Beacham et al.: Population identification of Oncorhynchus tshawytscha by variation at microsatellite loci 



253 



it is necessary that the annual variation in population- 

 discriminating characters within populations be substan- 

 tially less than the differences among populations. If the 

 annual variation in population-discriminating characters 

 within populations is less, then annual baseline sampling 

 of populations would not be necessary, and samples from 

 individual populations could be pooled over time to in- 

 crease the reliability of observed allele frequencies. This 

 procedure is required in order that a stock identification 

 method be feasible from both technical and financial 

 perspectives. For Fraser River chinook salmon, the ge- 

 netic variation attributable to population differentiation 

 was about eight times the variation attributable to an- 

 nual variation within populations (Beacham et al., 2003), 

 rendering annual variation in allele frequencies of little 

 practical significance in estimation of stock composition for 

 fisheries in the drainage. In particular, annual estimation 

 of microsatellite allele frequencies in baseline populations 

 would not be required for practical applications, although 

 some level of monitoring of allele frequencies over time 

 would clearly be desirable. The annual stability of micro- 

 satellite allele frequencies for Fraser River chinook salmon 

 in relation to population differentiation is very similar to 

 that reported for other salmonids (Beacham et al., 1999; 

 Tessier and Bernatchez, 1999). 



The two major fall-return populations in the lower 

 Fraser River are from the Harrision River and Chilli- 

 wack River. Analysis of simulated mixtures and the CWT 

 sample suggested that discrimination between the Harri- 

 sion River and Chilliwack River populations was possible. 

 Transplants have occurred between these two populations 

 (Candy and Beacham, 2000), but the level of transplanta- 

 tion has not been sufficient to homogenize genetic differ- 

 entiation between the populations. 



Application to commercial and test fisheries 



Analysis of estimated stock compositions of the 1997-99 

 lower river commercial gillnet fishery and the 1995 lower 

 river test gillnet fishery indicated a discrepancy between 

 the relative abundance of lower Thompson River popula- 

 tions, particularly the Nicola River drainage populations. 

 In the commercial gillnet fishery, Nicola River drainage 

 populations comprised 10-30% of the samples in April 

 and May, but only 0-5% of the test fishery samples. Abso- 

 lute population abundance may have differed between 

 the two time periods, but a more likely explanation was 

 the fact that the 1995 test fishery was conducted with a 

 single mesh gillnet of 20.3 cm, a mesh size selective for 

 larger-bodied chinook salmon. Lower Thompson River 

 chinook salmon populations are substantially smaller in 

 body size than other chinook salmon populations in the 

 Fraser River drainage (Beacham and Murray, 1993), and 

 thus were not likely to have been sampled in proportion 

 to their abundance by the gear used in the test fishery. 

 Multipanel, multimesh gillnets have been used in the test 

 fishery since 1997 in order to obtain more representative 

 sampling of migrating chinook salmon. 



Timing of return of specific populations through the lower 

 Fraser River has been outlined by DFO.' The designation 



of populations as "spring run," "summer run," or "fall run" 

 is based upon a number of factors, of which peaks of occur- 

 rence of CWTs in the test fishery in the lower river and 

 peak of arrival on the spawning grounds are key factors. 

 Recoveries of CWTs are largely restricted to tagged, en- 

 hanced populations because little CWT marking has been 

 conducted for wild populations. There was, in general, good 

 correspondence between run timing determined by CWTs 

 or other factors and those observed in our analyses of the 

 lower river commercial fishery. For example, the Birkenhead 

 River population is known to return very early through the 

 lower Fraser River (Fraser et al., 1982). Highest proportions 

 of Birkenhead River chinook salmon were consistently ob- 

 served in the lower Fraser River commercial fishery prior 

 to 19 April, indicative of an early passage through the 

 lower Fraser River. The Coldwater River, Spins Creek, and 

 Nicola River populations are all found in the Nicola River 

 drainage, and all are classified as spring-run populations 

 (DFOM. The Nicola River drainage aggregrate was a major 

 contributor to catch in the commercial fishery from April to 

 early June. The other lower Thompson River populations, 

 the Deadman River and Bonaparte River, were classified as 

 spring-run populations, and they were detected in the lower 

 river commercial fishery. The Chilcotin River stock aggre- 

 grate (upper and lower Chilcotin populations) was classified 

 as spring run (DFOM, and again this stock was a dominant 

 contributor to the lower river commercial fishery in April 

 and May. In the upper Fraser River, the mainstem spawning 

 population at Tete Jaune and the Bowron River population 

 are thought to be spring run, and this timing was observed 

 in both the commercial fishery and the test fishery. 



The summer-run populations migrate through the lower 

 Fraser River mainly after 15 July and originate primarily 

 from the North and South Thompson River watersheds (a 

 few major populations come from the middle Fraser River 

 ( DFO ^ ). Analysis of the lower Fraser River test fishery sup- 

 ports this conclusion, with 60-75% of the fish sampled in 

 the test fishery in August of North and South Thompson 

 River origin. Populations contributing significantly to the 

 test fishery included the Clearwater River, Adams River, 

 and Shuswap River, and these have been defined as sum- 

 mer-run populations. Fall-run populations occur after 1 

 September and are thought to be largely restricted to the 

 lower Fraser River (DFO^ ). Lower Fraser River populations 

 certainly dominated the test fishery catch in October, but 

 lower Fraser populations were estimated to have comprised 

 only 45% of the catch in September. Summer-run popula- 

 tions were clearly present in the lower river in September, 

 and in fact comprised the majority of the catch. 



There was one significant discrepancy between the 

 previous designation of timing of return (DFOM and that 

 observed in the fishery sampling in our study. The popula- 

 tions in the Nechako River and Stuart River in the mid 

 Fraser region have been defined as summer run, based 

 largely on the timing of recoveries of CWTs from Stuart 

 River chinook salmon in the lower river test fishery. How- 

 ever, in the analysis of the lower river commercial and test 

 fisheries, the Stuart-Nechako population was estimated to 

 have comprised up to 20*7^ of the catch in a period prior to 

 15 July. The Stuart-Nechako drainage is large, and there 



