Data from: Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex

The processes responsible for cytonuclear discordance frequently remain
unclear. Here, we employed an exon capture dataset and demographic methods
to test hypotheses generated by species distribution models to examine how
contrasting histories of range stability vs. fluctuation have caused
cytonuclear concordance and discordance in ground squirrel lineages from
the Otospermophilus beecheyi species complex. Previous studies in O.
beecheyi revealed three morphologically cryptic and highly divergent
mitochondrial DNA lineages (named the Northern, Central, and Southern
lineages based on geography) with only the Northern lineage exhibiting
concordant divergence for nuclear genes. Here, we showed that these mtDNA
lineages likely formed in allopatry during the Pleistocene, but responded
differentially to climatic changes that occurred since the last
interglacial (~120,000 years ago). We find that the Northern lineage
maintained a stable range throughout this period, correlating with genetic
distinctiveness among all genetic markers and low migration rates with the
other lineages. In contrast, our results suggested that the Southern
lineage expanded from Baja California Sur during the Late Pleistocene to
overlap and potentially swamp a contracting Central lineage. High rates of
intraspecific gene flow between Southern lineage individuals among
expansion origin and expansion edge populations largely eroded Central
ancestry from autosomal markers. However, male-biased dispersal in this
system preserved signals of this past hybridization and introgression
event in matrilineal-biased X-chromosome and mtDNA markers. Our results
highlight the importance of range stability in maintaining the persistence
of phylogeographic lineages, whereas unstable range dynamics can increase
the tendency for lineages to merge upon secondary contact.