Genetic Variations and Expansion of the Blue Swimmer Crab (Portunus pelagicus) in Southeast Asia

Blue swimmer crabs (Portunus pelagicus) primarily inhabit the coastal regions of Southeast Asia. This study aimed to examine their population genetic structure, phylogeography, and historical demography by applying partial sequences to the control region in the mitochondrial DNA. The analysis focused on 6 populations comprising 166 individual samples collected from Taiwan (Kezailiao Kaohsiung (KK) and Penghu (PH)), mainland China (Xiamen (XM) and Hong Kong (HK)), Vietnam (Hanoi (VN)), and Singapore (SGP). The estimated nucleotide diversity (π) for all of the samples was 0.062, with values ranging between 0.018 (PH) and 0.045 (HK). Our study collected 116 haplotypes and classified them into lineages A and B. The XM, HK, VN, and SGP populations made up lineage A, and the PH and KK populations comprised lineage B. For each lineage, the results highlighted indications of demographic expansion. Lineage A can be traced back to the second-to-last interglacial period, while lineage B possibly originated in the last glacial period. There were significant differences in the FST values among the six populations, except for the pairs HK–XM and PH–KK. In conclusion, the phylogeography and genetic structure of P. pelagicus in Southeast Asia were potentially affected by the Pleistocene glacial cycles and human introduction. These findings further highlight the possible dispersal routes of P. pelagicus throughout Southeast Asia.

Genetic population subdivision of the blue swimming crab (Portunus pelagicus) across Indonesia inferred from mitochondrial DNA: Implication to sustainable fishery

The blue swimming crab (BSC), Portunus pelagicus (Linnaeus 1758), inhabits coastal areas of Southeast and East Asia, and is one of high fisheries commodities with an export value for Indonesia and an increasing global market demand, annually. However, the data of genetic diversity and their spatial connectivity of populations in Indonesia are not yet known, even when it is important to inform stock unit management and sustainable use. This study aimed to determine the genetic diversity and differentiation of blue swimming crabs across Indonesian populations in different Fishery Management Area (FMA), and their spatial genetic connectivity, as well as to deliver implications for sustainable fishery. A total of 297 individuals were collected and amplified using cytochrome oxidase I mitochondrial DNA. This study has showed the highest values for haplotype and nucleotide diversity in the eastern part of Indonesia, where exploitation is relatively low. Significant genetic differentiation between populations (FST = 0.954; p < 0.001) and the fisheries management areas (FST = 0.964; p < 0.001) were revealed. Low spatial connectivity was observed between populations in a distance of at least more than 60 kilometers. This study suggests that BSC populations in Indonesia, likely have several stock units, and preferably different fisheries management plans and actions across the region thoroughly and simultaneously. This would be effective for management and their sustainable conservation.

Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline

The blue swimming crab (Portunus pelagicus Linnaeus, 1758) is one of the commercially exploited crab fishery resources in Vietnam. This is the first study to provide a broad survey of genetic diversity, population structure and migration patterns of P. pelagicus along the Vietnamese coastline. The crab samples were collected from northern, central and southern Vietnam. Here, we used a panel of single nucleotide polymorphisms (SNPs) generated from restriction site-associated DNA sequencing (RADseq). After removing 32 outlier loci, 306 putatively neutral SNPs from 96 individuals were used to assess fine-scale population structure of blue swimming crab. The mean observed heterozygosity (Ho) and expected heterozygosity (He) per locus was 0.196 and 0.223, respectively. Pairwise Fst and hierarchical AMOVA supported significant differentiation of central and northern from southern populations (P<0.01). Population structure analyses revealed that P. pelagicus in the south is a separate fisheries unit from the north and center. Contemporary migration patterns supported high migration between northern and central populations and restricted genetic exchange within the southern population. In contrast, historic gene flow provides strong evidence for single panmictic population. The results are useful for understanding current status of P. pelagicus in the wild under an environment changing due to natural and anthropogenic stresses, with implications for fisheries management.

Genetic structure and historical demography of the blue swimming crab (Portunus pelagicus) from southeastern sea of China based on mitochondrial COI gene

In this study, the population genetic structure and historical demography of the blue swimming crab, Portunus pelagicus, from southeastern sea of China were investigated using cytochrome c oxidase subunit I (COI) gene of mitochondrion. A total of 889 bp segment of COI gene was sequenced, which showed a high haplotype diversity (0.6833-0.8142) and low nucleotide diversity (0.0021-0.0034). Among 30 haplotypes defined in this study, one (H1) was the most dominant (47.7%) and shared by each locality, while the majority (23) were rare and only existed in one individual. The AMOVA analysis revealed a limited population genetic structure, which suggested a high level of gene flow along the distribution areas of China. This conclusion was supported by the pairwise F_ST comparison values. The topology of the neighbour-joining tree constructed using 30 haplotypes from four localities presented two distinct clades (clade A and clade B). Meanwhile, three sequences of P. pelagicus downloaded from NCBI database showed a high-level divergence with the individuals collected in our study, which might form a new cryptical species. The individuals of clade B were cryptically embedded in the whole population, with a low frequency (7.7-24.2%), while clade A accounted for 75.8-92.3%. Neutrality tests and mismatch analyses suggested a late Pleistocene population expansion for both clade A (47,000-66,000 years ago) and clade B (74,000-100,000 years ago). This study should provide insight into phylogeny, population genetic structure, conservation genetics, and sustainable management of P. pelagicus.

Genetic heterogeneity of the blue swimming crab (Portunus pelagicus) in Thailand determined by AFLP analysis

Genetic diversity and population differentiation of the blue swimming crab (Portunus pelagicus) in Thailand, originating from Ranong and Krabi located in the Andaman Sea (west) and Chanthaburi, Prachuap Khiri Khan, and Suratthani located in the Gulf of Thailand (east), were examined by AFLP analysis. High genetic diversity of P. pelagicus in Thai waters was found (N=72). The four primer combinations generated 227 AFLP fragments, and the percentage of polymorphic bands in each geographic sample was 66.19-94.38%. The mean genetic distance between pairs of samples was 0.1151-0.2440. Geographic heterogeneity analyses using the exact test and FST-based statistics between all pairwise comparisons were statistically significant (P<0.01), indicating a fine-scale level of intraspecific population differentiation of Thai P. pelagicus. The estimated number of migrants per generation (Nem) was 0.26-0.76, suggesting restricted gene flow levels of P. pelagicus in Thai waters.