Publications
Molecular Genetics Laboratory primary publications
2016 and in press
195. Beamish, R. J., Ruth Withler, Joy Wade, and Terry Beacham. 2016. The Morrison Creek lamprey enigma. In: Jawless Fishes of the World. Volume 1. Alexei Orlov and Richard Beamish (editors). Cambridge Scholars Publishing.
194. Hertz, E., M.Trudel, S. Tucker, T. D. Beacham, C. Parken, D. Mackas, and A. Mazumder. In press. Influences of ocean conditions and feeding ecology on the survival of juvenile Chinook Salmon (Oncorhynchus tshawytscha). Fisheries Oceanography.
193. Beamish, R. J., Chrys M. Neville, Ruston M. Sweeting, Terry D. Beacham, Joy Wade, and Lingbo Li. 2016. Early ocean life history of Harrison River Sockeye Salmon and their contribution to the biodiversity of Sockeye Salmon in the Fraser River, British Columbia, Canada. Transactions of the American Fisheries Society 145: 348-362.
192. Hertz, E. J. M., Marc Trudel, Rana W. El-Sabaawi, Strahan Tucker, John F. Dower, Terry D. Beacham, Andrew M. Edwards, and Asit Mazumder. In press. Hitting the moving target: modelling gradual ontogenetic niche shifts using stable iostopes. Journal of Animal Ecology
191. Beacham,T. D., Richard J. Beamish, Chrys M. Neville, John R. Candy, Colin Wallace, Strahan Tucker, and Marc Trudel. In press. Stock-specific size and migration of juvenile Coho Salmon in British Columbia and southeastern Alaskan waters. Marine and Coastal Fisheries
190. Freshwater, C., Marc Trudel, Terry D. Beacham, L. Godbout, C.-E. Neville, Strahan Tucker, and F. Juanes. In press. Disentangling individual- and population-scale processes affecting a latitudinal size-gradient in Sockeye Salmon. Canadian Journal of Fisheries and Aquatic Sciences.
189. Beacham, T. D., J. R. Candy, S. Sato, and S. Urawa. In press. Microsatellite identification of Sockeye Salmon rearing in the Bering Sea during 2009-2014. NPAFC Research Bulletin.
2015
188. Raby, G. D., Donaldson, M. R., Hinch, S. G., Clark, T. D., Eliason, E. J., Jeffries, K. M., Cook, K.V., Teffer, A., Bass, A.L., Miller, K.M., Patterson, D.A., Farrell, A.P., & Cooke, S. J. 2015. Fishing for Effective Conservation: Context and Biotic Variation are Keys to Understanding the Survival of Pacific Salmon after Catch-and-Release. Integrative and comparative biology, icv088.
187. Muttray, A.F., D. Sakhrani, R.E. Withler and Robert H. Devlin. 2015. Low variation in a Y-chromosomal growth hormone pseudogene relative to its functional autosomal progenitor gene in Chinook Salmon. Transactions of the American Fisheries Society 144 (5): 1029-1039. DOI: 10.1080/00028487.2015.1059886.
186. King J.R, M. Wetklo, K. J. Supernault, M. Taguchi, K. Yokawa, O. Sosa-Nishizaki, and R. E. Withler. 2015. Genetic analysis of stock structure of Blue Shark (Prionace glauca) in the north Pacific ocean. Fisheries Research 172: 181-189.
185. Braun, D. C, J. W. Moore, J. R. Candy and R E Bailey. 2015. Population diversity in Fraser River Chinook salmon: linkages among response, genetic and life history diversity. Ecography 38: 1-12.
184. Candy, J. R., Nathan R. Campbell, Mathew H. Grinnell, Terry D. Beacham, Wesley A. Larson, and Shawn R. Narum. 2015. Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt. Molecular Ecology Resources 15: 1421-1434.
183. Freshwater, C., M. Trudel, Terry D. Beacham, Chrys Neville, Strahan Tucker, and F. Juanes. 2015. Validation of daily increments and a marine entry check in the otoliths of Sockeye Salmon post-smolts. Journal of Fish Biology 87: 169-178.
182. Taguchi, M., J. King, M. Wetklo, R. Withler and K. Yokawa. 2015. Population genetic structure and demographic history of Pacific blue sharks (Prionace glauca) inferred from mitochondrial DNA analysis. Marine and Freshwater Research 66: 267–275.
181. Tucker, S., M. E. Thiess, J. F. T. Morris, D. Mackas, W. T. Peterson, J. R. Candy, T. D. Beacham, E. M. Iwamoto, D. Teel, M. Peterson, and M. Trudel. 2015. Ocean distribution and consequent factors influencing marine survival of endangered Redfish Lake sockeye salmon. Transactions of the American Fisheries Society 144: 107-123.
2014
180. Jeffries, K.M. Scott G. Hinch, Marika Kirstin Gale, Timothy D. Clark, Andrew G. Lotto, Matthew T. Casselman, Shaorong Li, Erin L. Rechisky, Aswea D. Porter, David W. Welch and Kristina M. Miller. 2014. Immune response genes and pathogen presence predict migration survival in wild salmon smolts. Molecular Ecology 23:5803-5815.
179. Beacham, T. D., S. Cox-Rogers, C. MacConnachie, B. McIntosh, and C. G. Wallace. 2014. Population structure and run timing of sockeye salmon in the Skeena River, British Columbia: Response to comment. North American Journal of Fisheries Management 34: 1171-1176.
178. Beacham,T. D., Richard J. Beamish, John R. Candy, Strahan Tucker, Jamal H. Moss, and Marc Trudel. 2014. Stock-specific migration pathways of juvenile sockeye salmon in British Columbia waters and in the Gulf of Alaska. Transactions of the American Fisheries Society 143: 1386-1403.
177. Miller, K.M., A. Teffer, S. Tucker, S. Li, A.D. Schulze, M. Trudel, F. Juanes, A. Tabata, K.H. Kaukinen, N.G. Ginther, T.J. Ming, S.J. Cooke, J.M. Hipfner, D.A. Patterson, and S.G. Hinch. 2014. Infectious disease, shifting climates and opportunistic predators: cumulative factors potentially impacting wild salmon declines. Evolutionary Applications 7: 812-855. doi: 10.1111/eva.12164.
176. Anttila, K, E.J. Eliason, K.H. Kaukinen, K.M. Miller, and A.P. Farrell. 2014. Facing warm temperatures during migration – cardiac mRNA responses of two adult sockeye salmon Oncorhynchus nerka populations to warming and swimming challenges. Journal of Fish Biology 84: 1439-1456.
175. Withler R.E., D.S. O’Brien, N.M. Watson, and K.J. Supernault. 2014. Maintenance of genetic diversity in natural spawning of captively-reared endangered sockeye salmon, Oncorhynchus nerka. Diversity 6: 354-379. doi:10.3390/d6020354
174. Donaldson, M.R., S.G. Hinch, K.M. Jeffries, D.A. Patterson, S.J. Cooke, A.P. Farrell, and K.M. Miller. 2014. Species- and sex-specific responses and recovery of wild, mature Pacific salmon to an exhaustive exercise and air-exposure stressor. Comparative Biochemistry and Physiology: A 173: 7-16.
173. Araujo, H. Andres, John R. Candy, Terry D. Beacham, Bruce White, and Colin Wallace. 2014. Advantages and challenges of genetic stock identification in fish stocks with low genetic resolution. Transactions of the American Fisheries Society 143: 479-488.
172. Beacham,T. D., Richard J. Beamish, John R. Candy, Strahan Tucker, Jamal H. Moss, and Marc Trudel. 2014. Stock-specific migration size of juvenile sockeye salmon in British Columbia waters and in the Gulf of Alaska. Transactions of the American Fisheries Society 143: 876-888.
171. Beacham, T. D., S. Cox-Rogers, C. MacConnachie, B. McIntosh, and C. G. Wallace. 2014. Population structure and run timing of sockeye salmon in the Skeena River, British Columbia. North American Journal of Fisheries Management 34: 335-348.
170. Jeffries, K.M., S.G. Hinch, T. Sierocinski, P. Pavlidis, and K.M. Miller. 2014. Transcriptomic responses to high water temperature in two species of Pacific salmon. Evolutionary Applications 7(2): 286-300.
2013
169. McClelland, E. K., Tobi J Ming, Amy Tabata, Terry D Beacham, Ruth E Withler, and Kristina M Miller. 2013. Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka). Molecular Ecology 22:4783-4800.
168. Siegle, M.R., E.B. Taylor, K.M. Miller, R.E. Withler and K.L. Yamanaka. 2013. Subtle population genetic structure in Yelloweye Rockfish (Sebastes ruberrimus) is consistent with a major oceanographic division in British Columbia, Canada. PLoS ONE 8(8): e71083.
167. Moran, P., David A. Teel, Shawn R. Narum, Jon E. Hess, John R. Candy, Colin G. Wallace, Terry D. Beacham, John Carlos Garza, Michael A. Banks, M. Renee Bellinger, Scott M. Blankenship, Lisa W. Seeb, William D. Templin, and Christian T. Smith. 2013. Divergent life-history races do not represent Chinook salmon coast-wide: the importance of scale in Quaternary biogeography. Canadian Journal of Fisheries and Aquatic Sciences 70: 415-435.
166. Araujo, H.A., C.A. Holt, J.M.R. Curtis, R.I. Perry, J.R. Irvine, and C.G.J. Michielsens 2013. Building an ecosystem model using mismatched and fragmented data: a probabilistic network of early marine survival for coho salmon, Oncorhynchus kisutch, in the Strait of Georgia. Progress in Oceanography 115:41-52.
2012
165. Jeffries, K. M., Scott G. Hinch Thomas Sierocinski, Timothy D. Clark,Erika J. Eliason, Michael R. Donaldson, Shaorong Li, Paul Pavlidis, and Kristi M. Miller. 2012. Consequences of high temperatures and premature mortality on the transcriptome and blood physiology of wild adult sockeye salmon (Oncorhynchus nerka). Ecology and Evolution 2: 1747-1764.
164. Shelley, L. K., Peter S. Ross, Kristina M. Miller, Karia H. Kaukinen, and Christopher J. Kennedy. 2012. Toxicity of atrazine and nonylphenol in juvenile rainbow trout (Oncorhynchus mykiss): Effects on general health, disease susceptibility and gene expression. Aquatic Toxicology 124–125: 217– 226.
163. Benham, C.E., Supernault, K.J., and Burton, R.S. 2012. Genetic assessment of the population connectivity of the red urchin (Strongylocentrotus franciscanus). Journal of Experimental Marine Biology and Ecology 432-433:47-54.
162. Gutierrez, A.P., Lubieniecki, K.P., Davidson, E.A., Lien, S., Kent, M.P., Fukui, S., Withler, R.E., Swift, B., and Davidson, W.S. 2012. Genetic mapping of quantitative trait loci (QTL) for body-weight in Atlantic salmon (Salmo salar) using a 6.5 K SNP array. Aquaculture 358: 61-70.
161. Martins, E.G., Hinch, S.G., Patterson, D.A., Hague, M.J., Cooke, S.J., Miller, K.M., Robichaud, D., English, K.K., Farrell, A.P. 2012. High river temperature reduces survival of sockeye salmon approaching spawning grounds and exacerbates female mortality. Canadian Journal of Fisheries and Aquatic Sciences 69: 330-342.
160. Cooke, S.J., Hinch, S.G., Donaldson, M.R., Clark, T.D., Eliason, E.J., Crossin, G.T., Raby, G., Jeffries, K.M., Lapointe, M., Miller, K.M., Patterson, D.A., Farrell, A.P. 2012. Conservation physiology in practice: has physiology improved our ability to sustainably manage Pacific salmon during upriver migration? Philosophical Transactions of the Royal Society of London B – Biological Sciences 367: 1757-1769.
159. Hinch, S. G., S. J. Cooke, A. P. Farrell, K. M. Miller, M. Lapointe, and D. A. Patterson. 2012. Dead fish swimming: a review of research on the early migration and high premature mortality in adult Fraser River sockeye salmon Oncorhynchus nerka. Journal of Fish Biology 81: 576-599.
158. Preikshot, D., R. J Beamish, R. M Sweeting, C. M. Neville and T. D. Beacham. 2012. The residence time of juvenile Fraser River sockeye salmon in the Strait of Georgia. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 4: 438-449.
157. Thomson, R., R. J. Beamish, T. D. Beacham, M. Trudel, P. H. Whitfield, and R. A. S. Hourston. 2012. Anomalous ocean conditions may explain the recent extreme variability in Fraser River sockeye salmon production. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 4: 415-437.
156. Flannery, B. G., P. A. Crane, J. H. Eiler, T. D. Beacham, W. D. Templin, O. L. Schlei, and J. K. Wenburg. 2012. Comparison of radio telemetry and genetic methods for determining the origin of Yukon River Chinook salmon. North American Journal of Fisheries Management 32: 720-730.
156. Beacham, T. D., Brenda McIntosh, Cathy MacConnachie, Brian Spilsted, and Bruce A. White. In review. Pink salmon (Oncorhynchus gorbuscha) population structure in British Columbia and Washington as determined with microsatellites. Fishery Bulletin - Supplemental material
155. Beacham, T. D., Brenda McIntosh, Cathy MacConnachie, Brian Spilsted, and Bruce A. White. 2012. Population structure of pink salmon (Oncorhynchus gorbuscha) in British Columbia and Washington, determined with microsatellites. Fishery Bulletin 110: 242-256.
154. Jeffries, K.M., Hinch, S.G., Martins, E.G., Clark, T.D., Lotto, A.G., Patterson, D.A., Cooke, S.J., Farrell, A.P., Miller, K.M. 2012. Sex and proximity to reproductive maturity influence the survival, final maturation, and blood physiology of Pacific salmon when exposed to high temperature during a simulated migration. Physiological and Biochemical Zoology 85: 62-73.
153. Hammill, E., Curtis, J.M.R., Patterson, D.A., Farrell, A.P., Sierocinski, T., Pavlidis, P., Hinch, S.G., Miller, K. 2012. Comparison of techniques for correlating survival and gene expression data from wild salmon. Ecology of Freshwater Fish 21: 189-199.
152. Beacham, T. D., Colin G. Wallace, Khai D. Le, and Mark Beere. 2012. Population structure and run timing of steelhead trout in the Skeena River, British Columbia. North American Journal of Fisheries Management 32: 262-275.
151. Beamish, R. J., R.M. Sweeting, C.M. Neville, K.L. Lange, T.D. Beacham and D. Preikshot. 2012. Wild Chinook salmon survive much better than hatchery salmon in a period of poor production. Environmental Biology of Fishes 94: 135-148. DOI 10.1007/s10641-011-9783-5
150. Beacham. T. D., J. R. Candy, C. Wallace, M. Wetklo, L. Deng, and C. MacConnachie. 2012. Microsatellite mixed-stock identification of coho salmon (Oncorhynchus kisutch) in British Columbia. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 4: 85-100.
149. Beacham, T. D., K. Jonsen, and C. Wallace. 2012. A comparison of stock and individual identification for Chinook salmon in British Columbia provided by microsatellites and single nucleotide polymorphisms (SNPs). Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 4: 1-22.
148. Tucker, M. Trudel, D.W. Welch, J.R. Candy, J.F.T. Morris, M.E. Thiess, C. Wallace, and T.D. Beacham. 2012. Annual coastal migration of juvenile Chinook salmon: Static stock-specific patterns in a dynamic ocean. Marine Ecology Progress Series 449: 245-262.
147. Evans, ML, Dionne, M., Miller, KM and L. Bernatchez. 2012. Mate choice for major histocompatibility complex genetic divergence as a bet-hedging strategy in the Atlantic salmon (Salmo salar). Proceedings of the Royal Society of London, B. 279: 379-386.
2011
146. Godbout, L., C.C. Wood, R.E. Withler, S. Latham, J. Nelson, L. Wetzel, R. Barnett-Johnson, M. J. Grove, A.K. Schmitt and K.D. McKeegan. 2011. Sockeye salmon (Oncorhynchus nerka) return after an absence of nearly 90 years: a case of reversion to anadromy. Canadian Journal of Fisheries and Aquatic Sciences 68: 1590-1602.
145. Withler, R.E., R.H. Devlin, S. Latham, C.C. Wood and K. J. Supernault. 2011. Analysis of gene origin in the first adult returns to the Cultus sockeye salmon captive breeding program. Conservation Genetics 12: 1469-1483.
144. Martins, E.G., Hinch, S.G., Patterson, D.A., Hague, M.J., Cooke, S.J., Miller, K.M., Lapointe, M.F., English, K.K., and A.P. Farrell. 2011. 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. doi: 10.1111/j.1365-2486.2010.02241.x
143. Evans, T.G., E.D.D. Hammill, K. Kaukinen, A.D. Schulze, D.A. Patterson, K.K. English, J.M.R. Curtis, and K.M. Miller. 2011. Transcriptomics of environmental acclimatization and survival in wild adult Pacific sockeye salmon (Oncorhynchus nerka) during spawning migration. Molecular Ecology 20(21): 4472-4489. doi: 10.1111/j.1365-294X.2011.05276.x
142. 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, A. G. Lotto, K. A. Hruska, I. C. Olsson, G. N. Wagner, R. Thomson, R. Hourston, K. K. English, S. Larsson, J. M. Shrimpton, and G. Van der Kraak. 2011. Developing a mechanistic understanding of fish migrations by linking telemetry with physiology, behavior, genomics, and experimental biology: An interdisciplinary case study on adult Fraser River sockeye salmon. Fisheries 33: 321-339.
141. McClelland, E. K., T. J. Ming, A. Tabata, and K. M. Miller. 2011. Sequence analysis of MHC class I α2 from sockeye salmon (Oncorhynchus nerka). Fish & Shellfish Immunology 31: 507-510.
140. Liu, J.-X., A. Tatarenkov, T. D. Beacham, V. Gorbachev, S. Wildes, and J. C. Avise. 2011. Effects of Pleistocene climatic fluctuations on the phylogeographic and demographic histories of Pacific Herring (Clupea pallasi). Molecular Ecology 20: 3879-3893.
139. Tucker, S., M. Trudel, D.W. Welch, J.R. Candy, J.F.T. Morris, M.E. Thiess, C. Wallace, Jr and T.D. Beacham. 2011. Life history and seasonal stock-specific ocean migration of juvenile Chinook salmon. Transactions of the American Fisheries Society 140: 1101-1119.
138. Jeffries, K. M., S. G. Hinch, M. R. Donaldson, M. K. Gale, J. M. Burt, L. A. Thompson, A. P. Farrell, D. A. Patterson, and K. M. Miller. 2011. Temporal changes in blood variables during final maturation and senescence in male sockeye salmon Oncorhynchus nerka: reduced osmoregulatory ability can predict mortality. Journal of Fish Biology 79: 449-465.
137. Beacham, T. D., J. R. Candy, E. Porszt, S. Sato, and S. Urawa. 2011. Microsatellite identification of Canadian sockeye salmon rearing in the Bering Sea. Transactions of the American Fisheries Society 140: 296-306.
136. Beacham, T. D., B. McIntosh, and C. Wallace. 2011. A comparison of polymorphism of genetic markers and population sample sizes required for mixed-stock analysis of sockeye salmon (Oncorhynchus nerka) in British Columbia. Canadian Journal of Fisheries and Aquatic Sciences 68: 550-562.
135. Ford, J.K.B., G.M. Ellis, C.O. Matkin, M.H. Wetklo, L.G. Barrett-Lennard and R.E. Withler. 2011. Shark predation and tooth wear in a population of northeastern Pacific killer whales. Aquatic Biology 11: 213-224.
134. 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: 214-217.
133. Candy, J. R., C. G. Wallace, and T. D. Beacham. 2011. Distance-based population classification software using mean-field annealing. Molecular Ecology Resources 11: 116-125.
132. Beacham, T. D., M. Wetklo, L. Deng, and C. MacConnachie. 2011. Coho salmon population structure in North America determined from microsatellites. Transactions of the American Fisheries Society 140: 253-270.
2010
131. Ford, J.K.B., G. M. Ellis, C. O. Matkin, M. H. Wetklo, L. G. Barrett-Lennard, and R. E. Withler. 2010. Shark predation and tooth wear in a population of northeastern Pacific killer whales. Aquatic Biology 11(3):213-224.
130. Flannery, B. G., T. D. Beacham, J. R. Candy, R. R. Holder, G. F. Maschmann, E. J. Kretschmer, and J. K. Wenburg. 2010. Mixed-stock analysis of Yukon River chum salmon: Application and validation in a complex fishery. North American Journal of Fisheries Management 30: 1324-1338.
129. Beacham, T. D., B. McIntosh, and C. Wallace. 2010. A comparison of stock and individual identification for sockeye salmon (Oncorhynchus nerka) in British Columbia provided by microsatellites and single nucleotide polymorphisms. Canadian Journal of Fisheries and Aquatic Sciences 67: 1274-1290.
128. 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 migration. Physiological and Biochemical Zoology 83:446-458.
127. Olsen, J. B., T. D. Beacham, M. Wetklo, L. W. Seeb, C. T. Smith, B. G. Flannery, and J. K. Wenburg. 2010. The influence of hydrology and waterway distance on population structure of Chinook salmon (Oncorhynchus tshawytscha) in a large river. Journal of Fish Biology 76: 1128-1148.
126. Beacham, T. D. 2010. Revisiting trends in evolution of egg size in hatchery-enhanced populations of Chinook salmon from British Columbia. Transactions of the American Fisheries Society 139: 579-585.
125. Beacham, T.D., and R. E. Withler. 2010. Comment on “Gene flow increases temporal stability of Chinook salmon (Oncorhynchus tshawytscha) populations in the Upper Fraser River, British Columbia, Canada”. Canadian Journal of Fisheries and Aquatic Sciences 67: 202-205.
124. Hanson, M.B., R.W. Baird, J.K.B. Ford, J. Hempelmann, D. Van Doornik, J. Candy, C. K. Emmons, G. S. Schorr, B. Gisborne, K. L. Ayres, S. K. Wasser, K. C. Balcomb, K. Balcomb-Bartok, and M. J. Ford. 2010. Species and stock identification of prey selected by endangered southern resident killer whales in their summer range. Endangered Species Research 11: 69-82.
123. Campbell, A., R.E. Withler and K.J. Supernault. 2010. Occurrence of the red abalone Haliotis rufescens in British Columbia, Canada. American Malacological Bulletin 28: 185-188.
122. Supernault, K.J., A. Demsky, A. Campbell, T.J. Ming, K.M. Miller and R.E. Withler. 2010. Forensic genetic identification of abalone (Haliotis spp.) of the northeastern Pacific Ocean. Conservation Genetics 11: 855 - 865. DOI: 10.1007/s10592-009-9925-x.
2009
121. 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.
120. Beacham, T. D., J. R. Candy, S. Urawa, S. Sato, K. D. Le, and M. Wetklo. 2009. Stock origins of chum salmon (Oncorhynchus keta) in the Gulf of Alaska and eastern Pacific Ocean during winter as estimated with microsatellites. North Pacific Anadromous Fish Commission Research Bulletin 5: 15-23.
119. Tucker, S., M. Trudel, D.W. Welch, J.R. Candy, J.F.T. Morris, M.E. Thiess, C. Wallace, D.J. Teel, W. Crawford, E.V. Farley, Jr and T.D. Beacham. 2009. Seasonal stock-specific migrations of juvenile sockeye salmon along the west coast of North America: implications for growth. Transactions of the American Fisheries Society 138: 1458-1480.
118. Beacham, T. D., J. R. Candy, C. Wallace, S. Urawa, S. Sato, N. V. Varnavskaya, K. D. Le, and M. Wetklo. 2009. Microsatellite stock identification of chum salmon on a Pacific Rim basis. North American Journal of Fisheries Management 29: 1757-1776.
117. 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. Comparative Biochemistry and Physiology D 4: 75-89.
116. McPhee, M., M. Zimmerman, T. Beacham, B. Beckman, J. Olsen, L. W. Seeb, and W. D. Templin. 2009. Hierarchies in pattern and process: genetics and ecology of Pacific salmon in the Alaska-Yukon-Kuskokwim region. Pages 1177-1198. 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.
115. Winther, I., and T. D. Beacham. 2009. The application of Chinook salmon stock composition data to management of the Queen Charlotte Islands troll fishery, 2006. Pages 977-1004. 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.
114. 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.
113. Macdonald, R. W., V. Forsland, R. E. Withler, D. A. Patterson, and A. Demsky. 2009. The use of stable oxygen isotope (δ18O) composition in sockeye salmon body fluid to determine whether a fish has been caught in freshwater. North American Journal of Fisheries Management 29: 560-569.
112. Beacham, T. D., J. R. Candy, K. D. Le, and M. Wetklo. 2009. Population structure of chum salmon (Oncorhynchus keta) across the Pacific Rim determined from microsatellite analysis. Fishery Bulletin 107: 244-260.
111. Candy, J. R., R. G. Bonnell, T. D. Beacham, C. G. Wallace, and R. E. Withler. 2009. Dividing population genetic data with the software Partitioning Optimization using Restricted Growth Strings (PORGS): an application to Chinook salmon (Oncorhynchus tshawytscha), Vancouver Island, British Columbia. Fishery Bulletin 107: 45-56.
110. 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.
109. Cooke, S.J. S.G. Hinch, A. P. Farrell, D.A. Patterson, K.M. Miller, D. Welch, M.R. Dondaldson, K.C. Hanson, G.T. Crossin, I. Olsson, M.S. Cooperman, M.T. Mathes, K.A. Hruscka, G.N. Wagner, R. Thomson. S. Larsson, K.K. English, J.M. Shrimpton, G.Van Der Kraak. 2009. Interdisciplinary applications of telemetry to the study of fish migration. Fisheries Management and Ecology 33(7): 321-338.
2008
108. Riddell, B.E., R. J. Beamish, L. J. Richards, and J. R. Candy. 2008. Comment on “Declining Wild Salmon Populations in Relation to Parasites from Farm Salmon”. Science 332: 1790.
107. Olsen, J. B., B. Flannery, T. D. Beacham, J. F. Bromaghin, P. A. Crane, C. F. Lean, K. M. Dunmall, and J. K. Wenburg. 2008. The influence of hydrographic structure and seasonal run-timing on genetic diversity and isolation-by-distance patterns in chum salmon (Oncorhynchus keta). Canadian Journal of Fisheries and Aquatic Sciences 65: 2026-2042.
106. Beacham, T. D., B. Spilsted, K. D. Le, and M. Wetklo. 2008. Population structure and stock identification of chum salmon Oncorhynchus keta from British Columbia determined with microsatellite DNA variation. Canadian Journal of Zoology 86: 1002-1014.
105. 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 single nucleotide polymorphisms. Molecular Ecology 17: 3464-3477.
104. Beacham, T. D., J. F. Schweigert, C. MacConnachie, K. D. Le, and L. Flostrand. 2008. Determination of population structure and migration of Pacific herring in British Columbia and adjacent regions with microsatellites. Transactions of the American Fisheries Society 137: 1795-1811.
103. 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: 901-906.
102. Beacham, T. D., S. Urawa, K. D. Le, and M. Wetklo. 2008. Population structure and stock identification of chum salmon from Japan determined with microsatellite DNA variation. Fisheries Science 74: 983-994.
101. Winans, G.A., M. L. McHenry, J. Baker, A. Eiz, A. Goodbla, E. Iwamoto, E. Kuligowski, K.M. Miller, M.P. Small, P. Spruell, and D. Van Doornik. 2008. Genetic inventory for anadromous Pacific salmonids of the Elwha River prior to dam removal. Northwest Science 82: 128-140.
100. Miller, K.M. and N. Maclean. 2008. Teleost microarrays: development in a broad phylogenetic range reflecting diverse applications. Journal of Fish Biology 72: 1-11.
99. 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.
98. Beacham, T. D., N. V. Varnavskaya, K. D. Le, and M. Wetklo. 2008. Determination of population structure and stock identification of chum salmon (Oncorhynchus keta) in Russia, determined with microsatellites. Fishery Bulletin 106: 245-256.
97. Beacham, T. D., M. Wetklo, C. Wallace, J. B. Olsen, B. G. Flannery, J. K. Wenburg, W. D. Templin, A. Antonovich, and L.. W. Seeb. 2008. The application of microsatellites for stock identification of Yukon River Chinook salmon. North American Journal of Fisheries Management 28: 283-295.
96. Parken, C. K., J. R. Candy, J. R. Irvine, and T. D. Beacham. 2008. Genetic and coded wire tag results combine to allow more precise management of a complex Chinook salmon aggregate. North American Journal of Fisheries Management 28: 328-340.
95. Beacham, T. D., I. Winther, K. L. Jonsen, M. Wetklo, L. Deng, and J. R. Candy. 2008. The application of rapid microsatellite-based stock identification to management of a Chinook salmon troll fishery off the Queen Charlotte Islands, British Columbia. North American Journal of Fisheries Management 28: 849-855.
2007
94. Rajakaruna, R. S., J. A. Brown, K. H. Kaukinen, and K. M. Miller. 2006. Major histocompatibility complex and kin discrimination in Atlantic salmon and Brook trout. Molecular Ecology 15: 4569-4575.
93. 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). Diseases of Aquatic Organisms 75: 239-49.
92. Dionne M, K. M. Miller, J. J. 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.
91. Lukacs, M. F., H. Harstad, U. Grimholt, M. Beetz-Sargent, G. A. cooper, L. Reid, H. G. Bakke, R. B. Phillips, K. M. Miller, W. S. Davidson, B. F. Koop. 2007. Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar). BMC Genomics 8: 251 (25 July 2007).
90. Withler, R. E., J. Supernault, B. Swift, R. Peterson and S. Fukui. 2007. Microsatellite DNA assignment of progeny to parents enables communal freshwater rearing in an Atlantic salmon selective breeding program. Aquaculture 272 (Supplement 1): S318.
89. Withler, R.E., T. Rundle and T.D. Beacham. 2007. Genetic identification of wild and domesticated strains of Chinook salmon in southern British Columbia, Canada. Aquaculture 272 (Supplement 1): S161-S171.
88. Miller, K.M., G. Traxler, K.H. 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 (Supplement 1): S217-S237.
87. Seeb, L. W., A. Antonovich, M. A. Banks, T. D. Beacham, M. R. Bellinger, M. Campbell, N. A. Decovich, J. C. Garza, C. M. Guthrie III, P. Moran, S. R. Narum, J. J. Stephenson, K. J. Supernault, D. J. Teel, W. D. Templin, J. K. Wenburg, S. F. Young, and C. T. Smith. 2007. Development of a standardized DNA database for Chinook salmon. Fisheries 32: 540-552.
86. Ikonomou, M.G., D.A Higgs, M. Gibbs, J. Oakes, B. Skura, S. McKinley, S.K. Balfry, S. Jones, R. Withler and C. Dubetz. 2007. Flesh quality of market-size farmed and wild British Columbia salmon. Environmental Science & Technology: 41:437-443.
85. Miller, K. M., K. Kaukinen, S. Li, T. Farrell, and D. Patterson. 2007. Expression profiling of late run sockeye salmon: Migration physiology uncovered using cDNA microarray technology. In: (C. A. Woody, editor). Sockeye salmon Evolution, Ecology, and Management. American Fisheries Society Symposium 54: 101-103.
2006
84. Beacham, K. L. Jonsen, J. Supernault, M. Wetklo, L. Deng, and N. Varnavskaya. 2006. Pacific Rim population structure of Chinook salmon as determined from microsatellite analysis. Transactions of the American Fisheries Society 135: 1604-1621.
83. Rajakaruna, R.S., J.A. Brown, K.H. Kaukinen, and K.M. Miller. 2006. Major histocompatibility complex and kin discrimination in Atlantic salmon and Brook trout. Molecular Ecology 15: 4569-4575.
82. Tymchuk, W.E., C. Biagi, R. E. Withler, and R. H. Devlin. 2006. Growth and behavioral consequences of introgression of a domesticated aquaculture genotype into a native strain of coho salmon. Transactions of the American Fisheries Society 135: 442-455.
81. Schulze, A.D., Alabi, A.O., Tattersall-Sheldrake, A.R. and K.M. Miller. 2006. Bacterial diversity in a marine hatchery: Balance between pathogenic and potentially probiotic bacterial strains. Aquaculture. 50-73.
80. 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.
79. Miller, K.M., K.J. Supernault, S. Li, and R.E. Withler. 2006. Population structure in two marine invertebrate species (Panopea abrupta and Stronylocentrotus franciscanus) targeted for aquaculture and enhancement in British Columbia. Journal of Shellfish Research: 33-42.
78. Miller, K.M, S. Li, T.J. Ming, K.H. Kaukinen, and A.D. Schulze. 2006. The salmonid MHC class I: More ancient loci uncovered. Immunogenetics: 571-589
77. 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.
76. Beacham, T.D., N. V. Varnavskaya, B. McIntosh, and C. MacConnachie. 2006. Population structure of sockeye salmon from Russia determined with microsatellite DNA variation. Transactions of the American Fisheries Society 135: 97-109.
2005
75. Beacham, T.D., B. McIntosh, and C. MacConnachie. 2005. Population structure and stock identification of sockeye salmon (Oncorhynchus nerka) in coastal lakes in British Columbia, Canada. Canadian Journal of Zoology 83: 834-844.
74. Beacham, T.D., J.R. Candy, B. McIntosh, C. MacConnachie, A.Tabata, K. Kaukinen, L. Deng, K. M. Miller, R. E. Withler, and N. V. Varnavskaya. 2005. Estimation of stock composition and individual identification of sockeye salmon on a Pacific Rim basis using microsatellite and major histocompatibility complex variation. Transactions of the American Fisheries Society 134: 1124-1146.
73. 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 in southeast Alaska and the Nass and Skeena rivers, British Columbia, with applications to stock identification. North American Journal of Fisheries Management. 25: 763-776.
72. Beacham, T.D., D. E. Hay, and K. D. Le. 2005. Population structure and stock identification of eulachon (Thaleichthys pacificus), an anadromous smelt, in the Pacific northwest. Marine Biotechnology. 7: 363-372.
71. 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.
70. King, J.R. and R.E. Withler. 2005. Male nest site fidelity and female serial polyandry in lingcod (Ophiodon elongatus, Hexagrammidae). Molecular Ecology 14: 653-660.
2004
69. Miller, K.M., K.H. Kaukinen, K Laberee, and K.J. Supernault. 2004. Microsatellite loci from red sea urchins (Strongylocentrotus franciscanus). Molecular Ecology Notes 4:722-724.
68. Kaukinen, K.H., K.J. Supernault, and K.M. Miller. 2004. Development of microsatellite loci in eulachon (Thaleichthys pacificus). Molecular Ecology Notes 4:632-634.
67. Kaukinen, K.H, K.J. Supernault, and K.M. Miller. 2004. Enrichment of tetranucleotide microsatellite loci from marine invertebrates. Journal of Shellfish Research 23: 621-626.
66. 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 using microsatellites and major histocompatibility complex variation. Transactions of the American Fisheries Society 133: 1117-1137.
65. Beacham, T.D., B. McIntosh, and C. MacConnachie. 2004. Population structure of lake-type and river-type sockeye salmon in transboundary rivers of northern British Columbia, Canada. Journal of Fish Biology 65: 389-402.
64. Beachem, 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. Conservation Genetics 5: 411-416.
63. Beacham, T.D., K.D. Le, and J.R. Candy. 2004. Population structure and stock identification of steelhead trout (Oncorhynchus mykiss) in British Columbia and the Columbia River based on microsatellite variation. Environmental Biology of Fishes 69: 95-109.
62. Kim, J.E., R.E. Withler, C. Ritland and K.M. Cheng. 2004. Genetic variation within and between domesticated chinook salmon (Oncorhynchus tshawytscha) strains and their progenitor populations. Environmental Biology of Fishes 69: 371-378.
61. 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. Environmental Biology of Fishes 69: 275-285.
60. 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. Environmental Biology of Fishes 69: 345-357.
59. 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. Environmental Biology of Fishes 69: 307-316.
2003
58. 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.
57. Withler, R.E., A. Campbell, S. Li, D. Brouwer, K.J. Supernault and K.M. Miller. 2003. Implications of high levels of genetic diversity and weak population structure for the rebuilding of northern abalone in British Columbia, Canada. Journal of Shellfish Research 22: 839-847.
56. Beacham, T.D. 2003. Comment on "Rapid evolution of egg size in captive salmon" (II). Science 302: 59d.
55. 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.
54. 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 .
2002
53. Miller, K.M., K.H. Kaukinen, and A.D. Schulze. 2002. Expansion and contraction of major histocompatibility complex (MHC) genes: a teleostean example. Immunogenetics 53: 941-963.
52. St-Hilaire, S., M. Boichuk, D. Barnes, M. Higgins, R. Devlin, R. Withler, J. Khattra, S. Jones and D. Kieser. 2002. Epizootiology of Parvicapsula minibicornis in Fraser River sockeye salmon, Oncorhynchus nerka (Walbaum). Journal of Fish Diseases 25: 107-120.
51. Beacham, T.D., B. McIntosh, and C. MacConnachie. 2002. Microsatellite identification of individual sockeye salmon (Oncorhynchus nerka) in Barkley Sound, British Columbia. Journal of Fish Biology 61: 1021-1032.
50. 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 Journal of Marine Science 59: 650-655.
2001
49. Miller, K.M., K. Laberee, K.H. Kaukinen, S. Li, and R.E. Withler. 2001. Development of microsatellite loci in pinto abalone (Haliotis kamtschatkana). Molecular Ecology Notes 1: 315-317.
48. Miller, K.M., K. Laberee, A.D. Schulze, and K.H. Kaukinen. 2001. Development of microsatellite loci in Pacific herring (Clupea pallasi). Molecular Ecology Notes 1: 131-132.
47. Miller, K.M., K.H. Kaukinen, T.D. Beacham, and R.E. Withler. 2001. Geographic heterogeneity in natural selection of an MHC locus in sockeye salmon. Genetica 111: 237-257.
46. 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. Transactions of the American Fisheries Society 130: 1116-1155.
45. 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. Marine Biology 139: 1-12.
44. Nelson, R.J., M.P. Small, T.D. Beacham, and K.J. Supernault. 2001. Population structure of Fraser River chinook salmon (Oncorhynchus tshawytscha): an analysis using microsatellite DNA markers. Fishery Bulletin 99: 94-107.
2000
43. Miller, K.M., T.J. Ming, A.D. Schulze, and R.E. Withler. 2000. Denaturing gradient gel electrophoresis (DGGE): a rapid and sensitive technique to screen nucleotide sequence variation in populations. P. 253-258. In: J.D. Burczak and E. Mardis (eds.). Polymorphism Detection and Analysis. Eaton Publishing.
42. Candy, J.R., and T. D. Beacham. 2000. Patterns of homing and straying in sothern British Columbia coded-wire tagged chinook salmon (Oncorhynchus tshawytscha) populations. Fisheries Research 47: 41-56.
41. Withler, R.E. 2000. Genetic tools for identification and conservation of exploited abalone (Haliotis spp.) species. In: A. Campbell (ed). Workshop on rebuilding abalone stocks in British Columbia. Canadian Special Publication of Fisheries and Aquatic Sciences 130: 101-110.
40. 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 9: 240-241.
39. 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: 238-239.
38. Beacham, T.D., S. Pollard, and K. Le. 2000. Microsatellite DNA population structure and stock identification of steelhead trout (Oncorhynchus mykiss) in the Nass River and Skeena Rivers in northern British Columbia. Marine Biotechnology 2: 587-600.
37. 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.
36. 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). North Pacific Anadromous Fish Commission Research Bulletin 2: 263-276.
35. Beacham, T.D., K.D. Le, M.R. Raap, K. Hyatt, W. Luedke, and R.E. Withler. 2000. Microsatellite DNA variation and estimation of stock composition of sockeye salmon (Oncorhynchus nerka) in Barkley Sound, British Columbia. Fishery Bulletin (US) 98: 14-24.
1999
34. 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.
33. Beacham, T.D., S. Pollard, and K.D. Le. 1999. Population Structure and Stock Identification of Steelhead in Southern British Columbia, Washington, and the Columbia River Based on Microsatellite DNA Variation. Transactions of the American Fisheries Society 128: 1068-1084.
32. Shaklee, J.B., T.D. Beacham, L. Seeb, and B. White. 1999. Managing Pacific salmon fisheries using genetic data: Case studies from four species of Pacific salmon. Fisheries Research 43: 45-78.
31. Nelson, R.J., and T.D. Beacham. 1999. Isolation and cross species amplification of microsatellite loci useful for study of Pacific salmon. Animal Genetics 30: 228-229.
30. Beacham, T.D., and C.C. Wood. 1999. Application of microsatellite DNA variation to estimation of stock composition and escapement of Nass River sockeye salmon (Oncorhynchus nerka). Canadian Journal of Fisheries and Aquatic Sciences 56: 297-310.
1998
29. Miller, K.M., and R.E. Withler 1998. The salmonid class I Mhc: Limited diversity in a primitive teleost. Immunological Reviews 166: 279-293.
28. Nelson, R.J., T.D. Beacham, and M.P. Small. 1998. Microsatellite analysis of the population structure of a Vancouver Island sockeye salmon (Oncorhynchus nerka) stock complex using non-denaturing gel electrophoresis. Molecular Marine Biology and Biotechnology 7: 312-319.
27. Beacham, T.D., and J.B. Dempson. 1998. Population structure of Atlantic salmon (Salmo salar) from the Conne River, Newfoundland as determined from microsatellite DNA. Journal of Fish Biology 52: 665-676.
26. Small, M.P., R.E. Withler, and T.D. Beacham. 1998. Population structure and stock identification of British Columbia coho salmon, Oncorhynchus kisutch, based on microsatellite DNA variation. Fishery Bulletin (US)96: 843-858.
25. Small, M.P., T.D. Beacham, R.E. Withler, and R.J. Nelson. 1998. Discriminating coho salmon (Oncorhynchus kisutch) populations within the Fraser River, British Columbia using microsatellite DNA markers. Molecular Ecology 7:141-155.
24. Beacham, T.D., L. Margolis, and R. J. Nelson. 1998. A comparison of methods of stock identification for sockeye salmon (Oncorhynchus nerka) in Barkley Sound, British Columbia. North Pacific Anadromous Fish Commission Bulletin 1: 227-239.
1997
23. Miller, K.M., and R.E. Withler. 1997. Mhc diversity in Pacific salmon: population structure and trans-species allelism. Hereditas 127:83-95.
22. Withler, R.E., T.D. Beacham, T.J. Ming and K.M. Miller. 1997. Species identification of Pacific salmon by means of a major histocompatibility complex gene. North American Journal of Fisheries Management 17: 929-938.
21. Withler, R.E., and K.M. Miller. 1997. Structure of an unusual minisatellite locus, Ssa1, in Pacific salmonids. Journal of Heredity 88: 415-422.
20. Miller, K.M., R.E. Withler, and T.D. Beacham. 1997. Molecular evolution at Mhc genes in two populations of chinook salmon Oncorhynchus tshawytscha. Molecular Ecology 6: 937-954.
1996
19. Miller, K.M, and R.E. Withler. 1996. Sequence analysis of a polymorphic Mhc class II gene in Pacific salmon. Immunogenetics 43: 337-351.
18. Beacham, T.D., K.M. Miller, and R.E. Withler. 1996. Minisatellite DNA variation and stock identification of coho salmon (Oncorhynchus kisutch). Journal of Fish Biology 49: 411-429.
17. Beacham, T.D. 1996. The use of minisatellite DNA variation for stock identification of chum salmon (Oncorhynchus keta). Fisheries Bulletin (U.S.) 94: 611-627.
16. Beacham, T.D., R.E. Withler, and T.A. Stevens. 1996. Stock identification of chinook salmon (Oncorhynchus tshawytscha) using minisatellite DNA variation. Canadian Journal of Fisheries and Aquatic Sciences 53: 380-394.
15. Miller, K.M., R.E. Withler, and T.D. Beacham. 1996. Stock identification of coho salmon (Oncorhynchus kisutch) using minisatellite DNA variation. Canadian Journal of Fisheries and Aquatic Sciences 53: 181-195.
14. Taylor, E.B., C.C. Foote, and C.C. Wood. 1996. Molecular genetic evidence for parallel life history evolution in a Pacific salmon (sockeye salmon and kokanee, Oncorhynchus nerka). Evolution 50: 401-416.
1995
13. Withler, R.E. and T.D. Beacham. 1995. Freshwater growth, smolting, and marine survival and growth of diploid and triploid coho salmon (Oncorhynchus kisutch). Aquaculture 136: 91-107.
12. Taylor, E.B. 1995. Genetic variation at minisatellite DNA loci among North Pacific populations of steelhead and rainbow trout (Oncorhynchus mykiss). Journal of Heredity 86: 354-363.
11. Beacham, T.D., R.E. Withler, and C.C. Wood. 1995. Stock identification of sockeye salmon by means of minisatellite DNA variation. North American Journal of Fisheries Management 15: 249-265.
1994
10. Withler, R.E., and T.D. Beacham. 1994. Genetic consequences of the simultaneous or sequential addition of milt from multiple males during hatchery spawning of chinook salmon (Oncorhynchus tshawytscha). Aquaculture 126: 11-23.
9. Withler, R.E., and T.D. Beacham. 1994. Genetic variation in growth and flesh colour of coho salmon (Oncorhynchus kisutch) in British Columbia. Aquaculture 119: 135-148.
8. Beacham, T.D., C.B. Murray, and L.W. Barner. 1994. Influence of photoperiod on the timing of reproductive maturation in pink salmon (Oncorhynchus gorbuscha), and its application to genetic transfers between odd- and even-year spawning populations. Can. J. Zool. 72: 826-833.
7. Withler, R.E., T.D. Beacham, R.F. Watkins, and T.A. Stevens. 1994. Identification of farm and native chinook salmon (Oncorhynchus tshawytscha) on the west coast of Vancouver Island, British Columbia, using the nuclear DNA probe B2-2. Canadian Journal of Fisheries and Aquatic Sciences 51(Supplement 1): 267-276.
6. Taylor, E.B., T.D. Beacham, and M. Kaeriyama. 1994. Population structure and identification of North Pacific Ocean chum salmon (Oncorhynchus keta) revealed by an analysis of minisatellite DNA variation. Canadian Journal of Fisheries and Aquatic Sciences 51: 1430-1442.
1993
5. Beacham, T.D., and C.B. Murray. 1993. Acceleration of maturity of pink salmon (Oncorhynchus gorbuscha) using photoperiod control. Aquaculture 109: 315-325.
4. Murray, C.B., T.D. Beacham, and L.W. Barner. 1993. Growth and survival of newly emerged and juvenile coho salmon (Oncorhynchus kisutch) reared at different salinities. Can. J. Zool. 71: 1230-1237.
3. Beacham, T.D. 1993. Competition between juvenile pink (Oncorhynchus gorbuscha) and chum salmon (O. keta) and its effect on growth and survival. Can. J. Zool. 71: 1270-1274.
2. Beacham, T.D., and C.B. Murray. 1993. Fecundity and egg size variation in North American Pacific salmon (Oncorhynchus). J. Fish. Biol. 42: 485-508.
1. Stevens, T.A., R.E. Withler, S.H. Goh, and T.D. Beacham. 1993. A new multi-locus probe for DNA fingerprinting in chinook salmon Oncorhynchus tshawytscha), and comparisons with a single locus probe. Canadian Journal of Fisheries and Aquatic Sciences 50: 1559-1567.
Secondary publications
2015
57. Tucker, S., T. D. Beacham, and M. Trudel. 2015. Seasonal distribution of juvenile Vancouver Island Chinook Salmon. NPAFC Document
2014
56. Ackerman P.A, S. Barnetson D, Lofthouse C, McClean A, Stobbart,and R.E. Withler. 2014. Back from the brink: The Cultus Lake Sockeye salmon enhancement program from 2000-2014. Canadian Manuscript Report of Fisheries and Aquatic Science 3032: vii + 63p.
55. Beacham, T. D., J. R. Candy, S. Sato, and S. Urawa. 2014. Microsatellite Identification of Sockeye Salmon Rearing in the Bering Sea During 2009-2013. NPAFC Document 1511. 18 pp. (Available at http://www.npafc.org).
2013
54. Beacham, T. D., Richard J. Beamish, John R. Candy, Strahan Tucker, Jamal H. Moss, and Marc Trudel. 2013. Stock-specific Migration Pathways and Size of Juvenile Sockeye Salmon (Oncorhynchus nerka) in Nearshore Waters and in the Gulf of Alaska. North Pacific Anadromous Commission Technical Report 9: 31-32.
53. Hertz, E., Marc Trudel, Rana W. El-Sabaawi, Strahan Tucker, Terry D. Beacham, and Asit Mazumder. 2013. Interannual and Spatial Variability in the Feeding Ecology of Juvenile Chinook Salmon and Effects on Survival and Growth. North Pacific Anadromous Commission Technical Report 9: 97-98.
52. Miller, K. M., Marc Trudel, David A. Patterson, Angela Schulze, Karia Kaukinen, Shaorong Li, Norma Ginther, Tobi Ming, and Amy Tabata. 2013. Are Smolts Healthier in Years of Good Ocean Productivity? North Pacific Anadromous Commission Technical Report 9: 165-168.
51. Moss, J., Marc Trudel, Brian Beckman, William Crawford, Wyatt Fournier, Emily Fergusson, and Terry Beacham. 2013. Benefits of Living Life on the Edge: Enhanced Growth and Foraging Opportunities for Juvenile Salmon Inhabiting the Margins of the Sitka Eddy. North Pacific Anadromous Commission Technical Report 9: 77-78.
50. Tucker, S., Mark Hipfner, John R. Candy, Colin Wallace, Terry D. Beacham, and Marc Trudel. 2013. Stock-Specific Predation of Rhinoceros Auklets (Cerorhinca monocerata) on Juvenile Salmon in Coastal British Columbia. North Pacific Anadromous Commission Technical Report 9: 95-96. 2012
49. Araujo, A., J. Candy, and T. Beacham. 2012. Advantages and limitations of genetic stock identification applied to pink salmon stocks. Proceedings of 25th Northeast Pacific Pink and Chum Salmon Workshop.
48. Irvine, J.R., T. Beacham, M. Trudel, A. Tompkins, and M. Saunders. 2012. Canadian bibliography of 2010-2012 publications linked to the current NPAFC Science Plan. NPAFC Doc. 1432. 47 pp. Fisheries and Oceans Canada. Pacific Biological Station.
47. Beacham, T. D., J. R. Candy,S. Sato and S. Urawa. 2012. Microsatellite identification of sockeye salmon rearing in the Bering Sea 2011. NPAFC Document 1389. 10 pp.
46. Beacham, T. D., J. R.Candy, S. Tucker, S. Sato, S. Urawa, J. H. Moss, and M. Trudel. 2012. Nonrandom distribution of Canadian sockeye salmon rearing in the Bering Sea and coastal Gulf of Alaska. NPAFC Document 1403. 11 pp.
45. Trudel, M., K. R. Middleton, S. Tucker, M. E. Thiess, J. F. T. Morris, J. R. Candy, A. Mazumder, and T. D. Beacham. 2012. Estimating winter mortality in juvenile Marble River Chinook salmon. NPAFC Document 1426. 10 pp.
44. Irvine, J.R., M. Trudel, A. Tompkins, T. Beacham, and M. Saunders. 2012. Canadian research in 2012 relevant to the NPAFC Salmon Science Plan for 2011-2015. NPAFC Document 1379. 5 pp.
2011
43. Beamish, R., K. Lange, C. Neville, R. Sweeting, and T. Beacham. 2011. Structural patterns in the distribution of ocean- and stream-type juvenile Chinook salmon populations in the Strait of Georgia in 2010 during the critical early marine period. NPAFC Document 1354.
42. Trudel, M., Jamal H. Moss, Strahan Tucker, John R. Candy, and Terry D. Beacham. 2011. Stock-Specific Distribution of Juvenile Sockeye Salmon in the Eastern Gulf of Alaska. NPAFC Document 1353.
2010
41. Bradford, M.J., J.M.B. Hume, R.E. Withler, D. Lofthouse, S. Barnetson, S. Grant, M. Folkes, N. Schubert and A-M. Huang. 2011. Status of Cultus Lake sockeye salmon. DFO Canadian Science Advisory Secretariat Research Document 2010/123. vi + 44p.
40. Beamish, R. J., R.M. Sweeting, T.D. Beacham, K.L. Lange, and C.M. Neville. 2010. A late ocean entry life history strategy improves the marine survival of Chinook salmon in the Strait of Georgia. North Pacific Anadromous Fish Commission Document Number 1282.
39. Beamish, R. J., K.L. Lange, C.M. Neville, R.M. Sweeting, and T.D. Beacham. 2010. Late ocean entry of sea type sockeye salmon from the Harrison River in the Fraser River drainage results in improved productivity. North Pacific Anadromous Fish Commission Document Number 1283.
2009
38. Ford, K.B., Wright B. M, Ellis, G. M, and J.R. Candy 2009. Chinook salmon predation by resident killer whales, seasonal and regional selectivity, stock identity of prey, and consumption rates. CSAS Research Document 2009/101.
2007
37. Flannery, B. G., T. D. Beacham, R. R. Holder, Kretschmer, and J. K. Wenburg. 2007. Stock structure and mixed stock analysis of Yukon River chum salmon. U. S. Fish and Wildlife Service, Alaska Fisheries Technical Report Number 97. 53p.
36. Schubert, N.D., Candy, J.R., Cook, R., Greenbank, J., Lofthouse, D., McNicol, R., J.A., Parken, C.K., Sneddon, D., Tadey, J.A., and Wilson, K. (in press) Status of Birkenhead River Chinook salmon (Oncorhynchus tshawytscha). Canadian Stock Assessment Secretariat Research Document 2007.
35. Urawa, S., S. Sato, N. Varnavskaya, P. A. Crane, and T. D. Beacham. 2007. Genetic stock identification of juvenile chum salmon caught in the Okhotsk Sea during the fall of 2003. North Pacific Anadromous Fish Commission Technical Report 7:72-74.
34. Trudel, M., M. E. Thiess, J. F. T. Morris, J. R. Candy, T. D. Beacham, D. A. Higgs, and D. W. Welch. 2007. Overwinter mortality and energy depletion in juvenile Pacific salmon off the west coast of British Columbia and Alaska. North Pacific Anadromous Fish Commission Technical Report 7:61-63
2006
33. Olsen J. B, T. D. Beacham, K. D. Le, M. Wetklo, L. D. Luiten, E. J. Kretschmer, J. K. Wenburg, C. F. Lean, K. M. Dunmall, and P. A. Crane PA. 2006. Genetic variation in Norton Sound chum salmon populations. Final report for study 45081, Arctic Yukon Kuskokwim Sustainable Salmon Initiative
32. Flannery, B., T. Beacham, M. Wetklo, C. Smith, B. Templin, A. Antonovich, L. Seeb, S. Miller, O. Schlei, and J. Wenburg. 2006. Run timing, migratory patterns, and harvest information of Chinook salmon stocks within the Yukon River. U.S. Fish and Wildlife Service Alaska Fisheries Technical Report Number 92: 44p.
31. Winther, I., and T. D. Beacham. 2006. The application of Chinook salmon stock composition data to management of the Queen Charlotte Islands troll fishery, 2002 to 2005. Canadian Technical Report of Fisheries and Aquatic Sciences 2665: 88 p.
2005
30. Candy J. R., B. G. Flannery, and T. D. Beacham. 2005. Building a collaborative chum salmon microsatellite baseline for Yukon River genetics stock identification. Proceedings of the 22d Pink and Chum Workshop 13 pp.
29. Beacham, T. D., K. D. Le, and M. Wetklo. 2005. Summary of chum salmon stock identification research conducted by the Molecular Genetics Laboratory, Pacific Biological Station. North Pacific Anadromous Fish Commission Document Number 900.
2004
28. Beacham, T.D., and J. R. Candy. 2004. Microsatellite analysis and stock identification of Pacific salmon using Pacific Rim baselines. North Pacific Anadromous Fish Commission Technical Report 6: 48-49.
27. Beacham, T.D., J.R. Candy, B. McIntosh, C. MacConnachie, A. Tabata, K.M. Miller, R.E, Withler, and N. Varnavskaya. 2004. Estimation of stock composition of sockeye salmon in the North Pacific Ocean. North Pacific Anadromous Fish Commission Document Number 783.
26. Latham, S.J., M. Lapointe, J. Gable, J.R. Candy, and T.D. Beacham. 2004. DNA analysis increases the utility of other stock identification methods in sockeye fisheries management. North Pacific Anadromous Fish Commission Technical Report 5: 123-124.
25. Welch, D.W., M. Trudel, T.D. Beacham, J.F.T. Morris, and J.R. Candy. 2004. DNA-based stock identification of coastal sockeye salmon: Evidence for stock-specific migration behaviour of central coast (Rivers Inlet) sockeye salmon. North Pacific Anadromous Fish Commission Technical Report 5: 65-66.
24. Trudel, M., D.W. Welch, J.F.T. Morris, J.R. Candy, and T.D. Beacham. 2004. Using genetic markers to understand the coastal migration of juvenile coho (Oncorhynchus kisutch) and chinook salmon (Oncorhynchus tshawytscha). North Pacific Anadromous Fish Commission Technical Report 5: 52-54.
23. Candy, J.R., and T.D. Beacham. 2004. Determining accuracy of a Bayesian approach to estimate individual indentification to stock-of-origin for Pacific salmon in marine fisheries using microsatellite and MHC loci. North Pacific Anadromous Fish Commission Technical Report 5: 43-44.
22. Beacham, T.D., K.D. Le, and J.R. Candy. 2004. Population structure and stock identification of chum salmon (Oncorhynchus keta) based upon microsatellite analysis. North Pacific Anadromous Fish Commission Technical Report 5: 31-33.
21. Withler, R.E., K.M. Miller, J.R. Candy, and T.D. Beacham. 2004. A sea change: Genetics in conservation of the rich and strange. North Pacific Anadromous Fish Commission Technical Report 5: 7-8.
2003
20. Withler, R.E., A. Campbell, D. Brouwer, S. Li, K.J. Supernault, and K.M. Miller. 2003. Implications of high levels of genetic diversity and weak population structure for the rebuilding of northern abalone populations in British Columbia, Canada. Canadian Technical Report of Fisheries and Aquatic Sciences 2482: 74-75.
19. Pepper, V, C. Collier and R.E. Withler. 2003. Newfoundland experience with salmonid broodstock for application to aquaculture industry needs. Aquaculture Association of Canada Special Publication 6: 27-30.
18. Withler, R.E., K.M. Miller, J. Candy and T.D. Beacham. 2003. Forensic identification of Pacific salmonid tissues to species and population of origin. Abstract. In: CSFS 2003: Forensic Science - a public or private enterprise? 50th Annual Meeting of the Canadian Society of Forensic Science. March 25-29, 2003. Vancouver BC. P. 55.
17. Beacham, T.D., J.F. Schweigert, C. MacConnachie, K.D. Le, K. Labaree, and K.M. Miller. 2003. Microsatellite population structure of herring (Clupea pallasi) in British Columbia, with comparisons to southeast Alaska and California. 2003 PSARC Fisheries Update.
2002
16. Candy, J.R., C.G. Wallace, and T.D. Beacham. 2002. Microsat Manager: an application for multi-locus genetic data, user’s guide and documentation (Version 2.4). Canadian Technical Report of Fisheries and Aquatic Sciences 2407. Manual; MS Access File
15. Miller, K.M., T.D. Beacham and R.E. Withler. 2002. Use of neutral and adaptive genetic ariation in the management and conservation of Pacific Salmon. Abstract. ICES 2002 Centennial meeting.
14. Candy, J.R., J.R. Irvine, C.K. Parken, S.L. Lemke, R.E. Bailey, M. Wetklo, and K. Jonsen. 2002. A discussion paper on possible new stock groupings (conservation units) for Fraser River chinook salmon. Canadian Stock Assessment Research Document 2002/085.
13. Schubert, N.D, T.D. Beacham, A.J. Cass, T.E. Cone, B.P. Fanos, M. Foy, J.H. Gable, J.A. Grout, J.M.B. Hume, M. Johnson, K.F. Morton, K.S. Shortreed, M.J. Staley and R.E. Withler. 2002. Status of Cultus Lake sockeye salmon (Oncorhynchus nerka). Canadian Stock Assessment Secretariat Research Document 2002/064.
12. Beacham, T.D., J.F. Schweigert, C. MacConnachie, K.D. Le, K. Labaree, and K.M. Miller. 2002. Population structure of herring (Clupea pallasi) in British Columbia determined by microsatellites, with comparisons to southeast Alaska and California. Canadian Stock Assessment Secretariat Research Document 2002/109.
2001
11. Beacham, T.D., J.R. Candy, B. McIntosh, C. MacConnachie, A. Tabata, K. Kaukinen, K.M. Miller, and R.E. Withler. 2001. Estimation of stock composition of sockeye salmon in the North Pacific Ocean. North Pacific Anadromous Fish Commission Document Number 552.
10. Beacham, T.D., J.F. Schweigert, C. MacConnachie, K.D. Le, K. Labaree, and K.M. Miller. 2001. Population structure of herring (Clupea pallasi) in British Columbia: an analysis using microsatellite loci. Canadian Stock Assessment Secretariat Research Document 2001/128.
9. Withler, R.E, A. Campbell, S. Li, K.M. Miller, D. Brouwer, and B. Lucas. 2001. High levels of genetic variation in northern abalone, Haliotis kamtschatkana, of British Columbia. Canadian Stock Assessment Secretariat Research Document 2001/097.
8. Irvine, J.R, C.K. Parken, D.G. Chen, J.R. Candy, T. Ming, J. Supernault, W. Shaw, and R.E. Bailey. 2001. 2001 assessment of stock status for coho salmon from the interior Fraser River. Canadian Stock Assessment Secretariat Research Document 2001/083.
7. Bailey, R.E., J.R. Irvine, J.R. Candy, C.K. Parken, S.L. Lemke, M. Sullivan, and M. Wetklo. 2001. Summary of stock assessment information for selected early returning chinook salmon populations of the Fraser River watershed. Canadian Stock Assessment Secretariat Research Document 2001/134.
2000
6. Noakes, D.J. and T. D. Beacham. 2000. A summary of genetic stock identification research conducted at the Pacific Biological Station, Canada. North Pacific Anadromous Fish Commission Document Number 494.
5. Yamanaka, K.L., R.E. Withler, and K.M. Miller. 2000. Structure of yelloweye rockfish (Sebastes ruberrimus) populations in British Columbia. Canadian Stock Assessment Secretariat Research Document 2000/172. Abstract Document
4. Beacham, T.D., R.S. Gregory, and J. Brattey. 2000. Origins of two recruitment pulses of 0-group Atlantic cod (Gadus morhua) in Bonvista Bay, Newfoundland during 1999, determined from genetic variation. Canadian Stock Assessment Secretariat Research Document 2000/93
3. Irvine, J.R., R.E. Withler, M.J. Bradford, R.E. Bailey, S. Lehmann, K. Wilson, J. Candy, and W.S. Shaw. 2000. Stock status and genetics of coho salmon from the interior Fraser River. Canadian Stock Assessment Secretariat Research Document 2000/125.
2. Beacham, T.D., J. Brattey, K.M. Miller, K.D. Le, A.D. Schulze, and R.E. Withler. 2000. Population structure of Atlantic cod (Gadus morhua) in the Newfoundland and Labrador area determined from genetic variation. Canadian Stock Assessment Secretariat Research Document 2000/099.
1999
1. Beacham, T.D., J. Brattey, K.M. Miller, K. D. Le, and R. E. Withler. 1999. Population structure of Atlantic cod (Gadus morhua) in the Newfoundland and Labrador area based on microsatellite variation. Canadian Stock Assessment Secretariat Research Document 99/35.
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