Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
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DOI：
10.1098/rspb.2016.2756
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发表时间：
2017-02-22
影响因子：
4.7
通讯作者：
Ellegren, Hans
中科院分区：
文献类型：
--
作者：
Dutoit, Ludovic;Vijay, Nagarjun;Ellegren, Hans
由于共享的祖先变异在现存物种中仍然分离，密切相关的物种可能在基因组的同源区域表现出相似水平的遗传多样性。然而，在谱系排序完成后，这种共变不一定是预期的。另一方面，如果控制遗传多样性的过程是保守的，那么即使在亲缘关系较远的物种之间，多样性也可能存在共变。我们绘制了两种不同鸟类（颈鹟和冠乌鸦）基因组之间的保守同线性区域，并鉴定了超过 600 Mb 的同源区域（基因组的 66%）。通过对两个物种的大量群体样本的全基因组重测序数据的分析，我们发现 200 kb 窗口中的核苷酸多样性具有良好的相关性（Spearman's rho = 0.407）。排除编码序列后相关性仍然高度相似。为了解释这种共变，我们认为稳定的鸟类核型和重组率变化的保守景观使得连锁选择的多样性减少效应在不同的鸟类谱系中相似。对驱动鹟多样性水平异质性的几个潜在解释变量的主成分回归分析揭示了重组率变化和选择编码序列目标密度的最强影响，与连锁选择一致。稳定的核型也可能与保守的基因组突变环境相关，从而导致谱系之间多样性水平的共变。我们的观察表明遗传多样性在某种程度上是可以预测的。
Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird speciescollared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman's rho = 0.407). The correlation remained highly similar after excluding coding sequences. To explain this covariation, we suggest that a stable avian karyotype and a conserved landscape of recombination rate variation render the diversity-reducing effects of linked selection similar in divergent bird lineages. Principal component regression analysis of several potential explanatory variables driving heterogeneity in flycatcher diversity levels revealed the strongest effects from recombination rate variation and density of coding sequence targets for selection, consistent with linked selection. It is also possible that a stable karyotype is associated with a conserved genomic mutation environment contributing to covariation in diversity levels between lineages. Our observations imply that genetic diversity is to some extent predictable.