Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species
由美國德州農(nóng)工大學(xué)的Willian J Murphy團(tuán)隊(duì)發(fā)表在Molecular Biology and Evolution上。
文章的出發(fā)點(diǎn)是探究基因流對系統(tǒng)發(fā)育關(guān)系推斷的影響。研究者對貓科動(dòng)物系統(tǒng)發(fā)育關(guān)系進(jìn)行了探究，探究基因組上重組率對物種樹推斷的影響。研究發(fā)現(xiàn)，由于古老的雜交漸滲的存在，常染色體上的信號并不總是能反應(yīng)真實(shí)的物種形成歷史。系統(tǒng)發(fā)育信號集中在低重組區(qū)域，尤其是X染色體上較大的低重組區(qū)；在哺乳動(dòng)物中，X染色體上大的低重組區(qū)域表現(xiàn)出了反復(fù)出現(xiàn)的遺傳分化和選擇清掃信號。而高重組區(qū)域則富集了古代基因流信號，并且使得對冠群的分化時(shí)間的估計(jì)少了約40%。總的來說，主流的系統(tǒng)發(fā)育重建方法沒有考慮到歷史雜交事件的影響。
Figure 1. 已發(fā)表研究中的系統(tǒng)發(fā)育關(guān)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).
看起來最核心的研究方法就是滑窗建樹。
