Revisiting the genetic diversity and population structure of the endangered Green Sea Turtle (Chelonia mydas) breeding populations in the Xisha (Paracel) Islands, South China Sea

The Green Sea Turtle (Chelonia mydas) is an umbrella species in the South China Sea, a Chinese national first-level protected wild animal, and the only sea turtle that nests in waters around China. The largest C. mydas nesting ground is distributed in the Xisha (Paracel) Islands, which plays a vital role in the survival of sea turtle populations in the region. This study reveals the genetic diversity and population structure of the breeding population of C. mydas in the Xisha (Paracel) Islands using three mitochondrial markers. A total of 15 D-loop, five Cytochrome b (Cyt b), and seven Cytochrome C Oxidase subunit I (COI) haplotypes were identified in the breeding population of C. mydas in the Xisha (Paracel) Islands. D-loop haplotypes are distributed in clades III, IV, and VIII of the C. mydas mitochondrial control region. It is the first time that one haplotype from Clade IV was found in this C. mydas population, and five new D-loop haplotypes were also identified. The haplotype and nucleotide diversity were calculated for each marker: D-loop (0.415 haplotype diversity, 0.00204 nucleotide diversity), Cyt b (0.140, 0.00038) and COI (0.308, 0.00083). The average genetic distance (p) of each molecular marker was less than 0.01. Neutral detection and nucleotide mismatch analysis suggested that the breeding population of C. mydas in the Xisha (Paracel) Islands did not experience a population expansion event in recent history. It is recommended that a sea turtle protection area be established in the Xisha (Paracel) Islands area to strengthen protection and effectively protect the uniqueness and sustainability of the breeding population of C. mydas in the South China Sea.