Data from: Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation

Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.在物种形成过程中，差异化基因流、连锁选择引发的多样性降低，以及基因组自身的特征，均可塑造基因组分化的整体格局。斯温氏夜鸫（Swainson's thrushes）的沿海与内陆亚种类群之间，繁殖隔离的潜在来源已得到充分研究，其中季节性迁徙行为的差异可能在降低杂交个体适合度方面发挥关键作用。本研究组装并注释了该物种的参考基因组（reference genome）草图，同时生成了分布于这两个类群杂交带（hybrid zone）邻近区域的种群的全基因组鸟枪测序（whole-genome shotgun sequencing）数据。本研究记录到两类群间遗传分化的相对估计值存在显著的全基因组异质性（genomewide heterogeneity）。在相对分化程度较高的基因组区域，种群内的遗传多样性更低，这一结果支持了选择性清除（selective sweep）在塑造该分化格局中发挥作用的假说。此类区域的绝对遗传分化水平反而有所降低，进一步表明在祖先种群中，或是二次接触（secondary contact）后的分化类群之间，可能曾发生过反复的选择性清除事件。着丝粒（centromere）附近以及Z染色体上的相对遗传分化水平同样更高，这说明基因组自身的特征同样会促成全基因组的异质性。与迁徙性状相关的基因集中分布于分化岛（islands of differentiation）区域内，这支持了此前的假说：斯温氏夜鸫的季节性迁徙受到了分化选择的作用。迁徙行为的差异可能在众多类群的物种形成过程中发挥核心作用；本研究搭建的研究框架，将为未来探究多个候选基因在降低斯温氏夜鸫乃至其他物种种间基因流中的作用提供支撑。