Mitochondrial DNA analysis reveals three stocks of yellowfin tuna Thunnus albacares (Bonnaterre, 1788) in Indian 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.

Shallow population structure of southern bluefin tuna, Thunnus maccoyii (Castelnau, 1872) between Indian and Atlantic Oceans inferred from mitochondrial DNA sequences

Southern bluefin tuna (Thunnus maccoyii Castelnau, 1872) is distributed across most of the southern temperate ocean and migrates extensively between 30°S and 50°S. Since T. maccoyii has been continually and heavily exploited, it is necessary to investigate the genetic diversity, population structure and demographic history of T. maccoyii for effective management and conservation. Thirty-seven gonad tissues of T. maccoyii were sampled from two locations, which were in the eastern Indian Ocean and the eastern Atlantic Ocean, by scientific observers onboard Korean T. maccoyii longline vessels in 2015. We compared 1240-bp sequences of combined mitochondrial DNA (mtDNA) from the cytochrome c oxidase subunit I (COI, 504-bp) and control region (CR, 736-bp) sequences. The pairwise fixation index (F_ST) and maximum-likelihood tree showed that two clades (A and B) were formed regardless of locations. Clade A occurred more commonly than clade B in both localities: the occurrence ratio of clade A was 69% in the Indian Ocean, and 79% in the Atlantic Ocean, respectively. Our findings suggest that a historic differentiation event may have occurred in T. maccoyii, but recently the connectivity between the two oceans may be possible in T. maccoyii populations.

Gene variation and population structure of Pampus chinensis in the China coast revealed by mitochondrial control region sequences

Pampus chinensis is a commercially important fishery species in the Indo-West Pacific region. In the present study, the genetic variation of P. chinensis among 10 sampling localities along the China coast and one from the Indonesia region was evaluated using mitochondrial DNA control region sequences. As a result, a total of 30 variable sites were detected in the 458 bp segment of the control region among 330 individuals from 11 localities, and 41 haplotypes were defined. Samples in the China coast present a high level of genetic diversity, with the values of haplotype diversity ranged from 0.674 to 0.860, and nucleotide diversity from 0.820% to 1.502%. Pairwise F_ST statistics showed a moderate genetic divergence (-0.027 to 0.384) among samples from different geographical locations. Median-joining network analysis revealed a similar pattern of phylogeographic structure in samples from Ningbo and Dongxing although they were far apart. Therefore, joint influences of dispersal capability, spatial distance, ocean current and geographic segregation on the formation of the present population structure in P. chinensis was proposed. The results of the present study would be helpful for the sustainable utilization and management of this species.

A review of the fisheries, life history and stock structure of tropical tuna (skipjack Katsuwonus pelamis, yellowfin Thunnus albacares and bigeye Thunnus obesus) in the Indian Ocean

Skipjack (Katsuwonus pelamis), yellowfin (Thunnus albacares) and bigeye (Thunnus obesus) tuna are the target species of tropical tuna fisheries in the Indian Ocean, with high commercial value in the international market. High fishing pressure over the past three decades has raised concerns about their sustainability. Understanding life history strategies and stock structure is essential to determine species resilience and how they might respond to exploitation. Here we provide a comprehensive review of available knowledge on the biology, ecology, and stock structure of tropical tuna species in the Indian Ocean. We describe the characteristics of Indian Ocean tropical tuna fisheries and synthesize skipjack, yellowfin, and bigeye tuna key life history attributes such as biogeography, trophic ecology, growth, and reproductive biology. In addition, we evaluate the available literature about their stock structure using different approaches such as analysis of fisheries data, genetic markers, otolith microchemistry and tagging, among others. Based on this review, we conclude that there is a clear lack of ocean basin-scale studies on skipjack, yellowfin and bigeye tuna life history, and that regional stock structure studies indicate that the panmictic population assumption of these stocks should be investigated further. Finally, we identify specific knowledge gaps that should be addressed with priority to ensure a sustainable and effective management of these species.

Ghaffar M, Sung YY, Danish-Daniel M, Tan MP. Recent population expansion of longtail tuna Thunnus tonggol (Bleeker, 1851) inferred from the mitochondrial DNA markers

The population genetic diversity and demographic history of the longtail tuna Thunnus tonggol in Malaysian waters was investigated using mitochondrial DNA D-loop and NADH dehydrogenase subunit 5 (ND5). A total of 203 (D-loop) and 208 (ND5) individuals of T. tonggol were sampled from 11 localities around the Malaysian coastal waters. Low genetic differentiation between populations was found, possibly due to the past demographic history, dispersal potential during egg and larval stages, seasonal migration in adults, and lack of geographical barriers. The gene trees, constructed based on the maximum likelihood method, revealed a single panmictic population with unsupported internal clades, indicating an absence of structure among the populations studied. Analysis on population pairwise comparison ФST suggested the absence of limited gene flow among study sites. Taken all together, high haplotype diversity (D-loop = 0.989-1.000; ND5 = 0.848-0.965), coupled with a low level of nucleotide diversity (D-loop = 0.019-0.025; ND5 = 0.0017-0.003), "star-like" haplotype network, and unimodal mismatch distribution, suggests a recent population expansion for populations of T. tonggol in Malaysia. Furthermore, neutrality and goodness of fit tests supported the signature of a relatively recent population expansion during the Pleistocene epoch. To provide additional insight into the phylogeographic pattern of the species within the Indo-Pacific Ocean, we included haplotypes from GenBank and a few samples from Taiwan. Preliminary analyses suggest a more complex genetic demarcation of the species than an explicit Indian Ocean versus Pacific Ocean delineation.

Genetic variation of reef-building polychaete Sabellaria chandraae in the south-eastern Arabian Sea based on mitochondrial COI gene sequences

The honeycomb worm Sabellaria chandraae is the most common reef-building polychaete in the intertidal area along the south-eastern Arabian Sea. We used the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene to examine the levels of genetic variation the population. The samples were collected from seven intertidal areas along the south-eastern Arabian Sea. The hierarchical Analysis of Molecular Variance (AMOVA) and conventional population statistics (F_ST) showed a low level of genetic differentiation (F_ST = 0.0864, p < .05), indicating no geographical patterning among seven populations. The present results were able to provide a reference for the single stock population along the south-eastern Arabian Sea.

Food functionality of protein isolates extracted from Yellowfin Tuna (Thunnus albacares) roe using alkaline solubilization and acid precipitation process

Four types of roe protein isolates (RPIs) were prepared through the alkaline solubilization and acid precipitation (ASAP) process, and their functional properties and in vitro bioactivities were evaluated. Higher buffer capacity in pH-shift range of 8-12 was found in RPI-1 (pH 11/4.5), required average 94.5 mM NaOH than that of other RPIs to change the pH by 1 unit. All the samples of 1% dispersion (w/v) showed the lowest buffering capacity near the initial pH. The water-holding capacities (WHC) of RPIs and casein as controls without pH-shift were in range of 3.7-4.0 g/g protein, and there were no significant differences (p > 0.05). At pH 2 and 8-12 with pH-shift, WHC and protein solubility of RPIs were significantly improved compared to those of controls. Foaming capacities of RPI-1 and RPI-3 were 141.9% and 128.1%, respectively, but those of RPI-2 and RPI-4 were not detected. The oil-in-water emulsifying activity index of RPI-1 and RPI-3 was 10.0 and 8.3 m2/g protein, which was not statistically different from casein (7.0 m2/g), but lower than that of hemoglobin (19.1 m2/g). Overall, RPIs, casein, and hemoglobin exhibited lower food functionality at pH 4-6 near isoelectric points. Through the pH-shift treatment, the food functionalities of RPIs were improved over the controls, especially in the pH 2 and pH 8-12 ranges. RPI also showed in vitro antioxidant and antihypertensive activities. Therefore, it has been confirmed that RPI extracted from yellowfin tuna roe has high utility as a protein- or food-functional-enhancing material or protein substitute resource for noodles, confectionery, baking, and surimi-based products.

Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations

Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population structure of the yellowfin tuna, and to investigate its demographic history. We detect significant differentiation of Atlantic and Indo-Pacific yellowfin tuna populations as well as the possibility of a third diverged yellowfin tuna group in the Arabian Sea. We further observe evidence for past population expansion as well as asymmetric gene flow from the Indo-Pacific to the Atlantic.

Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna (Thunnus albacares)

Global population genetic structure of yellowfin tuna (Thunnus albacares) is still poorly understood despite its relevance for the tuna fishery industry. Low levels of genetic differentiation among oceans speak in favour of the existence of a single panmictic population worldwide of this highly migratory fish. However, recent studies indicated genetic structuring at a much smaller geographic scales than previously considered, pointing out that YFT population genetic structure has not been properly assessed so far. In this study, we demonstrated for the first time, the utility of 2b-RAD genotyping technique for investigating population genetic diversity and differentiation in high gene-flow species. Running de novo pipeline in Stacks, a total of 6772 high-quality genome-wide SNPs were identified across Atlantic, Indian and Pacific population samples representing all major distribution areas. Preliminary analyses showed shallow but significant population structure among oceans (FST=0.0273; P-value<0.01). Discriminant Analysis of Principal Components endorsed the presence of genetically discrete yellowfin tuna populations among three oceanic pools. Although such evidence needs to be corroborated by increasing sample size, these results showed the efficiency of this genotyping technique in assessing genetic divergence in a marine fish with high dispersal potential.

Population genetics of four heavily exploited shark species around the Arabian Peninsula

The northwestern Indian Ocean harbors a number of larger marine vertebrate taxa that warrant the investigation of genetic population structure given remarkable spatial heterogeneity in biological characteristics such as distribution, behavior, and morphology. Here, we investigate the genetic population structure of four commercially exploited shark species with different biological characteristics (Carcharhinus limbatus, Carcharhinus sorrah, Rhizoprionodon acutus, and Sphyrna lewini) between the Red Sea and all other water bodies surrounding the Arabian Peninsula. To assess intraspecific patterns of connectivity, we constructed statistical parsimony networks among haplotypes and estimated (1) population structure; and (2) time of most recent population expansion, based on mitochondrial control region DNA and a total of 20 microsatellites. Our analysis indicates that, even in smaller, less vagile shark species, there are no contemporary barriers to gene flow across the study region, while historical events, for example, Pleistocene glacial cycles, may have affected connectivity in C. sorrah and R. acutus. A parsimony network analysis provided evidence that Arabian S. lewini may represent a population segment that is distinct from other known stocks in the Indian Ocean, raising a new layer of conservation concern. Our results call for urgent regional cooperation to ensure the sustainable exploitation of sharks in the Arabian region.

Mitochondrial DNA variation and phylogenetic relationships among five tuna species based on sequencing of D-loop region

In order to assess the DNA sequence variation and phylogenetic relationship among five tuna species (Auxis thazard, Euthynnus affinis, Katsuwonus pelamis, Thunnus tonggol, and T. albacares) out of all four tuna genera, partial sequences of the mitochondrial DNA (mtDNA) D-loop region were analyzed. The estimate of intra-specific sequence variation in studied species was low, ranging from 0.027 to 0.080 [Kimura's two parameter distance (K2P)], whereas values of inter-specific variation ranged from 0.049 to 0.491. The longtail tuna (T. tonggol) and yellowfin tuna (T. albacares) were found to share a close relationship (K2P = 0.049) while skipjack tuna (K. pelamis) was most divergent studied species. Phylogenetic analysis using Maximum-Likelihood (ML) and Neighbor-Joining (NJ) methods supported the monophyletic origin of Thunnus species. Similarly, phylogeny of Auxis and Euthynnus species substantiate the monophyly. However, results showed a distinct origin of K. pelamis from genus Thunnus as well as Auxis and Euthynnus. Thus, the mtDNA D-loop region sequence data supports the polyphyletic origin of tuna species.