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Article

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

by
Yijin Di
1,
Lingyu Zheng
1,
Jingzhao Ke
1,
Yinyin Zhou
1,*,
Shaoyang Mo
2,
Xiangbo Liu
3,
Jiquan Lin
4,
Yuxiao Ren
4,
Duanjie Huang
4,
Rouwen Chen
1 and
Xiubao Li
1,5,6,*
1
School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
2
School of Marine Science and Engineering, Hainan University, Haikou 570228, China
3
School of Ecology, Hainan University, Haikou 570228, China
4
Hainan Provincial Ecological and Environmental Monitoring Centre, Haikou 571126, China
5
State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
6
Hainan International Joint Research Center for Coral Reef Ecology, Hainan University, Haikou 570228, China
*
Authors to whom correspondence should be addressed.
Oceans 2025, 6(4), 72; https://doi.org/10.3390/oceans6040072
Submission received: 15 April 2025 / Revised: 18 October 2025 / Accepted: 29 October 2025 / Published: 4 November 2025
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Abstract

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.
Keywords: Acropora hyacinthus; genetic diversity; genetic connectivity; ddRAD; mitochondrial putative control region; conservation genomics Acropora hyacinthus; genetic diversity; genetic connectivity; ddRAD; mitochondrial putative control region; conservation genomics

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MDPI and ACS Style

Di, Y.; Zheng, L.; Ke, J.; Zhou, Y.; Mo, S.; Liu, X.; Lin, J.; Ren, Y.; Huang, D.; Chen, R.; et al. Low Genetic Diversity and Decreased Effective Population Sizes of Acropora hyacinthus Populations Inhabiting Inshore and Offshore Reefs in the South China Sea. Oceans 2025, 6, 72. https://doi.org/10.3390/oceans6040072

AMA Style

Di Y, Zheng L, Ke J, Zhou Y, Mo S, Liu X, Lin J, Ren Y, Huang D, Chen R, et al. Low Genetic Diversity and Decreased Effective Population Sizes of Acropora hyacinthus Populations Inhabiting Inshore and Offshore Reefs in the South China Sea. Oceans. 2025; 6(4):72. https://doi.org/10.3390/oceans6040072

Chicago/Turabian Style

Di, Yijin, Lingyu Zheng, Jingzhao Ke, Yinyin Zhou, Shaoyang Mo, Xiangbo Liu, Jiquan Lin, Yuxiao Ren, Duanjie Huang, Rouwen Chen, and et al. 2025. "Low Genetic Diversity and Decreased Effective Population Sizes of Acropora hyacinthus Populations Inhabiting Inshore and Offshore Reefs in the South China Sea" Oceans 6, no. 4: 72. https://doi.org/10.3390/oceans6040072

APA Style

Di, Y., Zheng, L., Ke, J., Zhou, Y., Mo, S., Liu, X., Lin, J., Ren, Y., Huang, D., Chen, R., & Li, X. (2025). Low Genetic Diversity and Decreased Effective Population Sizes of Acropora hyacinthus Populations Inhabiting Inshore and Offshore Reefs in the South China Sea. Oceans, 6(4), 72. https://doi.org/10.3390/oceans6040072

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