Development and evaluation of 200 novel SNP assays for population genetic studies of westslope cutthroat trout and genetic identification of related taxa

Molecular Ecology Resources

Volumn 12, Issue 5, 2012, Pages 942-949

  Campbell, N R ^a   Amish, S J ^b   Pritchard, V L ^c   Mckelvey, K S ^d   Young, M K ^d   Schwartz, M K ^d   Garza, J C ^c   Luikart, G ^b,e   Narum, S R ^a  

^a Columbia River Inter Tribal Fish Commission ^*  (United States)

^b UNIVERSITY OF MONTANA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d USDA Forest Service Forestry Science Lab   (United States)

^e UNIVERSITY OF MONTANA   (United States)

Author keywords

Admixture; Hybridization; KASPar; Oncorhynchus clarki; Population genomics; Rainbow trout; SNP; Taqman; Westslope cutthroat trout

Indexed keywords

ANIMAL; ARTICLE; CLASSIFICATION; EVALUATION; GENETICS; GENOTYPE; METHODOLOGY; MOLECULAR TYPING; ONCORHYNCHUS; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES;

ANIMALS; GENETICS, POPULATION; GENOTYPE; MOLECULAR TYPING; ONCORHYNCHUS; POLYMORPHISM, SINGLE NUCLEOTIDE; UNITED STATES;

ONCORHYNCHUS; ONCORHYNCHUS CLARKII; ONCORHYNCHUS MYKISS; SALMONIDAE;

EID: 84865284083     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2012.03161.x     Document Type: Article

References (36)

1. Abadía-Cardoso A, Clemento AC, Garza JC (2011) Discovery and characterization of single nucleotide polymorphisms in steelhead/rainbow trout, Oncorhynchus mykiss. Molecular Ecology Resources, 11(Suppl. 1), 31-49.
2. Allendorf FW, Leary RF (1988) Conservation and distribution of genetic variation in a polytypic species, the cutthroat trout. Conservation Biology, 2, 170-184.
3. Behnke RJ (1992) Native Trout of Western North America. American Fisheries Society, Bethesda, MD.
4. Behnke RJ (2002) Trout and Salmon of North America. The Free Press, New York, NY.
5. Belkhir K, Borsa P, Chikhi L, Raufaste M, Bonhomme F (2004) GENETIX 4.05, logiciel sous WindowsTM pour la Génétique des Populations. Montpellier, France, Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II.
6. Brunelli JP, Thorgaard GH (2008) Single-Nucleotide polymorphisms associated with allozyme differences between inland and coastal rainbow trout. Transactions of the American Fisheries Society, 137, 1292-1298.
7. Campbell NR, Narum SR (2011) Development of 54 novel single-nucleotide polymorphism (SNP) assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River. Molecular Ecology Resources, 11(Suppl. 1), 20-30.
8. Castaño-Sanchez C, Smith TPL, Wiedmann RT et al. (2009) Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics, 10, 559-567.
9. COSEWIC (2006) COSEWIC Assessment and Update Status Report on the Westslope Cutthroat trout Oncorhynchus Clarkii lewisi (British Columbia population and Alberta population) in Canada. Committee on the Status of Endangered Wildlife in Canada, Ottawa.
10. Drinan DP, Kalinowski ST, Vu NV, Shepard BB, Muhlfeld CC, Campbell MR (2011) Genetic variation in westslope cutthroat trout Oncorhynchus clarkii lewisi: implications for conservation. Conservation Genetics, 12, 1513-1523.
11. Fausch KD, Rieman BE, Dunham JB, Young MK, Peterson DP (2009) Invasion versus isolation: trade-offs in managing native salmonids with barriers to upstream movement. Conservation Biology, 23, 859-870.
12. Finger AJ, Stephens MR, Clipperton NW, May B (2009) Six diagnostic single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trouts. Molecular Ecology Resources, 9, 759-763.
13. Griffith JS (1988) Review of competition between cutthroat trout and other salmonids. In: Status and Management of Cutthroat Trout (ed. Gresswell RE), pp. 134-140. American Fisheries Society Symposium 4, Bethesda, MD.
14. Harwood AS, Phillips RB (2011) A suite of twelve single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trout. Molecular Ecology Resources, 11, 382-385.
15. Hitt NP, Frissell CA, Muhlfeld CC, Allendorf FW (2003) Spread of hybridization between native westslope cutthroat trout, Oncorhynchus clarki lewisi, and nonnative rainbow trout, Oncorhynchus mykiss. Canadian Journal of Fisheries and Aquatic Science, 60, 1440-1451.
16. Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources, 11(Suppl. 1), 117-122.
17. Kalinowski ST, Novak BJ, Drinan DP, Jennings RDeM, Vu NV (2010) Diagnostic single nucleotide polymorphisms for identifying westslope cutthroat trout (Onchorhynchus clarki lewisi), Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri), and rainbow trout (Oncorhynchus mykiss). Molecular Ecology Resources, 11, 389-393.
18. Leary RF, Allendorf FW, Knudsen KL (1985) Developmental instability and high meristic counts in interspecific hybrids of salmonid fishes. Evolution, 39, 1318-1326.
19. May BE (2009) Westslope Cutthroat Trout Status Update Summary. Wild Trout Enterprises LLC, Bozeman.
20. Muhlfeld CC, Kalinowski ST, McMahon TE et al. (2009) Hybridization rapidly reduces fitness of a native trout in the wild. Biology Letters, 5, 328-331.
21. Narum SR (2006) Beyond Bonferroni: less conservative analyses for conservation genetics. Conservation Genetics, 7, 783-787.
22. Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A (2004) GeneClass2: a software for genetic assignment and first-generation migrant detection. Journal of Heredity, 95, 536-539.
23. Pritchard VL, Abadía-Cardoso A, Garza JC (2012) Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarki. Molecular Ecology Resources, doi: 10.1111/j.1755-0998.2012.03149.x.
24. Pritchard VL, Jones K, Cowley DE (2007) Estimation of introgression in cutthroat trout populations using microsatellites. Conservation Genetics, 8, 1311-1329.
25. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proceedings of the National Acadamy of Science, 94, 9197-9221.
26. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248-249.
27. Ruzycki JR, Beauchamp DA, Yule DL (2003) Effects of introduced lake trout on native cutthroat trout in Yellowstone Lake. Ecological Applications, 13, 23-37.
28. Shepard BB, May BE, Urie W (2005) Status and conservation of westslope cutthroat trout within the western United States. North American Journal of Fisheries Management, 25, 1426-1440.
29. Smith GR, Dowling TE, Gobalet KW, Lugaski T, Shiozawa DK, Evans RP (2002) Biogeography and timing of evolutionary events among Great Basin fishes. Great Basin Aquatic Systems History, Hershler R, Madsen DB & Curry DR, editors. Smithsonian Contributions to the Earth Sciences 33, 175-234.
30. Taylor EB, Stamford MD, Baxter JS (2003) Population subdivision in westslope cutthroat trout (Oncorhynchus clarki lewisi) at the northern periphery of its range: evolutionary inferences and conservation implications. Molecular Ecology, 12, 2609-2622.
31. Waples RS, Gustafson RG, Weitkamp LA et al. (2001) Characterizing diversity in salmon from the Pacific Northwest. Journal of Fish Biology, 59(Suppl. A), 1-41.
32. Wilson WD, Turner TF (2009) 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, 52, 406-415.
33. Wofford JEB, Gresswell RE, Banks MA (2005) Influence of barriers to movement on within-watershed genetic variation of coastal cutthroat trout. Ecological Applications, 15, 628-637.
34. Young MK(ed.) (1995) Conservation Assessment for Inland Cutthroat Trout. US Forest Service General Technical Report. RM-256. Rocky Mountain Research Station, Fort Collins, CO, 61pp.
35. Young MK (2011) Generation-scale movement patterns of cutthroat trout (Oncorhynchus clarkii pleuriticus) in a stream network. Canadian Journal of Fisheries and Aquatic Sciences, 68, 941-951.
36. Young SF, McLellan JG, Shaklee JB (2004) Genetic integrity and microgeographic population structure of westslope cutthroat trout, Oncorhynchus clarki lewisi, in the Pend Oreille Basin in Washington. Environmental Biology of Fishes, 69, 127-142.