Thunnus Species Research Articles

Unidirectional trans-Atlantic gene flow and a mixed spawning area shape the genetic connectivity of Atlantic bluefin tuna.

The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have challenged this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome-wide single-nucleotide polymorphisms (SNPs) from 500 larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore (Thunnus alalunga) into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species.

Automated Identification of Morphological Characteristics of Three Thunnus Species Based on Different Machine Learning Algorithms

Tuna are economically important fish species. The automated identification of tuna species is of importance in fishery production and resource assessment in that it would facilitate the informed monitoring of tuna fishing vessels and the establishment of electronic observer systems. As morphological characteristics are important for tuna identification, this study aims to verify the performance of the automated identification of three Thunnus species through morphological characteristics based on different machine learning algorithms. Firstly, morphological outlines were visually analyzed using EFT (elliptic Fourier transform) and CNN (convolutional neural network). Then, the EFT feature data and deep feature data of the tuna outline images were extracted, and principal component analysis of the two different morphological characteristics was performed. Finally, different machine learning algorithms were used to analyze the identification performance of tuna of the same genus and different species. The experimental results showed that EFT features had the highest identification accuracy in KNN (K-nearest neighbor), with 90% for T. obesus, 90% for T. albacores, and 85% for T. alalunga. Deep features had the best identification performance in SVM (support vector machine), with 80% for T. obesus, 90% for T. albacores, and 100% for T. alalunga. Deep features were better than EFT features in identification performance. The biodiversity and intergeneric differences among tuna species can be well analyzed using these two different morphological characteristics. Machine learning algorithms open up the way for rapid near-real-time electronic observer systems in these important international fisheries.

Automatic classification of the phenotype textures of three Thunnus species based on the machine learning SVM algorithm

Tuna resources are an important part of China's pelagic fishery production. However, for China's tuna fishery, tuna species caught at sea are still manually classified, which is a time-consuming and inefficient process; so China's tuna fishery needs to develop toward automation. This study uses gray-level co-occurrence matrix (GLCM) and VGG16 to visualize phenotypic texture through local images of three Thunnus species. At the same time, texture feature index data (TFD), deep feature data (DFD), and their combined feature data (CFD) are obtained from texture images. Support vector machine (SVM) with different kernel functions is used to classify phenotypic texture of tuna automatically. The study shows that visualized texture images of different tuna using GLCM and VGG16 have biological characteristics. In the classification results without cross-validation, the average classification accuracy of TFD in polynomial was 83%, the average classification accuracy of DFD in RBF (Radial basis function) was 93%, and the average classification accuracy of CFD in RBF was 95%. It is concluded that tuna phenotype texture can be efficiently classified by using SVM with different kernel functions.

Rapid endothermal development of juvenile pacific bluefin tuna.

An important trait of Pacific bluefin tuna (PBT) is their ability to maintain their body temperature above the ambient temperature, which allows them to occupy a wider ecological niche. However, the size at which this ability in nature develops is unclear. Therefore, this study aimed to clarify this point by monitoring the body temperature and the surrounding ambient temperature as the fish grew. PBT with fork lengths (FLs) ranging from 19.5 to 28.0 cm were implanted with archival electronic tags and released into the ocean. Data from 41 fish were obtained (recorded body and water temperatures, light level, and swimming depth (pressure) at 30-s intervals) and analyzed to elucidate the development of the ability of PBT to maintain a high body temperature. Body temperature of a PBT (< FL of ca. 40 cm) decreased in response to a vertical movement down to cooler depths, but higher body temperatures were maintained as the fish grew. The body temperature was then continuously maintained above ambient temperatures and fluctuated independently when fish attained more than 40 cm FL. Estimation of the whole-body heat-transfer coefficient and heat-production rate indicated that the latter decreased slowly with growth, while the former decreased by one order of magnitude when tuna reached 52 cm FL. Additionally, in the daytime, the whole-body heat-transfer coefficient was significantly higher than that at nighttime. Unlike other fishes including other Thunnus species, inhabiting tropical/subtropical waters, PBT rapidly acquire higher thermo-conservation ability when young, allowing capture of high-quality prey abundant in temperate waters to support high growth rates during early life.

Comparative study of DNA extraction to initiate harmonized protocol for a simple method of species identification: Fresh and canned Tuna case study

ABSTRACT Seven different methods of DNA extraction were performed and compared in order to have the better DNA recovery in terms of quality and quantity. A PCR assay was realised based on the Cytb mitochondrial gene to identify 53 commercial food products of wide range diversity (Scombridae Thunnus species) commercialised in the Tunisian market, and we checked whether these products were correctly labelled under European and national legislations. Phylogenetic analyses on Cytb mitochondrial gene were used to study the relationships among the considered species. Tuna species was easily differentiated and confirmed by direct sequencing. The results showed a high deficiency in labelling: 96% of canned tuna did not specify the species, although the name of the species had to be mentioned. Partial least squares regression (PLS) showed relatively high values (45%) in all analysed data, suggesting substantial difference between the extraction procedures and matrices with SDS/PCI method being the most convenient.

Product Authentication Using Two Mitochondrial Markers Reveals Inconsistent Labeling and Substitution of Canned Tuna Products in the Taiwanese Market.

Fish of the tribe Thunnini represent a significant proportion of the stock caught by the fishing industry, with many of these fishes being collectively called tuna. However, only certain species can be used legally as an ingredient in canned tuna products, depending on regional food regulations. In Taiwan, only Thunnus species or Katsuwonus pelamis can be used as canned tuna. Here, we authenticated 90 canned tuna products, including 25 cat food samples, by sequencing two mitochondrial regions, 16S rRNA (16S) and the control region (CR). BLAST analysis revealed that Sarda orientalis, Euthynnus affinis, Auxis rochei, and Auxis thazard are all used as substitutes for legitimate tuna products. We found that 63.33% of investigated samples are true canned tuna, i.e., contain Thunnus species or skipjack tuna. We advocate that the Taiwanese government publishes an official standardized list of fishes, especially so that scientific, Chinese and vernacular names can be assigned unambiguously based on a “one species-one name policy”, thereby clarifying which species can be used in seafood products such as tuna. Furthermore, we feel that the large-scale and long-term monitoring of canned tuna products is warranted to fully assess the extent of tuna product adulteration in Taiwan.

Restricted vertical and cross-shelf movements of longtail tuna (Thunnus tonggol) as determined by pop-up satellite archival tags

The global catch of longtail tuna (Thunnus tonggol) has almost tripled over the past two decades, with recent stock assessments suggesting overexploited stocks. Nine longtail tuna were tracked for 2–115 days with pop-up satellite archival tags off eastern Australia (27.5°S 153.4°E to 27.5°S 153.4°E) to better understand their movements, habitat specificity, and post-capture mortality. Fish primarily utilised coastal waters of 0–25 m (maximum 90 m) and water temperatures of 23–28 °C (17.1–28.5 °C). All fish moved north for distances of up to 654 km, with three fish moving to a known spawning area where their vertical movement behaviour changed abruptly. Their occupation of shallow waters and a lack of diel vertical migrations differ markedly to the habits of oceanodromous Thunnus species. This may be due to the absence of a swim bladder and highly evolved heat exchanging vascular networks that may limit their niche breadth. The tagging data may help improve stock assessment model inputs and subsequent outcomes to guide the development of science-based conservation and management measures.

Identification of four Thunnus tuna species using mitochondrial cytochrome b gene sequence and PCR-RFLP analysis

Sequence analysis and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique were used to identify the species of Thunnus thynnus, T. alalunga, T. obesus and T. albacares. Genetic variation of 376bp fragments in mitochondrial cytochrome b gene of 4 Thunnus species captured from northern Pacific Ocean, northern Atlantic Ocean and Indian Ocean was analyzed. The restriction enzymes and restriction fragment length pattern in each Thunnus species were obtained. It was found that the 376bp fragment of cytochrome b gene in T. obesus showed the obvious divergence of 4.235% different from other 3 species. The highest interspecific similarity ranged 98.687~99.674% between T. thynnus and T. alalunga. PCR-RFLP by using 3 specific restriction enzymes Bsp1286, Hinc Ⅱ and Rsa Ⅰ could precisely and quickly identify the species of the 4 common Thunnus species. Furthermore, this technique successfully detected the species of 12 samples of commercial tuna fillets (sashimi).

Character-based identification system of scombrids from Indian waters for authentication and conservation purposes

Scombrids are the important component of pelagic fishery resources which include 54 species under 15 genera commonly known as mackerels, bonitos, and tunas. Due to the high commercial value attained, there are real chances of fraudulent substitution by species of inferior value. DNA based species identification methods can be applied to detect product adulteration, as well as to better contribute to the conservation and management of these species by providing accurate species identification independently of the age of the individuals or the tissue processed. In this study, a total of 15 commercially important scombrid species from Indian waters were analyzed. Due to the inadequacy of mitochondrial COI barcoding gene in discriminating between some Thunnus species, cytochrome b sequences were used instead. For all the 15 species, we propose a DNA character-based keys which uses a diagnostic combination of nucleotides and respective probes, including the first character-based keys and probes to differentiate between Thunnus albacares and T. obsesus.

In situ and real-time authentication of Thunnus species by iKnife rapid evaporative ionization mass spectrometry based lipidomics without sample pretreatment

Tuna adulteration and mislabeling are serious problem worldwide and have caused economic loss and consumer rights violation. In this study, an electrometric knife (iKnife) coupling rapid evaporative ionization mass spectrometry (REIMS) and a multivariate recognition model were developed and employed for in situ and real-time authentication of four tuna species without sample preparation. The results showed that the lipidomic profiles were successfully acquired and the differences in fatty acids and phospholipids were statistically analyzed to be significant (p < 0.05). The model displayed the superb classification accuracy (>93%) and validation (R2(Y) = 0.992, Q2 = 0.986), and the main contributors of m/z 817.64, m/z 809.68, etc. were screened out to be used as potential biomarkers. Based on this technique, the identity of blind tuna samples could be unambiguously authenticated with the results displayed on a monitor screen directly. This study provided a front-line rapid detection method to prove the authenticity of tuna species.

A quantitative comparison of two kits for DNA extraction from canned tuna

The most common methods that can be used for species identification of tuna include methods based on detection of species-specific DNA via the polymerase chain reaction (PCR) method. The problem with DNA detection in processed products is the possibility of DNA fragmentation during the technological process. The quantity and quality of extracted DNA is a crucial step for species identification based on the DNA analysis. In this study, two DNA extraction methods (DNeasy Blood &amp; Tissue Kit and DNeasy mericon Food Kit) for tuna DNA isolation were compared. Eight food products of canned tuna (three of them were declared as Thunnus albacares and five products were declared as Katsuwonus pelamis) with a different addition of various ingredients were tested. Furthermore, three different times of proteolysis (30 min, 60 min, overnight) for each sample and each extraction kit were evaluated. The DNA concentration was determined by a Qubit dsDNA HS Assay Kit fluorescence method and quantified using a Qubit fluorometer. The DNA purity was evaluated using the A260/A280 ratio of absorbances measured on a spectrophotometer. The main indicator of DNA quality and quantity was its amplifiability in the subsequent real-time PCR for Thunnus species, Thunnus albacares and Katsuwonus pelamis. Based on the results, both kits can be used for tuna species determination in highly heat-treated products with different composition, nevertheless, the DNeasy mericon Food Kit provided better statistical values in some parameters. The effect of different times of proteolysis was significant in most of the samples with regard to the crossing point values determined by real-time PCR.

Phylotranscriptomic Insights into the Diversification of Endothermic Thunnus Tunas.

Birds, mammals, and certain fishes, including tunas, opahs and lamnid sharks, are endothermic, conserving internally generated, metabolic heat to maintain body or tissue temperatures above that of the environment. Bluefin tunas are commercially important fishes worldwide, and some populations are threatened. They are renowned for their endothermy, maintaining elevated temperatures of the oxidative locomotor muscle, viscera, brain and eyes, and occupying cold, productive high-latitude waters. Less cold-tolerant tunas, such as yellowfin tuna, by contrast, remain in warm-temperate to tropical waters year-round, reproducing more rapidly than most temperate bluefin tuna populations, providing resiliency in the face of large-scale industrial fisheries. Despite the importance of these traits to not only fisheries but also habitat utilization and responses to climate change, little is known of the genetic processes underlying the diversification of tunas. In collecting and analyzing sequence data across 29,556 genes, we found that parallel selection on standing genetic variation is associated with the evolution of endothermy in bluefin tunas. This includes two shared substitutions in genes encoding glycerol-3 phosphate dehydrogenase, an enzyme that contributes to thermogenesis in bumblebees and mammals, as well as four genes involved in the Krebs cycle, oxidative phosphorylation, β-oxidation, and superoxide removal. Using phylogenetic techniques, we further illustrate that the eight Thunnus species are genetically distinct, but found evidence of mitochondrial genome introgression across two species. Phylogeny-based metrics highlight conservation needs for some of these species.

Complete mitochondrial genome of the yellowfin tuna (Thunnus albacares) and the blackfin tuna (Thunnus atlanticus): notes on mtDNA introgression and paraphyly on tunas

The genus Thunnus is composed of eight species, which are separated into two groups, the temperate subgenus Thunnus (bluefin tunas group) and the tropical subgenus Neothunnus (yellowfin tunas group). We obtained the mitochondrial genome for two species from the yellowfin group, Thunnus albacares and Thunnus atlanticus, and compared to those from extant Thunnus species to reconstruct the mtDNA phylogenetic relationship within the genus. Our results coincide with previous studies using mtDNA and nuclear loci in the paraphyly of the bluefin group mainly as a result of the position of Thunnus obesus within the tree. Also, we support the introgression hypothesis of the mtDNA from albacore into Pacific Bluefin tuna.

Abundance and habitat associations of tuna larvae in the surface water of the Gulf of Mexico

Summer ichthyoplankton surveys were conducted in the northern Gulf of Mexico from 2007 to 2010 to characterize the distribution and abundance of tuna larvae. Larval assemblages of tunas were comprised of four genera: Thunnus, Auxis, Euthynnus, and Katsuwonus. Thunnus were the most abundant and four species were detected; T. atlanticus [blackfin tuna], T. obesus [bigeye tuna], T. albacares [yellowfin tuna], and T. thynnus [bluefin tuna]. Intra- and inter-annual variability in the distribution and abundance of Thunnus species were observed with higher densities in 2008 and 2009, with a decline in abundance observed in 2010. Distribution and abundance of Thunnus larvae were influenced by physical and chemical conditions of the water mass, notably sea surface temperature and salinity. Distinct species-specific habitat preferences were observed and the location of mesoscale oceanographic features influenced larval abundance with higher densities of T. atlanticus, T. obesus, and T. albacares near anticyclonic (warm core) regions and the Loop Current, while T. thynnus was observed in higher densities near cyclonic (cold core) regions. This study demonstrates that spatial and temporal variability in the location of mesoscale oceanographic features may be important to partitioning nursery habitat among Thunnus species.

The First Record of Peritoneal Cavity Temperature Recording in Free-Swimming Dolphin Fish Coryphaena hippurus by Using Archival Tags, on the East Coast of Taiwan

The ambient water temperature and peritoneal cavity temperature of two dolphin fish Coryphaena hippurus, in relation to their vertical movements were examined using archival tags, on the east coast of Taiwan. The peritoneal cavity temperature of the dolphinfish nearly corresponds to the ambient water temperature on a half-day scale, suggesting that they are typical ectothermic fish. This is quite different from Thunnus species, such as big eye, T.obesus and bluefin tuna, T. orientalis, as reported elsewhere. It is known that dolphinfish are predominantly confined to the surface mixed layer, in contrast to the immature bluefintuna that repeatedly dive across the thermocline for short periods; this is when the horizontal distributions of these species overlap. By using a simple heat budget model, we compared the thermo conservation abilities of dolphinfish and immature bluefin tuna, which revealed that the peritoneal cavity temperature of dolphinfish showed more rapid decrease when they dived beyond the thermocline that of the immature bluefin tuna that could maintain a relatively constant body temperature. This is one possible reason why these two species display such markedly different patterns of vertical movement, which is influenced by the

Identification of five highly priced tuna species by quantitative real-time polymerase chain reaction

Tunas are economically important fishery worldwide, and are often used for commercial processed production. For effective fishery management and protection of consumers′ rights, it is important to develop a molecular method to identify species in canned tuna products rapidly and reliably. Here, we have developed a duplex quantitative real-time PCR (qPCR) for identification of five highly priced tuna species (Thunnus maccoyii, Thunnus obesus, Thunnus albacares, Thunnus alalunga and Katsuwonus pelamis) from processed as well as fresh fish. After amplification and sequencing of seven genetic markers commonly used for species identification, 16S rDNA and control region (CR) of mitochondrial DNA were selected as the reference gene markers for genus Thunnus and tuna species identification, respectively. Subsequently, a 73 bp fragment of 16S rDNA and 85–99 bp fragment of CR were simultaneously amplified from each target species by qPCR. The qPCR efficiency of each reaction was calculated according to the standard curves, and the method was validated by amplification DNA extracted from single or mixed tuna specimen. The developed duplex qPCR system was applied to authenticate species of 14 commercial tuna products successfully, which demonstrated it was really a useful and academic technique to identify highly priced tuna species.

Development of a multiplex PCR–ELISA method for the genetic authentication of Thunnus species and Katsuwonus pelamis in food products

In the present work a PCR–ELISA technique for the authentication of Thunnus species was developed. This method is composed by four systems that can be used in a hierarchical way allowing the identification of several scombroids species; or each individual system independently. The hierarchical strategy, proposes a first step, to assign one sample to the Thunnus genus. Next, if the result is positive, several tests can be applied to assign the sample to some particular species of the Thunnus genus. In the case that the result is negative (absence of Thunnus species), it is possible to verify if Katsuwonus pelamis is included in the sample. The method even allows the detection of mixtures of these species in relatively low amounts (up to 1%). Finally, this method was applied to 11 commercial samples to verify the labelling status of tuna products in the market, detecting that 18% were mislabelling.

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.

Karyotype stasis in four Atlantic Scombridae fishes: mapping of classic and dual-color FISH markers on chromosomes

Fish from the family Scombridae exhibit a biogeographical pattern that includes pelagic habits, high swimming ability, and migratory behavior of its species. Although genetic studies aimed at the management and conservation of some of its more intensely exploited species are available, cytogenetic analyses of Scombridae are scarce. In the present study, individuals of four species of this family were obtained in the vicinity of the St. Peter and St. Paul Archipelago in the Mid-Atlantic region. The chromosomes of these four species were analyzed using conventional staining, Ag-NORs, C-banding, CMA3/DAPI fluorochrome staining, and dual-color FISH with 18S and 5S rDNA probes. Acanthocybium solandri and Scomberomorus brasiliensis showed 2n = 48 chromosomes (2st + 46a; FN = 50), while Thunnus albacares and T. obesus, which also had 2n = 48 chromosomes, share another karyotype structure (2m + 2st + 44a; FN = 52). Discrete heterochromatic blocks are present in the centromeric regions of the chromosomes. 18S rDNA/Ag-NORs/CMA3+/DAPI−sites are located on the short arms of a subtelocentric pair that is apparently homeologous among the four species. The 5S rDNA genes on pair 24 are conserved in all of the species. Cytogenetic patterns showed a high degree of chromosomal conservation between the species. However, Thunnus species displayed greater karyotypic differentiation than A. solandri and S. brasiliensis. Pericentric inversions seem to be the primary mechanism involved in karyotype differentiation in this important fish group.

Establishment of a mitochondrial DNA sequence database for the identification of fish species commercially available in South Africa

The limitations intrinsic to morphology-based identification systems have created an urgent need for reliable genetic methods that enable the unequivocal recognition of fish species, particularly those that are prone to overexploitation and/or market substitution. The aim of this study was to develop a comprehensive reference library of DNA sequence data to allow the explicit identification of 53 commercially available fish species in South Africa, most of which were locally caught marine species. Sequences of approximately 655 base pairs were generated for all species from the cytochrome c oxidase I (COI) gene, the region widely adopted for DNA barcoding. Specimens of the genus Thunnus were examined in further detail, employing additional mitochondrial DNA control region sequencing. Cumulative analysis of the sequences from the COI region revealed mean conspecific, congeneric and confamilial Kimura 2-parameter distances of 0.10%, 4.58% and 15.43%, respectively. The results showed that the vast majority (98%) of fish species examined could be readily differentiated by their COI barcodes, but that supplementary control region sequencing was more useful for the discrimination of three Thunnus species. Additionally, the analysis of COI data raised the prospect that Thyrsites atun (snoek) could constitute a species pair. The present study has established the necessary genetic information to permit the unambiguous identification of 53 commonly marketed fish species in South Africa, the applications of which hold a plethora of benefits relating to ecology research, fisheries management and control of commercial practices.