Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species
由美国德州农工大学的Willian J Murphy团队发表在Molecular Biology and Evolution上。
文章的出发点是探究基因流对系统发育关系推断的影响。研究者对猫科动物系统发育关系进行了探究，探究基因组上重组率对物种树推断的影响。研究发现，由于古老的杂交渐渗的存在，常染色体上的信号并不总是能反应真实的物种形成历史。系统发育信号集中在低重组区域，尤其是X染色体上较大的低重组区；在哺乳动物中，X染色体上大的低重组区域表现出了反复出现的遗传分化和选择清扫信号。而高重组区域则富集了古代基因流信号，并且使得对冠群的分化时间的估计少了约40%。总的来说，主流的系统发育重建方法没有考虑到历史杂交事件的影响。
Figure 1. 已发表研究中的系统发育关系不一致
Figure 2. (A) Left: the top three most frequently recovered phylogenies for six felid lineages, inferred from window-based ML supermatrix analysis of the 1.5-Gb whole-genome alignment. Right: the frequency of each topology within autosomes and chrX, based on partitioning into low (<0.5 cM/Mb) and high (>2 cM/Mb) recombination rates (Li, Hillier, et al. 2016). Red arrows indicate three lineages in which the most frequent topology in the LRchrX was not the same as the most frequent genome-wide topology. (B) Distribution of different topologies on chrX, and their relationship to recombination rate (bottom).
看起来最核心的研究方法就是滑窗建树。
