Phylogeography of Diadophis punctatus: extensive lineage diversity and repeated patterns of historical demography in a trans-continental snake

Dynamic climatic oscillations during the Pleistocene had profound effects on the distributions of species across North America. Although the role of historical climate change on speciation remains controversial, the impact on genetic variation within species has been well documented. We examined mtDNA sequences from the cytochrome b gene (1117 bp) and a portion of the NADH-4 gene (659 bp) for 286 individuals of Diadophis punctatus to infer phylogeographic patterns and population structure and to examine historical demographic patterns in both glaciated and unglaciated regions of North America. We inferred 14 lineages that replace each other geographically across the United States. Several of these lineages appear to be confined to specific habitats (floodplains, grasslands, montane environments) and traverse previously identified genetic barriers for terrestrial vertebrates including the Mississippi and Apalachicola Rivers, the Appalachian Mountains, and the western continental divide. We also observed overlapping ranges between some haplotype groups and several instances of secondary contact associated with ecological transition zones in eastern South Carolina, southern Oklahoma and central California. Within the US, diversification began during the late Miocene and continued into the mid-Pleistocene, suggesting these lineages pre-dated the last glacial maximum. Coalescent and non-coalescent demographic analyses indicate that independent lineages currently occupying previously glaciated or unsuitable areas in eastern, central and western US underwent post-glacial population expansion likely from southern refugia during the late Pleistocene/early Holocene. Conversely, southern lineages display patterns consistent with long-term population stability. Such long-term persistence of genetic structure may be due to the competitive effects between lineages or ecosystem stability in more southern latitudes.