Abstract
Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the least. Neighbor-joining trees grouped populations according to major river drainages. A great amount of genetic differentiation was present among and within all drainages. Based on Nei’s D S , populations in the Snake River were the most differentiated, while populations in the Missouri River were the least. This pattern of differentiation is consistent with a history of sequential founding events through which westslope cutthroat trout may have experienced a genetic bottleneck as they colonized each river basin from the Snake to the Clark Fork to the Missouri river. These data should serve as a starting point for a discussion on management units and possible distinct population segments. Given the current threats to the persistence of westslope cutthroat trout, and the substantial genetic differentiation between populations, these topics warrant attention.
Similar content being viewed by others
References
Allendorf FW, Leary RF (1988) Conservation and distribution of genetic variation in a polytypic species, the cutthroat trout. Conserv Biol 2:170–184
Amos W (2006) The hidden value of missing genotypes. Mol Biol Evol 23:1995–1996
Behnke RJ (1992) Native trout of western North America. American Fisheries Society Monograph 6, Bethesda, Maryland
Behnke RJ (2002) Trout and salmon of North America. The Free Press, New York
Bernatchez L, Wilson CC (1998) Comparative phylogeography of Nearctic and Palearctic fishes. Mol Ecol 7:431–452
Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631
COSEWIC (2006) COSEWIC assessment and update status report on the westslope cuttthroat trout Oncorhynchus clarkii lewisi (British Columbia population and Alberta population) in Canada. Committee on the Status of Endangered Wildlife in Canada, Ottawa
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. Cons Biol 23:859–870
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Guo SW, Thompson EA (1992) Performing the exact test of Hardy–Weinberg proportion for multiple alleles. Biometrics 48:361–372
Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59:1633–1638
Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913
Hughes CF, Queller DC (1993) Detection of highly polymorphic microsatellite loci in a species with little allozyme polymorphism. Mol Ecol 2:131–137
Kalinowski ST (2002a) Evolutionary and statistical properties of genetic distances. Mol Ecol 11:1263–1273
Kalinowski ST (2002b) How many alleles per locus should be used to estimate genetic distances? Heredity 88:62–65
Kalinowski ST (2004) Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conserv Genet 5:539–543
Kalinowski ST (2005a) Do polymorphic loci require larger sample sizes to estimate genetic distances? Heredity 94:33–36
Kalinowski ST (2005b) HP-Rare: a computer program for performing rarefaction on measures of allelic diversity. Mol Ecol Notes 5:187–189
Kalinowski ST (2009) How well do evolutionary trees describe genetic relationships between populations? Heredity 102:506–513
Kalinowski ST, Taper ML (2006) Maximum likelihood estimation of the frequency of null alleles at microsatellite loci. Conserv Genet 7:991–995
Kalinowski ST, Novak BJ, Drinan DP, Jennings R, Vu NV (2010) Diagnostic single nucleotide polymorphisms for identifying westslope cutthroat trout (Oncorhynchus clarki lewisi), Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (Oncorhynchus mykiss). Mol Ecol Resour 11:389–393
Kozfkay CC, Campbell MR, Yundt SP, Peterson MP, Powell MS (2007) Incidence of hybridization between naturally sympatric westslope cutthroat trout and rainbow trout in the Middle Fork Salmon River drainage, Idaho. T Am Fish Soc 136:624–638
Kozfkay CC, Campbell MR, Meyer KA, Schill DJ (2011) Influences of habitat and hybridization on the genetic structure of Redband trout in the upper Snake River basin, Idaho. T Am Fish Soc 140:282–295
Leary RF, Allendorf FW, Phelps SR, Knudsen KL (1988) Population genetic structure of westslope cutthroat trout: genetic variation within and among populations. Proc Mont Acad Sci 48:57–70
Liknes GA, Graham PJ (1988) Westslope cutthroat trout in Montana: life history, status and management. Status and management of interior stocks of cutthroat trout. Am Fish Soc Symp 4:53–60
May BE (2009) Westslope cutthroat trout status update summary. Wild Trout Enterprises LLC, Bozeman
McPhail JD, Lindsey CC (1986) Zoogeography of the freshwater fishes of Cascadia (the Columbia system and rivers north to the Stikine). In: Hocutt CH, Wiley EO (eds) The zoogeography of North American freshwater fishes. J Wiley and Sons, New York, pp 615–637
Montana Fisheries Information System (MFISH) (2011) Montana Department of Fish, Wildlife and Parks. http://fwp.mt.gov/fishing/mFish/ Accessed Jan 2011
Muhlfeld CC, Kalinowski ST, McMahon TE, Painter S, Leary RF, Taper ML, Allendorf FW (2009) Hybridization reduces fitness of cutthroat trout in the wild. Biol Lett 5:328–331
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590
Nielsen JL, Byrne A, Graziano SL, Kozfkay CC (2009) Steelhead genetic diversity at multiple spatial scales in a managed basin: Snake River, Idaho. T Am Fish Soc 29:680–701
Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mole Ecol Notes 6:288–295
Pielou EC (1991) After the ice age. University of Chicago Press, Chicago
Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249
R Development Core Team (2010). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org
Rieman BE, Apperson KA (1989) Status and analysis of salmonid fisheries: westslope cutthroat trout synopsis and analysis of fishery information. Idaho Department of Fish and Game, Federal Aid in Sport Fish Restoration, Project F-73-R-11, Boise, Idaho
Rousset F (2008) GENEPOP’007: a complete reimplementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour 8:103–106
Rousset F, Raymond M (1995) Testing heterozygote excess and deficiency. Genetics 140:1413–1419
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sánchez JA, Clabby C, Ramos D, Blanco G, Flavin F, Vázquez E, Powell R (1996) Protein and microsatellite single locus variability in Salmo salar L. (Atlantic salmon). Heredity 77:423–432
Shepard BB, Sanborn B, Ulmer L, Lee DC (1997) Status and risk of extinction for westslope cutthroat trout in the upper Missouri River basin, Montana. N Am J Fish Manag 17:1158–1172
Shepard BB, May BE, Urie W (2005) Status and conservation of westslope cutthroat trout within the western United States. N Am J Fish Manag 25:1426–1440
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. Mol Ecol 12:2609–2622
USFWS (US Fish, Wildlife Service), NOAA (National Oceanic, Atmospheric Administration) (1996) Policy regarding the recognition of distinct vertebrate population segments under the Endangered Species Act. Fed Regist 61:4721–4725
Van Eimeren P (1996) Westslope cutthroat trout Oncorhynchus clarki lewsi. In: Duff DA (ed) Conservation assessment for inland cutthroat trout: distribution, status and habitat management implications. US Department of Agriculture, Forest Service, Intermountain Region, Ogden, Utah, pp 1–10
Vu NV, Kalinowski ST (2009) Twelve tetranucleotide microsatellite loci for westslope cutthroat trout Oncorhynchus clarki lewisi (Salmonidae). Conserv Genet Resour 1:249–251
Weir BS, Cockerham CC (1984) Estimating F-Statistics for the analysis of population structure. Evolution 38:1358–1370
Acknowledgments
This research was funded by National Science Foundation grant DEB 0717456. Thanks to Robb Leary, Paul Spruell, and Jim Mogen for samples. Thanks to Matt Boyer and two anonymous reviewers. Their suggestions greatly improved the manuscript.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Drinan, D.P., Kalinowski, S.T., Vu, N.V. et al. Genetic variation in westslope cutthroat trout Oncorhynchus clarkii lewisi: implications for conservation. Conserv Genet 12, 1513–1523 (2011). https://doi.org/10.1007/s10592-011-0249-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10592-011-0249-2