Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species
Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species
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DOI：
10.1093/molbev/msz139
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发表时间：
2019-10-01
影响因子：
10.7
通讯作者：
Murphy, William J.
中科院分区：
文献类型：
--
作者：
Li, Gang;Figueiro, Henrique;Murphy, William J.
目前的系统基因组学方法隐含地假设基因组中的主要系统发育信号反映了生物体的真实进化史，而没有评估物种形成后基因流动的混杂效应，这可能产生与重组变异相互作用的系统发育信号的马赛克。在这里，我们通过对猫科27种物种的系统发育分析来检验这一假设的有效性，评估了重组率对物种树推断和跨基因组的分歧时间估计的局部影响。我们发现，常染色体中的系统发育信号并不总是代表最可能的物种形成历史，这是由于在猫科动物进化过程中的古老杂交。相反，系统发育信号集中在低重组率的区域，并显著丰富在大的X染色体重组冷点，这些冷点表现出强烈的遗传分化和跨哺乳动物目的选择性扫描的反复模式。相比之下，高重组率的区域被丰富了古代基因流的特征，这些序列将皇冠-谱系分化时间扩大了近40%。我们得出结论，现有的推断生命树的系统基因组学方法可能是高度误导的，没有考虑系统发育信号相对于重组率的基因组结构及其与历史杂交的相互作用。
Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of postspeciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here, we tested the validity of this assumption with a phylogenomic analysis of 27 species of the cat family, assessing local effects of recombination rate on species tree inference and divergence time estimation across their genomes. We found that the prevailing phylogenetic signal within the autosomes is not always representative of the most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within regions of low recombination, and notably enriched within large X chromosome recombination cold spots that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by similar to 40%. We conclude that existing phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic architecture of phylogenetic signal relative to recombination rate and its interplay with historical hybridization.