Current research and/or projects
I have overseen a diverse molecular genetics research program within DFO for over 15 years. The overarching goal of my program is the development and application of molecular genetic tools that can be applied towards sustainable fisheries management and aquaculture development of aquatic species. Population genetics research has been applied to establish management and conservation units within species, develop stock identification databases in salmon, and in forensic identification for enforcement. Genetic studies have been conducted on a variety of marine fish and shellfish species, including salmonids, rockfish, sablefish, Atlantic cod, herring, urchins, geoduck, and abalone. While we have developed and utilized a variety of molecular markers, including minisatellite and microsatellite loci and mitochondrial DNA, my main interest is in adaptive variation. The Major Histocompatibility Complex (MHC) is the premiere adaptive gene complex in vertebrates, and my lab has conducted extensive research on MHC gene discovery in teleosts, adaptive population genetics of MHC genes in salmon, and mechanisms of selection on the MHC in teleosts.
My group has also developed genetic markers and techniques for species identification and applied these in forensic analysis for enforcement, scat analysis in stellar sea lions, and identification of escaped farmed salmon. Our work on bacterial typing has been applied to the development of probiotics for aquaculture, delineation of bacterial complexity in salmon streams and lakes, and pathogen screening in fish. For aquaculture, we have developed quantitative RT-PCR assays for pathogens, identified the Kudoa thyrsites protein responsible for the post-mortem liquefication of salmon tissue, and identified “expressed” QTLs associated with rapid muscle growth in scallops.
In 2004, with the introduction of the first GRASP (Genomics Research on Atlantic Salmon Project; Ben Koop and Willie Davidson) salmon cDNA microarray, I initiated the formation of a new functional genomics program, the Marine Ecological Genomics and Adaptation Group, within the Molecular Genetics Laboratory. This new program expands my interest in adaptive evolution to the molecular control of phenotypic adaptation. Research within this program has included species-specific salmonid host response to the IHN virus, aimed at elucidating effective host responses for targeted vaccine research, salmon migration physiology, to identify physiological profiles associated with river entry timing and fate of late-run Fraser river sockeye salmon, and density stress in pen-reared salmon, to identify stress biomarkers for aquaculture. This program focuses largely, although not exclusively, on wild ecological genomics research to elucidate phenotype-environment interactions and limits to adaptability. See the MEGA tab under the Molecular Genetics Laboratory for more details.
Research and/or project statements
- McClelland, E.K., T.J. Ming, A. Tabata, K.M. Miller. 2011. Sequence analysis of MHC class I α2 from sockeye salmon (Oncorhynchus nerka). Fish and Shellfish Immunol. Doi: 10.1016/j.fsi.2011.06.012.
- Miller, K.M., Li, S, Kaukinen, K.H., Ginther, N., Hammill, E., Curtis, J.M.R., Patterson, D.A., Sierocinski, T., Donnison, L., Pavlidis, P., Hinch, S.G., Hruska, K.A., Cooke, S.J., English, K.K., and Farrell, A.P. 2011. Genomic signatures predict migration and spawning failure in wild Canadian salmon. Science: 331: 214-218.
- Donaldson, M.R., Hinch, S.G., Patterson, D.A., Farrell, A.P., Shrimpton, J.M., Miller-Saunders, K.M., Robichaud, D., Hills, J., Hruska, K.A., Hanson, K.C., English, K.K., Van Der Kraak, G., and Cooke, S.J. 2010. Physiological condition differentially affects the behaviour and survival of two populations of sockeye salmon during their freshwater spawning migrations. Physiological and Biochemical Zoology 83: 446-458.
- Martins, E.G., S.G. Hinch, D.A. Patterson, M.J. Hague, S.J. Cooke, K.M. Miller, M.F. Lapointe, K.K. English, A.P Farrell. 2010. Effects of river temperature and climate warming on stock-specific survival of adult migrating Fraser River sockeye salmon (Oncorhynchus nerka). Global Change Biology 17: 99-114.
- Beacham, T.D., K.M. Miller and R.E. Withler. 1996. Minisatellite DNA variation and stock identification of coho salmon. J. Fish Biol. 49: 411-429.
- Withler, R.E., and K.M. Miller. 1996. Structure of an unusual minisatellite locus, Ssa1, in Pacific salmonids. J. Heredity 88:415-422.
- Evans, M.L., M. Dionne, K.M. Miller, L Bernatchez. 2011. Mate choice for major histocompatibility complex genetic divergence as a bet-hedging strategy in the Atlantic salmon (Salmo salar). Proc. R. Soc. B: doi: 10.1098/rspb.2011.0909.
- Miller, K.M., A.D. Schulze, N. Ginther, S. Li, D.A. Patterson, A.P. Farrell, S.G. Hinch. 2009. Salmon Spawning Migration: Metabolic Shifts and Environmental Triggers. Comp. Biochem Physiol D 4: 75-89.
- Hinch, S.G., A.P. Farrell, S.J. Cooke, D.A. Patterson, M.F. Lapointe, D.W. Welch, K.K. English, G.T. Crossin, K. Miller, R.E. Thomson, G. Van Der Kraak, I. Olssen, M. Shrimpton, and M.S. Cooperman. Using physiological telemetry and intervention experiments to examine the maladaptive shift in Fraser River's Late-Run Sockeye Salmon spawning migration. American Fisheries Society Symposium 69:891-894.
- Dionne, M., K.M. Miller, J.J. Dodson, and L. Bernatchez. 2009. MHC standing genetic variation and pathogen resistance in wild 1 Atlantic salmon. Philosophical Transactions of the Royal Society of London B. 364: 1555-1565.
- Tollit, D. J., A. D. Schulze, A. W. Trites, T.F. Olesiuk, S. J. Crockford, T. S. Gelatt, R. R. Ream, and K. M. Miller. 2009. Development and application of DNA techniques for validating and improving pinniped diet estimates. Ecological Applications 19(4): 889-905.
- Beacham, T. D., K. D. Le, M. Wetklo, B. McIntosh, T. Ming, and K. M. Miller. 2009. Population structure and stock identification of chum salmon from western Alaska determined with microsatellite and major histocompatibility complex variation. Pages 141-160. In C. C. Krueger, and C. E. Zimmerman, editors. Pacific Salmon: Ecology and Management of Western Alaska’s Populations. American Fisheries Society, Symposium 70, Bethesda, Maryland.
- Beacham, T. D., K. J. Supernault, and K. M. Miller. 2008. Population structure of Dungeness crab (Cancer magister) in British Columbia. Journal of Shellfish Research 27(4): 901-906.
- Cooke, S.J., S.G. Hinch, A.P. Farrell, D.A. Patterson K. Miller-Saunders, D.W. Welch, M.R. Donaldson K.C. Hanson, G.T. Crossin, M.T. Mathes et al. 2008a. Developing a mechanistic understanding of fish migrations by linking telemetry with physiology, behaviour, genomics and experimental biology: an interdisciplinary case study on adult Fraser River sockeye salmon. Fisheries 33(7) 321-338.
- Narum, S. R. , M. Banks, T. Beacham, R. Bellinger, M. Campbell, J. DeKoning, A. Elz, C. Guthrie, C. Kozfkay, K. Miller, P. Moran, R. Phillips, L. Seeb, C. Smith, K. Warheit, S. Young, and J.C. Garza. 2008. Differentiating populations at broad and fine geographic scales with microsatellites and SNPs. Molecular Ecology 17: 3464-3477
- Funk, V.A., R.W. Olsen, M. Raap, D. Smith, L. Aitken, J.D. Haddow, D. Wang, J.A. Dawson-Coates, R.D. Burke, and K.M. Miller. 2008. Identification, characterization, and deduced amino acid sequence of the dominant protease from Kudoa paniformis and K. Thyrsites: A unique cytoplasmic cysteine protease. Comparative Biochemistry and Physiology, Part B 149: 477-489.
- Lukacs, MF, H Harstad, U Grimholt, M Beetz-Sargent, GA cooper, L Reid, HG Bakke, RB Phillips, KM Miller, WS Davidson, BF Koop. 2007. Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar). BMC Genomics 8: 251 (25 July 2007).
- Dionne M, KM Miller, JJ Dodson, F Caron, L Bernatchez. 2007. Clinal varaiation in MHC diversity with temperature: evidence for the role of host-pathogen interaction on local adaptation in atlantic salmon. Evolution. 61: 2154-64.
- Funk, V, M Raap, K Sojonky, S Jones, J Robinson, C Falkenberg, and K Miller. 2007. Development and validation of an RNA- and DNA-based quantitative PCR assay for the quantitative detection of Kudoa thyrsites (Gilchrist) in Atlantic salmon (Salmo salar). Dis. Aquat. Org. 75: 239-49.
- Miller, KM, G Traxler, KH Kaukinen, S Li, J Richard and N Ginther. 2007. A cDNA microarray study of Atlantic salmon (Salmo salar) response to Infectious Hematopoietic Necrosis (IHN) virus. Aquaculture. 272 (sup1): S217-S237.
- Rajakaruna, RS, JA Brown, KH Kaukinen, and KM Miller. 2006. Major histocompatibility complex and kin discrimination in Atlantic salmon and Brook trout. Mol. Ecol. 15: 4569-4575.
- Miller, KM, S Li, TJ Ming, KH Kaukinen, and AD Schulze. 2006. The salmonid MHC class I: more ancient loci uncovered. Immunogenetics 58: 571-589.
- Miller, KM, KJ Supernault, S Li and RE Withler. 2006. Population structure in two marine invertebrate species (Panopea abrupta and Strongylocentrotus franciscanus) targeted for aquaculture and enhancement in British Columbia. J. Shellfish Res 25: 33-42.
- Schulze, AD, AO Alabi, A Sheldrake, and KM Miller. 2006. Bacterial diversity in a marine hatchery: balance between pathogenic and potentially probiotic bacterial strains. Aquaculture 256: 50-73.
- Beacham, T. D., J. R. Candy, K. L. Jonsen, J. Supernault, M. Wetklo, L. Deng, K. M. Miller, and R. E. Withler. 2006. Estimation of stock composition and individual identification of Chinook salmon across the Pacific Rim using microsatellite variation. Transactions of the American Fisheries Society 135: 861-888.
- Beacham, T. D., B. McIntosh, C. MacConnachie, K. M. Miller, R. E. Withler, and N. V. Varnavskaya. 2006. Pacific Rim population structure of sockeye salmon as determined from microsatellite analysis. Transactions of the American Fisheries Society 135: 174-187.
- Beacham, T.D., J.R. Candy, B. McIntosh, C. MacConnachie, A. Tabata, K.M. Miller, and R.E. Withler. 2005. DNA-level variation of sockeye salmon (Oncorhynchus nerka) in southeast Alaska and the Nass and Skeena rivers, British Columbia, with applications to stock identification. N. Amer. J. Fish. Manage.
- Withler, R.E., K.J. Supernault and K.M. Miller. 2005. Genetic variation within and among domesticated Atlantic salmon broodstocks in British Columbia, Canada. Animal Genetics 36: 43-50.
- Beacham, T.D., M. Lapointe, J.R. Candy, B. McIntosh, C. MacConnachie, A. Tabata, K. Kaukinen, L. Deng, K.M. Miller, and R.E. Withler. 2004. Stock identification of Fraser River sockeye salmon (Oncorhynchus nerka) using microsatellites and major histocompatibility complex variation. Trans. Am. Fish. Soc. 133: 1106-1126.
- Kaukinen, K.H, K.J. Supernault, and K.M. Miller. 2004. Enrichment of Tetranucleotide Microsatellite Loci from Marine Invertebrate species. J. Shellfish Res 23(2): 621-626.
- Kaukinen, K.H., K.J. Supernault, and K.M. Miller. 2004. Development of microsatellite loci in eulachon (Thaleichthys pacificus). Mol. Ecol. Notes 4: 632-634.
- Beacham, T.D., M. Lapointe, J.R. Candy, K.M. Miller, and R.E. Withler. 2004. DNA in action: Rapid application of DNA variation to sockeye salmon fisheries management. Cons. Gen. in Press.
- Miller, K.M., K.Hl Kaukinen, K. Laberee, and K.J. Supernault. 2004. Microsatellite loci from red sea urchins (Strongylocentrotus franciscanus). Mol. Ecol. Notes 4: 722-724.
- Miller, K.M., J.R. Winton, A. Schulze, M.K. Purcell, and T. Ming. 2004. Major Histocompatibility Complex loci are associated with susceptibility of Atlantic salmon to infectious hematopoietic necrosis virus. Env. Biol. Fish. 69: 307-316.
- Withler, R.E., J.R. Candy, T.D. Beacham and K.M. Miller. 2004. Forensic DNA analysis of Pacific salmonid samples for species and stock identification. Env. Biol. Fish. 69: 275-285.
- Withler, R.E., J.R. King, J.B. Marliave, B. Beaith, S. Li, K.J. Supernault, K.M. Miller. 2004. Polygamous mating and high levels of genetic variation in lingcod (Ophiodon elongatus) of the Strait of Georgia, British Columbia. Env. Biol. Fish. 69: 345-357.
- Withler, RE, A Campbell, S Li, D Brouwer, KJ Supernault, and KM Miller. 2003. Implications of high levels of genetic diversity and weak population structure for the rebuilding of northern abalone in British Columbia, Canada. J Shellfish Res 22: 839-847.
- Flajnik, M.F., K.M. Miller and L. Du Pasquier. 2003. Evolution of the immune system. In: Fundamental Immunology, Fifth Edition, Chapter 18. WE Paul (ed.), Lippincott-Raven Publishers, Philadelphia.
- Beacham, T.D., J.R. Candy, K.J. Supernault, M. Wetklo, B. Deagle, K. Labaree, J.R. Irvine, K.M. Miller, R.J. Nelson, and R.E. Withler. 2003. Evaluation and application of microsatellites for population identification of Fraser River chinook salmon (Oncorhynchus tshawytscha). Fishery Bulletin 101: 243-259.
- Beacham, T.D., K.J. Supernault, M. Wetklo, B. Deagle, K. Labaree, J.R. Irvine, J.R. Candy, K.M. Miller, R.J. Nelson and R.E. Withler. 2003. The geographic basis for population structure in Fraser River chinook salmon, Oncorhynchus tshawytscha. Fishery Bulletin 101: 229-242.
- Beacham, T.D., J. Brattey, K.D. Le, K.M. Miller, and R.E. Withler. 2002. Multiple stock structure of Atlantic cod (Gadus morhua) off Newfoundland and Labrador determined from genetic variation. ICES J. Mar. Sci. 59(4): 650-655.
- Miller, KM, KH Kaukinen, and AD Schulze. 2002. Expansion and contraction of major histocompatibility complex (MHC) genes: a teleostean example. Immunogenetics 53: 941-963.
- Miller, KM, KH Kaukinen, TD Beacham, and RE Withler. 2001 Geographic heterogeneity in natural selection on an MHC locus in sockeye salmon. Genetica 111: 237-257.
- Miller, KM, K Laberee, KH Kaukinen, S Li, and RE Withler. 2001. Development of microsatellite loci in pinto abalone (Haliotis kamtschatkana). Molecular Ecology Notes 1(4): 315-317.
- Miller, KM, K Laberee, AD Schulze, and KH Kaukinen. 2001. Development of microsatellite loci in Pacific herring (Clupea pallasi). Molecular Ecology Notes 1(3): 131-133.
- Withler, R.E., T.D. Beacham, A.D. Schulze, L.J. Richards, and K.M. Miller. 2001. Co-existing populations of Pacific Ocean perch, Sebastes alutus, in Queen Charlotte Sound, British Columbia. Mar. Biol. 139: 1-12.
- Beacham, T.D., J.R. Candy, K.J. Supernault, T. Ming, B. Deagle, A. Schultz, D. Tuck, K. Kaukinen, J.R Irvine, K.M. Miller, and R. E. Withler. 2001. Evaluation and application of microsatellite and major histocompatibility complex variation for stock identification of coho salmon in British Columbia. Trans. Am. Fish. Soc. 130: 1116-1155.
- Beacham, T.D., C.C. Wood, R.E. Withler, K.D. Le and K.M. Miller. 2000. Application of microsatellite DNA variation to estimation of stock composition and escapement of Skeena River sockeye salmon (Oncorhynchus nerka). N. Pac. Anadr. Fish Comm. Bull. No. 2: 263-276.
- Miller, K.M., K.D. Le and T.D. Beacham. 2000. Development of tri- and tetranucleotide repeat microsatellite loci in Atlantic cod (Gadus morhua). Molecular Ecology 9(2): 238-240.
- Miller, K.M., A.D. Schulze and R.E. Withler. 2000. Characterization of microsatellite loci in Sebastes alutus and their conservation in congeneric rockfish species. Molecular Ecology 12: 240-242.
- Withler, R.E., K.D. Le, R.J. Nelson, K.M.Miller, and T.D. Beacham. 2000. Intact genetic structure and high levels of genetic diversity in bottlenecked sockeye salmon, Oncorhynchus nerka, populations of the Fraser River, British Columbia, Canada. Canadian Journal of Fisheries and Aquatic Sciences 57 : 1985-1998.
- Miller, K.M., T.J. Ming, A.D. Schulze and R.E. Withler. 1999. Denaturing gradient gel electrophoresis (DGGE): A rapid and sensitive technique to screen nucleotide sequence variation in populations. BioTechniques 27: 1016-1030.
- Miller, K.M. and R.E. Withler. 1998. The salmonid class I MHC: limited diversity in a primitive teleost. Immunological Reviews166: 279-293.
- Miller, K.M., R.E. Withler and T.D. Beacham. 1997. Population differentiation at Mhc genes in chinook salmon Oncorhynchus tshawytscha. Molecular Ecology 6: 937-954.
- Withler, R.E., T.D. Beacham and K.M. Miller. 1997. Species identification of Pacific salmon by PCR-RFLP of a MHC gene. N. Amer. J. Fish. Manage. 17: 929-938.
- Miller, K.M. and R.E. Withler. 1997. Mhc diversity in Pacific salmon: Population structure and trans-species allelism. Hereditas 127: 83-95.
- Miller, K.M., R.E. Withler, and T.D. Beacham. 1996. Stock identification of coho salmon (Oncorhynchus kisutch) using minisatellite DNA variation. Can. J. Fish. Aquat. Sci. 53(1): 181-195.
- Miller, K.M. and R.E. Withler. 1996. Sequence analysis of a polymorphic Mhc class II gene in Pacific salmon. Immunogenetics 43: 337-351.