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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
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Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

机译：侧向基因转移的系统发育建模可重构物种形成的模式和相对时间

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摘要

The timing of the evolution of microbial life has largely remained elusive due to the scarcity of prokaryotic fossil record and the confounding effects of the exchange of genes among possibly distant species. The history of gene transfer events, however, is not a series of individual oddities; it records which lineages were concurrent and thus provides information on the timing of species diversification. Here, we use a probabilistic model of genome evolution that accounts for differences between gene phytogenies and the species tree as series of duplication, transfer, and loss events to reconstruct chronologically ordered species phytogenies. Using simulations we show that we can robustly recover accurate chronologically ordered species phytogenies in the presence of gene tree reconstruction errors and realistic rates of duplication, transfer, and loss. Using genomic data we demonstrate that we can infer rooted species phytogenies using homologous gene families from complete genomes of 10 bacterial and archaeal groups. Focusing on cyanobacteria, distinguished among prokaryotes by a relative abundance of fossils, we infer the maximum likelihood chronologically ordered species phytogeny based on 36 genomes with 8,332 homologous gene families. We find the order of speciation events to be in full agreement with the fossil record and the inferred phytogeny of cyanobacteria to be consistent with the phylogeny recovered from established phylogenomics methods. Our results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record.
机译：由于原核生物化石记录的稀缺以及可能在遥远的物种之间进行基因交换的混杂影响，微生物生命进化的时机在很大程度上仍然难以捉摸。然而，基因转移事件的历史并不是一系列个别的怪事。它记录了哪些宗族是并发的，从而提供了有关物种多样化时间的信息。在这里，我们使用基因组进化的概率模型，将基因植物和树种之间的差异作为重复，转移和丢失事件的序列，以重建按时间顺序排列的物种植物。使用模拟表明，在存在基因树重建错误以及实际的重复，转移和丢失率的情况下，我们可以稳健地恢复准确的按时间顺序排列的物种植物遗传学。使用基因组数据，我们证明我们可以使用来自10个细菌和古细菌组的完整基因组的同源基因家族来推断生根的植物。着眼于蓝细菌，通过相对丰富的化石在原核生物之间进行区分，我们基于36个具有8,332个同源基因家族的基因组，推断出按时间顺序排列的最大植物种的最大可能性。我们发现物种形成事件的顺序与化石记录完全一致，并且推断的蓝细菌的植物遗传学与从已建立的系统发育组学方法中恢复的系统发育一致。我们的结果表明，通过基因组进化的概率模型检测到的侧向基因转移可以用作进化时间信息的来源，为有限的原核化石记录提供了有价值的补充。

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    Gergely J. Szoelloesi; Bastien Boussau; Sophie S. Abby; EricTannier; Vincent Daubin;

  • 作者单位

    Iaboratoire de Biometrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unite Mixte de Recherche 5558, Universite Lyon 1, F-69622 Villeurbanne, France,Universite de Lyon, F-69000 Lyon, France;

    Iaboratoire de Biometrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unite Mixte de Recherche 5558, Universite Lyon 1, F-69622 Villeurbanne, France,Universite de Lyon, F-69000 Lyon, France,Department of Integrative Biology, University of California, Berkeley, CA 94720-3140;

    Microbial Evolutionary Genomics, Departement Genomes et Genetique, Institut Pasteur, F-75015 Paris, France,Centre National de la Recherche Scientifique, Unite Mixte de Recherche 3525, F-75015 Paris, France;

    Iaboratoire de Biometrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unite Mixte de Recherche 5558, Universite Lyon 1, F-69622 Villeurbanne, France,Universite de Lyon, F-69000 Lyon, France,Institut National de Recherche en Informatique et en Automatique Rhdne-alpes, F-38334 Montbonnot, France;

    Iaboratoire de Biometrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unite Mixte de Recherche 5558, Universite Lyon 1, F-69622 Villeurbanne, France,Universite de Lyon, F-69000 Lyon, France;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    molecular dating; gene tree reconciliation; birth-death model;

    机译：分子测年基因树和解;出生死亡模型;

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