229 



Abstract— We surveyed variation at 

 13 microsatellite loci in approximately 

 7400 Chinook salmon sampled from 

 52 spawning sites in the Fraser River 

 drainage during 1988-98 to examine 

 the spatial and temporal basis of 

 population structure in the watershed. 

 Genetically discrete chinook salmon 

 populations were associated with almost 

 all spawning sites, although gene flow 

 within some tributaries prevented or 

 limited diiTerentiation among spawn- 

 ing groups. The mean Fgj- value over 

 52 samples and 13 loci surveyed was 

 0.039. Geographic structuring of popu- 

 lations was apparent: distinct groups 

 were identified in the upper, middle, 

 and lower Fraser River regions, and 

 the north, south, and lower Thompson 

 River regions. The geographically and 

 temporally isolated Birkenhead River 

 population of the lower Fraser region 

 was sufficiently genetically distinctive 

 to be treated as a separate region in a 

 hierarchial analysis of gene diversity. 

 Approximately 95% of genetic varia- 

 tion was contained within populations, 

 and the remainder was accounted for by 

 differentiation among regions (3.1%), 

 among populations within regions 

 ( 1 .39c), and among years within popula- 

 tions (0.5%). Analysis of allelic diversity 

 and private alleles did not support the 

 suggestion that genetically distinctive 

 populations of chinook salmon in the 

 south Thompson were the result of 

 postglacial hybridization of ocean-type 

 and stream-type chinook in the Fraser 

 River drainage. However, the relatively 

 small amount of differentiation among 

 Fraser River chinook salmon popula- 

 tions supports the suggestion that gene 

 flow among genetically distinct groups 

 of postglacial colonizing groups of 

 chinook salmon has occurred, possibly 

 prior to colonization of the Fraser River 

 drainage. 



The geographic basis for population 

 structure in Fraser River chinook salmon 

 iOncorhynchus tshawytscha) 



Terry D. Beacham 

 K. Janine Supernault 

 Michael Wetklo 

 Bruce Deagle 

 Karen Labaree 

 James R. Irvine 

 John R. Candy 

 Kristlna M. Miller 

 R. John Nelson 

 Ruth E. Withler 



Department of Fisheries and Oceans 



Pacific Biological Station 



3190 Hammond Bay Road 



Nanaimo, Britistn Columbia, Canada V9T 6N7 



E-mail address (for T D Beacham) Beachamt(a)pac.dfo-mpo gcca 



Manuscript accepted 22 October 2002. 



Manuscript received 31 December 2002 

 at NMFS Scientific Publications Office. 



Fish. Bull. 101(2):229-242 (2003). 



The Fraser River drainage supports 

 the largest group of chinook salmon 

 iOncorhynchus tshawytscha) popula- 

 tions in North America, and the most 

 abundant individual chinook salmon 

 population in British Columbia (the 

 Harrison River in the lower Fraser 

 River drainage). Chinook salmon are 

 distributed throughout the entire 

 Fraser River drainage, and spawning 

 populations exist in approximately 65 

 tributaries (Fraser etal., 1982). There is 

 substantial variation among and within 

 populations for life history traits such 

 as length of juvenile freshwater resi- 

 dence, size and age at maturity, and 

 timing of adult migration and spawning. 

 Juveniles (largely from the Harrison 

 River population) can migrate to the 

 marine environment immediately after 

 fry emerge in the spring, or during the 

 first summer after developing in fresh 

 water for several months ("ocean-type"), 

 or they can remain in fresh water for 

 a year or longer ("stream-type") before 

 migrating to the ocean (Fraser et al., 

 1982;Healey, 1983, 1991). 



Migrating adult chinook salmon re- 

 turning to spawn in Fraser River tribu- 



taries enter the drainage from April to 

 October — individual populations having 

 characteristic migration times (Fraser 

 et al., 1982 ). Spring or "early run" popu- 

 lations are designated as those in which 

 at least 50% of the fish pass through 

 the lower Fraser by 15 July and include 

 populations of the mid and upper Fra- 

 ser areas, the lower Thompson area, 

 and a small lower Fraser population 

 that spawns in the upper reaches of the 

 Harrison drainage (Birkenhead River). 

 Summer or "mid run" populations are 

 those in which the majority of the fish 

 pass through the lower Fraser after 15 

 July, but before 31 August, and include 

 populations of the mid Fraser area, and 

 the north and south Thompson areas. 

 Chinook salmon of the large Harrison 

 River population are fall or "late run" 

 fish and enter the lower Fraser in Sep- 

 tember and October. Thus, in the Fraser 

 drainage, it is the late-run Harrison 

 population of the lower Fraser that is 

 characterized by ocean-type juveniles, 

 whereas the earlier migrating spring 

 and summer populations of the interior 

 Fraser drainage are characterized by 

 stream-type juveniles. Exceptions are 



