Genetic support for discrete conservation units of the fossorial rodent Geomys pinetis

Knowledge of the population genetic structure and diversity of at-risk species is essential to accurately evaluate population viability and define units for conservation and management. The southeastern pocket gopher (Geomys pinetis) is a fossorial rodent native to the imperiled longleaf pine savannas of the southeastern United States. Its recent decline has made it a species of ‘high conservation concern’ by state agencies. Previous phylogenetic analyses suggested two distinct lineages within the species occurring east (G. p. pinetis) and west (G. p. mobilensis) of the Apalachicola-Chattahoochee-Flint River (ACF) Basin, a phylogeographic break for many species. However, little is known about the genetic substructure within each region. We examined neutral and putatively adaptive variation in 9373 single nucleotide polymorphisms (SNPs) to assess the extent of genetic structure across the species' geographic range. We confirmed significant genetic divergence of populations east–west of the ACF Basin, predating the Last Glacial Maximum, supporting the presence of two evolutionary independent lineages. Our results indicate additional strong genetic substructuring within each lineage and possible non-neutral variation across latitudes. Given the high degree of genetic differentiation and lack of evidence for secondary contact among populations within the ACF Basin, we recommend that G. pinetis be managed as two conservation units corresponding to distinct lineages representing G. pinetis and G. mobiliensis.