Molecular biology and evolution最新文献_第4页

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-29 DOI: 10.1093/molbev/msaf022

Brandon Gaut, Claudia Russo

引用次数: 0

Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history. 人类历史进程中人类肠道共生菌群的人口历史和选择效应的推断。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-22 DOI: 10.1093/molbev/msaf010

Jonathan C Mah, Kirk E Lohmueller, Nandita Garud

引用次数: 0

Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads. 读取长度支配古代DNA读取的系统发育定位精度。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-17 DOI: 10.1093/molbev/msaf006

Ben Bettisworth, Nikolaos Psonis, Nikos Poulakakis, Pavlos Pavlidis, Alexandros Stamatakis

{"title":"Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads.","authors":"Ben Bettisworth, Nikolaos Psonis, Nikos Poulakakis, Pavlos Pavlidis, Alexandros Stamatakis","doi":"10.1093/molbev/msaf006","DOIUrl":"https://doi.org/10.1093/molbev/msaf006","url":null,"abstract":"A common problem when analyzing ancient DNA (aDNA) data is to identify the species which corresponds to the recovered aDNA sequence(s). The standard approach is to deploy sequence similarity based tools, such as BLAST. However, as aDNA reads may frequently stem from unsampled taxa due to extinction, it is likely that there is no exact match in any database. As a consequence, these tools may not be able to accurately place such reads in a phylogenetic context. Phylogenetic placement is a technique where a read is placed onto a specific branch of a phylogenetic reference tree, which allows for a substantially finer resolution when identifying reads. Prior applications of phylogenetic placement has deployed only on data from extant sources. Therefore, it is unclear how the aDNA damage affects phylogenetic placement's applicability to aDNA data. To investigate how aDNA damage affects placement accuracy, we re-implemented a statistical model of aDNA damage. We deploy this model, along with a modified version of the existing assessment pipeline PEWO, to seven empirical datasets with four leading tools: APPLES, EPA-NG, pplacer, and RAPPAS. We explore the aDNA damage parameter space via a grid search in order to identify the aDNA damage factors that exhibit the largest impact on placement accuracy. We find that the frequency of DNA backbone nicks (and consequently read length) has the, by far, largest impact on aDNA read placement accuracy, and that other factors, such as misincorporations, have a negligible effect on overall placement accuracy.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008447","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}

引用次数: 0

Navigating a Fine Balance: Point-Mutant Cheater Viruses Disrupt the Viral Replication Cycle. 微妙的平衡：点突变作弊病毒扰乱病毒复制周期。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-06 DOI: 10.1093/molbev/msae258

Moran Meir, Arielle Kahn, Carmel Farage, Yael Maoz, Noam Harel, Adi Ben Zvi, Shir Segev, Maria Volkov, Ravit Yahud, Uri Gophna, Adi Stern

{"title":"Navigating a Fine Balance: Point-Mutant Cheater Viruses Disrupt the Viral Replication Cycle.","authors":"Moran Meir, Arielle Kahn, Carmel Farage, Yael Maoz, Noam Harel, Adi Ben Zvi, Shir Segev, Maria Volkov, Ravit Yahud, Uri Gophna, Adi Stern","doi":"10.1093/molbev/msae258","DOIUrl":"10.1093/molbev/msae258","url":null,"abstract":"Cheater viruses cannot replicate on their own yet replicate faster than the wild type (WT) when the 2 viruses coinfect the same cell. Cheaters must possess dual genetic features: a defect, which leads to their inability to infect cells on their own, and a selective advantage over WT during coinfection. Previously, we have discovered 2 point-mutant cheaters of the MS2 bacteriophage. Here, we set out to discover the possible repertoire of cheater MS2 viruses by performing experimental evolution at a very high multiplicity of infection. Our results revealed a third point-mutant cheater that arose in 8 biological replicas. Each of the 3 primary cheaters disrupts the fine balance necessary for phage replication, in different ways that create a defect + advantage. We found that over time, the point-mutant cheaters accumulate additional secondary mutations, which alter other stages of the viral replication cycle, complementing the disruptions created by the original cheater. Intriguingly, cheater and secondary mutations almost always reside in very close proximity on the genome. This region encodes for multiple functions: overlapping reading frames as well as overlapping RNA structures critical for transitioning from one stage to another in the viral replication cycle. This region of overlap explains the dual functions of cheaters, as one mutation can have pleiotropic effects. Overall, these findings underscore how viruses, whose dense genomes often have overlapping functions, can easily evolve point-mutant cheaters, and how cheaters can evolve to alter the intricate balance of the viral replication cycle.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864802","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}

引用次数: 0

Selection Can Favor a Recombination Landscape That Limits Polygenic Adaptation. 自然选择倾向于限制多基因适应的重组景观。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-06 DOI: 10.1093/molbev/msae273

Tom Parée, Luke Noble, Denis Roze, Henrique Teotónio

引用次数: 0

Adaptive Significance of Non-coding RNAs: Insights from Cancer Biology. 非编码rna的适应性意义：来自癌症生物学的见解。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-06 DOI: 10.1093/molbev/msae269

John F McDonald

{"title":"Adaptive Significance of Non-coding RNAs: Insights from Cancer Biology.","authors":"John F McDonald","doi":"10.1093/molbev/msae269","DOIUrl":"10.1093/molbev/msae269","url":null,"abstract":"The molecular basis of adaptive evolution and cancer progression are both complex processes that share many striking similarities. The potential adaptive significance of environmentally-induced epigenetic changes is currently an area of great interest in both evolutionary and cancer biology. In the field of cancer biology intense effort has been focused on the contribution of stress-induced non-coding RNAs (ncRNAs) in the activation of epigenetic changes associated with elevated mutation rates and the acquisition of environmentally adaptive traits. Examples of this process are presented and combined with more recent findings demonstrating that stress-induced ncRNAs are transferable from somatic to germline cells leading to cross-generational inheritance of acquired adaptive traits. The fact that ncRNAs have been implicated in the transient adaptive response of various plants and animals to environmental stress is consistent with findings in cancer biology. Based on these collective observations, a general model as well as specific and testable hypotheses are proposed on how transient ncRNA-mediated adaptive responses may facilitate the transition to long-term biological adaptation in both cancer and evolution.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11725524/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979419","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 de novo Gene Promotes Seed Germination Under Drought Stress in Arabidopsis. 一个新生基因促进拟南芥在干旱胁迫下的种子萌发。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-06 DOI: 10.1093/molbev/msae262

Guang-Teng Jin, Yong-Chao Xu, Xing-Hui Hou, Juan Jiang, Xin-Xin Li, Jia-Hui Xiao, Yu-Tao Bian, Yan-Bo Gong, Ming-Yu Wang, Zhi-Qin Zhang, Yong E Zhang, Wang-Sheng Zhu, Yong-Xiu Liu, Ya-Long Guo

{"title":"A de novo Gene Promotes Seed Germination Under Drought Stress in Arabidopsis.","authors":"Guang-Teng Jin, Yong-Chao Xu, Xing-Hui Hou, Juan Jiang, Xin-Xin Li, Jia-Hui Xiao, Yu-Tao Bian, Yan-Bo Gong, Ming-Yu Wang, Zhi-Qin Zhang, Yong E Zhang, Wang-Sheng Zhu, Yong-Xiu Liu, Ya-Long Guo","doi":"10.1093/molbev/msae262","DOIUrl":"10.1093/molbev/msae262","url":null,"abstract":"The origin of genes from noncoding sequences is a long-term and fundamental biological question. However, how de novo genes originate and integrate into the existing pathways to regulate phenotypic variations is largely unknown. Here, we selected 7 genes from 782 de novo genes for functional exploration based on transcriptional and translational evidence. Subsequently, we revealed that Sun Wu-Kong (SWK), a de novo gene that originated from a noncoding sequence in Arabidopsis thaliana, plays a role in seed germination under osmotic stress. SWK is primarily expressed in dry seed, imbibing seed and silique. SWK can be fully translated into an 8 kDa protein, which is mainly located in the nucleus. Intriguingly, SWK was integrated into an extant pathway of hydrogen peroxide content (folate synthesis pathway) via the upstream gene cytHPPK/DHPS, an Arabidopsis-specific gene that originated from the duplication of mitHPPK/DHPS, and downstream gene GSTF9, to improve seed germination in osmotic stress. In addition, we demonstrated that the presence of SWK may be associated with drought tolerance in natural populations of Arabidopsis. Overall, our study highlights how a de novo gene originated and integrated into the existing pathways to regulate stress adaptation.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11721784/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886062","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

Dampened TLR2-mediated Inflammatory Signaling in Bats. 抑制蝙蝠中tlr2介导的炎症信号。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-06 DOI: 10.1093/molbev/msae253

Jiaming Zeng, Xiangyi Zhang, Chen Huang, Shilin Tian, Huabin Zhao

{"title":"Dampened TLR2-mediated Inflammatory Signaling in Bats.","authors":"Jiaming Zeng, Xiangyi Zhang, Chen Huang, Shilin Tian, Huabin Zhao","doi":"10.1093/molbev/msae253","DOIUrl":"10.1093/molbev/msae253","url":null,"abstract":"Bats are considered natural hosts for numerous viruses. Their ability to carry viruses that cause severe diseases or even death in other mammals without falling ill themselves has attracted widespread research attention. Toll-like receptor 2 forms heterodimers with Toll-like receptor 1 or Toll-like receptor 6 on cell membranes, recognizing specific pathogen-associated molecular patterns and playing a key role in innate immune responses. Previous studies have shown that moderate Toll-like receptor 2-mediated immune signals aid in pathogen clearance, while excessive or inappropriate Toll-like receptor 2-mediated immune signals can cause self-damage. In this study, we observed that TLR2, unlike TLR1 or TLR6, has undergone relaxed selection in bats compared with other mammals, indicating a reduced functional constraint on TLR2 specifically in bats. Indeed, our cell-based functional assays demonstrated that the ability of Toll-like receptor 2 to bind with Toll-like receptor 1 or Toll-like receptor 6 was significantly reduced in bats, leading to dampened inflammatory signaling. We identified mutations unique to bats that were responsible for this observation. Additionally, we found that mutations at residues 375 and 376 of Toll-like receptor 2 in the common ancestor of bats also resulted in reduced inflammatory response, suggesting that this reduction occurred early in bat evolution. Together, our study reveals that the Toll-like receptor 2-mediated inflammatory response has been specifically dampened in bats, which may be one of the reasons why they could harbor many viruses without falling ill.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11702297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813579","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

MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses. MixtureFinder：估计DNA混合模型用于系统发育分析。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-06 DOI: 10.1093/molbev/msae264

Huaiyan Ren, Thomas K F Wong, Bui Quang Minh, Robert Lanfear

{"title":"MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses.","authors":"Huaiyan Ren, Thomas K F Wong, Bui Quang Minh, Robert Lanfear","doi":"10.1093/molbev/msae264","DOIUrl":"10.1093/molbev/msae264","url":null,"abstract":"In phylogenetic studies, both partitioned models and mixture models are used to account for heterogeneity in molecular evolution among the sites of DNA sequence alignments. Partitioned models require the user to specify the grouping of sites into subsets, and then assume that each subset of sites can be modeled by a single common process. Mixture models do not require users to prespecify subsets of sites, and instead calculate the likelihood of every site under every model, while co-estimating the model weights and parameters. While much research has gone into the optimization of partitioned models by merging user-specified subsets, there has been less attention paid to the optimization of mixture models for DNA sequence alignments. In this study, we first ask whether a key assumption of partitioned models-that each user-specified subset can be modeled by a single common process-is supported by the data. Having shown that this is not the case, we then design, implement, test, and apply an algorithm, MixtureFinder, to select the optimum number of classes for a mixture model of Q-matrices for the standard models of DNA sequence evolution. We show this algorithm performs well on simulated and empirical datasets and suggest that it may be useful for future empirical studies. MixtureFinder is available in IQ-TREE2, and a tutorial for using MixtureFinder can be found here: http://www.iqtree.org/doc/Complex-Models#mixture-models.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881819","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

Direct Measurement of the Mutation Rate and Its Evolutionary Consequences in a Critically Endangered Mollusk. 一种极度濒危软体动物突变率的直接测量及其进化后果。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-06 DOI: 10.1093/molbev/msae266

T Brock Wooldridge, Sarah M Ford, Holland C Conwell, John Hyde, Kelley Harris, Beth Shapiro

{"title":"Direct Measurement of the Mutation Rate and Its Evolutionary Consequences in a Critically Endangered Mollusk.","authors":"T Brock Wooldridge, Sarah M Ford, Holland C Conwell, John Hyde, Kelley Harris, Beth Shapiro","doi":"10.1093/molbev/msae266","DOIUrl":"10.1093/molbev/msae266","url":null,"abstract":"The rate at which mutations arise is a fundamental parameter of biology. Despite progress in measuring germline mutation rates across diverse taxa, such estimates are missing for much of Earth's biodiversity. Here, we present the first estimate of a germline mutation rate from the phylum Mollusca. We sequenced three pedigreed families of the white abalone Haliotis sorenseni, a long-lived, large-bodied, and critically endangered mollusk, and estimated a de novo mutation rate of 8.60 × 10-9 single nucleotide mutations per site per generation. This mutation rate is similar to rates measured in vertebrates with comparable generation times and longevity to abalone, and higher than mutation rates measured in faster-reproducing invertebrates. The spectrum of de novo mutations is also similar to that seen in vertebrate species, although an excess of rare C > A polymorphisms in wild individuals suggests that a modifier allele or environmental exposure may have once increased C > A mutation rates. We use our rate to infer baseline effective population sizes (Ne) across multiple Pacific abalone and find that abalone persisted over most of their evolutionary history as large and stable populations, in contrast to extreme fluctuations over recent history and small census sizes in the present day. We then use our mutation rate to infer the timing and pattern of evolution of the abalone genus Haliotis, which was previously unknown due to few fossil calibrations. Our findings are an important step toward understanding mutation rate evolution and they establish a key parameter for conservation and evolutionary genomics research in mollusks.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 1","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951710","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