Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches.
Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches.
复制标题
基因流、古老的多态性以及生态适应塑造了达尔文雀之间差异的基因组格局。
DOI：
10.1101/gr.212522.116
复制
发表时间：
2017-06
期刊：
影响因子：
7
通讯作者：
Webster MT
中科院分区：
文献类型：
--
作者：
Han F;Lamichhaney S;Grant BR;Grant PR;Andersson L;Webster MT
密切相关的物种的基因组比较已经确定了“岛屿”的局部升高的序列分歧。基因组岛可能包含参与局部适应或生殖隔离的功能变体，因此可能在物种形成过程中发挥重要作用。然而，基因组岛也可以通过与物种形成无关的进化过程产生，对它们的性质的研究可以阐明新物种是如何进化的。在这里，我们进行了扫描区域的高相对分歧（FST）在12个物种对达尔文的雀在不同的遗传距离。在每一对中，我们鉴定出平均在相对趋异度（FST）和绝对趋异度（dXY）上都升高的基因组岛。该信号表明这些基因组区域内的单倍型比基因组的其余部分更早地彼此分离。有趣的是，在同域和异域物种对中观察到类似数量的升高的dXY基因组岛，这表明最近的基因流不是它们形成的主要因素。我们发现，两个最明显的基因组岛屿包含ALX1和HMGA2基因座，这是与喙的形状和大小的变化，分别，这表明他们参与了生态适应。包括这些基因座在内的基因组岛区域的一个子集似乎代表了在达尔文雀的辐射早期进化的古代分歧单倍型。比较基因组学数据表明，这些基因座和基因组岛一般具有非常低的重组率，这可能在它们的建立中发挥作用。
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 (FST) 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 (FST) and absolute divergence (dXY). 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 dXY 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 ALX1 and HMGA2 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.