MFWGL Publications
Allendorf, F.W., D.M. Espeland, D.T. Scow, and S.R. Phelps. 1980. Coexistence of native and introduced rainbow trout in the Kootenai River drainage. Proc. Montana Acad. Sciences 39:28-36.
Allendorf, F.W., and S.R. Phelps. 1980. Loss of genetic variation in a hatchery stock of cutthroat trout. Trans. Amer. Fish. Soc. 109:537-543.
Phelps, S.R., and F.W. Allendorf. 1982. Genetic comparison of upper Missouri River cutthroat trout to other Salmo clarki lewisi populations. Proc. Mont. Acad. Sci. 41:14-22.
Phelps, S.R., and F.W. Allendorf. 1983. Genetic identity of pallid and shovelnose sturgeon (Scaphirhynchu albus and S. platorynchus). Copeia 1983(3):696-700.
Leary, R.F., F.W. Allendorf, and K.L. Knudsen. 1983. Developmental stability and enzyme heterozygosity in rainbow trout. Nature 301:71-72.
F.W. Allendorf, and K.L. Knudsen. 1983. Consistently high meristic counts in natural hybrids between brook trout and bull trout. Syst. Zool. 32:369-376.
Leary, R.F., F.W. Allendorf, S.R. Phelps, and K.L. Knudsen. 1984. Introgression between westslope cutthroat and rainbow trout in the Clark Fork River drainage, Montana. Proc. Montana Acad. Sci. 43:1-18.
Leary, R.F., F.W. Allendorf, and K.L. Knudsen. 1985. Developmental instability as an indicator of reduced genetic variation in hatchery trout. Trans. Amer. Fish. Soc. 114:230-235.
Leary, R.F., F.W. Allendorf, K.L. Knudsen, and G.H. Thorgaard. 1985. Heterozygosity and developmental stability in gynogenetic diploid and triploid rainbow trout. Heredity 54:219-225.
Ferguson, M.M., R.G. Danzmann, and F.W. Allendorf. 1985. Developmental divergence among hatchery strains of rainbow trout (Salmo gairdneri). II. Hybrids. Can. J. Genet. and Cytol. 27:298-307.
Leary, R.F., F.W. Allendorf, and K.L. Knudsen. 1985. Developmental instability and high meristic counts in interspecific hybrids of salmonid fishes. Evolution 39:1318-1326.
Gyllensten, U., R.F. Leary, F.W. Allendorf, and A.C. Wilson. 1985. Introgression between two cutthroat trout subspecies with substantial karyotypic, nuclear, and mitochondrial genomic divergence. Genetics 111:905-915.
Ferguson, M.M., R.G. Danzmann, and F.W. Allendorf. 1985. Absence of developmental incompatibility in hybrids between rainbow trout and two subspecies of cutthroat trout. Biochemical Genetics 23:557-570.
Danzmann, R.G., M.M. Ferguson, and F.W. Allendorf. 1985. Does enzyme heterozygosity influence developmental rate in rainbow trout? Heredity 56:417-425.
Danzmann, R.G., M.M. Ferguson, and F.W. Allendorf. 1986. Heterozygosity and developmental rate in a strain of rainbow trout. Evolution 40:86-93.
Marnell, L.F., R.J. Behnke, and F.W. Allendorf. 1987. Genetic identification of the cutthroat trout (Salmo clarki) in Glacier National Park, Montana. Can. J. Fish. Aquat. Sci. 44:1830-1839.
Leary, R.F., F.W. Allendorf, S.R. Phelps, and K.L. Knudsen. 1987. Genetic divergence and identification of seven subspecies of cutthroat trout and rainbow trout. Trans. Amer. Fish. Soc. 116:580-587.
Allendorf, F.W. 1987. Leary, R.F., F.W. Allendorf, and K.L. Knudsen. 1987. Differences in inbreeding coefficients do not explain the association between heterozygosity at isozyme loci and developmental stability in rainbow trout. Evolution 41:1413-1415.
Ferguson, M.M., R.G. Danzmann, and F.W. Allendorf. 1988. Developmental success of hybrids between two taxa of salmonid fishes with moderate structural gene divergence. Can. J. Zool. 66:1389-1395.
Allendorf, F.W., and R.F. Leary. 1988. Conservation and distribution of genetic variation in a polytypic species, the cutthroat trout. Conservation Biology 2:170-184.
Leary, R.F., F.W. Allendorf, S.R. Phelps, and K.L. Knudsen. 1988. Population genetic structure of westslope cutthroat trout: Genetic variation within and among populations. Proc. Montana Acad. Sci. 48:57-70.
Danzmann, R. G., M. M. Ferguson, and F. W. Allendorf. 1988. Heterozygosity and components of fitness in a strain of rainbow trout. Biol. J. Linnean Soc. 33:285-304.
Ferguson, M.M., K. L. Knudsen, R. G. Danzmann, and F. W. Allendorf. 1988. Developmental rate and viability of rainbow trout with a null allele at a lactate dehydrogenase locus. Biochem. Genet. 26:177-189.
Ferguson, M.M., R.G. Danzmann, and F.W. Allendorf. 1988. Developmental success of hybrids between two taxa of salmonid fishes with moderate structural gene divergence. Can. J. Zool. 66:1389-1395.
Allendorf, F.W., and R.F. Leary. 1988. Conservation and distribution of genetic variation in a polytypic species, the cutthroat trout. Conservation Biology 2:170-184.
Danzmann, R. G., M.M. Ferguson, and F.W. Allendorf. 1989. Genetic variability and components of fitness in hatchery strains of rainbow trout. J. Fish Biol. 35 (Suppl. A):313-320.
Leary, R.F., F.W. Allendorf, and K.L. Knudsen. 1991. Effects of rearing density on meristics and developmental stability of rainbow trout. Copeia 1991(1):44-49.
Forbes, S.H., and F.W. Allendorf. 1991. Associations between mitochondrial and nuclear genotypes in cutthroat trout hybrid swarms. Evolution 45:1332-1349.
Forbes, S.H., and F.W. Allendorf. 1991. Mitochondrial genotypes have no detectable phenotypic effects in cutthroat trout hybrid swarms. Evolution 45:1350-1359.
Leary, R.F., F.W. Allendorf, and K.L. Knudsen. 1992. Genetic, environmental, and developmental causes of meristic variation in rainbow trout. Acta Zoologica Fennica 191:77-93.
Leary, R.F., F.W. Allendorf, and S.H. Forbes. 1993. Conservation genetics of bull trout in the Columbia and Klamath River drainages. Conservation Biology 7:856-865.
Leary, R.F., F.W. Allendorf, and G.K. Sage. 1995. Hybridization and introgression between introduced and native fish. Amer. Fish. Soc. Symposium 15:91-101.
Kanda, N., and F.W. Allendorf. 2001. Genetic population structure of bull trout from the Flathead River basin as shown by microsatellites and mitochondrial DNA markers. Trans. Amer. Fish. Soc. 130:92-106.
Thelen, G.C., and F. W. Allendorf. 2001. Heterozygosity-fitness correlations in rainbow trout: effects of allozyme loci or associative overdominance? Evolution 55:1180-1187.
Rieman, B., and F.W. Allendorf. 2001. Effective population size and genetic conservation criteria for bull trout. N.A. Jour. Fish. Management 21:756-764.
Allendorf, F.W., R.F. Leary, P. Spruell, and J.K. Wenburg. 2001. The problems with hybrids: Setting conservation guidelines. Trends Ecol. Evol. 16:613-622.
Allendorf, F.W., P. Spruell, and F.M. Utter. 2001. Response. Whirling disease and wild trout. Fisheries 26(8):36.
Spruell, P.S., M.L. Bartron, N. Kanda, and F.W. Allendorf. 2001. Detection of hybrids between bull trout Salvelinus confluentus) and brook trout (S. fontinalis) using PCR primers complementary to interspersed nuclear elements. Copeia 2001:1093–1099.
Kanda, N., R.F. Leary, P. Spruell, and F.W. Allendorf. 2002. Molecular genetic markers identifying hybridization between Colorado River cutthroat trout and Yellowstone cutthroat trout or rainbow trout. Trans. Amer. Fish. Soc. 130:312-319.
Kanda, N., R.F. Leary, and F.W. Allendorf. 2002. Evidence of introgressive hybridization between bull trout and brook trout. Trans. Amer. Fish. Soc. 131:772-782.
Spruell, P., A.R. Hemmingsen, P.J. Howell, N. Kanda, and F.W. Allendorf. 2003. Conservation genetics of bull trout: Geographic distribution of variation at microsatellite loci. Conservation Genetics 4:17-29.
Hitt, N.P., C.A. Frissell, C. Muhlfeld, and F.W. Allendorf. 2003. Spread of hybridization between native westslope cutthroat trout, Oncorhynchus clarki lewisi, and non-native rainbow trout, O. mykiss. Canadian J. Fish. Aquat. Sci. 60:1440-1451.
Allendorf, F.W., R.F. Leary, N.P. Hitt, K.L. Knudsen, L.L. Lundquist, and P. Spruell. 2004. Intercrosses and the U.S. Endangered Species Act: should hybridized populations be included as westslope cutthroat trout? Conservation Biology 18:1203-1213.
Whiteley, A.R., P. Spruell, and F.W. Allendorf. 2004. Ecological and life history characteristics predict population genetic divergence of two salmonids in the same landscape. Molec. Ecol. 13:3665-3688.
Allendorf, F.W., R.F. Leary, N.P. Hitt, K.L. Knudsen, M.L. Boyer, and P. Spruell. 2005 Cutthroat trout hybridization and the U.S. Endangered Species Act: One species, two policies. Conservation Biology 19:1326-1328.
Whiteley, A.R., P. Spruell, and F.W. Allendorf. 2006. Can common species provide valuable information for conservation? Molec. Ecol. 15:2767-2786.
Whiteley, A.R., P. Spruell, B.E. Rieman, and F.W. Allendorf. 2006. Fine-scale genetic structure of bull trout at the southern limit of their distribution. Trans. Amer. Fish. Soc. 135:1238-1253.
Boyer, M., C. Muhlfeld, C., and F. W. Allendorf. 2008. Rainbow trout (Oncorhynchus mykiss) invasion and the spread of hybridization with native westslope cutthroat trout (Oncorhynchus clarkii lewisi) Canadian J. Fish. Aquat. Sci. 65: 658-659.
Muhlfeld, C. C., Kalinowski, S.T., McMahon, T.E., Taper, M.L., Painter, S., Leary, R.F., and Allendorf, F. W. 2009. Hybridization rapidly reduces fitness of a native trout in the wild. Biology Letters 5:328-331.
Bingham, D., R.F. Leary, S. Painter, and F.W. Allendorf. 2012. Near absence of hybridization between sauger and introduced walleye despite massive releases. Conservation Genetics 13:509-523.
Hohenlohe, P.A., M.D. Day, S.J. Amish, M.R. Miller, N. Kamp-Hughes, M.C. Boyer, C.C. Muhlfeld, F,W. Allendorf, E.A. Johnson, and G. Luikart. 2013. Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Molecular Ecology 22:3002-3013.
Muhlfeld, C.C., R. P. Kovach, L. A. Jones, R. Al-Chokhachy, M. C. Boyer, R. F. Leary, W. H. Lowe, G. Luikart, and F. W. Allendorf. 2014. Invasive hybridization is accelerated by climate change in a threatened species. Nature Climate Change 4:620-624.
Kovach, R. P., C. C. Muhlfeld, M. C. Boyer, W. H. Lowe, F. W. Allendorf, and G. Luikart. 2015. Dispersal and selection mediate hybridization between a native and invasive species. Proceedings of the Royal Society B: Biological Sciences 282:20142454.
Kovach, R.P., C.C. Muhlfeld, A.A. Wade, B.K. Hand, D.C. Whited, P.W. DeHaan, R. Al-Chokhachy, and G. Luikart. 2015. Genetic diversity is related to climatic variation and vulnerability in threatened bull trout. Global Change Biology 21:2510-2524.
Muhlfeld, C.C., V.S. D’Angelo, C.C. Downs, J. Powell, S. Amish, G. Luikart, R. Kovach, M. Boyer and S. Kalinowski. 2016. Genetic status and conservation of westslope cutthroat trout in Glacier National Park. Transactions of the American Fisheries Society 145:1093-1109.
Kovach, R.P., B.K. Hand, P.A. Hohenlohe, T.F. Cosart, M.C. Boyer, H.H. Neville, C.C. Muhlfeld, S.J. Amish, K. Carim, S.R. Narum, W.H. Lowe, F.W. Allendorf, and G. Luikart. 2016. Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones. Proceedings of the Royal Society B: Biological Science. 283: 20161380.
Muhlfeld, C.C., R.P. Kovach, R. Al-Chokhachy, S.J.Amish, J. Kershner, R.F. Leary, W.H. Lowe, G. Luikart, P. Matson, B. Shepard, P. Westley, D. Whited, A. Whiteley, and F. W. Allendorf. 2017. Legacy introductions and climatic variation explain spatiotemporal patterns of invasive hybridization in a native trout. Global Change Biology.
Kovach, R.P., C.C. Muhlfeld, Al-Chokhachy, S.J.Amish, J. Kershner, R.F. Leary, W.H. Lowe, G. Luikart, P. Matson, B. Shepard, P. Westley, D. Whited, A. Whiteley, and F. W. Allendorf. 2017. No evidence for ecological segregation protecting native trout from invasive hybridization. Global Change Biology.
2000. P. Kovach, A. R. Whiteley, M. E. Jaeger, S. Painter, A. Lodmell, R. F. Leary. 2020. Genetic monitoring informs conservation status and trend of Arctic grayling at the southern edge of their distribution. Canadian Journal of Fisheries and Aquatic Sciences 77:1934-1942.
Strait, J. T., L. A. Eby, R. P. Kovach, C. C. Muhlfeld, M. C. Boyer, S. J. Amish, S. Smith, W. H. Lowe, G. Luikart. 2021. Hybridization alters growth and migratory life-history expression of native trout. Evolutionary Applications 14:821-833.
Bell, D. A., R. P., Kovach, C. C. Muhlfeld, R. Al-Chokhachy, T. J. Cline, D. C. Whited, D. A. Schmetterling, P. M. Lukacs, A. R. Whiteley. 2021. Climate change and expanding invasive species drive widespread declines of native trout in the northern Rocky Mountains, USA. Science Advances 7:eabj5471.
Bohling, J., J. Von Bargen, M. Piteo, A. Louden, M. Small, T. A. Delomas, R. Kovach. 2021. Developing a standardized single nucleotide polymorphism panel for rangewide genetic monitoring of bull trout. North American Journal of Fisheries Management 6:1920-1931.
Bell, D. A., R. P. Kovach, Z. L. Robinson, A. R. Whiteley, T. E. Reed. 2021. The ecological causes and consequences of hard and soft selection. Ecology Letters 24:1505-1521.
Bourret, S.L., R.P. Kovach, T. J. Cline, J. T. Straight, C.C. Muhlfeld. 2022. High dispersal rates drive expansion of maladaptive hybridization. Proceedings of the Royal Society B 289: 20221813.
2022. P. Kovach, R. F. Leary, D. A. Bell, S. Painter, A Lodmell, A. R. Whiteley. 2022. Genetic variation in westslope cutthroat trout reveals that widespread genetic rescue is warranted. Canadian Journal of Fisheries and Aquatic Sciences 79:936-946.
Lampton, J., R. P. Kovach, J. L. Dunnigan. 2023. Efficacy of one-time rotenone application for Westslope Cutthroat Trout restoration in Boulder Creek, Montana. North American Journal of Fisheries Management 43:1081-1092.
Dangora, A. J., Eby, L. A., Barfoot, C. A., & Whiteley, A. R. 2023. Evaluating the effects of selective passage of migratory Westslope Cutthroat Trout on nonnative admixture. Transactions of the American Fisheries Society, 152(6), 772-787.
Harris, A.C., D.K. Coykendall, H. Lamson, R.P. Kovach, J.L. Dunnigan, M.R. Campbell. 2024. An improved genetic marker panel for conservation monitoring of upper Kootenay River burbot. Conservation Genetic Resources 16:195-197.
Bell, D.A., R.P. Kovach, A.R. Whiteley. 2024. Inbreeding avoidance and cost in a small, isolated trout population. Proceedings of the Royal Society B 291:20241164.
Feuerstein, C.A., R.P. Kovach, C.G. Kruse, M.E. Jaeger, D.A. Bell, Z.L. Robinson, A.R. Whiteley. 2024. Genetic variation and hybridization determine the outcomes of conservation reintroductions. Conservation Letters 17:e13049.
2025. Kovach, D. Bell, S. Amish, S. Smith, K. Cook, D. Schmetterling, M Jaeger, A. Whiteley. 2025. Defining hybridization thresholds for native species conservation in the genomic era. Fisheries vuaf:023.
Flores, A.M., K. Cristensen, T. Godin, et al. 2025. The genome assembly of westslope cutthroat trout, Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow trout, Oncorhynchus mykiss. G3: Genes, Genomes, Genetics 15:jkaf064.
Bell, D.A., K.J. Carim, R.P. Kovach, L.A. Eby, C. Barfoot, S. Painter, A. Lodmell, S.J. Amish, S. Smith, L. Rosenthal, B. Larkin, P. Ramsey, A.R. Whiteley. 2025. Genomic insights into inbreeding and adaptive divergence of trout populations to inform genetic rescue. Evolutionary Applications 18:e70090.
Bell, D. A., R. P. Kovach, Z. Robinson, A. Dangora, J. Mullen, A. Poole, J. Olsen, R. Spoon, C. Pipinich, L. Nelson, A. R. Whiteley. 2026. Inbred source populations result in genetic rescue of imperiled trout populations. Biological Conservation 314: 111677.