Data from: Evidence of linked selection on the Z chromosome of hybridizing hummingbirds

Levels of genetic differentiation vary widely along the genomes of
recently diverged species. What processes cause this variation? Here I
analyze geographic population structure and genome-wide patterns of
variation in the Rufous, Allen's, and Calliope Hummingbirds
(Selasphorus rufus/sasin/calliope) and assess evidence that linked
selection on the Z chromosome drives patterns of genetic differentiation
in a pair of hybridizing species. Demographic models, introgression tests,
and genotype clustering analyses support a reticulate evolutionary history
consistent with divergence during the late Pleistocene followed by gene
flow across migrant Rufous and Allen's Hummingbirds during the
Holocene. Relative genetic differentiation is elevated and
within-population diversity depressed on the Z chromosome in all
interspecific comparisons. The ratio of Z to autosomal within-population
diversity is much lower than that expected from population size effects
alone, and Tajima's D is depressed on the Z chromosome in S.
rufus and S. calliope. These results suggest that conserved
structural features of the genome play a prominent role in shaping genetic
differentiation through the early stages of speciation in northern
Selasphorus hummingbirds, and that the Z chromosome is a likely
site of genes underlying behavioral and morphological variation in the
group.