Low Genetic Diversity and Decreased Effective Population Sizes of Acropora hyacinthus Populations Inhabiting Inshore and Offshore Reefs in the South China Sea

Coral reefs, with their high biodiversity and ecological service functions, face significant threats due to climate change, overfishing, and pollution. The South China Sea (SCS) hosts rich coral biodiversity, particularly Acropora hyacinthus, a critical species for reef restoration. However, the region’s coral reefs are increasingly degraded, highlighting the urgent need for conservation efforts. In the present study, the genetic diversity and population structure of A. hyacinthus were examined based on two types of data: double-digest restriction-site-associated DNA (ddRAD) sequencing data and mitochondrial putative control region DNA (mtCR) sequences. Coral tissue samples were collected from 74 colonies inhabiting two inshore reefs (Sanya) and three offshore reefs (Xisha islands), and 748 single nucleotide polymorphisms (SNPs) and 74 mtCR sequences were obtained and utilized for downstream analysis. The results were consistent in analyses and did not cluster into two geographical groups for the inshore and offshore sites. Phylogenetic analysis showed that individuals of A. hyacinthus inhabiting the five detected sites were likely cryptic species HyaD. Furthermore, AMOVA and pairwise FST estimations based on both data types revealed no differentiation among five populations and between inshore and offshore reefs, which could be due to the reproductive mode of broadcast spawning for this species. However, a prevalent low level of genetic diversity was observed when compared with nearby Taiwan regions and Japan, and the geographic history results showed that the effective population size (Ne) had been decreasing for the past 300 years. Thus, we speculated that the populations of A. hyacinthus inhabiting the SCS lack the potential to cope with future climate change adequately, and multiple conservation measures should be implemented based on considering genetic diversity.