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Article

Genetic Diversity and Environmental Adaptation Signatures of the Great Seahorse (Hippocampus kelloggi) in the Coastal Regions of the Indo-Pacific as Revealed by Whole-Genome Re-Sequencing

1
College of Fisheries, Hubei Hongshan Laboratory/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
2
CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2025, 26(3), 1387; https://doi.org/10.3390/ijms26031387
Submission received: 16 December 2024 / Revised: 30 January 2025 / Accepted: 4 February 2025 / Published: 6 February 2025
(This article belongs to the Section Molecular Genetics and Genomics)

Abstract

The great seahorse (Hippocampus kelloggi) is one of the larger species within the seahorse group and is widely distributed in coastal areas of the Indo-Pacific. However, the natural resources of this species continue to decrease, rendering it a vulnerable species that faces a high risk of extinction. Therefore, there is an urgent need to conduct research on the genetic diversity of this species to protect its genetic resources. In this study, we conducted whole-genome re-sequencing (WGRS) on three H. kelloggi populations from the Red Sea (RS, n = 30), the Andaman Sea (AS, n = 13), and the South China Sea (SCS, n = 13), and a total of 1,398,936 high-quality single-nucleotide polymorphisms (SNPs) were identified. The results indicate that the average observed heterozygosity (Ho) and the average expected heterozygosity (He) for the RS, AS, and SCS populations are 0.2031 and 0.1987, 0.1914 and 0.1822, and 0.2083 and 0.2001, respectively. The three geographic populations exhibit a high degree of genetic differentiation with only a minimal gene flow between them. Consistently, in a population structure analysis, the three groups are also clearly distinguished, which is consistent with the results of the population differentiation coefficient. Demographic analyses revealed that the effective population size (Ne) of the SCS population underwent a dramatic bottleneck during the Last Glacial Maximum (LGM), followed by a substantial recovery, whereas the RS and AS populations maintained stable Ne values throughout this period. To investigate adaptive responses to climate change in the SCS population, we employed selective elimination analysis, which identified 21 candidate genes potentially involved in environmental adaptation. Of particular significance were myo5a, hps4, znf385a, msh3, and pfkfb4, which likely play crucial roles in the adaptive mechanisms of H. kelloggi. This comprehensive study not only illuminates the genetic diversity patterns of H. kelloggi but also provides a valuable foundation for future investigations into the species’ evolutionary adaptations.
Keywords: Hippocampus kelloggi; whole-genome re-sequencing; genetic diversity; environmental adaptation; Indo-Pacific Hippocampus kelloggi; whole-genome re-sequencing; genetic diversity; environmental adaptation; Indo-Pacific

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MDPI and ACS Style

Hao, W.-X.; Zhang, Y.-Y.; Wang, X.; Qu, M.; Wan, S.-M.; Lin, Q. Genetic Diversity and Environmental Adaptation Signatures of the Great Seahorse (Hippocampus kelloggi) in the Coastal Regions of the Indo-Pacific as Revealed by Whole-Genome Re-Sequencing. Int. J. Mol. Sci. 2025, 26, 1387. https://doi.org/10.3390/ijms26031387

AMA Style

Hao W-X, Zhang Y-Y, Wang X, Qu M, Wan S-M, Lin Q. Genetic Diversity and Environmental Adaptation Signatures of the Great Seahorse (Hippocampus kelloggi) in the Coastal Regions of the Indo-Pacific as Revealed by Whole-Genome Re-Sequencing. International Journal of Molecular Sciences. 2025; 26(3):1387. https://doi.org/10.3390/ijms26031387

Chicago/Turabian Style

Hao, Wen-Xin, Ying-Yi Zhang, Xin Wang, Meng Qu, Shi-Ming Wan, and Qiang Lin. 2025. "Genetic Diversity and Environmental Adaptation Signatures of the Great Seahorse (Hippocampus kelloggi) in the Coastal Regions of the Indo-Pacific as Revealed by Whole-Genome Re-Sequencing" International Journal of Molecular Sciences 26, no. 3: 1387. https://doi.org/10.3390/ijms26031387

APA Style

Hao, W.-X., Zhang, Y.-Y., Wang, X., Qu, M., Wan, S.-M., & Lin, Q. (2025). Genetic Diversity and Environmental Adaptation Signatures of the Great Seahorse (Hippocampus kelloggi) in the Coastal Regions of the Indo-Pacific as Revealed by Whole-Genome Re-Sequencing. International Journal of Molecular Sciences, 26(3), 1387. https://doi.org/10.3390/ijms26031387

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