Data from: Mitochondrial DNA assessment of the phylogeography of the gopher tortoise

Identifying geographic barriers that define genetic structure within a
species is crucial in formulating an effective conservation plan. The
identification of appropriate management units is critical for the
protection and recovery of the gopher tortoise Gopherus polyphemus, which
have declined across their entire range. Previous molecular work at
various spatial scales has identified distinct population assemblages of
the gopher tortoise. The goal of this study was to assess the genetic
structure in gopher tortoises through a more complete sampling of the
federally listed as threatened portion of the range and evaluate the
extent of genetic isolation imposed by several potential geographic
barriers. We sequenced a 712–base-pair portion of a mitochondrial gene
(NADH dehydrogenase 4) for 322 individuals from 42 sites across the range.
We found two major assemblages of haplotypes separated by a modest
phylogenetic break (average uncorrected p distance  =  0.015). The
biogeographic barrier that best explained the geographic partitioning of
genetic variation was the Apalachicola–Chattahoochee rivers and not the
one used to delimit the federally listed as threatened portion of the
range (Tombigbee–Mobile). However, the presence of distinct (group 1 and
2) haplotypes on either side of Apalachicola–Chattahoochee rivers
indicates that the two lineages experienced historical isolation and
divergence, after which they came back into contact. If one were to define
genetic units of conservation for gopher tortoises, then the
Apalachicola–Chattahoochee rivers delineation would be the most
appropriate based on the analysis of molecular variance of the
mitochondrial sequence data. However, a model that combines the
Apalachicola–Chattahoochee and Tombigbee–Mobile rivers as geographic
breaks was the second-best model in this analysis, which suggests that the
federally listed as threatened portion of the range also contains
important geographic structure. Thus, we recommend that making management
decisions on the basis of mitochondrial data alone is premature, and that
prior to any status review additional work that examines finer scale
patterns of genetic structure by using microsatellite loci is required.