PDF(Pubmed)
Abstract：
A growing number of recent studies have demonstrated that introgression is common across the tree of life. However, we still have a limited understanding of the fate and fitness consequence of introgressed variation at the whole-genome scale across diverse taxonomic groups. Here, we implemented a phylogenetic hidden Markov model to identify and characterize introgressed genomic regions in a pair of well-diverged, nonsister sea urchin species: Strongylocentrotus pallidus and Strongylocentrotus droebachiensis. Despite the old age of introgression, a sizable fraction of the genome (1% to 5%) exhibited introgressed ancestry, including numerous genes showing signals of historical positive selection that may represent cases of adaptive introgression. One striking result was the overrepresentation of hyalin genes in the identified introgressed regions despite observing considerable overall evidence of selection against introgression. There was a negative correlation between introgression and chromosome gene density, and two chromosomes were observed with considerably reduced introgression. Relative to the nonintrogressed genome-wide background, introgressed regions had significantly reduced nucleotide divergence (dXY) and overlapped fewer protein-coding genes, coding bases, and genes with a history of positive selection. Additionally, genes residing within introgressed regions showed slower rates of evolution (dN, dS, dN/dS) than random samples of genes without introgressed ancestry. Overall, our findings are consistent with widespread selection against introgressed ancestry across the genome and suggest that slowly evolving, low-divergence genomic regions are more likely to move between species and avoid negative selection following hybridization and introgression.
摘要：
最近越来越多的研究表明，渗入在整个生命树中很常见。然而,我们对跨不同分类群体的全基因组尺度内渗变异的命运和适应性后果的理解仍然有限。这里,我们实现了一个系统发育隐马尔可夫模型来识别和表征一对分化良好的基因组区域，非姐妹海胆物种：苍白条和S.droebachiensis。尽管年代久远，相当一部分基因组(1%-5%)表现出渗入的祖先，包括许多显示历史阳性选择信号的基因，这些基因可能代表适应性基因渗入的情况。一个惊人的结果是，尽管观察到针对基因渗入的选择的大量总体证据，但在确定的基因渗入区域中hyalin基因的过度表达。基因渗入与染色体基因密度呈负相关,观察到两条染色体的渗入大大减少。相对于非基因渗入的全基因组背景，基因渗入区域的核苷酸差异（dXY）显着降低，并且重叠的蛋白质编码基因较少，编码基础，和有阳性选择史的基因。此外,存在于渗入区域内的基因显示出较慢的进化速度(dN，dS,dN/dS）比没有渗入血统的基因的随机样本。总的来说,我们的发现与基因组中针对渗入祖先的广泛选择一致，并表明进化缓慢，低分化基因组区域更有可能在物种之间移动，并避免杂交和基因渗入后的阴性选择。
