GENETIC POPULATION STRUCTURE OF CHINOOK SALMON, 

 ONCORHYNCHUS TSHAWYTSCHA, IN THE PACIFIC NORTHWEST 



F. Utter,' G. Milner.i G. StIhl,^ and D. Teel' 



ABSTRACT 



Variation at 25 polymorphic protein coding loci was examined for 86 populations of chinook salmon, 

 Oncorhynchus tshaun/tscha, ranging from the Babine River in British Columbia to the Sacramento River 

 in California. Substantial differences in allele frequencies identified patterns of genetic variability over 

 the geographic range of the study. The following nine major genetically defined regions were formu- 

 lated: 1) the Fraser River tributaries east of the Cascade Crest (no downstream drainages were sam- 

 pled). 2) Georgia Strait, 3) Puget Sound, 4) a broad coastal region ranging from the west coast of Vancouver 

 Island southward through northern California, 5) the Columbia River below The Dalles Dam, 6) the 

 Columbia River above The Dalles Dam, 7) the Snake River. 8) the Klamath River, and 9) the Sacramento 

 River. Populations sampled within a region tended to be genetically distinct from each other although 

 they exhibited the general patterns of variability that defined the region. Within a region there was little 

 distinction among populations returning to spawn at different times. The persistence of these geographic 

 patterns in the face of natural opportunities for introgression, and sometimes massive transplantations, 

 suggests that genetically adapted groups within regions have resisted large-scale introgression from other 

 regions. Repopulation of deglaciated areas in the Fraser River, Georgia Strait, and Puget Sound ap- 

 parently occurred from multiple sources; most likely sources included Columbia River populations and 

 northern refuges rather than from the large coastal group of populations. Patterns of genetic distribu- 

 tion of chinook salmon differed from those of other anadromous salmonids studied within this region. 

 A conservative policy for stock transfers was suggested based on distinct genetic differences observed 

 both between and within regions. 



Population studies of chinook salmon, Oncorhynchus 

 tshawytscha, based on electrophoretically detected 

 genetic variation have been carried out since the late 

 1960s. As data have accumulated, an increasingly 

 clear picture of the breeding structure of this species 

 has emerged. While early investigations based on 

 only a few polymorphic loci identified differences 

 among populations, they failed to identify any geo- 

 graphic trends (e.g.. Utter et al. 1973; Kristiansson 

 and Mclntyre 1976). Differences within and among 

 drainages became apparent as additional polymor- 

 phic loci were found and a more comprehensive 

 sampling of populations was made (Utter et al. 1976, 

 1980; Gharrett et al. 1987). 



This paper outlines the genetic structure of 

 chinook salmon in the Pacific Northwest using allele 

 frequency data collected for the purpose of esti- 

 mating the stock composition of ocean caught 

 Chinook salmon (Milner et al. 19813; 19834. MiUej. 



et al. 1983; Utter et al. 1987). Our purpose is to ex- 

 amine these data in the light of other relevant bio- 

 logical and historical information 1) to understand 

 genetic relationships among chinook salmon popu- 

 lations better and 2) to provide biologists with new 

 insights to assist in the preservation and manage- 

 ment of this important biological resource. 



MATERIALS AND METHODS 



Our data were obtained from samples of juvenile 

 or adult fish collected at 86 locations ranging from 

 British Columbia through California (Table 1, Fig. 

 1). These data include allele frequencies from 25 

 protein-coding loci with sample sizes between 38 and 

 200 individuals. Data were accumulated between 

 1980 and 1984 and were reported in part in Milner 

 et al. (fn. 3, 4). 



Electrophoretic procedures followed those de- 



'Coastal Zone and Estuarine Studies Division. Northwest and 

 Alaska Fisheries Center, National Marine Fisheries Service, 

 NOAA, 2725 Montlake Boulevard East, Seattle, WA 98112. 



^Department of Genetics. Stockholm University, S-10691, Stock- 

 holm, Sweden. 



'Milner, G. B.. D. J. Teel. F. M. Utter, and C. L. Burley. 1981. 

 Columbia River stock identification study: Validation of genetic 



Manuscript accepted January 1989. 

 Fishery Bulletin. U.S. 87:239-264. 



method. Report to Bonneville Power Administration under con- 

 tract DE-A179-80BP18488, 51 p. Available Bonneville Power Ad- 

 ministration, P.O. Box 3621, Portland, OR 97208. 



'Milner, G. B., D. J. Teel, and F. M. Utter. 1983. Genetic stock 

 identification study. Report to Bonneville Power Administration 

 under contract DE-A179-82BP28044M001, 95 p. Available Bonne- 

 ville Power Administration, P.O. Box 3621, Portland, OR 97208. 



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