Data from: Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits

Linking population genetic variation to the spatial heterogeneity of the environment is of fundamental interest to evolutionary biology and ecology, in particular when phenotypic differences between populations are observed at biologically small spatial scales. Here, we applied restriction-site associated DNA sequencing (RAD-Seq) to test whether phenotypically differentiated populations of wild blue tits (Cyanistes caeruleus) breeding in a highly heterogeneous environment exhibit genetic structure related to habitat type. Using 12106 SNPs in 197 individuals from deciduous and evergreen oak woodlands, we applied complementary population genomic analyses, which revealed that genetic variation is influenced by both geographical distance and habitat type. A fine-scale genetic differentiation supported by genome- and transcriptome-wide analyses was found within Corsica, between two adjacent habitats where blue tits exhibit marked differences in breeding time while nesting less than 6 km apart. Using redundancy analysis (RDA), we show that genomic variation remains associated with habitat type when controlling for spatial and temporal effects. Finally, our results suggest that the observed patterns of genomic differentiation were not driven by a small proportion of highly differentiated loci, but rather emerged through a process such as habitat choice, which reduces gene flow between habitats across the entire genome. The pattern of genomic isolation-by-environment closely matches differentiation observed at the phenotypic level, thereby offering significant potential for future inference of phenotype-genotype associations in a heterogeneous environment.

将种群遗传变异与环境的空间异质性相关联，是进化生物学与生态学的基础研究议题。当种群间的表型差异仅出现在生物学意义上极小的空间尺度下时，这一方向的研究价值尤为凸显。本研究运用限制性酶切位点相关DNA测序（restriction-site associated DNA sequencing, RAD-Seq）技术，针对栖息于高度异质化环境、且存在表型分化的野生青山雀（Cyanistes caeruleus）种群，检验其是否存在与栖息地类型相关的遗传结构。我们对取自落叶栎林与常绿栎林的197个个体的12106个单核苷酸多态性位点（single nucleotide polymorphism, SNPs）进行分析，采用互补性群体基因组学研究方法，结果显示遗传变异同时受到地理距离与栖息地类型的双重影响。在科西嘉岛境内，两处相距不足6公里的相邻栖息地中，青山雀的繁殖时间存在显著差异，全基因组与全转录组分析均证实此处存在精细尺度的遗传分化。通过冗余分析（redundancy analysis, RDA），我们证实即便控制空间与时间效应，基因组变异仍与栖息地类型显著相关。最终，本研究结果表明，观测到的基因组分化模式并非由少量高度分化的基因座所驱动，而是通过诸如栖息地选择这类过程形成——这类过程可降低不同栖息地间全基因组范围内的基因流。这种环境隔离的基因组分化模式与表型层面观测到的分化高度吻合，为未来在异质化环境中推断表型-基因型关联提供了重要的研究潜力。