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

Abstract

Simple Summary Mackerel scad is an important pelagic fish supporting purse-seine fisheries in the South China Sea, but its population genomic structure remains poorly understood. We analyzed genome-wide genetic variation in 112 fish from the Xisha, Dongsha, and Nansha Islands using restriction-site-associated DNA sequencing. Dongsha and Nansha were sampled in April 2025, whereas Xisha was sampled in September 2025. The three sampling groups retained moderate-to-high genetic diversity and showed low genetic differentiation. Analyses of ancestry, principal components, phylogenetic relationships, and historical relationships consistently indicated extensive genetic similarity across the surveyed regions. We also detected putative genotype–environment associations, with chlorophyll-a, salinity, and nitrate yielding the largest numbers of candidate loci; these results are exploratory and require further validation. The results provide the first genome-scale baseline for mackerel scad in the South China Sea. Because sampling month was confounded with location and the inference is based mainly on neutral genomic markers, definitive fishery management-unit delineation requires broader, seasonally matched and temporally replicated sampling.