Population Genomic Assessment of Genetic Diversity and Structure in Mackerel Scad (Decapterus macarellus) in the South China Sea Based on RAD-seq

The mackerel scad (Decapterus macarellus) is an important pelagic fish in the South China Sea (SCS), where it supports light purse-seine fisheries. Genome-wide information on its genetic diversity and population structure remains limited, although it is needed for stock identification and sustainable management. Restriction-site-associated DNA sequencing (RAD-seq) was used to analyze 112 D. macarellus individuals collected from Xisha, Dongsha, and Nansha Islands in the SCS, with Dongsha and Nansha sampled in April 2025 and Xisha sampled in September 2025; the congener Decapterus macrosoma was included as an outgroup for analyses requiring an external reference. A total of 12,080 high-quality single-nucleotide polymorphisms (SNPs) across 1087 retained loci were used for within-species analyses. The three sampling groups showed moderate-to-high genetic diversity (π = 0.02045–0.03191; HO = 0.01669–0.02497). Pairwise FST values ranged from 0.0086 to 0.0120 and DXY values ranged from 0.00156 to 0.00174, while principal component analysis, ADMIXTURE, and phylogenetic analyses indicated low genome-wide differentiation among the sampled regions. The TreeMix results were treated as exploratory and showed close allele–frequency relationships among the sampling groups. Genotype–environment association analysis identified putative association signals across the environmental variables examined, with chlorophyll-a, salinity, and nitrate yielding the largest numbers of candidate loci. Overall, these results indicate low neutral genetic differentiation among the sampled groups. Because sampling location and month were confounded and the data are based primarily on neutral genomic markers, the present results should be considered a genomic baseline rather than definitive evidence for a single fishery management unit.