Phylogenetic analysis of the Pacific cutthroat trout (Oncorhynchus clarki ssp.: Salmonidae) based on partial mtDNA ND4 sequences: A closer look at the highly fragmented inland species

Molecular Phylogenetics and Evolution

Volumn 52, Issue 2, 2009, Pages 406-415

  Wilson, Wade D ^a   Turner, Thomas F ^a  

^a UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

Apache trout; Cutthroat; Gila trout; ND4; Oncorhynchus; Oncorhynchus clarki; Pacific trout; Salmonidae

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; CLASSIFICATION; DNA SEQUENCE; GENETICS; ONCORHYNCHUS; PHYLOGENY; POPULATION GENETICS; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; DNA, MITOCHONDRIAL; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; ONCORHYNCHUS; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

AMADINA FASCIATA; MYA; ONCORHYNCHUS; ONCORHYNCHUS CLARKII; ONCORHYNCHUS GILAE; ONCORHYNCHUS GILAE APACHE; ONCORHYNCHUS GILAE GILAE; ONCORHYNCHUS GORBUSCHA; ONCORHYNCHUS KISUTCH; ONCORHYNCHUS MASOU; ONCORHYNCHUS MYKISS; ONCORHYNCHUS NERKA; ONCORHYNCHUS TSHAWYTSCHA; SALMONIDAE; SALVELINUS;

EID: 65649084829     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.03.018     Document Type: Article

References (57)

1. Allendorf F.W., and Leary R.F. Conservation and distribution of genetic variation in a polytypic species, the cutthroat. Conserv. Biol. 2 (1988) 170-184
2. Behnke R.J., Koh T.P., and Needham P.R. Status of the landlocked salmonid fishes of Formosa with a review of Oncorhynchus masou (Brevoort). Copeia 2 (1962) 400-407
3. Behnke, R.J., 1988. Phylogeny and classification of cutthroat trout. pp 1-7. In: Gresswell, R.E. (Ed.), Status and Management of Interior Stocks of Cutthroat Trout, p. 140.
4. Behnke R.J. Trout and Salmon of North America (2002), The Free Press, New York p. 352
5. Brown K.H., Drew R.E., Weber L.A., and Thorgaard G.H. Intraspecific variation in the rainbow trout mitochondrial DNA genome. Comp. Biochem. Physiol. D Genomics Proteomics 1 (2006) 219-226
6. Campbell M.R., Dillon J., and Powell M.S. Hybridization and introgression in a managed, native population of Yellowstone cutthroat trout: genetic detection and management implications. Trans. Am. Fish. Soc. 131 (2002) 364-375
7. Cavender T.M., and Miller R.R. Salmo australis, a new species of fossil salmonid from southwestern Mexico. Contrib. Mus. Paleontol. Univ. Mich. 26 (1982) 1-17
8. Crandall K.A., Bininda-Emonds O.R.P., Mace G.M., and Wayne R.K. Considering evolutionary processes in conservation biology: returning to the original meaning of evolutionary significant units. Trends Ecol. Evol. 15 (2000) 290-295
9. Crespi B., and Fulton M.J. Molecular systematics of Salmonidae: combined nuclear data yields a robust phylogeny. Mol. Phylogenet. Evol. 31 (2004) 658-679
10. Docker M.F., Dale A., and Heath D.D. Erosion of interspecific reproductive barriers resulting from hatchery supplementation of rainbow trout sympatric with cutthroat trout. Mol. Ecol. 12 (2003) 3515-3521
11. Drummond A.J., Ho S.Y.W., Phillips M.J., and Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4 (2006) e88
12. Drummond A.J., and Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7 (2007) 214
13. Gold J.R. Systematics of western North American trout (Salmo), with notes on the redband trout of Sheepheaven Creek, California. Can. J. Zool. 55 (1977) 1858-1873
14. Gyllensten U., and Wilson A.C. Mitochondrial DNA of salmonids: inter- and intraspecific variability detected with restriction enzymes. In: Ryman N., and Utter F. (Eds). Population Genetics and Fishery Management (1987), Univ. of Wash. Press, Seattle
15. Hedgecock D., Siri P., and Strong D.R. Conservation biology of endangered Pacific salmonids: introductory remarks. Conserv. Biol. 8 (1994) 863-894
16. Hendrickson D.A., Espinosa H., Findley L.T., Forbes W., Tomelleri J.R., Mayden R.L., Nielsen J.L., Jensen B., Campos G.R., Romero A.V., van der Heiden A., Camarena F., and Garcia de León F.J. Mexican native trouts: a review of their history and current systematic and conservation status. Rev. Fish. Biol. Fish. 12 (2002) 273-316
17. Hitt N.P., Frissell C.A., Muhlfeld C.C., and Allendorf F.W. Spread of hybridization between native westslope cutthroat trout, Oncorhynchus clarki lewisi, and nonnative rainbow trout, Oncorhynchus mykiss. Can. J. Fish. Aquat. Sci. 60 (2003) 1440-1451
18. Huelsenbeck J.P., and Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
19. Hurst C.D., Bartlett S.E., Davidson W.S., and Bruce I.J. The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar. Gene 239 (1999) 237-242
20. Kimmel P.G. Fishes of the Miocene-Pliocene deer butte formation, southeast Oregon. University of Michigan Museum of Paleontology Papers on Paleontology 14 (1975) 69-87
21. LaRivers I. A new trout from the Barstovian (Miocene) of western Nevada. Biological Society of Nevada Occasional Papers 3 (1964) 1-4
22. Leary R.F., Allendorf F.W., and Knudsen K.L. Major morphological effects of a regulatory gene: Pgm1-t in rainbow trout. Mol. Biol. Evol. 1 (1984) 183-194
23. Leary R.F., Allendorf F.W., Phelps S.R., and Knudsen K.L. Genetic divergence and identification of seven cutthroat trout subspecies and rainbow trout. Trans. Am. Fish. Soc. 116 (1987) 580-587
24. Loudenslager E.J., and Gall G.A.E. Geographic patterns of protein variation and subspeciation in cutthroat trout, Salmo clarki. Syst. Zool. 29 (1980) 27-42
25. Loudenslager E.J., and Thorgaard G.H. Karyotypic and evolutionary relationships of the Yellowstone (Salmo clarki bouvieri) and west-slope (SC. lewisi) cutthroat trout. J. Fish. Res. Board Can. 36 (1979) 630-635
26. Loudenslager E.J., Rinne J.N., Gall G.A.E., and David R.E. Biochemical genetic studies of native Arizona and New Mexico trout. Southwestern Nat. 31 (1986) 221-234
27. Metcalf J.L., Pritchard V.L., Silvesteri S.M., Jenkins J.B., Wood J.S., Cowley D.E., Evans R.P., Shiozawa D.K., and Martin A.P. Across the great divide: genetic forensics reveals misidentification of endangered cutthroat trout populations. Mol. Ecol. 16 (2007) 4445-4454
28. Miya M., and Nishida M. Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol. Phylogenet. Evol. 17 (2000) 437-455
29. Montgomery D.R. Coevolution of the Pacific salmon and Pacific Rim topography. Geology 28 (2000) 1107-1110
30. Neave F. The orgin and speciation of Oncorhynchus. Trans. Royal Soc. Can. 52 (1958) 25-39 (series 3,. section 3)
31. Nehlsen W., Williams J.E., and Lichatowich J.A. Pacific salmon at the crossroads: stocks at risk from California, Oregon, Idaho, and Washington. Fish 16 (1991) 4-21
32. Nielsen J.L., Fountain M.C., Favela J.C., Cobble K., and Jensen B.L. Oncorhynchus at the southern extent of their range: a study of mtDNA control-region sequence with special reference to an undescribed subspecies of O. Mykiss from Mexico. Environ. Biol. Fish. 51 (1998) 7-23
33. Oakley T.H., and Phillips R.B. Phylogeny of Salmoninae fish based on growth hormone introns: Atlantic (Salmo) and Pacific (Oncorhynchus) salmon are not sister taxa. Mol. Phylogenet. Evol. 11 (1999) 381-393
34. Oohara I., Sawano K., and Okazaki T. Mitochondrial DNA sequence analysis of the Masu salmon - phylogeny in the genus Oncorhynchus. Mol. Phylogenet. Evol. 7 (1997) 71-78
35. Osinov A.G., and Lebedev V.S. Genetic divergence and phylogeny of the Salmoninae based on allozyme data. J. Fish Biol. 57 (2000) 354-381
36. Phillips R.B., Matsuoka M.P., Konkol N.R., and McKay S. Molecular systematics and evolution of the growth hormone introns in the Salmoninae. Environ. Biol. Fish. 69 (2004) 433-440
37. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
38. Pritchard V.L., Jones K., and Cowley D.E. Estimation of introgression in cutthroat trout populations using microsatellites. Conserv. Genet. 8 (2007) 1311-1329
39. Ronquist, F., Huelsenbeck, J.P., van der Mark, P., 2005. MrBayes 3.1 Manual.
40. Rubidge E.M., and Taylor E.B. An analysis of spatial and environmental factors influencing hybridization between native westslope. Conserv. Genet. 6 (2005) 369-384
41. Smith G.R. Fishes of the Pliocene Glenns Ferry Formation, southwest Idaho. Papers on Paleontology, Univ. of Michigan 14 (1975) 1-68
42. Smith G.R., and Stearley R.F. The classification and scientific names of rainbow and cutthroat trouts. Fish 14 (1989) 4-10
43. Smith, G.R., Swirydczuk, K., Kimmel, P.G., Wilkinson, B.H., 1982. Fish biostratigraphy of late Miocene to Pleistocene sediments of the western Snake River plain, Idaho. In: Bonnichsen, B., Breckenridge, R.M. (Eds.), Cenozoic Geology of Idaho, Bull. Idaho. Bur. Mine Geol., vol. 26, Moscow.
44. Smith, G.R., Dowling, T.E., Gobalet, K.W., Lugaski, T., Shiozawa, D.K., Evans, R.P., 2002. Biogeography and timing of evolutionary events among Great Basin fishes. In: Hershler, R., Madsen, D.B., Currey, D.R. (Eds.), Great Basin Aquatic Systems History. Smithson. Contrib. Earth Sci., vol. 33, Washington.
45. Stearly R.F., and Smith G.R. Phylogeny of the Pacific trouts and salmons (Oncorhynchus) and genera of the family Salmonidae. Trans. Amer. Fish. Soc. 122 (1993) 1-33
46. Sunnucks P., Wilson A.C.C., Beheregaray L.B., Zenger K., French J., and Taylor A.C. SSCP is not so difficult: the application and utility of single-stranded conformational polymorphism in evolutionary biology and molecular ecology. Mol. Ecol. 9 (2000) 1699-1710
47. Swofford, D.L., 2001. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods) Version 4. Sinauer Associates, Sunderland, Massachusetts.
48. Taylor D.W., and Smith G.R. Pliocene molluscs and fishes from northeastern California and northwestern Nevada. Contrib. Mus. Paleo. Univ. Mich. 25 (1981) 339-413
49. 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. Nucleic Acids Res. 24 (1997) 4876-4882
50. Thorgaard G.H. Chromosomal differences among rainbow trout populations. Copeia 1983 (1983) 650-662
51. Utter F. Patterns of subspecific anthropogenic introgression in two salmonid genera. Rev. Fish. Biol. Fish. 10 (2000) 265-279
52. Utter F.M., and Allendorf F.W. Phylogenetic relationships among species of Oncorhynchus: a consensus view. Conserv. Biol. 8 (1994) 864-867
53. Waples R.S., Adams P.B., Bohnsack J., and Barbara L.T. A biological framework for evaluating whether a species is threatened or endangered in a significant portion of its range. Conserv. Biol. 21 (2007) 964-974
54. Wares J.P., Alo D., and Turner T.F. A genetic perspective on management and recovery of federally endangered trout (Oncorhynchus gilae) in the American southwest. Can. J. Fish. Aquat. Sci. 61 (2004) 1890-1899
55. Young W.P., Ostberg C.O., Keim P., and Thorgaard G.H. Genetic characterization of hybridization and introgression between anadromous rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki). Mol. Ecol. 10 (2001) 921-930
56. Zardoya R., Garrido-Pertierra A., and Bautista J.M. The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. J. Mol. Evol. 41 (1995) 942-951
57. Zuckerkandl E., and Pauling L. Evolutionary Divergence and Convergence in Proteins (1965), Academic Press, New York