DOI: 10.5061/dryad.f1vhhmh90
title: Pleistocene speciation and isolation-by-distance within North American mud and rainbow snakes

description: 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.
description: README: Pleistocene speciation and isolation-by-distance within North
 American Mud and Rainbow snakes **Dataset Overivew** This dataset contains
 genomic data in vcf, Structure, and SFS formart. With these files all
 analyses in the above mentioned paper can be recreated. **Files**
 *Farancia_full_data_set.vcf* This file contains all samples across both
 Farancia abacura and F. erytrogramma in vcf format. These data have not
 been thinned and contain more than one SNP per GBS locus.
 *F_abacura_only.vcf* This file contains only F. abacura samples in vcf
 format, note this this file has not been thinned and may contain more than
 one SNP per locus. *F_erytrogramma_only.vcf* This file contains only F.
 erytrogramma samples in vcf format, note this this file has not been
 thinned and may contain more than one SNP per locus. *F_abacura_only.str*
 This file contains only F. abacura samples in Structure format. This file
 can be used to run conStruct for population structure.
 *F_erytrogramma_only.str* This file contains only F. erytrogramma samples
 in Structure format. This file can be used to run conStruct for population
 structure. *abacura_w-abacura_e-erytrogramma_for_gadma.sfs* Site frequency
 spectrum format file used in Gadma analysis for demographic inference.