Data from: Pleistocene range expansions promote divergence with gene flow between migratory and sedentary populations of Calothorax hummingbirds

We investigate the influence of postglacial population expansion on
genetic structure of reproductively isolated populations that come into
secondary contact and produce hybrid zones. We test migratory behaviour to
explain geographic patterns of genetic diversity and phylogeographic
structure in migratory and sedentary populations of hummingbirds in the
Chihuahuan Desert. We assessed genetic structure, demographic expansion
and introgression in Calothorax hummingbirds using mitochondrial DNA
(mtDNA) and nuclear microsatellites (nSSRs), and ecological niche
modelling (ENM) to predict where migratory and sedentary populations
resided during Pleistocene climate events. Bayesian analysis yielded three
clusters. However, only two clusters match mtDNA haplogroups, one parental
in the south (pulcher) and a cluster with two admixed taxa (sedentary and
migratory lucifer) that cannot be attributed to any pure parental
population. Demographic expansion, gene flow and admixture in the lucifer
range, postglacial northern expansion predicted by ENM, and approximate
Bayesian computation strongly supported a scenario of divergence with gene
flow: a Pleistocene basal split separating pulcher and the other two
clades are derived from a second split (migratory and sedentary lucifer).
Population genetic admixture was higher in localities with lower inferred
habitat suitability stability. The genetic differentiation of Calothorax
may be explained by the combined effects of (1) gene flow and recent
postglacial northern expansion from southern sedentary populations, (2)
increased genetic admixture with lower stability of habitat suitability,
and (3) the evolution of long-distance seasonal migration during
glacial/interglacial cycles, suggesting a role for diversification through
the divergence of migratory subpopulations that become sedentary.