Population Genetics Study of Saccostrea malabonensis (Bivalvia: Ostreidae) in Hainan Island

Hainan Island is one of the largest islands in China and is located in the Indo-Burma biodiversity hotspot region. Despite its ecological significance, comprehensive population genetic studies of key marine organisms along the entire coastline of Hainan Island have not been reported. This study examined the genetic diversity and population structure of the widely distributed oyster Saccostrea malabonensis around Hainan Island with analyzing mitochondrial COI gene sequences. The impacts of geographical, environmental and anthropogenic factors on genetic differentiation were also investigated. The results revealed a significant AT bias in the COI gene sequences, with transitions as the main mutation type. A total of 103 variable sites and 107 haplotypes were identified from 480 COI sequences, with haplotype diversities from 0.067 to 0.782, and nucleotide diversities between 0.00011 and 0.00278. AMOVA analysis indicated that 86.65% of the variation occurred within one population while 13.35% among different populations. The average genetic distance across 16 populations was 0.00169, and the average genetic differentiation index was 0.13353. Distinct population patterns can be observed. The populations of Tonghai Village (THV) and Gangmen Mountain (GMM) in Lingshui showed similar genetic structures while those of Wanquan River Estuary (WQRE, Qionghai) and Wuzhizhou Island (WZZI, Sanya) displayed divergent evolutionary trends. Cluster analysis grouped the 480 individuals of S. malabonensis into six subpopulations. These findings are helpful for developing conservation strategies and genetic breeding programs, and are also helpful for understanding the evolutionary history of this oyster species in Hainan Island.