Influences of habitat and hybridization on the genetic structure of redband trout in the upper Snake River Basin, Idaho

Transactions of the American Fisheries Society

Volumn 140, Issue 2, 2011, Pages 282-295

  Kozfkay, Christine C ^a   Campbell, Matthew R ^a   Meyer, Kevin A ^a   Schill, Daniel J ^a  

^a IDAHO DEPARTMENT OF FISH AND GAME   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONSERVATION GENETICS; DESERT; ENDANGERED SPECIES; FISHERY MANAGEMENT; GENE FLOW; GENETIC MARKER; GENETIC STRUCTURE; GENETIC VARIATION; HABITAT FRAGMENTATION; HABITAT MANAGEMENT; HATCHERY; HYBRIDIZATION; MARICULTURE; MONTANE FOREST; SALMONID FISHERY;

IDAHO; SNAKE BASIN; UNITED STATES;

ONCORHYNCHUS CLARKII; ONCORHYNCHUS MYKISS; ONCORHYNCHUS MYKISS GAIRDNERII; ONCORHYNCHUS MYKISS IRIDEUS; SALMONIDAE;

EID: 80855124955     PISSN: 00028487     EISSN: 15488659     Source Type: Journal    
DOI: 10.1080/00028487.2011.567837     Document Type: Article

References (82)

1. Avise, J. C. 1994. Molecular markers: natural history and evolution. Chapman and Hall, New York.
2. Banks, M. A., M. S. Blouin, B. A. Baldwin, V. K. Rashbrook, H. A. Fitzgerald, S. M. Blankenship, and D. Hedgecock. 1999. Isolation and inheritance of novel microsatellites in Chinook salmon (Oncorhynchus tshawytscha). Journal of Heredity 90:281-288.
3. Behnke, R. J. 1992. Native trout of western North America. American Fisheries Society, Monograph 6, Bethesda, Maryland.
4. Beitinger, T. L., W. A. Bennett, and R. W. McCauley. 2000. Temperature tolerances of North American freshwater fishes exposed to dynamic changes in temperature. Environmental Biology of Fishes 58:237-275.
5. Bennett, S. N., J. R. Olson, J. L. Kershner, and P. Corbett. 2010. Propagule pressure and stream characteristics influence introgression: cutthroat trout and rainbow trout in British Columbia. Ecological Applications 20:263-277.
6. Blankenship, S. M., M. R. Campbell, J. E. Hess, M. A. Hess, T. W. Kassler, C. C. Kozfkay, A. P. Matala, S. R. Narum, M. M. Paquin, M. P. Small, J. J. Stephenson, K. I. Warheit, and P. Moran. In press. Major lineages and metapopulations in Columbia River Oncorhynchus mykiss are structured by dynamic landscape features and environments. Transactions of the American Fisheries Society 140.
7. Boecklen, W. J., and D. J. Howard. 1997. Genetic analysis of hybrid zones: number of markers and power of resolution. Ecology (Washington, D.C.) 78:2611-2616.
8. Brunelli, J. P., G. H. Thorgaard, R. F. Leary, and J. L. Dunnigan. 2008. Singlenucleotide polymorphisms associated with allozyme differences between inland and coastal rainbow trout. Transactions of the American Fisheries Society 137:1292-1298.
9. Busby, P. J., T. C. Wainwright, G. J. Bryant, L. J. Lierheimer, and R. S. Waples. 1996. Status review of west coast steelhead fromWashington, Idaho, Oregon, and California. NOAA Technical Memorandum NMFS-NWFSC-27.
10. Cairney, M., J. B. Taggart, and B. Hoyheim. 2000. Characterization of microsatellite and minisatellite loci in Atlantic salmon (Salmo salar L.) and cross-species amplification in other salmonids. Molecular Ecology 9:2175-2178.
11. Cassinelli, J. D., and C. M. M. Moffitt. 2010. Comparison of growth and stress in resident redband trout held in laboratory simulations of montane and desert summer temperature cycles. Transactions of the American Fisheries Society 139:339-352.
12. Cavalli-Sforza, L. L., and A.W. F. Edwards. 1967. Phylogenetic analysis: models and estimation procedures. Evolution 32:550-570.
13. Cegelski, C. C., M. R. Campbell, K. A. Meyer, and M. S. Powell. 2006. Multiscale genetic structure of Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri in the upper Snake River basin, Idaho. Transactions of the American Fisheries Society 135:711-726.
14. Clemento, A. J., E. C. Anderson, D. Boughton, D. Girman, and J. C. Garza. 2009. Population genetic structure and ancestry of Oncorhynchus mykiss populations above and below dams in south-central California. Conservation Genetics 10:1321-1336.
15. Cordes, J. F., M. R. Stephens, M. A. Blumberg, and B. May. 2006. Identifying introgressive hybridization in native populations of California golden trout based on molecular markers. Transactions of the American Fisheries Society 125:110-128.
16. Crawford, N. G. 2010. SMOGD: software for the measurement of genetic diversity. Molecular Ecology Resources 10:556-557.
17. Currens, K. P., C. B. Schreck, and H. W. Li. 2009. Evolutionary ecology of redband trout. Transactions of the American Fisheries Society 138:797-817.
18. Deiner, K., J. C. Garza, R. Coey, and D. J. Girman. 2007. Population structure and genetic diversity of trout (Oncorhynchus mykiss) above and below natural and man-made barriers in the Russian River, California. Conservation Genetics 8:437-454.
19. Dunham, J., R. Schroeter, and B. Rieman. 2003. Influence of maximum water temperature on occurrence of Lahontan cutthroat trout within streams. North American Journal of Fisheries Management 23:1042-1049.
20. Eldridge, W. H., and K. A. Naish. 2007. Long-term effects of translocation and release numbers on fine-scale population structure among coho salmon (Oncorhynchus kisutch). Molecular Ecology 16:2407-2421.
21. Fausch, K. D., B. E. Rieman, J. B. Dunham, M. K. Young, and D. P. Peterson. 2009. Invasion versus isolation: trade-offs in managing native salmonids with barriers to upstream movement. Conservation Biology 23:859-870.
22. Fausch, K. D., Y. Taniguchi, S. Nakano, G. D. Grossman, and C. R. Townsend. 2001. Flood disturbance regimes influence rainbow trout invasion success among five holartic regions. Ecological Applications 11: 1438-1455.
23. Gamperl, A. K., K. J. Rodnick, H. A. Faust, E. C. Venn, and M. T. Bennett. 2002. Metabolism, swimming performance, and tissue biochemistry of high desert redband trout (Oncorhynchus mykiss ssp.): evidence for phenotypic differences in physiological function. Physiological and Biochemical Zoology 75:413-431.
24. Goudet, J. 1995. FSTAT (version 1.2): a computer program to calculate Fstatistics. Journal of Heredity 86:485-486.
25. Hansen, M.M., J. J. Fraser, K. Meier, and K.-L. D. Mensberg. 2009. Sixty years of anthropogenic pressure: a spatio-temperal genetic analysis of brown trout populations subject to stocking and population declines. Molecular Ecology 18:2549-2562.
26. Hansen, M. M., E. E. Nielsen, D. Bekkevold, and K.-L. D. Mensberg. 2001. Admixture analysis and stocking impact assessment in brown trout (Salmo trutta), estimated with incomplete baseline data. Canadian Journal of Fisheries and Aquatic Sciences 58:1853-1860.
27. Heath, D. D., S. Pollard, and C. Herbinger. 2001. Genetic structure and relationships among steelhead trout (Oncorhynchus mykiss) populations in British Columbia. Heredity 86:618-627.
28. Hindar, K., N. Ryman, and F. M. Utter. 1991. Genetic effects of cultured fish on natural populations. Canadian Journal of Fisheries and Aquatic Sciences 48:945-957.
29. Jakobsson, M., and N. A. Rosenberg. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801-1806.
30. Jensen, L. F., M. M. Hansen, G. Pertoldi, G. Holdensgaard, K-L. D. Mensberg, and V. Loeschcke. 2008. Local adaptation in brown trout early life-history traits: implications for climate change adaptability. Proceedings of the Royal Society B 275:2859-2868.
31. Jost, L. 2008. GST and its relatives do not measure differentiation. Molecular Ecology 17:4015-4026.
32. Jug, T., P. Berrebi, and A. Snoj. 2005. Distribution of non-native trout in Slovenia and their introgression with native trout populations as observed through microsatellite DNA analysis. Biological Conservation 123:381-388.
33. Koizumi, I., S. Yamamato, and K. Maekawa. 2006. Decomposed pairwise regression analysis of genetic and geographic distances reveals a metapopulation structure of stream-dwelling Dolly Varden charr. Molecular Ecology 15:3175-3189.
34. Kozfkay, J. R., J. C. Dillon, and D. J. Schill. 2006. Routine use of sterile fish in salmonid sport fisheries: are we there yet? Fisheries 31:392-401.
35. Langella, O. 2001. Populations 1.2.24: population genetic structure (individuals or populations distances, phylogenetic trees). Available: pge. cnrs. gif. fr/bioinfo/populations. (March 2005).
36. Lee, R. M., and J. N. Rinne. 1980. Critical thermal maxima of five trout species in the southwestern United States. Transactions of the American Fisheries Society 109:632-635.
37. Li, H. W., G. A. Lamberti, T. N. Persons, C. K. Tait, J. L. Li, and J. C. Buckhouse. 1994. Cumulative effects of riparian disturbances along high desert trout streams of the John Day basin, Oregon. Transactions of the American Fisheries Society 123:627-640.
38. McConnell, S. K., P. O'Reilly, L. Hamilton, J. M. Wright, and P. Bentzen. 1995. Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations. Canadian Journal of Fisheries and Aquatic Sciences 52:1863-1872.
39. Meyer, K. A., J. A. Lamansky, and D. J. Schill. 2010. Biotic and abiotic factors related to redband trout occurrence and abundance in desert and montane streams. Western North American Naturalist 1:77-91.
40. Narum, S. R., S. Boe, P. Moran, and M. Powell. 2006. Small-scale genetic structure and variation in steelhead of the Grande Ronde River, Oregon, USA. Transactions of the American Fisheries Society 135:979-986.
41. Narum, S. R., N. R. Campbell, C. C. Kozfkay, and K. A. Meyer. 2010. Adaptation of redband trout in desert andmontane environments. Molecular Ecology 19:4622-4637.
42. Narum, S. R., J. S. Zendt, D. Graves, and W. R. Sharp. 2008. Influence of landscape on resident and anadromous life history types of Oncorhynchus mykiss. Canadian Journal of Fisheries and Aquatic Sciences 65:1013-1023.
43. Neraas, L. P., and P. Spruell. 2001. Fragmentation of riverine system: the genetic effects of dams on bull trout (Salvelinus confluentus) in the Clark Fork River system. Molecular Ecology 10:1153-1164.
44. Neville, H., J. Dunham, A. Rosenberger, J. Umek, and B. Nelson. 2009. Influences of wildfire, habitat size, and connectivity on trout in headwater streams revealed by patterns of genetic diversity. Transactions of the American Fisheries Society 138:1314-1327.
45. Neville, H., J. B. Dunham, and M. Peacock. 2006. Assessing connectivity in salmonid fishes with DNA microsatellite markers. Pages 318-342 in K. R. Crooks andM. Sanjayan, editors. Connectivity conservation. Cambridge University Press, Cambridge, UK.
46. Nielsen, E. E., J. Hemmer-Hanssen, P. F. Larsen, and D. Bekkevold. 2009. Population genomics of marine fishes: identifying adaptive variation in space and time. Molecular Ecology 18:3128-3150.
47. Nielsen, J. L., A. Byrne, S. L. Graziano, and C. C. Kozfkay. 2009. Steelhead genetic diversity at multiple spatial scales in a managed basin: Snake River, Idaho. Transactions of the American Fisheries Society 29:680-701.
48. Nielsen, J. L., C. Carpanzano, M. C. Fountain, and C. A. Gan. 1997. Mitochondrial DNA and nuclear microsatellite diversity in hatchery and wild Oncorhynchus mykiss from freshwater habitats in southern California. Transactions of the American Fisheries Society 126:397-417.
49. O'Connell, M., R. G. Danzmann, J.-M. Cornuet, J. M. Wright, and M. M. Ferguson. 1997. Differentiation of rainbow trout (Oncorhynchus mykiss) populations in Lake Ontario and the evaluation of the stepwise mutation and infinite alleles models using microsatellite variability. Canadian Journal of Fisheries and Aquatic Sciences 54:1391-1399.
50. Olsen, J. B., P. Bentzen, and J. E. Seeb. 1998. Characterization of seven microsatellite loci derived from pink salmon. Molecular Ecology 7:1087-1089.
51. Orr, E. L., andW. N. Orr. 1996. Geology of the PacificNorthwest. McGraw-Hill, New York.
52. Ostberg, C. O., and R. J. Rodriguez. 2002. Novel microsatellite markers differentiate Oncorhynchus mykiss (rainbow trout and steelhead) and the O. clarki (cutthroat trout) subspecies. Molecular Ecology Notes 2:197-202.
53. Ostberg, C. O., and R. J. Rodriguez. 2004. Bi-parentally inherited speciesspecific markers identify hybridization between rainbow trout and cutthroat trout subspecies. Molecular Ecology Notes: 4:26-29.
54. Page, R. D. M. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12:357-358.
55. Paragamian, V. L., M. S. Powell, and J. C. Faler. 1999. MitochondrialDNAanalysis of burbot stocks in the Kootenai River Basin of British Columbia, Montana, and Idaho. Transactions of theAmerican Fisheries Society 128:868-874.
56. Peterson, D. P., B. E. Rieman, J. B. Dunham, K. D. Fausch, and M. K. Young. 2008. Analysis of trade-offs between the threat of invasion by nonnative brook trout (Salvelinus fontinalis) and intentional isolation for native westslope cutthroat trout (Oncorhynchus clarkii lewisi). Canadian Journal of Fisheries and Aquatic Sciences 65:557-573.
57. Pritchard, J. K., M. Stephens, and P. Donnely. 2000. Inferences of population structure using multilocus genotype data. Genetics 155:945-959.
58. Pritchard, V. L., J. L. Metcalf, K. Jones, A. P. Martin, and D. E. Cowly. 2009. Population structure and genetic management of Rio Grande cutthroat trout (Oncorhynchus clarkii virginalis). Conservation Genetics 10:1209-1221.
59. Raymond, M., and F. Rousset. 1995. GENEPOP, version 1.2: a population genetics software for exact tests and ecumenicism. Journal ofHeredity 86:248-249.
60. Rhew, R. 2007. Redband trout and the endangered species act. Pages 123-126 in R. K. Schroeder and J. D. Hall, editors. Redband trout: resilience and challenge in a changing landscape. American Fisheries Society, Oregon Chapter, Corvallis.
61. Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223-225.
62. Rodnick, K. J., A. K. Gamperl, K. R. Lizars, M. T. Bennett, R. N. Rausch, and E. R. Keeley. 2004. Thermal tolerance and metabolic physiology among redband trout populations in southeastern Oregon. Journal of Fish Biology 64:310-335.
63. Sanz, N., R. M. Araguas, R. Fernandez, M. Vera, and J.-L. Garcia-Marin. 2009. Efficiency of markers and methods for detecting hybrids and introgression in stocked populations. Conservation Genetics 10:225-236.
64. Schneider, S., D. Roessli, and L. Excoffier. 2000. Arlequin version 2.0: a software for population genetic data analysis. University of Geneva, Geneva, Switzerland.
65. Schrank, A. J., F. J. Rahel, and H. C. Johnstone. 2003. Evaluating laboratoryderived thermal criteria in the field: an example involvingBonneville cutthroat trout. Transactions of the American Fisheries Society 132:100-109.
66. Scribner, K. T., J. R. Gust, and R. L. Fields. 1996. Isolation and characterization of novel salmon microsatellite loci: cross-species amplification. Canadian Journal of Fisheries and Aquatic Sciences 53:833-841.
67. Simmons, R. E., P. Lavretsky, and B. May. 2009. Introgressive hybridization of redband trout in the upper McCloud River watershed. Transactions of the American Fisheries Society 139:201-213.
68. Small, M. P., J. G. McLellan, J. Loxterman, and J. Von Bargen. 2007. Finescale population structure of rainbow trout in the Spokane River drainage in relation to hatchery stocking and barriers. Transactions of the American Fisheries Society 136:301-317.
69. Stephens, M. R. 2007. Systematics, genetics and conservation of golden trout. Doctoral dissertation. University of California, Davis.
70. Stephenson, J. J., M. R. Campbell, J. Hess, C. Kozfkay, and A. P. Matala. 2009. A centralized model for creating, shared standardized microsatellite data that simplifies inter-laboratory collaboration. Conservation Genetics 10:1145-1149.
71. Susnik, S., P. Berrebi, P. Dovc, M. M. Hansen, and A. Snoj. 2004. Genetic introgression between wild and stocked salmonids and the prospects for using molecular markers in population rehabilitation: the case of the Adriatic grayling (Thymallus thymallus L. 1785). Heredity 93:273-282.
72. USFWS (U.S. Fish and Wildlife Service). 1997. Endangered and threatened species: listing of several evolutionary significant units (ESUs) ofWest Coast steelhead. Federal Register 62:159(18 August 1997):43937-43954.
73. Vaha, J. P., and C. R. Primmer. 2006. Efficiency of model-based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci. Molecular Ecology 15:63-72.
74. Waples, R. S., G. R. Pess, and T. Beechie. 2008. Evolutionary history of Pacific salmon in dynamic environments. Ecological Applications 1:189-206.
75. Weber, E. D., and K. D. Fausch. 2003. Interactions between wild and hatchery salmonids in streams: differences in biology and evidence for competition. Canadian Journal of Fisheries and Aquatic Sciences 60:1018-1036.
76. Wenburg, J. K., P. Bentzen, and C. J. Foote. 1998. Microsatellite analysis of genetic population structure in an endangered salmonid: the coastal cutthroat trout (Oncorhynchus clarki clarki). Molecular Ecology 7:733-749.
77. Williams, R. N., R. F. Leary, and K. P. Currens. 1997. Localized genetic effects of a long-term hatchery stocking program on resident rainbow trout in the Metolius River, Oregon. North American Journal of Fisheries Management 17:1079-1093.
78. Wishard, L. N., J. E. Seeb, F. M. Utter, and D. Stefan. 1984. A genetic investigation of suspected redband trout populations. Copeia 1984:120-132.
79. Wofford, J. E. B., R. E. Gresswell, andM. A. Banks. 2005. Influence of barriers to movement on within-watershed genetic variation of coastal cutthroat trout. Ecological Applications 15:628-637.
80. Zoellick, B. W. 1999. Stream temperatures and the elevational distribution of redband trout in southwestern Idaho. Great Basin Naturalist 59: 136-143.
81. Zoellick, B.W., D. B. Allen, and B. J. Flatter. 2005. A long-term comparison of redband trout distribution, density, and size structure in southwestern Idaho. North American Journal of Fisheries Management 25:1179-1190.
82. Zoellick, B. W., and B. S. Cade. 2006. Evaluating redband trout habitat in sagebrush desert basins in southwestern Idaho. North American Journal of Fisheries Management 26:268-281.