Genetic variation in populations of the threatened seagrass Halophila beccarii (Hydrocharitaceae)

• Genetic variation of Halophila beccarii was evaluated using six microsatellites.
• Very low genetic diversity was found within populations.
• A total of 16 multi-locus genotypes were revealed in the studied populations.
• Strong genetic differentiation was found among the populations.

Halophila beccarii (Hydrocharitaceae), a small monoecious seagrass, has been listed as a threatened species. In this study, a total of 106 samples were collected from four Chinese populations located at the northern limit of its distribution range. Using six polymorphic microsatellites, we found low genetic variation in this species, in which the mean number of alleles per locus was 2.8, and 16 multi-locus genotypes were revealed. In the four populations, the mean number of alleles per locus ranged from 1.2 to 2, one to eight genotypes were found, and clonal diversity ranged from 0 to 0.23; observed and expected heterozygosity ranged from 0.17 to 0.40 and from 0.09 to 0.24, respectively. Strong genetic differentiation was found among the populations, and the standardized fixation index (F′ST) was 0.787. Species traits (i.e., clonal growth) and bottleneck effects due to drastic population fluctuation may contribute to the observed low genetic variation.