Abstract
<jats:p> A central goal when assessing patterns of population structure for conservation is to identify populations with unique genetic compositions. The use of genomic sequencing to identify distinct populations has become an increasingly popular method of delineating conservation units. Reduced costs associated with sequencing make it possible to generate larger, more informative datasets to assess genetic diversity within and among populations. In species that exhibit nest-site philopatry, genetic population structure can emerge on much finer scales, particularly in maternally inherited mitochondrial genomes. We demonstrate the feasibility and insight gained by using whole mitochondrial genome sequencing for evaluating population genetic structure and comparing to previous single marker studies in a vulnerable turtle. We used whole mitochondrial genome sequences from diamond-backed terrapin ( <jats:italic>Malaclemys terrapin</jats:italic> ) to evaluate whether nest-site philopatry generates fine-scale genetic structure among <jats:italic>M. terrapin</jats:italic> nesting beaches in western Mobile Bay (Alabama, USA). We then compared haplotype diversity between the Alabama population and <jats:italic>M. terrapin</jats:italic> populations from the Atlantic and Gulf coasts and evaluated the utility of using whole mitochondrial genomes rather than a subset of loci to characterize unique haplotypic diversity. We found no genetic structure associated with nest-site philopatry within Alabama, but none of the haplotypes in this region were shared with other Gulf Coast sites. This genetic structure is consistent with strong female natal philopatry within western Mobile Bay relative to the Gulf of Mexico and suggests that the Mobile Bay population is genetically unique relative to other <jats:italic>M. terrapin</jats:italic> populations and merits a unique conservation and management plan. </jats:p>