243 



Abstract— Variation at 13 microsat- 

 ellite loci was previously surveyed in 

 approximately 7400 chinook salmon 

 (Oncorhynchus tshawytscha) sampled 

 from 50 localities in the Fraser River 

 drainage in southern British Colum- 

 bia. Evaluation of the utility of the 

 microsatellite variation for popula- 

 tion-specific stock identification appli- 

 cations indicated that the accuracy 

 of the stock composition estimates 

 generally improved with an increasing 

 number of loci used in the estimation 

 procedure, but an increase in accuracy 

 was generally marginal after eight loci 

 were used. With 10-14 populations in 

 a simulated fishery sample, the mean 

 error in population-specific estimated 

 stock composition with a 50-popula- 

 tion baseline was <1.4'7f. Identification 

 of individuals to specific populations 

 was highest for lower Fraser River and 

 lower and North Thompson River popu- 

 lations; an average of 70% of the indi- 

 vidual fish were correctly assigned to 

 specific populations. The average error 

 of the estimated percentage for the 

 seven populations present in a coded- 

 wire tag sample was 2% per population. 

 Estimation of stock composition in the 

 lower river commercial net fishery prior 

 to June is of key local fishery manage- 

 ment interest. Chinook salmon from the 

 Chilcotin River and Nicola River drain- 

 ages were important contributors to the 

 early commercial fishery in the lower 

 river because they comprised approxi- 

 mately 50% of the samples from the net 

 fishery prior to mid April. Mid Fraser 

 River populations were the dominant 

 group of chinook salmon in the catch 

 in April and comprised at least 307c of 

 the catch until late May. Upper Fraser 

 River populations did not occur in any 

 significant proportions in the fishery 

 until the last week of April. By late May, 

 they were the dominant contributors to 

 the lower river fishery, and by June 

 generally comprised approximately 

 70'%- of the weekly catch. Microsatellite 

 variation allows accurate estimation 

 of population-specific contributions to 

 lower river fisheries. 



Evaluation and application of microsatellites 

 for population identification of Fraser River 

 chinook salmon (Oncorhynchus tshawytscha) 



Terry D. Beacham 

 John R. Candy 

 K. Janine Supernault 

 Michael Wetklo 

 Bruce Deagle 

 Karen Labaree 

 James R. Irvine 

 Kristina M. Miller 

 R. John Nelson 



Ruth E. Withler 



Department ol Fisheries and Oceans 



Pacific Biological Station 



3190 Hammond Bay Road 



Nanalmo, British Columbia, Canada V9T 6N7 



E-mail address (for T D Beacham) BeachamtiSpacdfo-mpogcca 



Manuscript accepted 22 October 2002. 



Manuscript received 31 December 2002 

 at NMFS Scientific Publications Office. 



Fish. Bull. 101(2):243-259 (2003). 



Chinook salmon iOncorhynchus tshaw- 

 ytscha) are widely distributed within 

 the Fraser River drainage, spawning 

 in tributaries ranging from the head- 

 waters to near the mouth of the river. 

 There is substantial variation in life 

 history features among populations 

 within the drainage; populations vary 

 in size at maturity, timing of spawn- 

 ing, and juvenile freshwater residence. 

 Juveniles (largely from the Harrison 

 River population) can migrate directly 

 to the marine environment after 

 fry emerge in the spring or perhaps 

 develop in nonnatal tributaries in the 

 lower river (Murray and Rosenau, 

 1989). Juveniles from some popula- 

 tions migrate to the ocean during the 

 first summer of rearing ("ocean-type"), 

 whereas in other populations juveniles 

 remain in fresh water for a year or 

 longer ("stream-type") before migrat- 

 ing to the ocean (Fraser et al., 1982). 

 Management for conservation of genetic 

 diversity within the drainage requires 

 knowledge of genetic variation among 

 populations, as well as population-spe- 

 cific information from fisheries. 



Effective management of fisheries 

 within major drainages like the Fraser 

 River generally requires information on 

 timing of return of specific populations, 

 should managers wish to change exploi- 

 tation rates on specific populations for 

 conservation purposes. To acquire this 

 information is a particularly daunting 

 task within the Fraser River because 

 chinook salmon spawn in approximately 

 65 tributaries of the Fraser River ( Fra- 

 ser et al., 1982). Maturing adults from 

 these populations return annually to the 

 Fraser River throughout the year — the 

 majority offish returning from February 

 through November. For management 

 purposes, Fraser River chinook salmon 

 are currently divided into three groups 

 based on their migration timing into 

 the lower river: the spring run consists 

 of all populations where at least 50% of 

 the individuals are estimated to migrate 

 through the lower river before 15 July; 

 the summer run consists of populations 

 that migrate through the lower river 

 from 15 July to 31 August; and the fall 

 run consists of populations that migrate 

 through the lower river primarily in 



