Population structure of bigeye tuna (Thunnus obesus) in the Indian Ocean inferred from mitochondrial DNA

Fisheries Research

Volumn 90, Issue 1-3, 2008, Pages 305-312

  Chiang, Hsin Chieh ^a   Hsu, Chien Chung ^a   Wu, Georgiana Cho Chen ^b   Chang, Shui Kai ^c   Yang, Hsi Yuan ^b  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^c NATIONAL SUN YAT SEN UNIVERSITY   (Taiwan)

Author keywords

Bigeye tuna (Thunnus obesus); Control region; Indian Ocean; Mitochondrial DNA; Population structure; Western Pacific Ocean

Indexed keywords

SCOMBRIDAE; THUNNUS OBESUS;

EID: 40649108873     PISSN: 01657836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fishres.2007.11.006     Document Type: Article

References (45)

1. Alvarado-Bremer J.R., Naseri I., and Ely B. Orthodox and unorthodox phylogenetic relationships among tunas revealed by the nucleotide sequence analysis of the mitochondrial DNA control region. J. Fish Biol. 50 (1997) 540-554
2. Alvarado-Bremer J.R., Stequert B., Robertson N.W., and Ely B. Genetic evidence for inter-oceanic subdivision of bigeye tuna (Thunnus obesus Lowe) populations. Mar. Biol. 132 (1998) 547-557
3. Alvarado-Bremer J.R., Vinas J., Mejutoc J., Ely B., and Pla C. 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. Mol. Phyl. Evol. 36 (2005) 169-187
4. Appleyard S.A., Grewe P.M., Innes B.H., and Ward R.D. Population structure of yellowfin tuna (Thunnus albacares) in the western Pacific Ocean, inferred from microsatellite loci. Mar. Biol. 139 (2001) 383-393
5. Appleyard S.A., Ward R.D., and Grewe P.M. Genetic stock structure of bigeye tuna in the Indian Ocean using mitochondrial DNA and microsatellites. J. Fish Biol. 60 (2002) 767-770
6. Avise J. Phylogeography (1998), Mass: Harvard University Press, Cambridge
7. Brown G.G., Gadaleta G., Pepe G., Saccone C., and Sbisa E. Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J. Mol. Biol. 192 (1986) 503-511
8. Buonnacorsi V.P., McDowell J.R., and Graves J.E. Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans). Mol. Ecol. 10 (2001) 1179-1196
9. Carlsson J., McDowell J.R., Diaz-Jaimes P., Carlsson J.E., Boles S.B., Gold J.R., and Graves J.E. Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea. Mol. Ecol. 13 (2004) 3345-3356
10. Chiang H.C., Hsu C.C., Lin H.D., Ma G.C., Chiang T.Y., and Yang H.Y. Population structure of bigeye tuna (Thunnus obesus) in the South China Sea, Philippine Sea and western Pacific Ocean inferred from mitochondrial DNA. Fish. Res. 79 (2006) 219-225
11. Chow S., Okamoto H., Miyabe N., Hiramatsu K., and Barut N. Genetic divergence between Atlantic and Indo-Pacific stocks of bigeye tuna (Thunnus obesus) and admixture around South Africa. Mol. Ecol. 9 (2000) 221-227
12. Durand J.D., Collet A., Chow S., Guinand B., and Borsa P. 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 (2005) 313-322
13. Ely B., Vinas J., Alvarado Bremer J.R., Black D., Lucas L., Covello K., Labrie A.V., and Thelen E. Consequences of the historical demography on the global population structure of two highly migratory cosmopolitan marine fishes: the yellowfin tuna (Thunnus albacares) and the skipjack tuna (Katsuwonus pelamis). BMC Evol. Biol. 5 (2005) 19
14. Excoffier L., Smouse P.E., and Quattro J.M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131 (1992) 479-491
15. Felsenstein J. Confidence limits on phylogenies: an approach using bootstrap. Evolution 39 (1985) 783-791
16. Fu Y.X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147 (1997) 915-925
17. Grant W.S., and Bowen B.W. Population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J. Hered. 89 (1998) 415-426
18. Grewe, P.M., Hampton, J., 1998. An assessment of bigeye (Thunnus obesus) population structure in the Pacific Ocean based on mitochondrial DNA and DNA microsatellite analysis. SOEST Publication 98-05, JIMAR Contribution 98-320.
19. Guo S., and Thompson E. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48 (1992) 361-372
20. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 41 (1999) 95-98
21. Harpending R.C. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol. 66 (1994) 591-600
22. ICCAT, 2005. Report of the Second World Meeting on Bigeye Tuna. Madrid, Spain, March 10-13, 2004. Col. Vol. Sci. Pap. ICCAT, 57, 2, 3-38.
23. ICCAT, 2006. Report for the Biennial Period, 2004-2005, Part II (2005), vol. 1. International Commission for the Conservation of Atlantic Tunas, Madrid, Spain.
24. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5 (2004) 150-163
25. Lynch M., and Crease T.J. The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol. 7 (1990) 337-394
26. Martínez P., Gonzalez E.G., Castilho R., and Zardoya R. Genetic diversity and historical demography of Atlantic bigeye tuna (Thunnus obesus). Mol. Phyl. Evol. 39 (2006) 404-416
27. Nei M. Molecular Evolutionary Genetics (1987), Columbia University Press, New York
28. Ramos-Onsins S.E., and Rozas J. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 19 (2002) 2092-2100
29. Rogers A.R., and Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9 (1992) 552-569
30. Rozas J., Sanchez-DeI Barrio J.C., Messeguer X., and Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
31. Saccone C., Attimonelli M., and Sbisa E. Structural elements highly preserved during the evolution of the D-loop containing region in vertebrate mitochondrial DNA. J. Mol. Evol. 26 (1987) 205-211
32. Satiou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic tree. Mol. Biol. Evol. 4 (1987) 406-425
33. Schneider S., and Excoffier L. 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 (1999) 1079-1089
34. Schneider S., Roessli D., and Excoffier L. ARLEQUIN, Version 2.000: A Software for Population Genetics Data Analysis (2000), University of Geneva, Switzerland
35. Scoles D.R., and Graves J.E. Genetic analysis of the population structure of yellowfin tuna, Thunnus albacares, from the Pacific Ocean. Fish. Bull. (Washington, DC) 91 (1993) 690-698
36. Slatkin M., and Hudson R.R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129 (1991) 555-562
37. Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics 105 (1983) 460-467
38. Tajima F. The effect of change in population size on DNA polymorphism. Genetics 123 (1989) 597-601
39. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
40. Tamura K., and Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 (1993) 512-526
41. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25 (1997) 4876-4882
42. Watterson G. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7 (1975) 256-276
43. Ward R.D., Elliott N.G., Grewe P.M., and Smolenski A.J. Allozyme and mitochondrial DNA variation in yellowfin tuna (Thunnus albacares) from the Pacific Ocean. Mar. Biol. 118 (1994) 531-539
44. Ward R.D., Elliott N.G., Innes B.H., Smolenski A.J., and Grewe P.M. Global population structure of yellowfin tuna Thunnus albacares, inferred from allozyme and mitochondrial DNA variation. Fish. Bull. (Washington, DC) 95 (1997) 566-575
45. Weir B.S., and Cockerham C.C. Estimating F-statistics for the analysis of population structure. Evolution 38 (1984) 1358-1370