Talla Venkat, Kalsoom Faheema, Shipilina Daria, Marova Irina, Backström Niclas
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 752 36, Sweden.
Department of Vertebrate Zoology, Lomonosov Moscow State University, 119991, Russia.
G3 (Bethesda). 2017 Dec 4;7(12):3983-3998. doi: 10.1534/g3.117.300152.
Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps toward understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations, since they allow us to study how genomes evolve as species exchange genetic material and to associate particular genetic regions with phenotypic traits of interest. Here, we use whole-genome resequencing of both allopatric and hybridizing populations of the European () and the Siberian chiffchaff ()-two recently diverged species which differ in morphology, plumage, song, habitat, and migration-to quantify the regional variation in genome-wide genetic diversity and differentiation, and to identify candidate regions for trait variation. We find that the levels of diversity, differentiation, and divergence are highly heterogeneous, with significantly reduced global differentiation, and more pronounced differentiation peaks in sympatry than in allopatry. This pattern is consistent with regional differences in effective population size and recurrent background selection or selective sweeps reducing the genetic diversity in specific regions prior to lineage divergence, but the data also suggest that postdivergence selection has resulted in increased differentiation and fixed differences in specific regions. We find that hybridization and backcrossing is common in sympatry, and that phenotype is a poor predictor of the genomic composition of sympatric birds. The combination of a differentiation scan approach with identification of fixed differences pinpoint a handful of candidate regions that might be important for trait variation between the two species.
识别分化谱系中性状变异的候选基因以及表征基因组分化的机制基础是理解新物种形成过程的关键步骤。杂交带为这类研究提供了宝贵资源，因为它们使我们能够研究随着物种交换遗传物质基因组如何进化，并将特定遗传区域与感兴趣的表型性状联系起来。在这里，我们对欧洲林莺（）和西伯利亚林莺（）的异域种群和杂交种群进行全基因组重测序——这两个最近分化的物种在形态、羽毛、歌声、栖息地和迁徙方面存在差异——以量化全基因组遗传多样性和分化的区域变异，并识别性状变异的候选区域。我们发现多样性、分化和分歧水平高度异质，全球分化显著降低，同域分布中的分化峰值比异域分布中更明显。这种模式与有效种群大小的区域差异以及反复的背景选择或选择性清除在谱系分化之前降低特定区域的遗传多样性一致，但数据也表明分化后的选择导致了特定区域的分化增加和固定差异。我们发现杂交和回交在同域分布中很常见，并且表型对同域分布鸟类的基因组组成预测能力较差。将分化扫描方法与固定差异识别相结合，确定了少数可能对两个物种间性状变异很重要的候选区域。
