Genetic stock compositions and natal origin of green turtle (Chelonia mydas) foraging at Brunei Bay

AbstractKnowledge of genetics composition and growth stages of endangered green turtles, as well as the connectivity between nesting and foraging grounds is important for effective conservation. A total of 42 green turtles were captured at Brunei Bay with curved carapace length ranging from 43.8 to 102.0 cm, and most sampled individuals were adults and large juveniles. Twelve haplotypes were revealed in mitochondrial DNA control region sequences. Most haplotypes contained identical sequences to haplotypes previously found in rookeries in the Western Pacific, Southeast Asia, and the Indian Ocean. Haplotype and nucleotide diversity indices of the Brunei Bay were 0.8444±0.0390 and 0.009350±0.004964, respectively. Mixed-stock analysis (for both uninformative and informative prior weighting by population size) estimated the main contribution from the Southeast Asian rookeries of the Sulu Sea (mean ≥45.31%), Peninsular Malaysia (mean ≥17.42%), and Sarawak (mean ≥12.46%). Particularly, contribution from the Sulu Sea rookery was estimated to be the highest and lower confidence intervals were more than zero (≥24.36%). When estimating contributions by region rather than individual rookeries, results showed that Brunei Bay was sourced mainly from the Southeast Asian rookeries. The results suggest an ontogenetic shift in foraging grounds and provide conservation implications for Southeast Asian green turtles

Standard Operating Procedures for Tissue Sample Collection and Preservation

Funded by: Japanese Trust Fund Program (Trust Fund II

Mitochondrial markers identify a genetic boundary of the Green Tiger Prawn (Penaeus semisulcatus) in the Indo-Pacific Ocean

A population genetics study of the commercially important Green Tiger Prawn (Penaeus semisulcatus) was conducted in the Indo-Pacific Ocean with a focus on the Indo-Malay Archipelago waters of the South China Sea (SCS), Sulu Sea (SLS), Celebes Sea (CLS) and the Strait of Malacca (SOM), the latter being the main waterway that connects the Indian Ocean with the Pacific Ocean. A 548-base-pair region of mitochondrial COI and 571 base pairs of the control region (CR) were analysed in 284 specimens from 15 locations. Genetic divergences (Tamura 3-parameter) for COI ranged from 0.1% to 7.2% and CR 2.3% to 21.7%, with Bagan Pasir (BGP) in central SOM being the most genetically different from other populations (COI: 3.3–4.2%; CR: 7.1–16.5%). All populations were differentiated into two lineages with a genetic break in the vicinity of BGP; Lineage I comprised populations south of this site (SCS, SLS, CLS and part of SOM) and Lineage II comprised populations north of BGP (part of the SOM). Specifically, most individuals of Bagan Pasir (BGP) and another site just south of it, Batu Pahat (BPT), clustered in Lineage I, while all SOM populations to the north of these sites clustered in Lineage II. The BGP population is believed to be a mixed gene pool between the two lineages. The results could be attributed to the fluctuations of Pleistocene sea levels and a possible influence of the One Fathom Bank in SOM. High genetic diversity was recorded, π (Lineage I: COI: 3.4%; CR: 7.4%) (Lineage II: COI: 3.8%; CR: 12.6%) and, h (Lineage I: COI: 0.81; CR: 1.0) (Lineage II: COI: 0.57; CR: 0.99). Demographic statistics revealed that both lineages underwent a sudden expansion and consequent stabilisation in genetic variability. The findings of this study have wide implications for fisheries in the Indo-Pacific. The increased sampling effort within a narrower geographical scale by the current study permitted a precise locality of the genetic break for this species within the Indo-Pacific Ocean to be identified. The substantial genetic diversity within both lineages should be considered in fishery management and aquaculture development programs of this species in this region

Phylogeography of the Japanese scad, Decapterus maruadsi (Teleostei; Carangidae) across the Central Indo-West Pacific: Evidence of strong regional structure and cryptic diversity

The Japanese scad Decapterus maruadsi (Carangidae) is an economically important marine species in Asia but its exploitation shows signs of overfishing. To document its stock structure, a population genetic and phylogeographic study of several populations of this species from the central part of the Indo-West Pacific region was conducted using the mitochondrial cytochrome b gene. Genetic homogeneity within the Sundaland region’s population, including Rosario (the Philippines) and Ranong (Andaman Sea) populations was revealed with low nucleotide diversity (π = 0.001–0.003) but high haplotype diversity (h = 0.503–0.822). In contrast, a clear genetic structure was observed between this group and the northern Vietnam populations as revealed by FST, AMOVA and SAMOVA, while the central Vietnam population of Khanh Hoa is an admixed group between the two differentiated regional populations. The neutrality and mismatch distribution analyses supported a demographic expansion of D. maruadsi in between last Pleistocene to early Holocene period which influenced present day distribution pattern. Contemporary factors such as oceanic currents and different life history traits are also believed to play significant roles in the observed population structure and biogeographical pattern. Based on these results, recommendations on how stocks of the Japanese scad should be managed are offered.All of the collected specimens were permitted by participating SEAFDEC Member Countries who involved in Project entitled “Information Collection for Sustainable Pelagic Fisheries in the South China Sea and Andaman Sea.” (Funded by Japanese Trust Fund II Program, Southeast Asia Fisheries Development Center (SEAFDEC) from 2010 to 2015)

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 FST, 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 FST pairwise 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

Standard Operating Procedure for Collection and Preservation of DNA Tissue Samples

Funded by: SEAFDEC-Sweden Projec