Orthodox and unorthodox phylogenetic relationships among tunas revealed by the nucleotide sequence analysis of the mitochondrial DNA control region

A phylogeny of all eight recognized taxa of the genus Thunnus was constructed from approximately 400 base pairs of sequence of the mitochondrial DNA (mtDNA) control region. The PCR-amplified control region I segment studied contained a total of 186 variable sites and 159 phylogenetically informative sites. Diagnostic sequences for every taxon were identified. Neighbour-joining phylogenies supported monophyletic origins of the temperate subgenus Thunnus and of the tropical subgenus Neothunnus . Similar results were obtained by maximum parsimony analyses except that there was no support for a monophyletic origin of the subgenus Thunnus . Bigeye tuna, which have been difficult to place in either subgenus using conventional morphological data, was identified as the sister species of Neothunnus . Within the subgenus Thunnus , the Atlantic bluefin and Southern bluefin tunas were shown to be sister taxa of the highly divergent monophyletic clade formed by the Pacific northern bluefin and the Albacore tunas. The conspecific Atlantic ( T. thynnus thynnus ) and Pacific ( T. t. orientalis ) northern bluefin tunas were more divergent (Tamura-Nei distance 0·145 ± 0·019) from each other than the average distance separating most species-pairs within the genus. Thus, a re-examination of their status as subspecies of T. thunnus is warranted.     

Phylogenetic relationships between tuna species of the genus Thunnus (Scombridae: Teleostei): Inconsistent implications from morphology,nuclear and mitochondrial genomes

In order to infer phylogenetic relationships between tuna species of the genus Thunnus, partial sequences of the mitochondrial cytochrome b and ATPase genes were determined in all eight species. Supplemental restriction analysis on the nuclear rRNA gene was also carried out. Pacific northern bluefin tuna (Thunnus thynnus orientalis) was found to have mtDNA distinct from that of the Atlantic subspecies (T. t. thynnus) but very similar to that from the species albacore (T. alaluga). In contrast, no differentiation in nuclear genome was observed between the Atlantic and Pacific northern bluefin tunas. The Atlantic northern bluefin and southern bluefin tunas possessed mtDNA sequences very similar to species of yellowfin tuna group and not so similar to albacore and bigeye tunas which were morphologically assigned to the bluefin tuna group. The molecular data indicate that (1) mtDNA from albacore has been incorporated into the Pacific population of northern bluefin tuna and has extensively displaced the original mtDNA, and (2) albacore is the earliest offshoot, followed by bigeye tuna in this genus, which is inconsistent with the phylogenetic relationships between these tuna species inferred from morphology. Correspondence to: S. Chow     

Population genetics of tunas

Population genetic studies on tunas are reviewed. These studies have focused on phylogenetic reconstructions, species identifications and stock delineation, and have used tools ranging from blood group and allozyme analysis to PCR-aided examination of mitochondrial DNA variation. Both allozyme and mtDNA approaches show tunas in the genus Thunnus to be very closely related to one another, but also indicate that the two presently recognized subspecies of northern bluefin tuna, Thunnus thynnus thynnus and T. t. orientalis , in fact may be worthy of species status. These techniques also permit the unequivocal recognition of specimens, which is not always possible on morphological grounds. However, it is arguable that, until recently, tunas have not received their due attention from geneticists given their commercial significance and the need for information on stock structure to ensure sustainable management. This may be because tunas are known to be highly vagile and therefore levels of population differentiation are expected to be low. None the less, population subdivision has been recorded in several species (skipjack, yellowfin, albacore), although this tends to be on a broad (intra- or inter-oceanic) rather than on a more local scale. New molecular tools, including the PCR-based analyses of nuclear genes and microsatellite loci, are yielding new, highly polymorphic markers, and will enable more powerful analyses of stock structure than have hitherto been possible.     

Mitochondrial DNA sequence variation within and between tuna Thunnus species and its application to species identification

Restriction analysis detected two types of bigeye tuna (α and β); the α type was in the majority in the Atlantic but nearly absent in the Indo-Pacific. The β type shared a larger number of restriction sites with other species than the conspecific β type, but bigeye-specific nucleotide substitutions with a novel diagnostic restriction profile were found. Although the nucleotide sequence difference between Atlantic and Pacific sub-species of the northern bluefin tuna was nearly the largest among species, individuals possessing the Atlantic type of mtDNA were found at very low frequency in the Pacific and vice versa. Previous RFLP markers were found to be diagnostic for the other five species (albacore, blackfin, longtail, southern bluefin and yellowfin tunas). Genetic information is provided to discriminate all Thunnus species regardless of their origin and to identify the ocean of capture in the northern bluefin and bigeye tunas.     

Comparative phylogeography of Atlantic bluefin tuna and swordfish: the combined effects of vicariance, secondary contact, introgression, and population expansion on the regional phylogenies of two highly migratory pelagic fishes

Comparative phylogeography has revealed remarkable patterns of concordance in the maternal phylogenies of many species. The phylogeography and historical demography of the mitochondrial control region I for 607 Atlantic bluefin tuna (Thunnus thynnus) and 275 swordfish (Xiphias gladius) were analyzed to clarify the complex phylogenetic signals in the North Atlantic-Mediterranean region where they are sympatric. Atlantic bluefin tuna mtDNA is polyphyletic, and includes rare sequences sister to Pacific bluefin tuna (Thunnus orientalis) and introgressed albacore (Thunnus alalunga) sequences. There is no geographic partitioning between Atlantic and Mediterranean samples of Atlantic bluefin tuna (Phi(ST)=0.002). In contrast, Atlantic and Mediterranean swordfish are differentiated (Phi(ST)=0.091) due to the combined effects of vicariance, secondary contact, and dissimilar regional demographic histories. Mediterranean swordfish has substantially less variation, and a more recent history (tau=2.42) than that of Atlantic swordfish (tau=7.02). In spite of the discordant phylogenetic and phylogeographic signals, the demographic history of Atlantic swordfish and Atlantic bluefin tuna (tau=7.51) suggests concordance in the timeline of population expansion. Possible scenarios of cladogenesis, expansion, and contraction, influenced by glacial cycles during the Pleistocene, are formulated.     

Microsatellite DNA markers for population‐genetic studies of Atlantic bluefin tuna (Thunnus thynnus thynnus) and other species of genus Thunnus

Twenty‐five microsatellites from Atlantic bluefin tuna (Thunnus thynnus thynnus) were characterized. All 25 microsatellites were polymorphic; the number of alleles among up to 56 individuals surveyed ranged from two to 23. Atlantic bluefin tuna are highly exploited and major questions remain as to stock structure and abundance in the eastern and western North Atlantic. The microsatellites will be useful in testing stock‐structure hypotheses and in generating estimates of effective population size. The polymerase chain reaction primer sets developed also amplified identifiable alleles in three other species of genus Thunnus: T. albacares (yellowfin tuna), T. alalunga (albacore tuna) and T. obesus (bigeye tuna).     

Habitat and behaviour of yellowfin tuna Thunnus albacares in the Gulf of Mexico determined using pop-up satellite archival tags

This study presents the first data on movement, habitat use and behaviour for yellowfin tuna Thunnus albacares in the Atlantic Basin. Six individuals were tracked in the Gulf of Mexico using pop-up satellite archival tags. Records up to 80 days in length were obtained, providing information on depth and temperature preferences as well as horizontal movements. Thunnus albacares in the Gulf of Mexico showed a strong preference for the mixed layer and thermocline, consistent with findings for this species in other ocean basins. Fish showed a diel pattern in depth distribution, remaining in surface and mixed layer waters at night and diving to deeper waters during the day. The vertical extent of T. albacares habitat appeared to be temperature limited, with fish generally avoiding waters that were >6° C cooler than surface waters. The vertical and thermal habitat usage of T. albacares differs from that of bigeye Thunnus obesus and bluefin Thunnus thynnus , Thunnus orientalis and Thunnus maccoyii tunas. These results are consistent with the results of earlier studies conducted on T. albacares in other oceans.     

Isolation and characterization of seven tetranucleotide microsatellite loci from Atlantic northern bluefin tuna Thunnus thynnus thynnus

Microsatellite‐enriched genomic libraries were obtained from the Atlantic northern bluefin tuna, Thunnus thynnus thynnus and seven tetranucleotide markers were successfully isolated and characterized from this library. These markers were found to have between 1 and 17 alleles in Atlantic northern bluefin tuna and heterozygosity ranged from 0 to 0.85. No deviations from the expectation of Hardy‐Weinburg equilibrium were found for any marker. Several of these markers amplify reliably in other tuna species.     

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

The optimal management of the commercially important, but mostly over‐exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded F_ST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between‐ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17‐SNP panel was developed in Atlantic BFT by cross‐species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (F_ST = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.     

First record of female germ cells in the testis of a wild Mediterranean northern bluefin tuna Thunnus thynnus L. 1758

The presence of female germ cells was observed in the central portion of the testis of a Mediterranean northern bluefin tuna Thunnus thynnus , 2250 mm fork length and 217 kg. This is the first report of intersex in this species.     

Large‐scale distribution of tuna species in a warming ocean

Tuna are globally distributed species of major commercial importance and some tuna species are a major source of protein in many countries. Tuna are characterized by dynamic distribution patterns that respond to climate variability and long‐term change. Here, we investigated the effect of environmental conditions on the worldwide distribution and relative abundance of six tuna species between 1958 and 2004 and estimated the expected end‐of‐the‐century changes based on a high‐greenhouse gas concentration scenario (RCP8.5). We created species distribution models using a long‐term Japanese longline fishery dataset and two‐step generalized additive models. Over the historical period, suitable habitats shifted poleward for 20 out of 22 tuna stocks, based on their gravity centre (GC) and/or one of their distribution limits. On average, tuna habitat distribution limits have shifted poleward 6.5 km per decade in the northern hemisphere and 5.5 km per decade in the southern hemisphere. Larger tuna distribution shifts and changes in abundance are expected in the future, especially by the end‐of‐the‐century (2080–2099). Temperate tunas (albacore, Atlantic bluefin, and southern bluefin) and the tropical bigeye tuna are expected to decline in the tropics and shift poleward. In contrast, skipjack and yellowfin tunas are projected to become more abundant in tropical areas as well as in most coastal countries' exclusive economic zones (EEZ). These results provide global information on the potential effects of climate change in tuna populations and can assist countries seeking to minimize these effects via adaptive management.     

Fast versus slow growing tuna species: age,growth, and implications for population dynamics and fisheries management

Growth models describe the change in length or weight as a function of age. Growth curves in tunas can take different forms from relatively simple von Bertalanffy growth curves (Atlantic bluefin, albacore tunas) to more complex two- or three-stanza growth curves (yellowfin, bigeye, skipjack, southern bluefin tunas). We reviewed the growth of the principal market tunas (albacore, bigeye, skipjack, yellowfin and the three bluefin tuna species) in all oceans to ascertain the different growth rates among tuna species and their implications for population productivity and resilience. Tunas are among the fastest-growing of all fishes. Compared to other species, tunas exhibit rapid growth (i.e., relatively high K) and achieve large body sizes (i.e., high L _∞ ). A comparison of their growth functions reveals that tunas have evolved different growth strategies. Tunas attain asymptotic sizes (L _∞ ), ranging from 75 cm FL (skipjack tuna) to 400 cm FL (Atlantic bluefin tuna), and reach L _∞ at different rates (K), varying from 0.95 year^?1 (skipjack tuna) to 0.05 year^?1 (Atlantic bluefin tuna). Skipjack tuna (followed by yellowfin tuna) is considered the “fastest growing” species of all tunas. Growth characteristics have important implications for population dynamics and fisheries management outcomes since tunas, and other fish species, with faster growth rates generally support higher estimates of Maximum Sustainable Yield (MSY) than species with slower growth rates.     

Characterization of two tropomyosin isoforms from the fast skeletal muscle of bluefin tuna Thunnus thynnusorientalis

Fast skeletal muscle tropomyosin (TM) of tunas is composed of nearly equimolar amount of two isoforms designated α-TM and β-TM expediently based on their migration behavior in SDS-PAGE, whereas corresponding TMs from the other fish species are homogenous (α-type). The presence of β-TM is thus specific to tunas so far. The amino acid sequence of β-TM from bluefin tuna Thunnus thynnus orientalis, which has not been revealed to date unlike α-TM, was successfully obtained in this study by cDNA cloning. The coding region of β-TM cDNA comprised of an open reading frame of 855 bp encoding 284 amino acid residues, like most of the TMs. Unexpectedly, the sequence of β-TM showed high similarity to those of other vertebrate α-type TMs including tuna α-TM. Phylogenetic analysis also showed that β-TM has the closest relationship with α-TM of tuna. This fact was quite unlike the relation of mammalian α- and β-TMs. Based on the distribution of amino acid substitutions, it was suggested that tuna TM isoforms are the products of different genes. By thermodynamic analysis of native and reconstituted TMs, it was demonstrated that β-TM is less thermostable than α-TM. Proteolytic digestion also supported the lower stability of the former.     

Cardicola opisthorchis n. sp. (Trematoda: Aporocotylidae) from the Pacific bluefin tuna, Thunnus orientalis (Temminck & Schlegel, 1844), cultured in Japan

A new aporocotylid blood fluke is described, based on specimens from the ventricle of the Pacific bluefin tuna, Thunnus orientalis (Temminck et Schlegel), cultured in Wakayama and Nagasaki Prefectures, Japan. The new species is morphologically similar to the members of the genus Cardicola Short, 1953, but shows distinct differences in the body form, location of the testis and the orientation of the ootype. The body of the new species is long and slender, whereas other Cardicola species are small and generally lanceolate. The testis is mostly located posterior to the caeca and anterior to the ovary, occupying 31–45% of body length, in contrast to the known Cardicola species, whose testis is typically intercaecal. The ootype is oriented anteriorly, while in most congeners, it is directed posteriorly or horizontally. Phylogenetic analyses of this aporocotylid, together with Cardicola orientalis Ogawa, Tanaka, Sugihara et Takami, 2010 from the same host, were conducted based on DNA sequences of the ITS2 rDNA and the 28S region of ribosomal RNA. The analyses revealed that the new blood fluke belongs to the genus Cardicola despite the marked morphological differences. Thus, this aporocotylid is named Cardicola opisthorchis n. sp. and the generic diagnosis is emended in this paper. In addition, 100% identity among the ITS2 sequences from the present species, Cardicola sp. from T. orientalis in Mexico and Cardicola sp. from the northern bluefin tuna, Thunnus thynnus (Linnaeus) in Spain suggests that C. opisthorchis n. sp. has a broad geographical distribution and that it infects both the Pacific and northern bluefin tuna.     

Influence of swimming speed on metabolic rates of juvenile pacific bluefin tuna and yellowfin tuna

Bluefin tuna are endothermic and have higher temperatures, heart rates, and cardiac outputs than tropical tuna. We hypothesized that the increased cardiovascular capacity to deliver oxygen in bluefin may be associated with the evolution of higher metabolic rates. This study measured the oxygen consumption of juvenile Pacific bluefin Thunnus orientalis and yellowfin tuna Thunnus albacares swimming in a swim-tunnel respirometer at 20 degrees C. Oxygen consumption (Mo2) of bluefin (7.1-9.4 kg) ranged from 235+/-38 mg kg(-1) h(-1) at 0.85 body length (BL) s(-1) to 498+/-55 mg kg(-1) h(-1) at 1.80 BL s(-1). Minimal metabolic rates of swimming bluefin were 222+/-24 mg O(2) kg(-1) h(-1) at speeds of 0.75 to 1.0 BL s(-1). Mo2 of T. albacares (3.7-7.4 kg) ranged from 164+/-18 mg kg(-1) h(-1) at 0.65 BL s(-1) to 405+/-105 mg kg(-1) h(-1) at 1.8 BL s(-1). Bluefin tuna had higher metabolic rates than yellowfin tuna at all swimming speeds tested. At a given speed, bluefin had higher metabolic rates and swam with higher tailbeat frequencies and shorter stride lengths than yellowfin. The higher M dot o2 recorded in Pacific bluefin tuna is consistent with the elevated cardiac performance and enhanced capacity for excitation-contraction coupling in cardiac myocytes of these fish. These physiological traits may underlie thermal-niche expansion of bluefin tuna relative to tropical tuna species.     

Genetic isolation between Atlantic and Mediterranean albacore populations inferred from mitochondrial and nuclear DNA markers

Genetic population structure of Atlantic and Mediterranean albacore Thunnus alalunga was investigated using nucleotide sequence variations of the glucose‐6‐phosphate dehydrogenase gene intron ( G6PD ) and the mitochondrial DNA (mtDNA) D‐loop region ( Dloop ). Restriction analysis using Ase I digestion detected two major restriction types ( A and B ) at the Dloop locus with strong frequency differences between Atlantic and Mediterranean samples. Thirty‐six individuals of 100 Mediterranean albacore were of the B type whereas no B type individuals were found in the Atlantic samples ( n  = 102). Phylogenetic analysis using nucleotide sequence data of the Dloop locus indicated that the B type lineage recently arose from the ancestral A lineage in the Mediterranean Sea and has not dispersed into the Atlantic Ocean. The frequencies of two alleles ( L and S ) at the G6PD locus were significantly different between the samples from the Atlantic ( L  = 0·495) and the Mediterranean ( L  = 0·725), but no significant heterogeneity was observed between mtDNA‐ A and ‐ B types of the Mediterranean sample. These molecular data indicate that gene flow between the Atlantic and Mediterranean albacore populations have been considerably restricted and strongly suggest these populations should continue to be treated as two distinct management units.     

Spawning of bluefin tuna in the black sea: historical evidence, environmental constraints and population plasticity

The lucrative and highly migratory Atlantic bluefin tuna, Thunnus thynnus (Linnaeus 1758; Scombridae), used to be distributed widely throughout the north Atlantic Ocean, Mediterranean Sea and Black Sea. Its migrations have supported sustainable fisheries and impacted local cultures since antiquity, but its biogeographic range has contracted since the 1950s. Most recently, the species disappeared from the Black Sea in the late 1980s and has not yet recovered. Reasons for the Black Sea disappearance, and the species-wide range contraction, are unclear. However bluefin tuna formerly foraged and possibly spawned in the Black Sea. Loss of a locally-reproducing population would represent a decline in population richness, and an increase in species vulnerability to perturbations such as exploitation and environmental change. Here we identify the main genetic and phenotypic adaptations that the population must have (had) in order to reproduce successfully in the specific hydrographic (estuarine) conditions of the Black Sea. By comparing hydrographic conditions in spawning areas of the three species of bluefin tunas, and applying a mechanistic model of egg buoyancy and sinking rate, we show that reproduction in the Black Sea must have required specific adaptations of egg buoyancy, fertilisation and development for reproductive success. Such adaptations by local populations of marine fish species spawning in estuarine areas are common as is evident from a meta-analysis of egg buoyancy data from 16 species of fish. We conclude that these adaptations would have been necessary for successful local reproduction by bluefin tuna in the Black Sea, and that a locally-adapted reproducing population may have disappeared. Recovery of bluefin tuna in the Black Sea, either for spawning or foraging, will occur fastest if any remaining locally adapted individuals are allowed to survive, and by conservation and recovery of depleted Mediterranean populations which could through time re-establish local Black Sea spawning and foraging.     

Genetic identification of Thunnus orientalis, T. thynnus, and T. maccoyii by a cytochrome b gene analysis

The three species of bluefin tunas, Thunnus orientalis, T. maccoyii, and T. thynnus, are morphologically similar, which can pose problems for fisheries management and marketing. We examined intraspecific genetic diversity and interspecific genetic boundaries among these three species by analyzing the cytochrome (Cyt) b gene. The full lengths of the nucleotide sequences were 1,141 bp in T. orientalis and T. thynnus and ranged 1,138?~?1,141 bp in T. maccoyii. Mean nucleotide diversities were 0.0019?±?0.0002 in T. thynnus (n?=?8), 0.0063?±?0.0005 in T. orientalis (n?=?22), and 0.0059?±?0.0007 in T. maccoyii (n?=?24). Average numbers of nucleotide differences and nucleotide substitutions per site among the three species were 18.748?±?2.879 and 0.017?±?0.003, respectively. The Neighbor-joining and minimum-evolution trees showed distinct clades with high bootstrapping value support, and the high Fst value indicated significant differentiation among the three species. T. thynnus, T. orientalis, and T. maccoyii could be individually distinguished from each other Thunnus tunas by the 132nd, 375th, and 1,023rd sites of the Cyt b sequences. In the mismatch analysis, Fu??s and Tajima??s tests of sequences from T. orientalis and T. maccoyii provided evidence of their population expansion dating to the middle Pleistocene.     

Trophic ecology of Atlantic bluefin tuna Thunnus thynnus larvae

Feeding intensity, diet composition, selectivity, energy ingestion and dietary niche breadth of larval Atlantic bluefin tuna Thunnus thynnus were studied on the eastern (Mediterranean) spawning grounds of the species. Larval T. thynnus were collected in the Balearic Archipelago (north-west Mediterranean Sea) during 2004 and 2005 using surveys specific for larval scombrids. Larvae between 2·6 and 8·7 mm standard length (L(S) ) are diurnal feeders, and 94% of the guts collected during daylight hours were full. The mean ±s.d. number of prey per gut was 7·1 ± 5·7, with mean ±s.d. ranging from 3·0 ± 1·6 in the smallest T. thynnus larvae to 11·1 ± 5·8 in 5·0-6·0 mm L(S) larvae. Up to 21 prey were found in a single larval gut (5·0-6·0 mm L(S) ) at the end of the day. Larvae progressively selected larger prey and exhibited increased carbon content concurrent with preflexion development of feeding and locomotory structures. Larvae of 5·0-6·0 mm L(S) exhibited positive selection of cladocerans over other prey (Chesson's index), whereas copepod nauplii dominated the diets of earlier stages. The dietary niche breadth measured increased initially but decreased at c. 5·5 mm L(S) . Appendicularians were found in the diet of larger larval sizes, but no piscivory was observed. Results are discussed in light of the sparse existing data for larval T. thynnus and other larval tuna species.     

Schooling behaviour and retinomotor response of juvenile Pacific bluefin tuna Thunnus orientalis under different light intensities

Schooling behaviour and histological retinal light adaptation in juvenile Pacific bluefin tuna Thunnus orientalis were examined under various light intensities to determine the effect of light intensity on behaviour. After monitoring the schooling behaviour of juveniles 35–36 and 45–46 days post hatching, schooling variables such as nearest neighbour distance and separation swimming index were measured under different light intensities. Furthermore, retinal indices of light adaptation were investigated histologically for each experimental light intensity. Under intensities >5 lx, schooling variables in the two juvenile growth stages were nearly constant, allowing schooling. In contrast, the schooling variables indicated that the fish gradually swam more widely and randomly with decreasing light intensities <5 lx. The retinal indices also showed a shift from light adaptation to dark adaptation at light levels <5 lx. From 5 to 0·01 lx, retinal adaptation and fish schooling behaviour changed with light intensity. These data suggest that the schooling behaviour of juvenile Pacific bluefin tuna is greatly affected by retinal adaptation.