Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio‐temporal variations in population demography and variations in recombination rate and in diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests, and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (F_ST = 0.003 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long‐lasting gene flow between populations inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (F_ST = 0.08 on average), in line with the inference of moderate ancestral migration, followed by isolation since the end of the last glaciation. Effective population sizes were large, yet smaller on the island than on the mainland. Weak and nonparallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds and were more often found in regions of low recombination, as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8 Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.

中文翻译：

---

蓝山雀种群的人口统计历史和当地适应的基因组学。


了解局部适应背后的基因组过程是现代进化生物学的中心目标。这项任务需要识别局部选择的足迹，还需要估计种群人口统计学的时空变化以及重组率和基因组多样性的变化。在这里，我们在先前描述的强烈表型分化的背景下，研究了居住在落叶林与常绿林、岛屿与大陆地区的蓝山雀种群的这些参数。落叶和常绿栖息地的邻近种群对的遗传差异较弱（平均F _ST = 0.003），但栖息地类型对整体遗传结构的影响具有统计显着性。这种低分化与人口模型推断出的人群之间强大而持久的基因流动是一致的。反过来，岛屿和大陆人口存在适度分化（平均F _ST = 0.08），符合祖先适度迁移的推论，随后自上次冰河时代结束以来就开始隔离。岛上的有效人口规模很大，但比大陆要少。落叶种群和常绿种群之间的差异选择的弱且不平行的足迹与其高连通性和这些栖息地局部适应的可能多基因性质一致。反过来，在长期孤立的岛屿鸟类与大陆鸟类之间发现了更强的发散选择足迹，并且更常见于低重组区域，正如理论所预期的那样。最后，我们在大陆发现了一个基因组倒置，跨度为 2.8 Mb。 这些结果为了解多个地理尺度的蓝山雀种群的人口历史和局部适应的遗传结构提供了见解。