Population Genomics of Kirtland’s Snake (Clonophis kirtlandii)

The semi-fossorial Kirtland’s Snake Clonophis kirtlandii is a relatively small species in the subfamily Natricinae that is endemic to the Midwest and prefers moist habitats such as open meadows and wetlands. Threatened or endangered over most of its range, a population genomic study for this species is necessary to better understand the status of its populations and provide a basis for developing management plans to further its protection. Here, a population genomics analysis using 3RAD was used to discover 166 SNPs within this species from across its geographic range. Multiple cluster analyses revealed populations formed three clusters, which were not clearly based on geographic location. Samples from Indiana and Ohio showed admixture and were assigned to two different clusters, while Illinois samples were all located in a single cluster. Michigan samples and some individuals collected from single site in southeast Indiana formed a third distinct cluster. Pairwise comparison of DAPC results revealed that the three identified clusters were distinct from each other. Individuals from non-urban habitats trended toward higher levels of nucleotide diversity and expected heterozygosity compared to individuals from urban habitats but without statistical support. This study successfully identified loci that were used to describe genetic variation between C. kirtlandii populations.