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.