Clonal diversity and connectedness of turtle grass (Thalassia testudinum) populations in a UNESCO Biosphere Reserve

•St. John, American Virgin Island turtlegrass are not clonal populations.•These seagrasses have high levels of genetic diversity and low levels of inbreeding.•The St. John’s populations have high connectivity to each other.•The outgroup from a stressed bay in Florida is diverse with few signs of inbreeding.

We assessed Thalassia testudinum population genetics among four bays in St. John (United States Virgin Islands), a protected UNESCO Biosphere Reserve. Our results suggest that the St. John T. testudinum populations have (1) high sexual reproduction rates, (2) high levels of genetic diversity and low levels of inbreeding relative to other seagrass populations in less protected geographic areas, and (3) high connectivity when separated by up to 12 km. Pairwise FST values among the island populations ranged from 0.035 to 0.148. Additionally, we found that the T. testudinum outgroup population from an anthropogenically stressed bay in Florida is surprisingly diverse and shows few signs of inbreeding.