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

<b>Abstract</b><br/>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.

摘要
在物种形成过程中，差异基因流（differential gene flow）、连锁选择导致的多样性降低以及基因组自身特征，均可塑造基因组分化的模式。斯温氏鸫（Swainson's thrushes）的沿海与内陆亚种群之间的生殖隔离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适合度方面发挥关键作用。本研究组装并注释了该物种的草图参考基因组（draft reference genome），同时为这两个亚种群之间杂交带邻近的种群生成了全基因组鸟枪测序数据（whole-genome shotgun sequence data）。我们记录到这两个亚种群间遗传分化相对估计值存在显著的全基因组异质性。在相对分化程度较高的区域，种群内多样性更低，这支持了选择性清除（selective sweeps）在塑造该分化模式中的作用。此类区域的绝对遗传分化水平有所降低，进一步表明祖先种群中以及二次接触后的分歧种群间可能发生了反复的选择性清除事件。相对遗传分化在着丝粒（centromeres）附近及Z染色体（Z chromosome）上也更高，提示基因组自身特征同样推动了全基因组异质性的形成。与迁徙性状相关的基因集中分布于分化岛（islands of differentiation）中，验证了此前提出的“季节性迁徙在斯温氏鸫种群间受到歧化选择（divergent selection）”的假说。迁徙行为差异可能在诸多类群的物种形成过程中扮演核心角色；本研究搭建的研究基础设施，将为未来探究多个候选基因在降低斯温氏鸫乃至其他物种种群间基因流中的作用提供支持。