Polyphyly of the pikeminnows (teleostei: Cyprinidae) inferred using mitochondrial dna sequences

Transactions of the American Fisheries Society

Volumn 139, Issue 1, 2010, Pages 303-315

  Houston, Derek D ^a   Ogden, T Heath ^b   Whiting, Michael F ^c   Shiozawa, Dennis K ^c  

^a UNIVERSITY OF NEVADA   (United States)

^b Nucl Eng Idaho State University   (United States)

^c BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77952558086     PISSN: 00028487     EISSN: 15488659     Source Type: Journal    
DOI: 10.1577/T09-075.1     Document Type: Article

References (79)

1. Arbogast, B. S., S. V. Edwards, J. Wakeley, P. Beerli, and J. B. Slowinski. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annual Review of Ecology and Systematics 33:707-740.
2. Avise, J. C., and F. J. Ayala. 1976. Genetic differentiation in speciose versus depauperate phylads: evidence from the California minnows. Evolution 30:46-58.
3. Baskin, J. A. 1979. Small mammals of the Hemphillian-age White Cone local fauna, northeastern Arizona. Journal of Paleontology 53:695-708.
4. Bell, M. A. 1976. Evolution of phenotypic diversity in Gasterosteus aculeatus superspecies on the Pacific Coast of North America. Systematic Zoologica 25:211-227.
5. Bell, M. A., and G. Orti. 1994. Pelvic reduction in threespine stickleback from Cook Inlet lakes: geographical distribution and intrapopulation variation. Copeia 1994:314-325.
6. Beranek, L. P., P. K. Link, and C. M. Fanning. 2006. Miocene to Holocene landscape evolution of the western Snake River Plain region, Idaho: using the SHRIMP detrital zircon provenance record to track eastward migration of the Yellowstone hotspot. Geological Society of America Bulletin 118:1027-1050.
7. Bernatchez, L., and J. J. Dodson. 1990. Allopatric origin of sympatric populations of lake whitefish (Coregonus clupeaformis) as revealed by mitochondrial-DNA restriction analysis. Evolution 44:1263-1271.
8. Briolay, J., N. Galtier, R. M. Brito, and Y. Bouvet. 1998. Molecular phylogeny of Cyprinidae inferred from cytochrome b DNA sequences. Molecular Phylogenetics and Evolution 9:100-108.
9. Carney, D. A., and L. M. Page. 1990. Meristic characteristics and zoogeography of the Ptychocheilus (Teleostei: Cyprinidae). Copeia 1990:171-181.
10. Coburn, M. M., and T. M. Cavender. 1992. Interrelationships of North American cyprinid fishes. Pages 328-373 in R. L. Mayden, editor. Systematics, historical ecology, and North American freshwater fishes. Stanford University Press, Palo Alto, California.
11. Colosimo, P. F., K. E. Hosemann, S. Balabhadra, G. Villarreal Jr., M. Dickson, J. Grimwood, J. Schmutz, R. M. Myers, D. Schluter, and D. M. Kingsley. 2005. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307:1928-1933.
12. Dallegge, T. A., M. H. Ort, W. C. McIntosh, and M. E. Perkins. 2001. Age and depositional basin morphology of the Bidahochi formation and implications for the ancestral Upper Colorado River. Pages 47-51 in R. A. Young and E. E. Spamer, editors. Colorado River: origin and evolution; proceedings of a symposium held at Grand Canyon Nation Park in June, 2000. Grand Canyon Association, Grand Canyon, Arizona.
13. Derome, N., P. Duchesne, and L. Bernatchez. 2006. Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchell) ecotypes. Molecular Ecology 15:1239-1249.
14. Diller, J. S. 1915. Guidebook of the western United States Part D: the Shasta Route and coast line. U.S. Geological Survey, Bulletin 546.
15. Dowling, T. E., and B. D. DeMarais. 1993. Evolutionary significance of introgressive hybridization in cyprinid fishes. Nature (London) 362:444-446.
16. Dowling, T. E., and G. J. P. Naylor. 1997. Evolutionary relationships of minnows in the genus Luxilus (Teleostei: Cyprinidae) as determined from cytochrome b sequences. Copeia 1997:758-765.
17. Dowling, T. E., C. A. Tibbets, W. L. Minckley, and G. R. Smith. 2002. Evolutionary relationships of the plagopter-ins (Teleostei: Cyprinidae) from cytochrome b sequences. Copeia 2002:665-678.
18. Drummond, A. J., S. Y. W. Ho, M. J. Phillips, and A. Rambaut. 2006. Relaxed phylogenetics and dating with confidence. PLOS Biology 4:e88.
19. Drummond, A., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7:214.
20. Estabrook, G. F., G. R. Smith, and T. E. Dowling. 2007. Body mass and temperature influence rates of mitochondrial DNA evolution in North American cyprinid fish. Evolution 61:176-1187.
21. Faulds, J. E., M. A. Wallace, L. A. Gonzalez, and M. T. Heizler. 2001. Depositional environment and paleogeo-graphic implications of the Late Miocene Hualapai limestone, northwestern Arizona and southern Nevada. Pages 81-87 in R. A. Young and E. E. Spamer, editors. Colorado River: origin and evolution; proceedings of a symposium held at Grand Canyon Nation Park in June, 2000. Grand Canyon Association, Grand Canyon, Arizona.
22. Felsenstein, J. 1985. Confidence limits on phylogenies—an approach using the bootstrap. Evolution 39:783-791.
23. Fenderson, O. C. 1964. Evidence of subpopulations of lake whitefish, Coregonus clupeaformis, involving a dwarfed form. Transactions of the American Fisheries Society 93:77-94.
24. Gard, M. 1997. Threatened fishes of the world: Ptychocheilus lucius Girard, 1856 (Cyprinidae). Environmental Biology of Fishes 49:292.
25. Gold, J. R., and Y. Li. 1994. Chromosomal NOR karyotypes and genome size variation among squawfishes of the genus Ptychocheilus (Teleostei: Cyprinidae). Copeia 1994:60-65.
26. Hershler, R., and H. Liu. 2004. A molecular phylogeny of aquatic gastropods provides a new perspective on biogeographic history of the Snake River region. Molecular Phylogenetics and Evolution 32:927-937.
27. Hershler, R., and D. W. Sada. 2002. Biogeography of Great Basin aquatic snails of the genus Pyrgulopsis. Pages 255-276 in R. Hershler, D. B. Madsen, and D. R. Currey, editors. Great Basin aquatic systems history. Smithsonian Institution Press, Smithsonian Contributions to the Earth Sciences 33, Washington, D.C.
28. Horton, T. W., D. J. Sjostrom, M. J. Abruzzese, M. A. Poage, J. R. Waldbauer, M. Hren, J. Wooden, and C. P. Chamberlain. 2004. Spatial and temporal variation of Cenozoic surface elevation in the Great Basin and Sierra Nevada. American Journal of Science 304:862-888.
29. Howard, K. A., and R. G. Bohannon. 2001. Lower Colorado River: upper Cenozoic deposits, incision, and evolution. Pages 101-105 in R. A. Young and E. E. Spamer, editors. Colorado River: origin and evolution; proceedings of a symposium held at Grand Canyon Nation Park in June, 2000. Grand Canyon Association, Grand Canyon, Arizona.
30. Hubbs, C. L., and R. R. Miller. 1948. The zoological evidence: correlation between fish distributions and hydrographic history in the desert basins of western United States. Pages 18-144 in The Great Basin, with emphasis on glacial and postglacial times. Bulletin of the University of Utah 38(20), Biological Series Volume X, Number 7, University of Utah, Salt Lake City.
31. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogeny. Biometrics 17:754-755.
32. Hunt, C. B. 1956. Cenozoic geology of the Colorado Plateau. U.S. Geological Survey, Professional Papers 279.
33. Jobb, G. 2005. TREEFINDER version of October 2005. Munich, Germany. Available: www.treefinder.de. (April 2009).
34. Johnson, J. B. 2002. Evolution after the flood: phylogeog-raphy of the desert fish Utah chub (Gila atraria). Evolution 56:948-960.
35. Johnson, J. B., T. E. Dowling, and M. C. Belk. 2004. Neglected taxonomy of rare desert fishes: congruent evidence for two species of leatherside chub. Systematic Biology 53:841-855.
36. Kelly, T. S. 1994. Two Pliocene (Blancan) vertebrate faunas from Douglas County, Nevada. PaleoBios 16:1-23.
37. Kimmel, P. G. 1975. Fishes of the Miocene-Pliocene Deer Butte Formation, southeast Oregon. University of Michigan Papers on Paleontology 14:69-87.
38. Kocher, T. D., W. K. Thomas, A. Meyer, S. V. Edwards, S. Paabo, F. X. Villablanca, and A. C. Wilson. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Science 86:6196-6200.
39. Lee, D. S., C. R. Gilbert, C. H. Hocutt, R. E. Jenkins, D. E. McAllister, and J. R. Stauffer Jr. 1980. Atlas of North American freshwater fishes. North Carolina Biological Survey, Publication 1980-12, Raleigh.
40. Link, P. K., H. G. McDonald, C. M. Fanning, and A. E. Godfrey. 2002. Detrital zircon evidence for Pleistocene drainage reversal at Hagerman Fossil Beds National Monument, central Snake River plain, Idaho. Idaho Geological Survey Bulletin 30:105-119.
41. Lu, G. Q., and L. Bernatchez. 1999. Correlated trophic specialization and genetic divergence in sympatric lake whitefish ecotypes (Coregonus clupeaformis): support for the ecological speciation hypothesis. Evolution 53:1491-1505.
42. Mayden, R. L. 1989. Phylogenetic studies of North American minnows, with emphasis on the genus Cyprinella (Teleostei: Cypriniformes). Miscellaneous Publications of the University of Kansas Museum of Natural History 80:1-189.
43. Mayden, R. L., W. J. Rainboth, and D. G. Buth. 1991. Phylogenetic systematics of the cyprinid genera Mylo-pharodon and Ptychocheilus: comparative morphometry. Copeia 1991:819-834.
44. McKell, M. D. 2003. Phylogeography of speckled dace, Rhinichthys osculus (Teleostei: Cyprinidae), in the intermountain west, USA. Master’s thesis. Brigham Young University, Provo, Utah.
45. McPhail, J. D., and C. C. Lindsey. 1970. Freshwater fishes of northwestern Canada and Alaska. Fisheries Research Board of Canada Bulletin 173:1-381.
46. Minckley, W. L., D. A. Hendrickson, and C. E. Bond. 1986. Geography of western North American freshwater fishes: description and relationships to intra-continental tecto-nism. Pages 519-614 in C. H. Hocutt and E. O. Wiley, editors. The zoogeography of North American freshwater fishes. Wiley, New York.
47. Mock, K. E., R. P. Evans, M. Crawford, B. L. Cardell, S. U. Janecke, and M. P. Miller. 2006. Rangewide molecular structuring in the Utah sucker (Catostomus ardens). Molecular Ecology 15:2223-2238.
48. Nylander, J. A. A. 2004. MrModelTest version 2 (program distributed by the author). Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
49. Pederson, J. L. 2001. Searching for the pre-Grand Canyon Colorado River: the Muddy Creek Formation north of Lake Mead. Pages 71-75 in R. A. Young and E. E. Spamer, editors. Colorado River: origin and evolution; proceedings of a symposium held at Grand Canyon Nation Park in June, 2000. Grand Canyon Association, Grand Canyon, Arizona.
50. Pederson, J. L. 2008. The mystery of the pre-Grand Canyon Colorado River—results from the Muddy Creek Formation. Geological Society of America Today 18:4-10.
51. Pigeon, D., A. Chouinard, and L. Bernatchez. 1997. Multiple modes of speciation involved in the parallel evolution of sympatric morphotypes of lake whitefish (Coregonus clupeaformis, Salmonidae). Evolution 51:196-205.
52. Posada, D. 2008. jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25:1253-1256.
53. Posada, D., and K. A. Crandall. 1998. ModelTest: testing the model of DNA substitution. Bioinformatics 14:817-818.
54. Powell, J. L. 2005. Grand Canyon: solving earth’s grandest puzzle. Pi Press, New York.
55. Repenning, C. A., T. R. Weasma, and G. R. Scott. 1995. The early Pleistocene (latest Blancan-earliest Irvingtonian) Froman Ferry fauna and history of the Glenns Ferry Formation, southwestern Idaho. U.S. Geological Survey Bulletin 2105:1-86.
56. Schluter, D., E. A. Clifford, M. Nemethy, and J. S. McKinnon. 2004. Parallel evolution and inheritance of quantitative traits. American Naturalist 163:809-822.
57. Schonhuth, S., I. Doadrio, O. Dominguez-Dominguez, D. M. Hillis, and R. L. Mayden. 2008. Molecular evolution of southern North American Cyprinidae (Actinopterygii), with the description of the new genus Tampichthys from central Mexico. Molecular Phylogenetics and Evolution 47:729-756.
58. Simons, A. M., P. B. Berendzen, and R. L. Mayden. 2003. Molecular systematics of North American phoxinin genera (Actinopterygii: Cyprinidae) inferred from mitochondrial 12S and 16S ribosomal RNA sequences. Zoological Journal of the Linnean Society 139:63-80.
59. Simons, A. M., and R. L. Mayden. 1998. Phylogenetic relationships of the western North American phoxinins (Actinopterygii: Cyprinidae) as inferred from mitochondrial 12S and 16S ribosomal RNA sequences. Molecular Phylogenetics and Evolution 9:308-329.
60. Smith, G. R. 1966. Distribution and evolution of the North American catostomid fishes of the subgenus Pantosteus, genus Catostomus. Miscellaneous Publications Museum of Zoology University of Michigan 129.
61. Smith, G. R. 1975. Fishes of the Pliocene Glenns Ferry Formation, southwest Idaho. University of Michigan Papers on Paleontology 14:1-68.
62. Smith, G. R. 1978. Biogeography of intermountain fishes. Great Basin Naturalist Memoirs 2:17-42.
63. Smith, G. R. 1981. Late Cenozoic freshwater fishes of North America. Annual Review of Ecological Systems 12:163-193.
64. Smith, G. R., and J. Cossel. 2002. Fishes from the late Miocene Poison Creek and Chalk Hills formations, Owyhee County, Idaho. Pages 23-35 in W. A. Akersten, M. E. Thompson, D. J. Meldrum, R. A. Rapp, and H. G. McDonald, editors. And whereas… papers on the vertebrate paleontology of Idaho honoring John A. White, Volume 2. Idaho Museum of Natural History, Occasional Paper 37, Pocatello.
65. Smith, G. R., T. E. Dowling, K. W. Gobalet, T. Lugaski, D. K. Shiozawa, and R. P. Evans. 2002. Biogeography and timing of evolutionary events among Great Basin fishes. Pages 175-234 in R. Hershler, D. B. Madsen, and D. R. Currey, editors. Great Basin aquatic systems history. Smithsonian Institution Press, Smithsonian Contributions to the Earth Sciences 33, Washington, D.C.
66. Smith, G. R., N. Morgan, and E. Gustafson. 2000. Fishes of the Mio-Pliocene Ringold Formation, Washington: Pliocene capture of the Snake River by the Columbia River. University of Michigan Papers on Paleontology 32:1-47.
67. Smith, G. R., K. Swirydczuk, K. Kimmel, and B. H. Wilkinson. 1982. Fish biostratigraphy of late Miocene to Pleistocene sediments of the western Snake River Plain, Idaho. Pages 519-541 in B. Bonnichson and R. M. Breckenridge, editors. Cenozoic geology of Idaho. Idaho Bureau of Mines and Geology, Bulletin 26, Moscow.
68. Sonder, L. J., and C. H. Jones. 1999. Western United States extension: how the west was widened. Annual Review of Earth Planetary Science 27:417-462.
69. Spencer, J. E., G. R. Smith, and T. E. Dowling. 2008. Middle to late Cenozoic geology, hydrography, and fish evolution in the American southwest. Pages 279-299 in M. C. Reheis, R. Hershler, and D. M. Miller, editors. Late Cenozoic drainage history of the Southwestern Great Basin and Lower Colorado River region: geologic and biotic perspectives. Geological Society of America Special Paper 439.
70. Swofford, D. L. 2002. PAUP* (Phylogenetic Analysis Using Parsimony *and other methods). Version 4.0b10. Sina-uer, Sunderland, Massachusetts.
71. Taylor, D. W. 1983. Late tertiary mollusks from the lower Colorado River valley. Contributions from the Museum of Paleontology University of Michigan 26:289-298.
72. Taylor, D. W. 1985. Evolution of freshwater drainages and mollusks in western North America. Pages 265-322 in C. J. Smiley, editor. Late Cenozoic history of the Pacific Northwest. American Association for the Advancement of Science, San Francisco.
73. Taylor, D. W., and G. R. Smith. 1981. Pliocene mollusks and fishes from northeastern California and northwestern Nevada. Contributions from the Museum of Paleontology University of Michigan 25:339-413.
74. Uyeno, T. 1961a. Osteology and phylogeny of the American cyprinid fishes allied to the genus Gila. Doctoral dissertation. University of Michigan, Ann Arbor.
75. Uyeno, T. 1961b. Late Cenozoic cyprinid fishes from Idaho with notes on other fossil minnows in North America. Papers of the Michigan Academy of Science Arts and Letters 46:329-344.
76. Uyeno, T., and R. R. Miller. 1965. Middle Pliocene cyprinid fishes from the Bidahochi Formation, Arizona. Copeia 1965:28-41.
77. Van Den Bussche, R. A., and S. R. Hoofer. 2004. Phylogenetic relationships among recent chiropteran families and the importance of choosing appropriate out-group taxa. Journal of Mammalogy 85:321-330.
78. Wallace, A. R., M. E. Perkins, and R. J. Fleck. 2008. Late Cenozoic paleogeographic evolution of northeastern Nevada: evidence from the sedimentary basins. Geosphere 4:36-74.
79. Wheeler, H. E., and E. F. Cook. 1954. Structural and stratigraphic significance of the Snake River capture, Idaho-Oregon. Journal of Geology 62:425-50.