Population structure of pink salmon 
(Oncorhynchus gorbuscha ) in British Columbia 
and Washington, determined with microsatellites 
E-mail address for contact author: Terry. Beacham@dfo-mpo.Qcc 
1 Fisheries and Oceans Canada 
Pacific Biological Station 
3190 Hammond Bay Road 
Nanaimo, B C., Canada V9T 6N7 
2 Fisheries and Oceans Canada 
417-2nd Avenue West 
Prince Rupert, B C Canada V8J 1G8 
3 Pacific Salmon Commission 
600-1155 Robson Street 
Vancouver, B C., Canada V6E 1B5 
Abstract — Population structure of 
pink salmon ( Oncorhynchus gorbus- 
cha) from British Columbia and Wash- 
ington was examined with a survey 
of microsatellite variation to describe 
the distribution of genetic variation. 
Variation at 16 microsatellite loci was 
surveyed for approximately 46,500 
pink salmon sampled from 146 loca- 
tions in the odd-year broodline and 
from 116 locations in the even-year 
broodline. An index of genetic differ- 
entiation, F st , over all populations 
and loci in the odd-year broodline was 
0.005, with individual locus values 
ranging from 0.002 to 0.025. Popula- 
tion differentiation was less in the 
even-year broodline, with a ^st value 
of 0.002 over all loci, and with individ- 
ual locus values ranging from 0.001 
to 0.005. Greater genetic diversity 
was observed in the odd-year brood- 
line. Differentiation in pink salmon 
allele frequencies between broodlines 
was approximately 5.5 times greater 
than regional differentiation within 
broodlines. A regional structuring 
of populations was the general pat- 
tern observed, and a greater regional 
structure in the odd-year broodline 
than in the even-year broodline. The 
geographic distribution of microsatel- 
lite variation in populations of pink 
salmon likely reflects a distribution 
of broodlines from separate refuges 
after the last glaciation period. 
Manuscript submitted 3 October 2011. 
Manuscript accepted 5 January 2012. 
Fish. Bull. 110:242-256(2012) 
The views and opinions expressed 
or implied in this article are those of the 
author (or authors) and do not necessarily 
reflect the position of the National Marine 
Fisheries Service, NOAA. 
Terry D. Beacham (contact author ) 1 
Brenda McIntosh' 
Cathy MacConnachie 1 
Brian Spilsted 2 
Bruce A. White 3 
Pink salmon ( Oncorhynchus gor- 
buscha ) spawn in more than 700 
rivers in British Columbia (Aro and 
Shepard, 1967), and the distribution 
of spawning populations varies in odd- 
numbered years and even-numbered 
years. Spawning occurs primarily 
only in odd years in the Fraser River 
drainage, mainly in even years on 
the Queen Charlotte Islands, and in 
both years in central and northern 
coastal areas of British Columbia 
(Neave, 1952). Because virtually all 
pink salmon mature at two years of 
age (Bilton and Ricker, 1965), two dis- 
tinct broodlines in the species have 
developed (odd-year and even-year), 
with virtually no gene flow between 
the broodlines. This reproductive iso- 
lation of the broodlines has resulted 
in reported differences in body size 
(Godfrey, 1959), morphological char- 
acteristics (Ricker, 1972; Beacham, 
1985), timing of spawning (Aro and 
Shepard, 1967; Dyagilev and Markev- 
ich, 1979), and genetic differentiation 
(Aspinwall, 1974; Beacham et al., 
1988). Evaluation of the genetic pop- 
ulation structure both between and 
within broodlines in British Columbia 
and Washington form the basis of the 
current study. 
Estimation of genetic population 
structure has been a key area of 
research in salmon assessment and 
management. Identification of a ge- 
netically distinct group of populations 
in the distribution of a species is a 
key step in conserving and maintain- 
ing genetic diversity. Genetically dis- 
tinct populations or regional groups of 
populations (stocks) were determined 
through surveys of genetic variation 
to evaluate the population structure 
of a species (Shaklee and Bentzen, 
1998). Identification of genetically 
distinct groups in the distribution of 
pink salmon in British Columbia and 
Puget Sound may lead to the conser- 
vation of genetic diversity by fisheries 
and resource management. An evalu- 
ation of genetic variation is effective 
in describing the population struc- 
ture of salmonids, is a key part in the 
elucidation of management units or 
conservation units for a species and 
can be applied to manage fisheries 
exploiting specific stocks of salmon. 
Determination of genetic population 
structure is an important part in de- 
veloping a genetically based method 
for estimation of stock composition. 
Allozymes were initially the key set 
of genetic markers used in evaluat- 
