Mitochondrial genetic diversity, population structure and late Pleistocene demographic expansion of Evynnis cardinalis in the northern South China Sea

Understanding how historical processes and contemporary oceanography shape population connectivity and demographic dynamics is essential for effective management of coastal marine fishes. In this study, we investigated the genetic diversity, population structure, and demographic history of Evynnis cardinalis (Lacepède 1802) across 25 sampling sites in the northern South China Sea and the Beibu Gulf using mitochondrial cytochrome c oxidase subunit I (COI) sequences. A total of 315 individuals were analyzed, revealing high haplotype diversity but low nucleotide diversity, together with a star-like haplotype network dominated by a few widespread haplotypes and numerous low-frequency private haplotypes. These patterns are characteristic of recent population expansion following a period of reduced effective population size. Pairwise Φ ST values, AMOVA, and principal coordinate analysis indicated weak genetic differentiation and extensive haplotype sharing across the region, suggesting limited mitochondrial genetic differentiation and widespread sharing of mitochondrial haplotypes across the study area, although the resolution of a single mitochondrial marker does not allow robust inference of contemporary gene flow. Nevertheless, a small but significant east-west genetic component across the Leizhou Peninsula was detected, suggesting that regional topography and oceanography may contribute to weak mitochondrial genetic differentiation without forming a strong barrier. Neutrality tests, mismatch distribution analyses, and Bayesian skyline plot reconstruction consistently supported a late Pleistocene demographic expansion, with estimated expansion times broadly between 18 and 90 ka. We infer that glacial-interglacial sea-level fluctuations, which repeatedly altered the extent and connectivity of continental shelf habitats, played a central role in shaping the demographic history of Evynnis cardinalis , while present-day monsoon-driven circulation and persistent transport through the Qiongzhou Strait help maintain contemporary connectivity. Together, our results highlight the combined influence of historical sea-level change and modern oceanographic processes in structuring genetic patterns of marginal-sea fishes and provide a genetic baseline for the conservation and management of Evynnis cardinalis in the northern South China Sea.