Data for: Additional complexity in historic and contemporary gene flow among hoary, Vancouver Island, and Olympic marmots revealed by microsatellites and ultraconserved elements

Alpine species are inordinately threatened by habitat loss and
precipitation changes resulting from climate change. In North America’s
Pacific Northwest, three closely related alpine mammal species – hoary,
Olympic, and Vancouver Island marmots – may face greater negative impacts
of climate change relative to species found at lower elevations.
Phylogenetic studies have found these three species form a monophyletic
complex; however, discordant evolutionary histories between mitochondrial
and nuclear genes suggest that gene flow may have occurred between these
marmot species. Furthermore, mitochondrial data find two reciprocally
monophyletic mitochondrial clades (haploclades) of hoary marmots. Nuclear
data do not recover this pattern, and interspecific relationships among
the markers are not consistent. We used nine microsatellite loci and
ultraconserved elements (UCEs) to explore patterns of nuclear gene flow
among marmot species in the PNW. Analyses of microsatellite data indicate
no current gene flow between hoary and Vancouver Island marmots or between
hoary and Olympic marmots, but do reveal nuclear gene flow among hoary
marmot haploclades. Additionally, UCE data reveal historic gene flow
between hoary and Vancouver Island marmots. Overall, our results suggest
that historic mitochondrial introgression between hoary and Vancouver
Island marmots, as well as male-biased dispersal, are driving mito-nuclear
discordance in this species complex.