Data from: Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation

Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as ‘Isolation by Adaptation’ (IBA). IBA can be complementary to the well-known pattern of ‘Isolation by Distance’ (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies, where divergent sexual selection is associated with phenotypic differentiation among allopatric populations. To investigate the relative contributions of selection and geographic distance to genome-wide differentiation, we compared genotypic and phenotypic variation from 350 barn swallows sampled across eight populations (28 pairwise comparisons) from four different subspecies. We report a draft whole genome sequence for H. rustica, to which we aligned a set of 9,493 single nucleotide polymorphisms (SNPs). Using statistical approaches to control for spatial autocorrelation of phenotypic variables and geographic distance, we find that divergence in traits related to migratory behavior and sexual signaling, as well as geographic distance together, explain over 70% of genome-wide divergence among populations. Controlling for IBD, we find 42% of genome-wide divergence is attributable to IBA through pairwise differences in traits related to migratory behavior and sexual signaling alone. By (i) combining these results with prior studies of how selection shapes morphological differentiation and (ii) accounting for spatial autocorrelation, we infer that morphological adaptation plays a large role in shaping population-level differentiation in this group of closely related populations.

地理隔离下的种群分化由多种因素共同驱动。自然选择与性选择可能在塑造种群分化模式中发挥关键作用，该模式被称为适应性隔离（Isolation by Adaptation, IBA）。适应性隔离可与广为人知的距离隔离（Isolation by Distance, IBD）模式互为补充：后者指亲缘关系较近的种群（通过任意进化过程）的分化与地理隔离相关联。家燕（Hirundo rustica）物种复合体包含6个亲缘关系密切的亚种，其异域种群间的表型分化与歧化性选择密切相关。为探究选择与地理距离对全基因组分化的相对贡献，本研究对来自4个亚种的8个种群（共28组成对比较）的350只家燕的基因型与表型变异进行了对比分析。本研究构建了家燕的全基因组草图序列，并将9493个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）位点比对至该参考基因组。通过采用控制表型变量空间自相关性与地理距离的统计方法，本研究发现：与迁徙行为、性信号相关的性状分化，结合地理距离，共同解释了种群间超过70%的全基因组分化。在控制距离隔离（IBD）效应的前提下，本研究发现：仅通过迁徙行为与性信号相关性状的成对差异，即可解释42%的全基因组分化，该分化可归因于适应性隔离（IBA）。本研究（1）将上述结果与此前关于选择如何塑造形态分化的研究相结合，（2）同时纳入空间自相关性校正，最终推断：在该亲缘关系密切的种群类群中，形态适应性在种群水平分化的形成过程中发挥了重要作用。