Twenty-five novel EST-derived simple sequence repeat (EST-SSR) markers were developed in the ark shell Scapharca broughtonii. Polymorphisms of these EST-SSR markers were evaluated in 48 wild individuals collected from Shidao, Shandong Province, China. A total of 202 alleles were detected at 25 loci. The numbers of alleles per locus ranged from 4 to 14, with an average of 8.08. The observed and expected heterozygosities varied from 0.2917 to 1.000 and from 0.3570 to 0.9002, respectively. After sequential Bonferroni correction for multiple tests, only one locus was found to deviate from Hardy-Weinberg equilibrium. Twenty-five EST-SSR markers showed a high rate of across-species transferability (100%) in Scapharca subcrenata and a low rate of across-genus transferability (20%) in Tegillarca granosa. These EST-SSRs will be helpful for QTL mapping, molecular breeding and investigation of population genetic diversity in ark shell S. broughtonii and other Scapharca species.

Twenty microsatellite markers were isolated and characterized for Solenocera crassicornis from a (GT)₁₃-enriched genomic library. Their polymorphisms were investigated using 44 wild individuals from the South Yellow Sea. Our investigation revealed that all the markers were polymorphic. The number of alleles per locus varied from 6 to 19 with an average of 12.35. The observed and expected heterozygosities ranged from 0.400 to 0.977 and from 0.609 to 0.940, with averages of 0.788 and 0.859, respectively. Four loci significantly deviated from Hardy-Weinberg equilibrium after Bonferroni’s correction. Cross-species amplification was also conducted in Solenocera melantho collected from the East China Sea. The result showed that 14 loci could be amplified from Solenocera melantho DNAs. These polymorphic markers would be useful for assessment of genetic variation and population structure of S. crassicornis and S. melantho.

Global coral reef ecosystems face various levels of disturbance pressure. Understanding the depth-structured variation in coral reef fish communities can help us to better grasp and predict the adaptive changes of the ecosystem under different stressors. This study applied eDNA metabarcoding technology to analyze the spatial distribution of the coral reef fish at various depths (0 m, 5 m, 10 m, 15 m, 20 m, 30 m, 40 m, 50 m, and 60 m) within the Xisha Islands of China. The results indicated that the eDNA technology detected a total of 213 amplicon sequence variants (ASVs), including 33 species that were not identified using traditional methods. Herbivorous fish generally dominated in relative abundance across different depths. Moreover, the similarity among depth groups was largely absent, and significant differences existed in fish assemblages across depth gradients, consistent with the unique depth preferences of fish microhabitats. Importantly, our findings revealed distinct depth-structured variation among different functional groups of coral reef fish. Large carnivorous fish initially increased and then decreased along the depth gradient from 0 to 60 m, with a turning point around 20 m, while large herbivorous fish displayed the opposite trend. Small carnivorous and small herbivorous fish consistently declined along the same depth gradient. Additionally, the Margalef index (D) and Function richness (FRic) both displayed a consistent downward trend with increasing depth, while the Shannon–Wiener index (H′), Pielou index (J′), Quadratic entropy (RaoQ), Functional dispersion (FDis), and Functional evenness (FEve) initially increased and then decreased, peaking around 20 m. This study revealed that eDNA metabarcoding is an effective tool for evaluating coral reef fish biodiversity, community composition, and spatial distribution. It enhances our understanding of distribution dynamics and offers valuable insights for coral reef conservation and restoration efforts.