Data from: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

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.

对近缘物种开展基因组比较研究，已发现局部序列分化程度升高的"基因组岛（genomic islands）"。基因组岛可能携带有参与局部适应或生殖隔离的功能性变异，因此在物种形成过程中发挥重要作用。不过，基因组岛也可通过与物种形成无关的进化过程产生，对其特性展开研究能够阐明新物种的演化机制。本研究针对不同遗传距离的12个达尔文雀物种对，开展了高相对分化区域（FST）的扫描分析。在每个物种对中，我们均鉴定出平均相对分化（FST）与绝对分化（dXY）均升高的基因组岛。这一信号表明，这些基因组区域内的单体型比基因组其余部分更早发生了相互隔离。有趣的是，在同域（sympatric）与异域（allopatric）物种对中，观测到的dXY升高的基因组岛数量相近，这提示近期的基因流并非其形成的主要因素。我们发现，两个最为显著的基因组岛分别包含ALX1与HMGA2基因座，二者分别与喙的形状和大小变异相关，表明它们参与了生态适应过程。包含上述基因座在内的部分基因组岛区域，似乎代表了在达尔文雀适应性辐射早期就已形成的古老分化单体型。比较基因组学数据显示，这些基因座以及基因组岛整体的重组率极低，这可能对其形成具有重要作用。

搜集汇总

背景与挑战

背景概述

该数据集包含达尔文雀14个种群的全基因组测序基因型信息，通过分析12个物种对，识别了基因组岛屿区域，这些区域与ALX1和HMGA2位点相关，涉及喙形和大小的生态适应。数据集旨在研究基因流、古老多态性和生态适应如何塑造物种分化的基因组景观，数据以VCF格式提供，总大小约657.87 MB。