Shallow population structure of southern bluefin tuna, Thunnus maccoyii (Castelnau, 1872) between Indian and Atlantic Oceans inferred from mitochondrial DNA sequences

References

• Alvarado Bremer JR, Ely B. 1999. Pronounced levels of genetic differentiation between two trans-Atlantic samples of little tunny (Euthynnus alletteratus). ICCAT Col Vol Sci Pap. 49(4):236–242.
   Google Scholar
• Alvarado Bremer JR, Naseri I, Ely B. 1997. Orthodox and unorthodox phylogenetic relationships among tunas revealed by the nucleotide sequence analysis of the mitochondrial DNA control region. J Fish Biol. 50:540–554.
   Web of Science ®Google Scholar
• Antoniou A, Kasapidis P, Kotoulas G, Mylonas CC, Magoulas A. 2017. Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: insights from genome-wide SNPs and microsatellites. J Biol Res. 24:3.
   Web of Science ®Google Scholar
• Bartlett SE, Davidson WS. 1991. Identification of Thunnus tuna species by the polymerase chain reaction and direct sequence analysis of their mitochondrial cytochrome b genes. Can J Fish Aquat Sci. 48(2):309–317.
   Web of Science ®Google Scholar
• Boustany AM, Reeb CA, Block BA. 2008. Mitochondrial DNA and electronic tracking reveal population structure of Atlantic bluefin tuna (Thunnus thynnus). Mar Biol. 156(1):13–24.
   Web of Science ®Google Scholar
• Carlsson J, McDowell JR, Diaz-Jaimes P, Carlsson JEL, Boles SB, Gold JR, Graves JE. 2004. Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea. Mol Ecol. 13(11):3345–3356.
   PubMed Web of Science ®Google Scholar
• Caton A, McLoughlin K, Staples D. 2000. Fishery Status Reports 1999: resource assessments of Australian Commonwealth fisheries. Fishery Status Reports. Canberra: Agriculture, Fisheries and Forestry; p. 159–168.
   Google Scholar
• CCSBT. 2018. Report on biology, stock status and management of southern bluefin tuna: 2018. Report of the Twenty Third Meeting of the Scientific Committee. Commission for the Conservation of Southern Bluefin Tuna. Available from: https://www.ccsbt.org/sites/default/files/userfiles/file/docs_english/meetings/meeting_reports/ccsbt_25/report_of_SC23.pdf.
   Google Scholar
• Chow S, Inoue S. 1993. Intra and interspecific restriction fragment length polymorphism in mitochondrial genes of Thunnus tuna species. Bull Nat Res Inst Far Seas Fish. 30:207–225.
   Google Scholar
• Chow S, Kishino H. 1995. Phylogenetic relationships between tuna species of the genus Thunnus (Scombridae: Teleostei): Inconsistent implications from morphology, nuclear and mitochondrial genomes. J Mol Evol. 41(6):741–748.
   PubMed Web of Science ®Google Scholar
• Donaldson KA, Wilson RR. 1999. Amphi-Panamic geminates of snook (Percoidei: Centropomidae) provide a calibration of the divergence rate in the mitochondrial DNA control region of fishes. Mol Phylogenet Evol. 13(1):208–213.
   PubMed Web of Science ®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.
   PubMed Web of Science ®Google Scholar
• Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147(2):915–925.
   PubMed Web of Science ®Google Scholar
• Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 41:95–98.
   Google Scholar
• Harpending HC. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol. 66(4):591–600.
   PubMed Web of Science ®Google Scholar
• Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN. 2007. Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes. 7(4):544–548.
   Google Scholar
• Kunal SP, Kumar G, Menezes MR, Meena RM. 2013. Mitochondrial DNA analysis reveals three stocks of yellowfin tuna Thunnus albacares (Bonnaterre, 1788) in Indian waters. Conserv Genet. 14(1):205–213.
   Web of Science ®Google Scholar
• Li WH. 1997. Molecular evolution. Sunderland (MA): Sinauer Associates, Inc.; p. 487.
   Google Scholar
• Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25(11):1451–1452..
   PubMed Web of Science ®Google Scholar
• Mandal A, Mohindra V, Singh RK, Punia P, Singh AK, Lal KK. 2012. Mitochondrial DNA variation in natural populations of endangered Indian Feather-Back Fish, Chitala chitala. Mol Biol Rep. 39(2):1765–1775.
   PubMed Web of Science ®Google Scholar
• Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press; p. 18–496.
   Google Scholar
• Nei M, Li WH. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA. 76(10):5269–5273.
   PubMed Web of Science ®Google Scholar
• Paine MA, McDowell JR, Graves JE. 2007. Specific identification of Western Atlantic Ocean scombrids using mitochondrial DNA cytochrome c oxidase subunit I (COI) gene region sequences. Bull Mar Sci. 80(2):353–367.
   Web of Science ®Google Scholar
• Patterson TA, Eveson JP, Hartog JR, Evans K, Cooper S, Lansdell M, Hobday AJ, Davies CR. 2018. Migration dynamics of juvenile southern bluefin tuna. Sci Rep. 8(1):14553.
   PubMedGoogle Scholar
• Pawson MG, Jennings S. 1996. A critique of methods for stock identification in marine capture fisheries. Fish Res. 25(3-4):203–217.
   Web of Science ®Google Scholar
• Polacheck T. 2012. Assessment of IUU fishing for southern bluefin tuna. Mar Policy. 36(5):1150–1165.
   Web of Science ®Google Scholar
• Ricker WE. 1981. Changes in the average size and average age of Pacific salmon. Can J Fish Aquat Sci. 38(12):1636–1656.
   Web of Science ®Google Scholar
• Rogers AR, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol. 9(3):552–569.
   PubMed Web of Science ®Google Scholar
• Suda A, Nishiki I, Iwasaki Y, Matsuura A, Akita T, Suzuki N, Fujiwara A. 2019. Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers. Sci Rep. 9(1):14450– 14412.
   PubMedGoogle Scholar
• Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123(3):585–595.
   PubMed Web of Science ®Google Scholar
• Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 10(3):512–526.
   PubMed Web of Science ®Google Scholar
• Thompson JD, Higgins DG, Gibson TJ. 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(22):4673–4680.
   PubMed Web of Science ®Google Scholar
• Viñas J, Bremen JA, Pla C. 2004a. Inter-oceanic genetic differentiation among albacore (Thunnus alalonga) populations. Mar Biol. 145(2):225–232.
   Web of Science ®Google Scholar
• Viñas J, Bremer JA, Pla C. 2004b. Phylogeography of the Atlantic bonito (Sarda sarda) in the northern Mediterranean: the combined effects of historical vicariance, population expansion, secondary invasion, and isolation by distance. Mol Phylogenet Evol. 33(1):32–42.
   PubMed Web of Science ®Google Scholar
• Waldman JR. 1999. The importance of comparative studies in stock analysis. Fish Res. 43(1–3):237–246.
   Web of Science ®Google Scholar
• Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD. 2005. DNA barcoding Australia's fish species. Philos Trans R Soc Lond B Biol Sci. 360(1462):1847–1857.
   PubMed Web of Science ®Google Scholar