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Yellowfin tuna, Thunnus albacares, is an important global fishery and of particular importance in the Eastern Pacific Ocean (EPO). According to the 2019 Inter-American Tropical Tuna Commission (IATTC) assessment, yellowfin tuna within the EPO is a single stock, and is being managed as one stock. However, previous studies indicate site fidelity, or limited home ranges, of yellowfin tuna which suggests the potential for multiple yellowfin tuna stocks within the EPO, which was supported by a population genetic study using microsatellites. If numerous stocks are present, management at the wrong spatial scales could cause the loss of minor yellowfin tuna populations in the EPO. In this study we used double digestion RADseq to assess the genetic structure of yellowfin tuna in the EPO. A total of 164 yellowfin tuna from Cabo San Lucas, México, and the Galápagos Islands and Santa Elena, Ecuador, were analysed using 18,011 single nucleotide polymorphisms. Limited genetic differentiation (FST = 0.00058-0.00328) observed among the sampling locations (México, Ecuador, Peru, and within Ecuador) is consistent with presence of a single yellowfin tuna population within the EPO. Our findings are consistent with the IATTC assessment and provide further evidence of the need for transboundary cooperation for the successful management of this important fishery throughout the EPO., Competing Interests: The authors have declared that no competing interests exist.

In population genetics, the amount of information for an analytical task is governed by the number of individuals sampled and the amount of genetic information measured on each of those individuals. In this work, we assessed the numbers of individual yellowfin tuna (Thunnus albacares) and genetic markers required for ocean-basin scale inferences. We assessed this for three distinct data analysis tasks that are often employed: testing for differences between genetic profiles; stock delineation, and; assignment of individuals to stocks. For all analytical tasks, we used real (not simulated) data from four sampling locations that span the tropical Pacific Ocean. Whilst spatially separated, the genetic differences between the sampling sites were not substantial, a maximum of approximately Fst = 0.02, which is quite typical of large pelagic fish. We repeatedly sub-sampled the data, mimicking a new survey, and performed the analyses. False positive rates were also assessed by re-sampling and randomly assigning fish to groups. Varying the sample sizes indicated that some analytical tasks, namely profile testing, required relatively few individuals per sampling location (n ≳ 10) and single nucleotide polymorphisms (SNPs, m ≳ 256). Stock delineation required more individuals per sampling location (n ≳ 25). Assignment of fish to sampling locations required substantially more individuals, more in fact than we had available (n > 50), although this sample size could be reduced to n ≳ 30 when individual fish were assumed to belong to one of the groups sampled. With these results, designers of molecular ecological surveys for yellowfin tuna, and users of information from them, can assess whether the information content is adequate for the required inferential task., Competing Interests: The authors have declared that no competing interests exist.

The Pacific bluefin tuna, Thunnus orientalis, is a highly migratory species that is widely distributed in the North Pacific Ocean. Like other marine species, T. orientalis has no external sexual dimorphism; thus, identifying sex-specific variants from whole genome sequence data is a useful approach to develop an effective sex identification method. Here, we report an improved draft genome of T. orientalis and male-specific DNA markers. Combining PacBio long reads and Illumina short reads sufficiently improved genome assembly, with a 38-fold increase in scaffold contiguity (to 444 scaffolds) compared to the first published draft genome. Through analysing re-sequence data of 15 males and 16 females, 250 male-specific SNPs were identified from more than 30 million polymorphisms. All male-specific variants were male-heterozygous, suggesting that T. orientalis has a male heterogametic sex-determination system. The largest linkage disequilibrium block (3,174 bp on scaffold_064) contained 51 male-specific variants. PCR primers and a PCR-based sex identification assay were developed using these male-specific variants. The sex of 115 individuals (56 males and 59 females; sex was diagnosed by visual examination of the gonads) was identified with high accuracy using the assay. This easy, accurate, and practical technique facilitates the control of sex ratios in tuna farms. Furthermore, this method could be used to estimate the sex ratio and/or the sex-specific growth rate of natural populations.

Yellowfin tuna, Thunnus albacares, is one of the most important seafood commodities in the world. Despite its great biological and economic importance, conflicting evidence arises from classical genetic and tagging studies concerning the yellowfin tuna population structure at local and global oceanic scales. Access to more powerful and cost effective genetic tools would represent the first step towards resolving the population structure of yellowfin tuna across its distribution range. Using a panel of 939 neutral Single Nucleotide Polymorphisms (SNPs), and the most comprehensive data set of yellowfin samples available so far, we found genetic differentiation among the Atlantic, Indian and Pacific oceans. The genetic stock structure analysis carried out with 33 outlier SNPs, putatively under selection, identified discrete populations within the Pacific Ocean and, for the first time, also within the Atlantic Ocean. Stock assessment approaches that consider genetic differences at neutral and adaptive genomic loci should be routinely implemented to check the status of the yellowfin tuna, prevent illegal trade, and develop more sustainable management measures.

The complete mitochondrial genome of the juvenile Pacific bluefin tuna Thunnus orientalis collected from Sea of Japan was determined by next-generation sequencing. The mitogenome is a circular molecule 16,529 bp in length, including the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The termination-associated sequence (TAS), central conserved sequence blocks (CSB) and CSB were detected in the control region. The gene contents of the mitogenome are identical to those observed in most bony fishes.

Tropical tuna fisheries are central to food security and economic development of many regions of the world. Contemporary population assessment and management generally assume these fisheries exploit a single mixed spawning population, within ocean basins. To date population genetics has lacked the required power to conclusively test this assumption. Here we demonstrate heterogeneous population structure among yellowfin tuna sampled at three locations across the Pacific Ocean (western, central, and eastern) via analysis of double digest restriction-site associated DNA using Next Generation Sequencing technology. The differences among locations are such that individuals sampled from one of the three regions examined can be assigned with close to 100% accuracy demonstrating the power of this approach for providing practical markers for fishery independent verification of catch provenance in a way not achieved by previous techniques. Given these results, an extended pan-tropical survey of yellowfin tuna using this approach will not only help combat the largest threat to sustainable fisheries (i.e. illegal, unreported, and unregulated fishing) but will also provide a basis to transform current monitoring, assessment, and management approaches for this globally significant species.

The yellowfin tuna, Thunnus albacares (Bonnaterre, 1788), covers majority of the Philippines' tuna catch, one of the major fisheries commodities in the country. Due to its high economic importance sustainable management of these tunas has become an imperative measure to prevent stock depletion. Currently, the Philippine yellowfin tuna is believed to be part of a single stock of the greater WCPO though some reports suggest otherwise. This study therefore aims to establish the genetic stock structure of the said species in the Philippines as compared to Bismarck Sea, Papua New Guinea using nine (9) DNA microsatellite markers. DNA microsatellite data revealed significant genetic differentiation between the Philippine and Bismarck Sea, Papua New Guinea yellowfin tuna samples. (FST = 0.034, P = 0.016), which is further supported by multilocus distance matrix testing (PCoA) and model-based clustering (STRUCTURE 2.2).With these findings, this study posits that the yellowfin tuna population in the Philippines is a separate stock from the Bismarck Sea population. These findings add evidence to the alternative hypothesis of having at least 2 subpopulations of yellowfin tuna in the WCPO and calls for additional scientific studies using other parameters to investigate this. Accurate population information is necessary in formulating a more appropriate management strategy for the sustainability of the yellowfin tuna not only in the Philippines but also in the WCPO.

Endothermy in vertebrates has been postulated to confer physiological and ecological advantages. In endothermic fish, niche expansion into cooler waters is correlated with specific physiological traits and is hypothesized to lead to greater foraging success and increased fitness. Using the seasonal co-occurrence of three tuna species in the eastern Pacific Ocean as a model system, we used cardiac gene expression data (as a proxy for thermal tolerance to low temperatures), archival tag data, and diet analyses to examine the vertical niche expansion hypothesis for endothermy in situ. Yellowfin, albacore, and Pacific bluefin tuna (PBFT) in the California Current system used more surface, mesopelagic, and deep waters, respectively. Expression of cardiac genes for calcium cycling increased in PBFT and coincided with broader vertical and thermal niche utilization. However, the PBFT diet was less diverse and focused on energy-rich forage fishes but did not show the greatest energy gains. Ecosystem-based management strategies for tunas should thus consider species-specific differences in physiology and foraging specialization.

Thunnus albacares is an important fishery species throughout the world. Polymorphisms of sequence variations in mtDNA COI genes were assessed to explore the genetic differentiations among 11 populations of T. albacares sampled from the central Pacific Ocean. Sixty-one mtDNA haplotypes and 38 variable sites were detected. Analysis of mtDNA COI sequences revealed that tuna from the 11 localities were characterized by moderately high haplotype diversity (h = 0.650 ± 0.040), while sequence divergence between haplotypes was relatively low (π = 0.00364 ± 0.00044). Analyses of molecular variance and FST analysis supported that significant genetic differentiations existed between some of the sampled populations. Tests of neutral evolution and mismatch distribution analysis suggested that T. albacares might have experienced a population expansion, which possibly occurred within the last 0.82 million years. Our study unraveled the genetic structure of the extant population of T. albacares and addressed the related fishery management issues including fishery stock identification and management.

The population genetic structure and phylogeography of wahoo, Acanthocybium solandri, were investigated on a global scale with intron six of lactate dehydrogenase-A (ldhA6, 8 locations, N = 213) and mtDNA cytochrome b (Cytb, 10 locations, N = 322). Results show extensive sharing of haplotypes across the wahoo's entire global range, and analyses were unable to detect significant structure (nuclear F(ST) = 0.0125, P = 0.106; mtDNA Phi(ST) < 0.0001, P = 0.634). Power analyses indicated 95% confidence in detecting nuclear F(ST) > or = 0.0389 and mtDNA Phi(ST) > or = 0.0148. These findings appear unique, as most other tunas, billfishes, and oceanic sharks exhibit significant population structure on the scale of East-West Atlantic, Atlantic vs. Indian-Pacific, or East-West Pacific. Overall nuclear heterozygosity (H = 0.714) and mtDNA haplotype diversity (h = 0.918) are both high in wahoo, while overall mtDNA nucleotide diversity (pi = 0.006) and nuclear nucleotide diversity (pi = 0.004) are uniformly low, indicating a recent increase in population size. Coalescence analyses yield an estimate of effective female population size (NeF) at approximately 816,000, and a population bottleneck approximately 690,000 years ago. However, conclusions about population history from our Cytb data set are not concordant with a control region survey, a finding that will require further investigation. This is the first example of a vertebrate with a single globally distributed population, a finding we attribute to extensive dispersal at all life stages. The indications of a worldwide stock for wahoo reinforce the mandate for international cooperation on fisheries issues.

Background: Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour) and physical (e.g. present-day ocean currents, past changes in sea temperature and levels) factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II), which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence., Results: We examined allele size variation of nine microsatellite loci in 380 individuals from the Gulf of Guinea, Canary, Azores, Canada, Indian Ocean, and Pacific Ocean. To investigate temporal stability of genetic structure, three Atlantic Ocean sites were re-sampled a second year. Hierarchical AMOVA tests, RST pairwise comparisons, isolation by distance (Mantel) tests, Bayesian clustering analyses, and coalescence-based migration rate inferences supported unrestricted gene flow within the Atlantic Ocean at the nuclear level, and therefore interbreeding between individuals belonging to both mitochondrial clades. Moreover, departures from HWE in several loci were inferred for the samples of Guinea, and attributed to a Wahlund effect supporting the role of this region as a spawning and nursery area. Our microsatellite data supported a single worldwide panmictic unit for bigeye tunas. Despite the strong Agulhas Current, immigration rates seem to be higher from the Atlantic Ocean into the Indo-Pacific Ocean, but the actual number of individuals moving per generation is relatively low compared to the large population sizes inhabiting each ocean basin., Conclusion: Lack of congruence between mt and nuclear evidences, which is also found in other species, most likely reflects past events of isolation and secondary contact. Given the inferred relatively low number of immigrants per generation around the Cape of Good Hope, the proportions of the mitochondrial clades in the different oceans may keep stable, and it seems plausible that the presence of individuals belonging to the mt Clade I in the Atlantic Ocean may be due to extensive migrations that predated the last glaciation.

Background: Yellowfin and skipjack tuna are globally distributed in the world's tropical and sub-tropical oceans. Since little, if any, migration of these fishes occurs between the Atlantic and Indo-Pacific Oceans, one might expect to see genetic differences between sub-populations in these ocean basins. However, yellowfin and skipjack tuna have extremely large population sizes. Thus, the rate of genetic drift should be slower than that observed for other tunas., Results: Low levels of genetic differentiation were observed between Atlantic and Pacific samples of yellowfin tuna. In contrast, no genetic differentiation was observed between Atlantic and Pacific samples of skipjack tuna., Conclusion: Much lower levels of genetic differentiation were found among sub-populations of yellowfin tuna compared to those observed for other large tunas, probably due to the large population size of yellowfin tuna. Since skipjack tuna appear to have even larger population sizes, it is not surprising that no genetic differentiation was detected between Atlantic and Pacific samples of these fish.

Two mitochondrial DNA segments of the bigeye tuna (Thunnus obesus) were amplified by polymerase chain reaction (PCR), and restriction fragment length polymorphism (RFLP) analyses of these segments were used for the genetic stock study. The variation in a segment flanking the ATPase and COIII genes was low; only two genotypes (alpha and beta) were detected by RsaI digestion. Yet a large difference in the genotype distribution was observed between ocean basin samples. The alpha type predominated in four Atlantic samples, where 178 of 244 individuals were the alpha type. In contrast, only one of 195 individuals collected in the Indo-Pacific was the alpha type? The frequency of the alpha type varied considerably from 0 to 80% among seven samples collected off the Cape of Good Hope. The variation found in the other segment, containing the D-loop region, was much higher; two endonucleases (DpnII and RsaI) detected five genotypes each and 15 composite genotypes. A highly significant difference in genotype frequencies was observed between the Atlantic and Indo-Pacific samples, but no heterogeneity was observed among the four Atlantic or among four Indo-Pacific samples. These results clearly indicate that not only gene flow, but also fish migration, between the Atlantic and Indian Oceans are severely restricted, and that fishes from these distinct stocks are intermingling around South Africa. The simple and diagnostic genetic marker found in this study can be used to estimate mixing ratios between Atlantic and Indian stocks around South Africa.