Population genetics and adaptive evolution of the Japanese crab (Charybdis japonica) in the northern and southern coastal waters of China based on resequencing technology

Abstract Charybdis japonica (A. Milne-Edwards, 1861) is an important marine species. Overfishing and environmental pressures have caused a decline in its fishery resources. This study examines the genetic diversity, population structure, and environmental adaptation of C. japonica to enhance its conservation and management strategies. Whole-genome resequencing was conducted on 122 samples collected from four populations along the coast of China. Our analyses revealed that the Dalian (DL) and Ningde (ND) populations have higher genetic diversity compared to the other populations. The populations were grouped into two distinct genetic clusters, with significant north-south differentiation, based on phylogenetic tree analysis, structure clustering, and principal component analysis (PCA). Additionally, GO and KEGG enrichment analyses identified key genes involved in protein synthesis, energy metabolism, and membrane stability, highlighting their potential roles in environmental adaptation. These findings provide the first genome-wide insights into the adaptive evolution of C. japonica , bridging population genetics and conservation genomics, offering a scientific basis for conservation efforts and the sustainable management of this commercially important species.