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The genetic structure and demography of the yellowbelly threadfin bream, Nemipterus bathybius, in the northern South China Sea were examined using the mitochondrial DNA cytochrome b gene (1141 bp). High levels of haplotype and nucleotide diversities (0.98 and 5.26 × 10−3, respectively) showed that all populations exhibited a high level of genetic diversity. Analysis of molecular variance (AMOVA), FST statistics, and haplotype networks suggested the absence of significant genetic differentiation along the coast of the northern South China Sea. Although the results suggested that the lack of differentiation within the population structure of N. bathybius was shaped by ocean currents, our results also showed that the Qiongzhou Strait limited their migration between Beibu Gulf and the northern South China Sea. Neutrality tests and mismatch distributions indicated population expansion, but the Bayesian skyline plots and approximate Bayesian computation approaches suggested that the population sizes recently contracted. The diversification of multiple stocks, which were induced by two ocean current systems, contributed to these discordant results. Although these analyses of demographic history revealed no evidence for recent population bottlenecks, the population demography needs to be evaluated further.

The population genetic structure and historical demography of the spotted scat Scatophagus argus along the coast of the South China Sea were examined on the basis of a 1141-bp segment of the mitochondrial DNA cytochrome b gene to resolve difficulties in artificial breeding in Taiwan. In all, 213 samples were collected from 15 locations, and 75 haplotypes were obtained. The haplotypes were divided into two sympatric lineages. The genetic distance between these two lineages was 2.55%. The observed genetic structures are the result of complex interactions of historical events and oceanographic currents. During glaciations, sea level fluctuations played major roles in isolation, and changes in environmental factors affected diversification. The observed genetic patterns imply that these two lineages are not only genetically distinct, but also ecologically distinct populations. Such divergence may contribute to the development of reproductive isolation. These results suggest the existence of cryptic species within S. argus. We considered it possible that many populations from Taiwan Island were introduced from South-east Asia and that the populations in the Gulf of Tonkin originated from these introduced populations from Taiwan. This study offers important resources for the further study of conservation genetics, hybridisation and speciation.

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