The influence of seasonal, monsoonal winds on the temporal and spatial variability of chlorophyll-a (chl-a) in the Beibu Gulf is studied based on long-term satellite data of sea surface winds, chl-a concentration and sea surface temperature (SST) and in-situ observations for the years from 2002 to 2014. The analysis results indicated that under northeasterly monsoonal winds, chl-a concentrations were substantially elevated in most area of the Beibu Gulf, with a high chl-a concentration (>2 mg m^-3) patch extending southwestward from the coastal water of the northeastern Gulf, consistent with the winter wind pattern. Meanwhile, the spatial distribution of high chl-a concentration is correlated with low SST in the northeastern Gulf. In the southern Gulf, there was generally low chl-a, except in the coastal waters southwest of Hainan Island. Here, the upwelling cold water prevails outside the mouth of the Beibu Gulf, driven by the southwesterly monsoonal winds and the runoff from the Changhua River, as implied by low observed SST. Correlation analysis indicated the chl-a concentration was strongly modulated by wind speed (r = 0.63, p0.7, p<0.001). Integrated analysis also showed that stratification is weak and mixing is strong in winter as affected by the high wind speed, which suggests that the wind-induced mixing is a dominant mechanism for entrainment of nutrients and the spatial distribution of chl-a in winter.

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), F_ST 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.

Four Trichiurus species, T. japonicus, T. lepturus, T. nanhaiensis, and T. brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T. gangeticus. The mitogenomes contained 16.568–16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNA^Pro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T. lepturus nor T. nanhaiensis but they are T. gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.

Sequences of the complete mitochondrial cytochrome oxidase subunit I gene were used to identify Trichiurus species and examine their population genetic structure and demographic history along the coast of China. Three Trichiurus species were found. Trichiurus japonicus lives in colder waters along the continental shelves in the China Seas, while Trichiurus nanhaiensis lives warmer waters along continental slopes in the South China Sea, and Trichiurus brevis lives in shallow and warmer waters in the South China Sea. The migrations of these species were mainly associated with feeding and spawning preferences. Two major wintering and spawning grounds in the East China Sea and South China Sea were found. All species showed a lack of population genetic structure resulting from their oceanodromous life cycle (the degree of population substructure index N_ST = 0.000–0.149), but the results of approximate Bayesian computational approaches suggested population declines or stabilization and differentiation. The results of the T_MRCA (time to the most recent common ancestor) showed that during glaciations, the Yellow Sea and the East China Sea were completely exposed, and the South China Sea acted as a refugium. Thus, the populations of these three species experienced differentiation during glaciations. This study also examined the limitations of Bayesian skyline plot analysis.

This paper presented the fish species richness at geographical unit of the Yangtze River. According to the fish taxonomic catalogs and biological traits, R language method was used to determine taxonomic diversity and functional diversity and the components of each unit. Regression analysis was used to test the varying tendency of taxonomic and functional diversity corresponding to the change of species richness. •Functional diversity is compared against taxonomic diversity in capturing the structure of dynamic ecosystem.•The β-diversity indices of taxonomy and function were calculated and decomposed to evaluate the role of species turnover and nestedness in the formation process of fish spatial pattern.•An integrated diversity index, balancing α and β diversity of species richness, taxonomic and functional diversity, is used to screen the prior conservation zone.