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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Phylogenetic incongruence arising from fragmented speciation in enteric bacteria
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Phylogenetic incongruence arising from fragmented speciation in enteric bacteria

机译：肠细菌中物种分化造成的系统发育不一致

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摘要

Evolutionary relationships among species are often assumed to be fundamentally unambiguous, where genes within a genome are thought to evolve in concert and phylogenetic incongruence between individual orthologs is attributed to idiosyncrasies in their evolution. We have identified substantial incongruence between the phylogenies of orthologous genes in Escherichia, Salmonella, and Citrobacter, or E. coli, E. fergusonii, and E. albertii. The source of incongruence was inferred to be recombination, because individual genes support conflicting topology more robustly than expected from stochastic sequence homoplasies. Clustering of phylogeneti-cally informative sites on the genome indicated that the regions of recombination extended over several kilobases. Analysis of phy-logenetically distant taxa resulted in consensus among individual gene phylogenies, suggesting that recombination is not ongoing; instead, conflicting relationships among genes in descendent taxa reflect recombination among their ancestors. Incongruence could have resulted from random assortment of ancestral polymorphisms if species were instantly created from the division of a recombining population. However, the estimated branch lengths in alternative phylogenies would require ancestral populations with far more diversity than is found in extant populations. Rather, these and previous data collectively suggest that genome-wide recombination rates decreased gradually, with variation in rate among loci, leading to pluralistic relationships among their descendent taxa.
机译：通常认为物种间的进化关系是基本明确的，其中基因组内的基因被认为是一致进化的，而各个直系同源物之间的系统发育不一致性归因于其进化过程中的特质。我们已经确定大肠埃希氏菌，沙门氏菌和柠檬酸直系同源基因或大肠杆菌，弗氏大肠杆菌和阿尔伯特氏大肠杆菌直系同源基因的系统发育之间的不一致。据推测，不一致的来源是重组，因为单个基因比随机序列同质异体更能支持冲突的拓扑。基因组上系统发育信息位点的聚簇表明重组区域扩展了几千个碱基。对植物遗传距离远的分类群的分析导致各个基因系统发育之间的共识，表明重组没有进行。相反，后代类群中基因之间的冲突关系反映了其祖先之间的重组。如果物种是通过重组种群的分裂而立即产生的，那么祖先多态性的随机分类可能会导致不一致。但是，在不同的系统发育中，估计的分支长度将要求祖先种群具有比现存种群更多的多样性。相反，这些数据和以前的数据共同表明，全基因组范围的重组率随着基因座速率的变化而逐渐降低，从而导致其后代分类单元之间的多元关系。

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