Pleistocene speciation and isolation-by-distance within North American mud and rainbow snakes

Understanding phylogeographic structure is a key step in examining the
processes related to lineage divergence and speciation. It is often
expected that wide-ranging taxa will be composed of deeply divergent
lineages and that codistributed species will have similar population
genetic structure. Within the southeastern coastal plain of North America,
a biodiversity hotspot, the evolutionary processes that have led to the
accumulation of diversity are underexplored. Several process within this
region could be responsible for species diversification, including past
changes in climate, fluctuating sea levels, and the formation of river
systems. However, it is also possible that a pattern of
isolation-by-distance can explain population genetic structure found in
widely distributed species, which can serve as a null hypothesis for
observed genetic structure. We generate a reduced representation genomic
dataset with population level sampling for two sister species of snakes
endemic to the southeastern coastal plain, the mudsnakes and rainbow
snakes (Farancia abacura and F. erytrogramma, respectively). With these
data we find a strong signal of population divergence in F. abacura, while
isolation-by-distance alone explains genetic divergence in F.
erytrogramma. We also identify several genomic regions associated with
environmental variation that may be key to local adaptation. Lastly, we
find that the best fit demographic model includes gene flow during the
initial divergence of these two species. This model also suggests that
there is current unidirectional gene flow from the eastern F. abacura
lineage into F. erytrogramma. However, the two F. abacura lineages appear
to be reproductively isolated. We suggest further comparative
phylogeographic work to understand the full suite of evolutionary
processes driving diversification and endemism in the southeastern coastal
plain.