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Fishery Bulletin 96(4), 1998 
biodiversity in the species (Bartley et al., 1992; 
Forbes et al., 1993; Weitkamp et al., 1995; Miller and 
Withler, 1997), to define the appropriate geographic 
scale of management to conserve the observed 
biodiversity (Weitkamp et al., 1995; McPhail, 1997; 
Small et al., 1998), and to develop stock composition 
methods that would enable the geographically based 
management required for conservation efforts 
(Bartley et al., 1992; Beacham et al., 1996; Miller et 
al., 1996; Van Doornik et al., 1996; Small et al., 1998). 
Coho salmon populations of California, Oregon, 
Washington, and southern British Columbia have 
been categorized into evolutionarily significant units 
(ESUs), that is to say, reproductively isolated popu- 
lations or groups of populations that represent the 
important phylogenetic components of genetic vari- 
ability in the species (Waples, 1991; Weitkamp et al., 
1995). The use of ESUs to delineate biodiversity in 
Pacific salmon is concordant with an emerging model 
of metapopulation structure that may supersede the 
stock concept that has long been applied to these 
species. Local spawning groups of salmon are no 
longer viewed as independent and persistent locally 
adapted “stocks” (Ricker, 1972), but rather as inter- 
related components, or subpopulations, of a geo- 
graphically based cluster of such components (the 
metapopulation) that share a relatively recent evo- 
lutionary history and among which gene flow still 
occurs (McPhail, 1997). Although adaptive differ- 
ences may arise among the subpopulations of a 
metapopulation as the result of an appropriate bal- 
ance between migration and natural selection within 
subpopulations, they are unlikely to persist over evo- 
lutionary time scales as subpopulations go extinct 
or are swamped by gene flow from adjacent subpopu- 
lations. Given this model of salmonid population 
structure, it is individual metapopulations (ESUs), 
rather than individual stocks, that managers must 
conserve to provide the reservoirs of genetic diver- 
sity for future evolution within the species. 
In coho salmon, and other Pacific salmonids, there 
is accumulating evidence that the dominant influ- 
ence on population structure has been the pattern of 
dispersal from isolated glacial refugia after the last 
ice age (Gharrett et al., 1987; Wood et al., 1994; 
Bickham et al., 1995, Miller and Withler 1997; Small 
et al., 1998). The distinct phylogenetic lineages that 
can be traced with molecular markers reveal patterns 
of recolonization of freshwater habitat from refugia 
located in the Columbia River drainage (Cascadia), 
the Bering Sea-Yukon River (Beringia), and coastal 
refugia that likely existed in British Columbia, as 
well as in more southern waters. For coho, chinook 
and sockeye salmon, many of these genetically dis- 
tinct intraspecific lineages converge in British Co- 
lumbia, providing us with the opportunity and chal- 
lenge of conserving biodiversity in situ. 
In this study, we examine variation among and 
within major river systems and coastal regions in 
British Columbia at three coho salmon microsatellite 
loci: OfslOl, Ots3, and Otsl03. Microsatellite DNA 
loci consist of highly variable single locus markers 
containing tandemly repeated arrays of noncoding 
1-6 basepair core sequences (Tautz, 1989). For each 
locus, variation in the number of core sequences cre- 
ates alleles differing in size by multiples of core-unit 
length. The rapid rate of mutation and high heterozy- 
gosity that characterize microsatellite loci have made 
them the molecular tool of choice in studies of popu- 
lation structure in vertebrates, including salmonid 
fish (Angers et al., 1995; McConnell et al., 1995; 
Scribner et al., 1996; Beacham et al., 1998; Small et 
al., 1998). In our study, we demonstrate the dual util- 
ity of microsatellite variation in defining the region- 
ally based phylogenetic lineages of coho salmon and 
in accurately detecting their presence in mixed-stock 
fisheries for management purposes. 
Methods 
DNA samples and PCR 
Adult coho salmon tissue samples were collected from 
34 coho salmon populations in British Columbia (Fig. 
1). Several populations were sampled in multiple 
years. See Miller et al., (1996) for descriptions of 
purified genomic DNA extractions from tissues col- 
lected up to 1993. Genomic DNA samples from 1994 
and 1995 were extracted by using a chelex resin pro- 
tocol (Small et al., 1998). Microsatellite alleles at 
three loci were polymerase chain reaction (PCR)-am- 
plified (Sakai et al., 1985) from DNA samples by us- 
ing primers for the tetranucleotide microsatellites 
OtslOl and Otsl03 (Small et al., 1998) and the di- 
nucleotide microsatellite, Ots3 (Banks 1 ). Primer se- 
quences, the PCR conditions, and size-fractionation 
of the PCR products are described in Small et al. 
(1998). PCR products from standard test fish were 
included on each gel to estimate the precision of al- 
lele sizing among gels. 
DNA band analysis 
Gels were scanned with a Kodak charge-coupled de- 
vice camera and the images were analyzed as out- 
lined in Small et al. (1998) with Bioimage Whole 
1 Banks, M. 1995. Bodega Marine Laboratory, POB 247, 
Bodega Bay, CA 94923. Personal commun. 
