Skip to main content

Advertisement

Log in

Genetic Population Structure of Thunnus albacares in the Central Pacific Ocean Based on mtDNA COI Gene Sequences

  • Original Article
  • Published:
Biochemical Genetics Aims and scope Submit manuscript

An Erratum to this article was published on 05 August 2015

Abstract

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 F ST 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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Abdussamad EM, Koya KP, Rohit P (2012) Fishery of yellowfin tuna Thunnus albacares (Bonnaterre, 1788) in the Indian EEZ with special reference to their biology and population characteristics. Indian J Fish 59(3):43–51

    Google Scholar 

  • Alvarado-Bremer JR, Stequert B, Robertson NW, Ely B (1998) Genetic evidence for inter-oceanic subdivision of bigeye tuna (Thunnus obesus) populations. Mar Biol 132:547–557

    Article  Google Scholar 

  • Appleyard SA, Grewe PM, Innes BH, Ward RD (2001) Population structure of Yellow-fin tuna (Thunnus albacares) in the western Pacific Ocean, inferred from microsatellite loci. Mar Biol 139:383–393

    Article  CAS  Google Scholar 

  • Appleyard SA, Ward RD, Grewe PM (2002) Genetic stock structure of bigeye tuna in the Indian Ocean using mitochondrial DNA and microsatellites. J Fish Biol 60:767–770

    Article  CAS  Google Scholar 

  • Avise J (1998) Phylogeography. Harvard University Press, Cambridge

    Google Scholar 

  • Avise JC, Arnold J, Ball RM (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Res 18:489–522

    Article  Google Scholar 

  • Campana SE, Frank KT, Hurley PCF, Koeller PA, Page FH, Smith PC (1989) Survival and abundance of young Atlantic cod Gadusmorhus andhaddock Melanogrammusaeglefinus as indicators of year-class strength. Can J Fish Aquat Sci 46:171–182

    Article  Google Scholar 

  • Chevaldonne P, Jollivet D, Desbruyeres D (2002) Sister-species of eastern Pacific hydrothermal vent worms (Ampharetidae, Alvinellidae, Vestimentifera) provide new mitochondrial COI clock calibration. Cahiers de Biologie Mar 43(3–4):367–370

    Google Scholar 

  • Chiang HC, Hsu CC, Wu GCC, Chang SK, Yang HY (2008) Population structure of bigeye tuna (Thunnus obesus) in the Indian Ocean inferred from mitochondrial DNA. Fish Res 90:305–312

    Article  Google Scholar 

  • Chow S, Okamoto H, Miyabe N, Hiramatsu K, Barut N (2000) Genetic divergence between Atlantic and Indo-Pacific stocks of bigeye tuna (Thunnus obesus) and admixture around South Africa. Mol Ecol 9:221–227

    Article  CAS  PubMed  Google Scholar 

  • Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1660

    Article  CAS  PubMed  Google Scholar 

  • Coates AG, Jackson JBG, Collins LS, Cronin TM, Dowsett HJ, Bybell LM, Jung P, Obando JA (1992) Closure of the Isthmus of Panama: the near-shore marine record of Costa Rica and western Panama. Geol Soc Am Bull 104:814–828

    Article  Google Scholar 

  • Collette B, Nauen C (1983) Scombrids of the world—an annotated and illustrated catalogue of tunas, mackerels, bonitos and related species known to date. FAO Spec Cat 2:137

    Google Scholar 

  • Coombs SH, Nichols JH, Fosh CA (1990) Plaice egg (Pleuronectes platessa L) in the southern North Sea: abundance, spawning area, vertical distribution, and buoyancy. J Mar Sci 47:133–139

    Google Scholar 

  • Durand JD, Collet A, Chow S, Guinand B, Borsa P (2005) Nuclear and mitochondrial DNA markers indicate unidirectional gene flow of Indo-Pacific to Atlantic bigeye tuna (Thunnus obesus) populations, and their admixture off southern Africa. Mar Biol 147:313–322

    Article  CAS  Google Scholar 

  • Ely B, Viànas J, Alvarado-Bremer JR, Black D, Lucas L, Covello K, Labrie A, Thelen VE (2005) Consequences of the historical demography on the global population structure of two highly migratory cosmopolitan marine fishes: the Yellow-fin tuna (Thunnus albacares) and the skipjack tuna (Katsuwonus pelamis). BMC Evol Biol 5:19

    Article  PubMed Central  PubMed  Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    CAS  PubMed Central  PubMed  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50

    CAS  PubMed Central  Google Scholar 

  • FAO (1996) Precautionary approach to capture fisheries and species introductions, elaborated by the technical consultation on the precautionary approach to capture fisheries (including species introductions) (6–13 June 1995, Lysekil, Sweden). (Fisheries FTGfR, ed.). Food and Agriculture Organization of the United Nations, Rome

  • Fink BD, Bayliff WH (1970) Migrations of yellowfin and skipjack tuna in the eastern Pacific Ocean as determined by tagging experiments. Bull Inter Am Trop Tuna Commun 15:1–227

    Google Scholar 

  • Grewe P, Hampton J (1998) An assessment of bigeye (Thunnus obesus) population structure in the Pacific Ocean based on mitochondrial DNA and DNA microsatellite analysis. SPEST Publication 98-05, JIMAR Contribution, pp 98–320

  • Hampton J, Gunn J (1998) Exploitation and movement of yellowfin tuna (Thunnus albacares) and bigeye tuna (T. obesus) tagged in the north-western Coral Sea. Mar Freshw Res 49:475–489

    Article  Google Scholar 

  • Harpending RC (1994) Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol 66:591–600

    CAS  PubMed  Google Scholar 

  • Hewitt GM (2000) The genetic legacy of the quaternary ice ages. Nature 405:907–913

    Article  CAS  PubMed  Google Scholar 

  • Hunter JR (1986) The dynamics of tuna movements: an evaluation of past and future research. FAO Fish Tech 13:277–278

    Google Scholar 

  • Itano DG, Willams PG (1992)Analysis of yellowfin tuna tagging data and related information collected by the Skipjack Survey and Assessment Programme. Technical report 28, SPC Tuna and Billfish Assessment Programme (TBAP), Noumea, New Caledonia

  • Joseph JFG, Alverson BD (1964)A review of the population structure of yellowfin tuna (Thunnus albacares) in the eastern Pacific Ocean. Inter Am Trop Tuna Commun Bull 9:53–112

  • Kamimura T, Honma M (1963) Distribution of the yellowfin tuna (Neothunnus macropterus) (Temminck and Schlegel) in the tuna longline fishing grounds of the Pacific Ocean. Nankai Reg Fish Res Lab Rept (17):31–53

    Google Scholar 

  • Keigwin L (1982) Pliocene closing of the Isthmus of Panama, based on stratigraphic evidence from nearby Pacific Ocean and Caribbean Sea cores. Geology 6:630–634

    Article  Google Scholar 

  • Kikawa S (1966) The distribution of maturing bigeye and yellowfin and an evaluation of their spawning potential in different areas in the tuna longline grounds in the Pacific. Rep Nankai Reg Fish Res Lab 23:131–208

    Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  • Lewis AD (1992) Stock structure of Pacific yellowfin tuna a review. South Pacific Commission, Noumea, New Caledonia: 14

  • Mac-Kenzie BR, Mosegaard H, Rosenberg AA (2009) Impending collapse of bluefin tuna in the northeast Atlantic and Mediterranean. Con Let 2:26–35

    Article  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Qiu F, Kitchen A, Beerli P, Miyamoto MM (2012) A possible explanation for the population size discrepancy in tuna (genus Thunnus) estimated from mitochondrial DNA and microsatellite data. Mol Phylogenet Evol 66(2):463–468

    Article  PubMed  Google Scholar 

  • Reiss H, Hoarau G, Dickey-Collas M, Wolff WJ (2009) Genetic population structure of marine fish: mismatch between biological and fisheries management units. Fish Fish 10:361–395

    Article  Google Scholar 

  • Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225

    Article  Google Scholar 

  • Rogers AR (1995) Genetic evidence for a Pleistocene population explosion. Evolution 49:608–615

    Article  Google Scholar 

  • Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–569

    CAS  PubMed  Google Scholar 

  • Rozas J, Sanchez-De I, Barrio JC, Messeguer X, Rozas R (2003) Dna SP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497

    Article  CAS  PubMed  Google Scholar 

  • Sambrook J, Fritsh EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  • Schneider S, Excoffier L (1999) Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152:1079–1089

    CAS  PubMed Central  PubMed  Google Scholar 

  • Schneider S, Roessli D, Excoffier L (2000) Arlequin, Version 2.000: A Software for Population Genetics Data Analysis. University of Geneva, Switzerland

  • Scoles DR, Grave JE (1993) Genetic analysis of the population structure of Yellow-fin tuna, Thunnus albacares, from the Pacific Ocean. Fish Bull 91:690–698

  • Sharp GD (1978) Behavioral and physiological properties of tunas and their effects on vulnerability to fishing gear. In: Sharp GD, Dizon AE (eds) The physiological ecology of tunas. Academic Press, New York, pp 397–449

    Chapter  Google Scholar 

  • Slatkin M (1993) Isolation by distance in equilibrium and nonequilibrium populations. Evolution 47:264–279

    Article  Google Scholar 

  • Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555–562

    CAS  PubMed Central  PubMed  Google Scholar 

  • Suzuki Z, Tomlinson PK, Honma M (1978) Population structure of Pacific yellowfin tuna. Bull Inter Am Trop Tuna Commun 17:273–441

    Google Scholar 

  • Tajima F (1989a) The effect of change in population size on DNA polymorphism. Genetics 123:597–601

    CAS  PubMed Central  PubMed  Google Scholar 

  • Tajima F (1989b) Statistical methods for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    CAS  PubMed Central  PubMed  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  CAS  PubMed  Google Scholar 

  • Templeton AR, Georgiadis NJ (1996) A landscape approach toconservation genetics: conserving evolutionary processes in the African Bovidae. In: Avise JC, Hamrick JL (eds) Conservation genetics: case histories from nature. Chapman & Hall, New York, pp 398–430

    Chapter  Google Scholar 

  • Templeton AR, Routman E, Phillips C (1995) Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the Tiger Salamander, Ambystomatigrinum. Genetics 140:767–782

    CAS  PubMed Central  PubMed  Google Scholar 

  • Thompson JD, Higgins DG, Gibson JJ (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Viànas J, Santiago J, Pla C (1999) Genetic characterization and Atlantic-Mediterranean stock structure of albacore, Thunnus alalunga. ICCAT Coll Vol Sci Pap 49:188–191

    Google Scholar 

  • Wan RJ, Sun S (2006) The category composition and abundance of ichthyoplankton in the ecosystem of the Yellow Sea and the East China Sea.ActaZoologicaSinica, 52(1):28–44 (in Chinese)

  • Waples RS, Punt AE, Cope JM (2008) Integrating genetic data into management of marine resources: how can we do it better? Fish Fish 9:423–449

    Article  Google Scholar 

  • Ward RD, Elliott NG, Grewe PM, Smolenski AJ (1994) Allozyme and mitochondrial DNA variation in Yellow-fin tuna (Thunnus albacares) from the Pacific Ocean. Mar Biol 118:531–539

    Article  CAS  Google Scholar 

  • Ward RD, Elliot NG, Innes BH, Smolenski AJ, Grewe PM (1997) Global population structure of yellowfin tuna (Thunnus albacares) inferred from allozyme and mitochondrial DNA variation. Fish Bull 95:566–575

    Google Scholar 

  • Wu GCC, Chiang HC, Chen KS, Hsu CC, Yang HY (2009) Population structure of albacore (Thunnus alalunga) in the Northwestern Pacific Ocean inferred from mitochondrial DNA. Fish Res 95:125–131

    Article  Google Scholar 

  • Zardoya R, Castilho R, Grande C, Favre-Krey L, Caetano S, Marcato S, Krey G, Patarnello T (2004) Differential population structuring of two closely related fish species, the mackerel (Scomberscombrus) and the chub mackerel (Scomberjaponicus), in the Mediterranean Sea. Mol Ecol 13:1785–1798

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We would like to express our thanks to all the people in the Tuna Technique Groups for their help with sample collection. This work was supported in part by the Major Research Plan Fostering Project of the National Natural Science Foundation of China (grant no. 91131006), the “Shu Guang” Project of the Shanghai Municipal Education Development Commission and the Shanghai Education Development Foundation (grant no. 13SG51). The grants from the Shanghai Municipal Project for First-class Discipline of Fisheries to Shanghai Ocean University and from the Opening Project of the Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, are appreciated.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Qianghua Xu.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, W., Chen, X., Xu, Q. et al. Genetic Population Structure of Thunnus albacares in the Central Pacific Ocean Based on mtDNA COI Gene Sequences. Biochem Genet 53, 8–22 (2015). https://doi.org/10.1007/s10528-015-9666-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10528-015-9666-0

Keywords

Navigation