Threatened, endangered, and at-risk species (TER-S) often exist as scattered metapopulations because of habitat fragmentation. Metapopulations often exhibit extinction-recolonization and source-sink dynamics. Sustainable metapopulations may be maintained through smaller, interconnected habitat patches if sufficient opportunities for dispersal occur between them. This concept is significant for the Department of Defense (DoD) because setting aside large tracts of undisturbed lands for conservation may impair the ability of a DoD installation to perform its mission. Genetic analyses can identify potential source and sink populations and, when combined with geographic information system (GIS) and landscape analyses, also can identify potential dispersal corridors necessary for sustaining metapopulations as well as habitats that are critical foci of genetic biodiversity and a priority for conservation. In particular, gopher tortoise (Gopherus polyphemus) populations are of concern. A large proportion of the remaining populations of these species reside on DoD lands.

The objective of this project was to conduct initial spatially explicit metapopulation genetic, landscape genetic, and phylogeographic analyses to determine relative levels of genetic diversity and gene flow for gopher tortoises on Camp Shelby, Mississippi. These data could then be used as a basis for a more intensive study of the metapopulation genetics of this species in relation to landscape structure, population demographics, and fitness components. Specific objectives included determining if (1) gopher tortoise populations were spatially structured, (2) the levels of genetic diversity and gene flow were affected by military activity and habitat quality, and (3) patterns of genetic diversity followed an "isolation by distance" model (i.e., if a correlation between geographic distance and genetic relatedness exists).

DNA was extracted from the blood of gopher tortoises collected from 22 colonies in and around Camp Shelby. Six major treatment groups were defined based on the habitat conditions and level of military activity descriptors used to describe the areas they inhabited. The amount of genetic diversity within each colony and treatment group was determined for microsatellite DNA markers and mitochondrial DNA. The amount of genetic diversity in mitochondrial DNA was analyzed in two different loci: a single-base sequence polymorphism in the cytochrome b gene (an enzyme in the electron transport chain) and the control region, a non-coding region that is the origin of DNA replication when the cell divides and replicates both nuclear and mitochondrial DNA. Spatially explicit metapopulation genetic, landscape genetic, and phylogeographic analyses were then used to determine relative levels of genetic diversity (within and between populations) and gene flow.

The data indicate that the amount of genetic diversity in the Camp Shelby gopher tortoise population may be affected by a combination of military activity and habitat quality. Data on gene flow indicate that military activity may have affected the rates of dispersal among the tortoise colonies. Genetic distances did not correlate well with geographic distance. This may indicate that gene flow is affected by factors other than geographic distance in these tortoises, possible by military activities on Camp Shelby. Overall, the data indicate that enough genetic diversity is present among these colonies to use genetic approaches in delimiting important habitat needs for conservation of gopher tortoises, which was the main goal of the research.

The approach developed under this project helped delineate important habitat and migration corridors for gopher tortoise metapopulations. It can be modified to analyze other species and installations. This approach also could extend to lands surrounding military installations to help identify potential source populations and foci of genetic diversity, buffering the effects of military activities on TER-S and reducing constraints to the use of DoD lands.