Population Genomic Assessment of Genetic Diversity and Structure in Mackerel Scad (Decapterus macarellus) in the South China Sea Based on RAD-seq.
4 affiliations
- 1South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
- 2College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China.
- 3Key Laboratory for Sustainable Utilization of Open-Sea Fishery, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China.
- 4Guangdong Provincial Observation and Research Station for Ecosystem in the Pearl River Estuary, Guangzhou 510300, China.
Abstract
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.
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BibTeX
@article{li2026population,
title = {{Population Genomic Assessment of Genetic Diversity and Structure in Mackerel Scad (Decapterus macarellus) in the South China Sea Based on RAD-seq.}},
author = {Yi Li and Shuai Zhang and Min Li and Jiangtao Fan and Yancong Cai and Yutao Yang and Shannan Xu and Zuozhi Chen},
journal = {Biology},
year = {2026},
month = sep,
doi = {10.3390/biology15191697},
url = {https://europepmc.org/article/MED/42883370},
note = {CC BY},
}
RIS
TY - JOUR
TI - Population Genomic Assessment of Genetic Diversity and Structure in Mackerel Scad (Decapterus macarellus) in the South China Sea Based on RAD-seq.
AU - Yi Li
AU - Shuai Zhang
AU - Min Li
AU - Jiangtao Fan
AU - Yancong Cai
AU - Yutao Yang
AU - Shannan Xu
AU - Zuozhi Chen
PY - 2026
DA - 2026/09/23
JO - Biology
DO - 10.3390/biology15191697
UR - https://europepmc.org/article/MED/42883370
AB - 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.
SN - 2079-7737
ER -