mutational input contribute to long-term trends. In the context of quantitative traits, mutational input is typically described by the mutational variance-covariance matrix, the M-matrix, which summarizes phenotypic variances and covariances introduced by new mutations per generation. However, as a summary statistic, the M-matrix does not fully capture all the relevant information from the underlying mutational architecture, and there exist a myriad of possible underlying mutational architectures that give rise to the same M-matrix. Using individual-based simulations, we demonstrate mutational architectures that produce the same M-matrix can lead to different levels of constraint on evolution and result in difference in within-population genetic variance, between-population divergence, and rate of adaptation. In particular, the rate of adaptation and that of neutral evolution are both reduced when a greater proportion of loci are pleiotropic. Our results reveal that aspects of mutational input not reflected by the M-matrix can have a profound impact on long-term evolution, and suggest it is important to take them into account in order to connect patterns of long-term phenotypic evolution to underlying microevolutionary mechanisms.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Genome of Apera spica-venti, a major grass weed. 一种主要的杂草——spica-venti的基因组。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-22 DOI: 10.1093/gbe/evaf096

John Lemas, Jevgenija Ņečajeva, Jacob Montgomery, Sofia Marques-Hill, Victor Llaca, Kevin Fengler, Lena Ulber, Dagmar Rissel, Josef Soukup, Kateřina Hamouzová, Fatemeh Abdollahi, David Nelson, Todd A Gaines, Eric Patterson

{"title":"The Genome of Apera spica-venti, a major grass weed.","authors":"John Lemas, Jevgenija Ņečajeva, Jacob Montgomery, Sofia Marques-Hill, Victor Llaca, Kevin Fengler, Lena Ulber, Dagmar Rissel, Josef Soukup, Kateřina Hamouzová, Fatemeh Abdollahi, David Nelson, Todd A Gaines, Eric Patterson","doi":"10.1093/gbe/evaf096","DOIUrl":"https://doi.org/10.1093/gbe/evaf096","url":null,"abstract":"Apera spica-venti (loose silky bent, or common windgrass) is a diploid grass-weed endemic to Europe and north Asia that has spread to the United States and Canada. This species has become a major grass weed in winter cereals, especially in eastern Europe mainly through the evolution of target site and non-target site resistance mechanisms. The scientific community currently lacks genomic resources to understand herbicide resistance evolution in this plant and therefore resistance is hard to diagnose and treat. To remedy this, we generated two reference haplome assemblies through phased genome assembly. Haplome 1 consists of 37 scaffolds with a total length of 4.06 Gbp and an N50 of 206.5 Mbp, while haplome 2 resulted in 34 scaffolds with a total length of 3.99 Gbp and an N50 of 270.1 Mbp. Both haplomes represent over 87% of the flow cytometry estimated genome size of 4.622 Gbp per 1C. Gene annotation was preformed via a modified Maker pipeline resulting in 44,208 and 43,844 genes for haplomes 1 and 2 respectively and capturing 90% of BUSCO annotated transcripts. Repeat analysis identified greater than 800,000 transposon elements spanning 2.3 Gbp of the genome and an average distance between genes of over 90 kbp. This reference genome addresses the lack of genomic resources and aims to better understand basic weed biology, ecology, and herbicide resistance evolution.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144119524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolutionary Insights into the Length Variation of DNA Damage Response Proteins Across Eukaryotes. 真核生物DNA损伤反应蛋白长度变异的进化见解。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-19 DOI: 10.1093/gbe/evaf089

Dominic Wiredu-Boakye, Laurence Higgins, Ondřej Gahura, Anzhelika Butenko, Guy Leonard, Mark A Freeman, Árni Kristmundsson, Karen Moore, Jamie W Harrison, Shani Mac Donald, Vyacheslav Yurchenko, Bryony A P Williams, Richard Chahwan

{"title":"Evolutionary Insights into the Length Variation of DNA Damage Response Proteins Across Eukaryotes.","authors":"Dominic Wiredu-Boakye, Laurence Higgins, Ondřej Gahura, Anzhelika Butenko, Guy Leonard, Mark A Freeman, Árni Kristmundsson, Karen Moore, Jamie W Harrison, Shani Mac Donald, Vyacheslav Yurchenko, Bryony A P Williams, Richard Chahwan","doi":"10.1093/gbe/evaf089","DOIUrl":"https://doi.org/10.1093/gbe/evaf089","url":null,"abstract":"Across the tree of life, DNA damage response (DDR) proteins play a pivotal, yet dichotomous role in organismal development and evolution. Here, we present a comprehensive analysis of 432 DDR proteins encoded by 68 genomes including that of Nucleospora cyclopteri, an intranuclear microsporidia sequenced in this study. We compared the DDR proteins encoded by these genomes to those of humans to uncover the DNA repair-ome across phylogenetically distant eukaryotes. We also performed further analyses to understand if organismal complexity and lifestyle play a role in the evolution of DDR protein length and conserved domain architecture. We observed that the genomes of extreme parasites such as Paramicrocytos, Giardia, Spironucleus and certain microsporidian lineages encode the smallest eukaryotic repertoire of DDR proteins and that pathways involved in modulation of nucleotide pools and nucleotide excision repair are most preserved DDR pathways in the eukaryotic genomes analysed here. We found that DDR and DNA repair proteins are consistently longer than housekeeping and metabolic proteins. This is likely due to the higher number of physical protein-protein interactions that DDR proteins are involved in. We find that although DNA repair proteins are generally longer than housekeeping proteins, their functional domains occupy a relatively smaller footprint. Notably, this pattern holds true across diverse organisms and shows no dependence on either lifestyle or mitochondrial status. Finally, we observed that unicellular organisms harbour proteins that are tenfold longer than their human homologs with the extra amino acids forming interdomain regions with clearly novel albeit undetermined function.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ParallelEvolCCM: Quantifying co-evolutionary patterns among genomic features. ParallelEvolCCM：量化基因组特征之间的共同进化模式。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-17 DOI: 10.1093/gbe/evaf092

Robert G Beiko, Chaoyue Liu, João Vitor Cavalcante, Ryan C Fink

引用次数: 0