Han Fan, Lamichhaney Sangeet, Grant B Rosemary, Grant Peter R, Andersson Leif, Webster Matthew T
Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75123 Uppsala, Sweden.
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544-2016, USA.
Genome Res. 2017 Jun;27(6):1004-1015. doi: 10.1101/gr.212522.116. Epub 2017 Apr 25.
Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence () in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence () and absolute divergence (). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the and loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.
亲缘关系相近物种的基因组比较已识别出局部序列差异升高的“岛屿”。基因组岛可能包含参与局部适应或生殖隔离的功能变异，因此可能在物种形成过程中发挥重要作用。然而，基因组岛也可能通过与物种形成无关的进化过程产生，对其特性的研究可以阐明新物种是如何进化的。在这里，我们对12对处于不同遗传距离的达尔文雀科物种进行了高相对差异（）区域的扫描。在每一对中，我们识别出平均相对差异（）和绝对差异（）均升高的基因组岛。这一信号表明这些基因组区域内的单倍型比基因组的其他部分更早地彼此隔离。有趣的是，在同域和异域物种对中观察到数量相似的升高的基因组岛，这表明近期的基因流不是其形成的主要因素。我们发现两个最显著的基因组岛包含 和 基因座，它们分别与喙的形状和大小的变异相关，这表明它们参与了生态适应。包括这些基因座在内的一部分基因组岛区域似乎代表了在达尔文雀科辐射早期就已分化的古老单倍型。比较基因组学数据表明，这些基因座以及一般的基因组岛具有极低的重组率，这可能在它们的形成过程中发挥作用。
