Historically believed to harbor unrecognized diversity, the taxonomy of the declining Alligator Snapping Turtle (genus Macrochelys) is debated. The original species, M. temminckii, was recently split into M. temminckii, M. apalachicolae, and M. suwanniensis. However, authors contest the status of M. apalachicolae. In this study, we generated thousands of genome-wide loci to quantify population structure and genetic differentiation across the range of Macrochelys spp. Our data indicate that M. apalachicolae is genetically distinct, with little gene flow between M. apalachicolae and other species, thus adding evidence that M. apalachicolae may be a distinct species. We also find genetic variation partitioned among river drainages, with very high intra- and interspecific genetic divergence among-river drainages. We suggest that translocations and re-introductions only move turtles in this genus within their natal river drainages to preserve existing patterns of genetic diversity.

These are raw SNPs that passed all filters from ipyrad.

Note: use population assignment file to assign individuals in the VCF to assemblages described in the manuscript.