Genetic population structure of the bigeye tuna Thunnus obesus in the central Pacific Ocean based on mtDNA Cytb sequences

Bigeye tuna Thunnus obesus is considered an important fishery species around the world. There is no adequate genetic data available for the T. obesus population. Polymorphism of sequence variations in mitochondrial Cytb genes were assessed to explore the level of genetic variability and differentiation among eight populations of T. obesus sampled from the central Pacific Ocean. Overall, a total of 44 mtDNA haplotypes and 26 variable sites were detected in the 686 bp segment of mtDNA Cytb gene. Nucleotide diversity ranged from 0.17 to 0.27 % and the haplotype diversity ranged from 0.604 to 0.793. An analysis of molecular variance (AMOVA) test of bigeye tuna revealed that 99.38 % of the genetic variation occurred within populations. Both the maximum likelihood tree and the haplotype network indicated that two lineages of bigeye tuna coexisted in the central Pacific Ocean. Hierarchical AMOVA tests and pairwise analysis revealed no geographical isolation among haplotypes within the two lineages. High Nm values from this investigation indicated high rates of gene flow between the two sampling regions. Furthermore, tests of neutrality and mismatch distribution suggested that T. obesus might have experienced a population expansion, one that possibly occurred 110,000 years ago. Our study firstly unraveled the population genetic structure of the T. obesus in the central Pacific Ocean, and addressed the related fishery management issues including fishery stock identification, management, and conservation.     

Effect of taurine enrichment in rotifer (Brachionus sp.) on growth of larvae of Pacific bluefin tuna Thunnus orientalis (Temminck & Schlegel) and yellowfin tuna T. albacares (Temminck & Schlegel)

To investigate the dietary effect of taurine on the larval stage of tuna species, Pacific bluefin tuna (PBF) and yellowfin tuna (YFT), larvae were reared until 16 days after hatching (dAH) and 14 dAH, respectively, and replicate samples were fed either non‐taurine‐enriched rotifers (T‐0) or rotifers enriched with 800 mg taurine L^?1 (T‐800). Most PBF and YFT larvae were at the preflexion stage until 7 and 8 dAH, and there were no differences in the growth performance and total protein content of larvae between the T‐0 and T‐800 groups (t‐test; P > 0.05). Thereafter, however, for larvae of both species, these parameters in the T‐800 group significantly increased with enhanced notochord development compared to those in T‐0 group (t‐test; P < 0.05). Except for the RNA content in PBF larvae, there were no significant differences in changes of DNA and RNA content with larval growth between the T‐0 and T‐800 groups, but both PBF and YFT larvae showed increased protein DNA^?1 and protein RNA^?1 ratios in the T‐800 group compared to the T‐0 group after notochord flexion. This indicates that taurine is an important nutrient for the rapid growth of early stage PBF and YFT larvae, and we conclude that the growth improvement of PBF and YFT larvae by dietary taurine supplementation is due to the increase in protein synthesis efficiency after notochord flexion.     

Environmental associations of Pacific bluefin tuna (Thunnus orientalis) catch in the California Current system

We investigate the impact of oceanographic variability on Pacific bluefin tuna (Thunnus orientalis: PBF) distributions in the California Current system using remotely sensed environmental data, and fishery‐dependent data from multiple fisheries in a habitat‐modeling framework. We examined the effects of local oceanic conditions (sea surface temperature, surface chlorophyll, sea surface height, eddy kinetic energy), as well as large‐scale oceanographic phenomena, such as El Niño, on PBF availability to commercial and recreational fishing fleets. Results from generalized additive models showed that warmer temperatures of around 17–21°C with low surface chlorophyll concentrations (<0.5 mg/m³) increased probability of occurrence of PBF in the Commercial Passenger Fishing Vessel and purse seine fisheries. These associations were particularly evident during a recent marine heatwave (the “Blob”). In contrast, PBF were most likely to be encountered on drift gillnet gear in somewhat cooler waters (13–18°C), with moderate chlorophyll concentrations (0.5–1.0 mg/m³). This discrepancy was likely a result of differing spatiotemporal distribution of fishing effort among fleets, as well as the different vertical depths fished by each gear, demonstrating the importance of understanding selectivity when building correlative habitat models. In the future, monitoring and understanding environmentally driven changes in the availability of PBF to commercial and recreational fisheries can contribute to the implementation of ecosystem approaches to fishery management.     

Sizes of adult bluefin tuna Thunnus orientalis in different areas of the western Pacific Ocean

ABSTRACT:   The length frequencies of adult Pacific bluefin tuna Thunnus orientalis caught near Japan, near Taiwan, in the tropical western Pacific Ocean, and in the South Pacific Ocean, were compared. The largest catches consisted of medium-sized adults (160–209 cm fork length) taken near Japan and large adults (≥210 cm) taken near Taiwan. Small adults (120–159 cm) were occasionally caught in the Sea of Japan. Small numbers of medium-sized and large adults were caught in the tropical western Pacific and the South Pacific. The length frequencies of the fish greater than 160 cm in length caught in different areas around Japan were similar to each other. As adult bluefin tuna grow older they spawn earlier, and their distribution, movements, and spawning areas change.     

Occurrence of Pacific bluefin tuna Thunnus orientalis larvae off the Pacific coast of Tohoku area,northeastern Japan: Possibility of the discovery of the third spawning ground

Recently, based on the histological studies it is suggested that Pacific bluefin tuna (PBF) spawns in the Kuroshio–Oyashio transition, off the Pacific coast of northeastern Japan, in addition to the previously identified two spawning areas of the northwestern Pacific around the Nansei Islands and the Sea of Japan. Distributional surveys for PBF larvae have not been conducted in the Kuroshio–Oyashio transition, and thus, we conducted PBF larval surveys at twenty stations in this area in early August 2018 to obtain evidence for the spawning of PBF. Twelve PBF larvae (3.9–7.2 mm in body length) were collected at six stations where sea surface temperature ranged from 27.2 to 28.2°C. Otolith microstructure analysis indicated that age of these larvae ranged from 4 to 11 days after hatching and the larvae hatched in late July. Growth of the collected larvae was comparable to those in the other two spawning grounds. Therefore, PBF spawns, hatches, and at least survives to the postflexion stage, 11 days after hatching in the Kuroshio–Oyashio transition. This fact potentially has a large impact on recruitment processes of PBF if they survive to recruitment in this third spawning ground.     

The distribution and early growth of juvenile Pacific bluefin tuna Thunnus orientalis around Sado Island in the eastern Sea of Japan

Fisheries Science - The distribution and early growth of juvenile Pacific bluefin tuna (PBF) Thunnus orientalis were studied based on trawl surveys conducted around Sado Island, eastern Sea of...     

南海大眼金枪鱼和黄鳍金枪鱼的群体遗传结构

测定了南海西沙和南沙群岛附近海区(11～12°N,15°N;110～112°E)黄鳍金枪鱼61尾(17尾成鱼、44尾幼鱼)和大眼金枪鱼26尾(22尾成鱼、4尾幼鱼)的线粒体基因组控制区部分序列(D-loop),结合GenBank数据库中印度洋、太平洋和大西洋群体的同源数据,分析结果:(1)黄鳍金枪鱼与大眼金枪鱼均具极高的单倍型多样性(Hd>99%),聚类树及群体间分化指数(FST和Snn)表明大眼金枪鱼群体分化程度明显高于黄鳍金枪鱼群体;(2)大眼金枪鱼和黄鳍金枪鱼的南海群体与印度洋群体之间基因流最强(Nm=51.638和261.280 10),其次为太平洋群体(Nm=10.868 8和-50.801 81);(3)黄鳍金枪鱼和大眼金枪鱼都基本服从群口扩张模型,而mismatch分布分别呈单、双峰,其中大眼金枪鱼的南海群体扩张较晚(Tau=7.902)且最为明显(θ1/θ0=99 999/14.752)。     

Identification of growth‐related nucleotide polymorphism in cultured Pacific bluefin tuna,Thunnus orientalis

Pacific bluefin tuna (PBF), Thunnus orientalis, is commercially one of the most important species of tuna. In this study, amplified fragment length polymorphism (AFLP) screening was conducted to find the growth‐related polymorphic DNA in cultured PBF. Fish hatched in 2007 were harvested at an age of 818–1994 days. They were categorized into superior, average and inferior growth groups, depending on their growth score at the time of harvest. On AFLP screening of 24 fish, with eight fish from each group, 215 polymorphic DNA fragments were observed. A second amplification, with EcoRI + ACC and MseI + CCC primers, generated a polymorphic fragment of 630 bp at a rate of 80.0% (n = 15) in the superior, 56.3% (n = 16) in the average and 20.0% (n = 15) in the inferior growth groups. Polymerase chain reaction (PCR) primers, which could amplify both AFLP‐positive and AFLP‐negative loci, were developed using the consensus sequence outside the AFLP target fragment. Eleven haplotypes were obtained by sequence analysis of the PCR product at the AFLP target loci. Among those, haplotype 1 was statistically significant in the superior and average growth groups and could be used as a molecular marker for distinguishing the individuals with superior and average growth from those with inferior growth.     

Habitat use and movement patterns of small (age‐0) juvenile Pacific bluefin tuna (Thunnus orientalis) relative to the Kuroshio

The habitat use of Pacific bluefin tuna (Thunnus orientalis; PBF) in nursery waters off the southern coast of Japan was investigated using archival tags over a 3 year study period (2012–2015), and the data were used to examine the free‐ranging habitat preferences of PBF and the relationship between their horizontal movements and the path of the Kuroshio off the Pacific coast of Japan. The path of the Kuroshio fluctuated seasonally, leading to changes in water temperature that strongly influenced the habitat use of small PBF (2–3 months after hatching). Most PBF were present in coastal waters inshore of the path of the current, and their habitat use changed in response to the distance of the current from the coast. The Kuroshio typically flowed along the coast from summer to autumn, and PBF remained in the coastal waters off Kochi Prefecture during this period. In contrast, PBF quickly moved eastward in winter when the current moved away from the coast. Throughout the winter and spring, the area of habitat use extended widely from the eastern end of the southern coast of Japan (the Boso Peninsula) to the offshore Kuroshio‐Oyashio transition region. These findings suggest that the seasonal habitat use and movement behavior of juvenile PBF are influenced by the distance of the Kuroshio axis from the coast, and the ultimate drivers are likely variations in oceanographic conditions and prey availability along the southern coast of Japan.     

Genetic characteristics of Pacific cod populations in Korea based on microsatellite markers

Pacific cod (Gadus macrocephalus) is a commercially important species in Korea. However, overfishing in the 1990s caused a strong decline in catch, and in response, artificially cultured juveniles have been released annually to enhance the stocks. Cod fishing has recently increased in Korea, and the variation within the cod population necessitates the study of their genetic characteristics. In this study, we utilized two newly developed and eight previously reported microsatellite markers to examine the genetic characteristics of Pacific cod populations. We compared the genetic diversity and genetic structure of three cod populations from the Korean coasts with three populations from the North Pacific Ocean. Genetic differences were identified in the eastern sea cod population from Korea. These genetic differences included a large number of alleles per locus, a large number of unique alleles, higher frequencies of the most common alleles, and lower gene diversity compared to the other Korean populations. Additionally, the eastern sea cod population was genetically significantly differentiated from the southern and western sea populations in Korea, in which no significant genetic differentiation was detected (F _ST = 0.033 and 0.031, respectively, P < 0.005).     

Energy partitioning in cultured juvenile Pacific bluefin tuna,Thunnus orientalis (Temminck & Schlegel, 1844)

The characteristics of dietary utilization, energy conversion efficiency, metabolic rate and energy partitioning were measured for cultured Pacific bluefin tuna (PBT) juveniles fed on an artificial diet. Thirty‐one juveniles (1.1 ± 0.3 g BW) were stocked into each of two 2500 L tanks to measure oxygen consumption (?O₂), swimming speed, digestibility and growth performance. ?O₂ elevated until 2.5 ± 0.3 times of pre‐feeding level within 1.5 h after feeding, except for the first feeding, and returned to pre‐feeding level within 3 h. Swimming speed fluctuation was corresponded with the ?O₂ fluctuation, and both parameters were stable from 02:00 to 06:00 and also during the whole day for starved fish. These indicate that feeding has strong influence on their metabolic rate. Energy partitioning for faecal, urinary and branchial, heat increment and voluntary activity, standard metabolism, and retained energy were calculated to be 17.2%, 5.9%, 14.9%, 41.3% and 20.7% of total ingested energy, respectively. The results indicate that, unlike other fish, juvenile PBT distribute large amount of energy for maintenance, which allows only a little proportion of ingested energy available for growth.     

Purification and characterization of glutathione peroxidase 1 in the red muscle of Pacific bluefin tuna Thunnus orientalis

Glutathione peroxidase GPx1 was purified from the red muscle of Pacific bluefin tuna Thunnus orientalis and its enzymatic properties were characterized. The enzyme was optimally active at pH 7.4 with a specific activity for hydrogen peroxide and a K _m of 6.7 μM. cDNA was also isolated and it contained a predicted open reading frame (ORF) encoding a 188 amino acid protein. The phylogenetic tree shows that fish including Pacific bluefin tuna, pufferfish, and zebrafish, but not mammals, possess two genetically distinct types of GPx1, i.e., GPx1a and GPx1b. The purified enzyme was classified as a fish GPx-1b enzyme on the basis of the phylogenetic tree of the GPx1 family.     

Reproductive biology of female Pacific bluefin tuna Thunnus orientalis from south-western North Pacific Ocean

Pacific bluefin is a highly valuable pelagic species that inhabits a broad range in the North Pacific Ocean. The reproductive biology, especially for the spawning aggregation in the south-western North Pacific Ocean, is not well understood. Thus, a total of 119 paired ovary specimens were collected from the Taiwanese longline fleet during the 1999 fishing season (late April through June) to gain a better understanding of important reproductivity-related stock parameters associated with this species. The following conclusions were made: (i) condition factor decreased from late May to early June; (ii) the sex ratio might be 1∶1 for spawners; (iii) the gonadosomatic index stayed at a relatively high level and markedly increased from late May to early June; (iv) histological examination of oocytes indicated that all specimens were sexually mature; (v) spawning activity appeared to start in May and peak in late May to early June; (vi) batch fecundity incre ased with fork length; and (vii) preliminary estimates of spawning frequency between batches ranged 2–4.5 days based on analysis of postovulatory follicles.     

Carrying capacity and survival strategy for the Pacific bluefin tuna, Thunnus orientalis, in the Western Pacific

The carrying capacity for the Pacific bluefin tuna at each life stage is estimated and its survival strategy is examined numerically, using a new method to define the hypothetical capacity, the standard population, and the search volumes that are necessary and are feasible for the tuna. The carrying capacity for the adult is estimated at 1–2 × 10⁶ individuals, which corresponds with 5–10% of the hypothetical capacity and is comparable with the maximum levels of the southern and the Atlantic bluefin tuna populations. It is hypothesized semiquantitatively that the migration at each life stage and the remarkable decrement of growth at 120 days and about 40 cm occur as an evolutionary response to population excess over the carrying capacity. It is also hypothesized semiquantitatively that the early larvae have minimal food available in the Subtropical Water and develop the predatory morphology, high growth rate, and high mobility, however, at the expense of a high mortality as an evolutionary response to the tuna spawning in the Subtropical Water. This method may be an available tool to not only investigate the carrying capacity and survival strategy of a specific fish species, but also predict when and in how much abundance the fish species occurs in a specific area of its habitat.     

Application of a habitat-based model to estimate effective longline fishing effort and relative abundance of Pacific bigeye tuna (Thunnus obesus)

A new habitat‐based model is developed to improve estimates of relative abundance of Pacific bigeye tuna (Thunnus obesus). The model provides estimates of `effective' longline effort and therefore better estimates of catch‐per‐unit‐of‐effort (CPUE) by incorporating information on the variation in longline fishing depth and depth of bigeye tuna preferred habitat. The essential elements in the model are: (1) estimation of the depth distribution of the longline gear, using information on gear configuration and ocean currents; (2) estimation of the depth distribution of bigeye tuna, based on habitat preference and oceanographic data; (3) estimation of effective longline effort, using fine‐scale Japanese longline fishery data; and (4) aggregation of catch and effective effort over appropriate spatial zones to produce revised time series of CPUE. Model results indicate that effective effort has increased in both the western and central Pacific Ocean (WCPO) and eastern Pacific Ocean (EPO). In the WCPO, effective effort increased by 43% from the late 1960s to the late 1980s due primarily to the increased effectiveness of effort (deeper longline sets) rather than to increased nominal effort. Over the same period, effective effort increased 250% in the EPO due primarily to increased nominal effort. Nominal and standardized CPUE indices in the EPO show similar trends – a decline during the 1960s, a period of stability in the 1970s, high values during 1985–1986 and a decline thereafter. In the WCPO, nominal CPUE is stable over the time‐series; however, standardized CPUE has declined by ～50%. If estimates of standardized CPUE accurately reflect relative abundance, then we have documented substantial reductions of bigeye tuna abundance for some regions in the Pacific Ocean. A decline in standardized CPUE in the subtropical gyres concurrent with stability in equatorial areas may represent a contraction in the range of the population resulting from a decline in population abundance. The sensitivity of the results to the habitat (temperature and oxygen) assumptions was tested using Monte Carlo simulations.     

Global population genetic structure of the sequential hermaphrodite,dusky grouper (Epinephelus marginatus)

1. The dusky grouper Epinephelus marginatus is a large epinephelid species that occurs in the eastern and south-western Atlantic and western Indian Oceans. Late maturity, protogynous hermaphroditism, site fidelity, and overfishing have all contributed to its demographic decline.
2. Connectivity and demography within a broad sampling of dusky grouper populations throughout its distribution were assessed. To do so, genetic variation at 11 polymorphic microsatellite loci and a partial sequence of the mitochondrial control region (mtCR) were evaluated.
3. Two major mtCR lineages with a sequence divergence of 1.6% were found. The magnitude of genetic differentiation for mtCR among north and south Atlantic and Indian Ocean populations was high, with Φ_ST = 0.528.
4. D_EST and results of discriminant analysis of principal component revealed significant microsatellite genetic differentiation between all collection areas. Significant pairwise D_EST showed moderate (0.084) to very great (0.603) differentiation. The effective population size was low for all localities, ranging between 25 (Azores Archipelago) and 311 (Rio Grande do Sul). The overall effective population size was estimated as 299 (confidence interval = 215–412), and there was no evidence of strong or recent bottleneck effects.
5. Local and regional genetic structuring among dusky grouper populations is the consequence of the species' site fidelity, distribution across multiple oceanographic boundaries, and probably also of sequential hermaphroditism that contributes to the intensity of random genetic drift.
6. The spatial pattern of genetic structuring of dusky groupers is such that fisheries management and conservation of population genetic integrity will have to be pursued at the local and regional scales.

     

Differential growth rates related to initiation of piscivory by hatchery-reared larval Pacific bluefin tuna Thunnus orientalis

Fast growth plays an important role in survival processes during the early life stages of both field-captured and hatchery-reared Pacific bluefin tuna Thunnus orientalis. Marked growth variations in hatchery-reared tuna larvae are frequently observed even for the same age and within the same rearing tank after the onset of the piscivory. We hypothesized that these small growth variations in the growth of tuna larvae at the onset of piscivory lead subsequently to large growth variations and tested the hypothesis using three size groups (large, intermediate and small) of hatchery-reared fish by nitrogen stable isotope and otolith analyses. Stable isotope analysis revealed that the large group rapidly utilized prey fish larvae, but the smaller groups depended more on rotifers as the main prey item relative to the large group. The otolith radius from the core to the increment corresponding to the first feeding on yolk-sac larvae was compared among the three size groups. The results revealed that the large group had larger otolith radii than the small and intermediate groups. Our findings suggest that small growth variations apparent during the early larval stage of tuna could induce further large growth variations in the late-larval and juvenile stages through differences in the initial ability to utilize piscivory.     

Spatial differentiation in the eastern Pacific yellowfin tuna revealed by microsatellite variation

ABSTRACT:   Five eastern Pacific yellowfin tuna samples (four northern: 10–25°N, 95–130°W, and one southern: 16–18°S, 95–97°W), collected from fishing vessels between 1994 and 2002 were analyzed for variation at seven microsatellite loci to evaluate their spatial genetic homogeneity. Single-locus homogeneity exact tests revealed significant genetic differentiation caused by three of seven loci. Pairwise sample comparisons of multilocus allele-frequency homogeneity tests and subpopulation division ( F _ST), revealed significant differentiation in comparisons between north equatorial samples and the south equatorial sample. amova analysis among collections grouped as northern and southern populations separated by the equator in the eastern Pacific confirmed the differentiation observed. These results may be considered as preliminary evidence of the presence of discrete populations in the eastern Pacific yellowfin tuna. The possibility that the spatial differentiation observed corresponds to temporal variation or non-random sampling cannot be discarded. The genetic differences encountered need to be corroborated by increasing sample sizes, including temporal replicates, and by the use of an alternative marker.     

基于线粒体COⅠ和Cytb基因序列的北太平洋柔鱼种群遗传结构研究

为准确掌握柔鱼的种群遗传结构,拟通过线粒体DNA的COI和Cytb基因序列分析方法对柔鱼不同产卵季节群体的遗传多样性和遗传结构进行研究。经PCR扩增与测序分别获得600 bp COI与481 bp Cytb基因序列。基于COI基因序列分析得到的单倍型数、单倍型多样性指数、核苷酸多样性指数及平均核苷酸差异数分别为24、(0.729 ±0.033)、(0.005 70 ± 0.003 25)和3.421。基于Cytb基因序列分析得到的单倍型数、单倍型多样性指数、核苷酸多样性指数及平均核苷酸差异数分别为28、(0.852 ± 0.016)、(0.006 45 ± 0.003 73)和3.101。分析认为, 北太平洋柔鱼2个产卵季节群体均具有较高的单倍型多样性指数和较低的核苷酸多样性指数。单倍型邻接树、两两群体间的F_st值以及AMOVA分析结果均表明, 北太平洋柔鱼2个产卵季节群体间的遗传差异不显著, 不存在显著的群体遗传结构。初步认为, 该海域因缺乏地理上的障碍, 加之北太平洋海流的作用以及柔鱼个体较强的游泳能力, 使得群体之间具有较强的基因流。     

Improving rearing performance in sea‐cage culture of Pacific bluefin tuna Thunnus orientalis juveniles (Temminck and Schlegel) using small sea cages

High levels of mortality occur in large net‐cage culture of Pacific bluefin tuna (PBF) Thunnus orientalis due to poor growth on commencement of sea‐cage culture obstructing the mass production of fingerlings. Therefore, we carried out this study to develop a countermeasure by using small sea cages (square with 13‐m sides). PBF juveniles were directly transferred to a 30‐m‐diameter cage (control) and compared them to fish transferred to small sea cages for 12 days before being merged into another 30‐m‐diameter cage. The survival rate, growth performance and potential factors increasing mortality were examined. The results of our study showed that survival rate in small sea cages was approximately 20% higher than that of the control. Poor growth also occurred in the small sea cages; however, its frequency and daily mortality rate were half those in the control. In addition, growth performance such as specific growth rate and weight gain of PBF juveniles in small sea cages significantly increased compared to the control. These results suggest that using small sea cages could be an effective countermeasure for poor growth, which may mitigate the high‐mortality conditions of current sea‐cage culture systems for PBF.