Data from: The role of ecological factors in determining phylogeographic and population genetic structure of two sympatric island skinks (Plestiodon kishinouyei and P. stimpsonii)

We conducted comparative phylogeographic and population genetic analyses
of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic
to islands in the southern Ryukyus, to explore different factors that have
influenced population structure. Previous phylogenetic studies using
partial mitochondrial DNA (mtDNA) indicate similar divergence times from
their respective closest relatives, suggesting that differences in
population structure are driven by intrinsic attributes of either species
rather than the common set of extrinsic factors that both presumably have
been exposed to throughout their history. In this study, analysis of mtDNA
sequences and microsatellite polymorphism demonstrate contrasting patterns
of phylogeography and population structure: P. kishinouyei exhibits a
lower genetic variability and lower genetic differentiation among islands
than P. stimpsonii, consistent with recent population expansion. However,
historical demographic analyses indicate that the relatively high genetic
uniformity in P. kishinouyei is not attributable to recent expansion. We
detected significant isolation-by-distance patterns among P. kishinouyei
populations on the land bridge islands, but not among P. stimpsonii
populations occurring on those same islands. Our results suggest that P.
kishinouyei populations have maintained gene flows across islands until
recently, probably via ephemeral Quaternary land bridges. The lower
genetic variability in P. kishinouyei may also indicate smaller effective
population sizes on average than that of P. stimpsonii. We interpret these
differences as a consequence of ecological divergence between the two
species, primarily in trophic level and habitat preference.