The large yellow croaker (Larimichthys crocea) is one of China’s most economically valuable marine fish. Its stock division and distribution have been debated since the 1960s due to their implications for ecological protection, germplasm recovery, and fishery resource management. In this study, we aimed to investigate the current population structure and habitat division of large yellow croaker populations living in the South China Sea using genomic signatures of selection.
We built a fine-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers. Compared with the previous Daiqu-Minyuedong-Naozhou division system proposed in the 1960s, our results revealed a climate-driven habitat change probably occurred between the Naozhou (Nanhai) Stock and the Min-yuedong (Mindong) Stock. The boundary between these two stocks’ habitats might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait, accompanied by highly asymmetric introgressions.
In addition, we found two divergent landscapes of natural selection existed in different stocks living in north and south areas. The northern population suffered highly-gathered and strong natural selection around developmental-process-related genes, which may help them exploit the rare growing periods efficiently. Meanwhile, we detected moderate and interspersed selective signatures from the southern populations. Moreover, many immune-related genes were associated with these signals, which aid in the adaptation to a high-pathogen-density warm environment.
Our results provide new insights into the evolutionary history and adaptation of this species and have implications for its conservation and management. We hope that our findings will contribute to a better understanding of large yellow croaker populations living in the South China Sea and inform future research on this important species.