Population genetic structure and genetic diversity of Chinese pomfret at the coast of the East China Sea and the South China Sea

Genetic Diversity and Connectivity of Ocypode ceratophthalmus in the East and South China Seas and Its Implications for Conservation

The East and South China Seas are rich in marine resources, but they are also under great pressure from climate change and human activities. Maintaining diversity and connectivity between communities is thought to be effective in mitigating these pressures. To assess the diversity and connectivity among the populations of Ocypode ceratophthalmus in the East and South China Seas, 15 populations from or near 15 marine protected areas in the two seas were studied using COI and D-Loop as genetic markers. The results showed that O. ceratophthalmus populations had high diversity, and the results of a hierarchical analysis of molecular variance and fixation index found that there were no significant genetic structures among these populations. High historical gene flow and high migration rates were further observed among populations by Migrate-n. Furthermore, the COI sequences further showed the asymmetric migration rate with a higher migration rate from south to north than from north to south. This information could provide recommendations for the management of marine protected areas in the East and South China Seas.

Mitochondrial marker implies fishery separate management units for spotted sardinella, Amblygaster sirm (Walbaum, 1792) populations in the South China Sea and the Andaman Sea

The spotted sardinella, Amblygaster sirm (Walbaum, 1792), is a commercial sardine commonly caught in Malaysia. Lack of management of these marine species in Malaysian waters could lead to overfishing and potentially declining fish stock populations. Therefore, sustainable management of this species is of paramount importance to ensure its longevity. As such, molecular information is vital in determining the A. sirm population structure and management strategy. In the present study, mitochondrial DNA Cytochrome b was sequenced from 10 A. sirm populations: the Andaman Sea (AS) (two), South China Sea (SCS) (six), Sulu Sea (SS) (one), and Celebes Sea (CS) (one). Accordingly, the intra-population haplotype diversity (Hd) was high (0.91-1.00), and nucleotide diversity (π) was low (0.002-0.009), which suggests a population bottleneck followed by rapid population growth. Based on the phylogenetic trees, minimum spanning network (MSN), population pairwise comparison, and F _ST,and supported by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA) tests, distinct genetic structures were observed (7.2% to 7.6% genetic divergence) between populations in the SCS and its neighboring waters, versus those in the AS. Furthermore, the results defined A. sirm stock boundaries and evolutionary between the west and east coast (which shares the same waters as western Borneo) of Peninsular Malaysia. In addition, genetic homogeneity was revealed throughout the SCS, SS, and CS based on the non-significant F _STpairwise comparisons. Based on the molecular evidence, separate management strategies may be required for A. sirm of the AS and the SCS, including its neighboring waters.

Comparative Phylogeography and Phylogeny of Pennah Croakers (Teleostei: Sciaenidae) in Southeast Asian Waters

A broad-scale comparative phylogeographic and phylogenetic study of pennah croakers, mainly Pennahia anea, P. macrocephalus, and P. ovata was conducted to elucidate the mechanisms that may have driven the diversification of marine organisms in Southeast Asian waters. A total of 316 individuals from the three species, and an additional eight and six individuals of P. argentata and P. pawak were employed in this study. Two genetically divergent lineages each of P. argentata and P. anea (lineages L1 and L2) were respectively detected from the analyses based on mitochondrial cytochrome b gene data. Historical biogeography analysis with a multi-gene dataset revealed that Pennahia species most likely originated in the South China Sea and expanded into the eastern Indian Ocean, East China Sea, and northwestern Pacific Ocean through three separate range expansions. The main diversifications of Pennahia species occurred during Miocene and Pliocene periods, and the occurrences of lineage divergences within P. anea and P. argentata were during the Pleistocene, likely as a consequence of cyclical glaciations. The population expansions that occurred after the sea level rise might be the reason for the population homogeneity observed in P. macrocephalus and most P. anea L2 South China Sea populations. The structure observed between the two populations of P. ovata, and the restricted distributions of P. anea lineage L1 and P. ovata in the eastern Indian Ocean, might have been hampered by the northward flowing ocean current at the Malacca Strait and by the distribution of coral reefs or rocky bottoms. While our results support S. Ekman’s center-of-origin hypothesis taking place in the South China Sea, the Malacca Strait serving as the center of overlap is a supplementary postulation for explaining the present-day high diversity of pennah croakers centered in these waters.

Comparative mitogenomic and phylogenetic analysis of Apalone spinifera and Apalone ferox (Testudines: Trionychidae)

The soft-shell turtles Apalone spinifera (AS) and Apalone ferox (AF) are two important economic species. AF is found in the Yellow River of China, and is a confirmed member of the Trionychidae family. However, the classification of AS was in dispute. Mitochondrial genomes (mitogenomes) have been widely used for species identification, as well as population and phylogenetic analysis. In order to understand the phylogenetic and mitogenomic features of AS and AF, the complete mitogenomes were sequenced, annotated and analyzed in this study. The complete mitogenomes of AS and AF are 16,817 bp and 16,756 bp in length, respectively. Both mitogenomes contain 37 genes, seven short intergenic spacers and two long intergenic spacers. Comparative analysis showed that there are 1,137 variation sites (6.79%) between the two mitogenomes. AS and AF mitogenomes both show a usage preference in terms of nucleotides, codons and amino acids. In addition, the non-synonymous substitution rate/synonymous substitution rate indicates that all protein-coding genes (PCGs) have undergone a strong purifying selection. Phylogenetic trees constructed by 13 PCGs show a clear phylogenetic relationship of the soft-shell turtles and suggest that AS is a sister species to AF of the genus Apalone. The data could be useful for further research of species identification, population analysis and the mitogenomic features of soft-shell turtles.