Data from: the great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

A major aim of evolutionary biology is to understand why patterns of
genomic diversity vary within taxa and space. Large-scale genomic studies
of widespread species are useful for studying how environment and
demography shape patterns of genomic divergence. Here, we describe one of
the most geographically comprehensive surveys of genomic variation in a
wild vertebrate to date; the great tit (Parus major) HapMap project. We
screened ca 500,000 SNP markers across 647 individuals from 29
populations, spanning ~30 degrees of latitude and 40 degrees of longitude
- almost the entire geographic range of the European subspecies.
Genome-wide variation was consistent with a recent colonisation across
Europe from a South-East European refugiam, with bottlenecks and reduced
genetic diversity in island populations. Differentiation across the genome
was highly heterogeneous, with clear “islands of differentiation”, even
among populations with very low levels of genome-wide differentiation. Low
local recombination rates were a strong predictor of high local genomic
differentiation (FST), especially in island and peripheral mainland
populations, suggesting that the interplay between genetic drift and
recombination causes highly heterogeneous differentiation landscapes. We
also detected genomic outlier regions that were confined to one or more
peripheral great tit populations, probably as a result of recent
directional selection at the species’ range edges. Haplotype-based
measures of selection were related to recombination rate, albeit less
strongly, and highlighted population-specific sweeps that likely resulted
from positive selection. Our study highlights how comprehensive screens of
genomic variation in wild organisms can provide unique insights into
spatio-temporal evolutionary dynamics.