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Pacific Rim Population Structure of Chinook Salmon asDetermined from Microsatellite Analysis

TERRY D. BEACHAM,* KIMBERLY L. JONSEN, JANINE SUPERNAULT, MICHAEL WETKLO, AND

LANGTUO DENG

Department of Fisheries and Oceans, Pacific Biological Station, Nanaimo,British Columbia V9T 6N7, Canada

NATALIA VARNAVSKAYA

Kamchatka Fishery and Oceanography Research Institute, 18 Naberezhnaya Street,Petropavlovsk-Kamchatsky 683000, Russia

Abstract.—The Pacific Rim population structure of Chinook salmon Oncorhynchus tshawytscha was

examined with a survey of microsatellite variation. Variation at 13 microsatellite loci was surveyed for over

52,000 Chinook salmon sampled from over 320 localities ranging from Russia to California. The genetic

differentiation index (FST

) over all populations and loci was 0.063; individual locus values ranged from 0.026

to 0.130. The most genetically diverse Chinook salmon were observed from northern British Columbia,

Washington (Puget Sound and coastal populations), and the upper Columbia River (spring run). Chinook

salmon from the Alsek River, northern British Columbia, and the Klamath River, California, displayed the

fewest number of alleles relative to Chinook salmon in other regions surveyed. Differentiation in Chinook

salmon allele frequencies among river drainages and populations within river drainages was approximately 13

times greater than that of annual variation within populations. We observed a general pattern of regional

structuring of populations, and Chinook salmon spawning in different tributaries within a major river drainage

or in smaller rivers within a geographic area were generally more similar to each other than to populations in

different major river drainages or geographic areas. Population structure of Chinook salmon on a Pacific Rim

basis supports the concept of a minimum of two refuges, northern and southern, during the last glaciation. The

distribution of microsatellite variation of Chinook salmon on a Pacific Rim basis reflects the origins of salmon

radiating from refuges after the last glaciation period.

The Chinook salmon Oncorhynchus tshawytscha is a

Pacific salmonid that has a wide geographic spawning

range. In Asia, the most abundant stocks are located on

the Kamchatkan Peninsula, but in North America

historically or currently abundant stocks range from the

Yukon River in the north to the Sacramento River in

California. Considerable life history variation is

observed within the spawning distribution. One major

component of life history variation is related to juvenile

life history in freshwater. Some populations are

considered to be stream type, in which juveniles rear

at least 1 year in freshwater before migrating to the

ocean (Healey 1983). Other populations are considered

to be ocean type, in which the juveniles migrate

directly to the ocean upon fry emergence, or they may

rear for a period in freshwater before migrating to the

ocean in their year of emergence. The stream-type life

history is dominant in large, northern rivers like the

Yukon, and in populations spawning in the headwaters

of more southern large rivers, like the Fraser and

Columbia. The ocean-type life history is common in

smaller coastal rivers south of 568N latitude, as well as

in larger rivers in the extreme southern portion of the

spawning distribution such as the Klamath and

Sacramento rivers (Healey 1991). Although these two

life history types have been considered as separate

races (Healey 1983, 1991), no clear genetic demarca-

tion exists between these two life history types over a

wide geographic area (Waples et al. 2004).

Chinook salmon populations also display a wide

variation in timing of return to freshwater for

spawning, which may occur during almost any month

of the year (Healey 1991). As outlined by Waples et al.

(2004), these run times are typically characterized as

spring (March–May), summer (June–August), fall

(September–November), and winter (December–Feb-

ruary). Populations can also differ in spawning

locations within a river drainage, with some popula-

tions migrating to the headwaters of major rivers like

the Columbia, Fraser, and Yukon rivers to spawn,

whereas other populations spawn in locations not far

removed from salt water.

Conservation of Chinook salmon genetic diversity

around the Pacific Rim requires an understanding of

* Corresponding author: [email protected]

Received March 28, 2006; accepted June 21, 2006Published online November 13, 2006

1604

Transactions of the American Fisheries Society 135:1604–1621, 2006� Copyright by the American Fisheries Society 2006DOI: 10.1577/T06-071.1

[Article]

their origins and the evolutionary processes promoting

and maintaining their differentiation, and delineation of

phylogenetically and adaptively distinct groups in the

distribution. Genetic variation can be employed as a

very effective tool to evaluate the population structure

of salmonids, is a key component in the elucidation of

management units or conservation units in a species,

and can be applied to manage fisheries exploiting

specific stocks of salmon. For Chinook salmon,

variation at allozymes was the initial principal genetic

technology employed in evaluation of population

structure, ranging from the Yukon River (Beacham et

al. 1989), Alaska (Gharrett et al. 1987), Southeast

Alaska and northern British Columbia (Guthrie and

Wilmot 2004), British Columbia (Teel et al. 2000), to

the U.S. Pacific Northwest (Winans 1989; Utter et al.

1989, 1995; Shaklee et al. 1999). Increased resolution

among populations relative to that detected with

allozymes became possible with the advent of DNA-

level assays. Initial surveys employed variation at

mitochondrial DNA (Wilson et al. 1987; Cronin et al.

1993) and minisatellites (Beacham et al. 1996), but

these techniques were soon replaced by surveys of

microsatellite variation (Banks et al. 2000; Nelson et al.

2001; Beacham et al. 2003). Microsatellites have been

recognized as providing the ability to evaluate fine-

scale population structure in salmonids (Banks et al.

2000), as well as the capability to investigate

population structure on a Pacific Rim basis (Beacham

et al. 2006b).

The structure of Chinook salmon populations has

certainly been associated with colonization events

following the last glaciation (Gharrett et al. 1987).

Before the last major glaciation, Chinook salmon were

probably fairly widely dispersed along the Pacific coast

of North America (McPhail and Lindsey 1970). The

advent of glaciation restricted the distribution of

Chinook salmon to some major and minor refuges.

Modern populations were thought to have originated

largely from a Bering Sea refuge in the north and a

Columbia River refuge in the south (McPhail and

Lindsey 1970). Local refuges may also have been

present in Kamchatka (Varnavskaya et al. 1994), and

on coastal islands in British Columbia (Warner et al.

1982; Wood 1995). Existing populations in southeast

Alaska, British Columbia, and Washington, if they

have a similar colonization history to sockeye salmon

O. nerka, may be derived primarily from the southern

Columbia River refuge, with perhaps some contribu-

tion from a coastal British Columbia refuge (Wood

1995). Microsatellite variation can be used to evaluate

relationships between existing Pacific Rim population

structure and proposed patterns of dispersal from

glacial refuges.

In this study, we evaluated whether juvenile life

history had any relationship to observed genetic

structure of populations to determine whether devel-

opment of juvenile life history was a relatively rare

event or occurred over many genetic lineages,

indicative of parallel evolution. We also evaluated

whether Chinook salmon in British Columbia may

have originated from more than one glacial refuge.

These objectives were accomplished by analyzing

variation at microsatellite loci to evaluate relationships

in Pacific Rim population structure of Chinook salmon.

In addition, the high levels of polymorphism and

heterozygosity at microsatellite loci allowed examina-

tion of regional differentiation in allelic frequencies

and levels of allelic diversity. The distribution of

genetic diversity among regions, populations, and

sampling years was estimated in the study, as well as

the stability of population structure.

Methods

Collection of DNA samples.—Genomic DNA was

extracted from either liver, scales, operculum punches

or fin clips from Chinook salmon sampled initially

using the phenol-chloroform protocol of Miller et al.

(1996) and later a chelex resin protocol (Withler et al.

2000). Samples were derived from adults in all areas

except for some locations at which juveniles were

sampled due to the difficulty of obtaining adults.

Adults could have been sampled and released, freshly

killed and sampled, or samples could have been

obtained from carcasses on the spawning grounds.

The study included a survey of microsatellite variation

for over 52,000 fish from over 320 populations, with

the populations ranging from Russia through California

(Table 1; Figure 1). The specific populations, collec-

tion years, and sample sizes included in the survey

have been outlined by Beacham et al. (2006a) in their

Appendix Table 1. A summary of the number of

populations surveyed by local geographic area is

outlined in Table 1.

Conversion of allele sizes between manual andautomated sizing systems.—As outlined by Beacham et

al. (2003), the initial survey of microsatellite variation

included amplifying products at six microsatellite loci:

Ots100, Ots101, Ots102, Ots104, Ots107 (Nelson and

Beacham 1999) and Ssa197 (O’Reilly et al. 1996), and

size fractionating the amplified products on non-

denaturing polyacrylamide gels by staining with 0.5

mg/mL ethidium bromide in water and illuminating

with ultraviolet light. Nelson et al. (1998) provided a

more complete description of gel electrophoretic

conditions. Beacham and Wood (1999) provided a

more complete description of the methods used to

identify alleles using this technology. With the

CHINOOK SALMON MICROSATELLITE ANALYSIS 1605

acquisition of automated sequencers (ABI 377) in our

laboratory, polymerase chain reaction products at seven

additional loci: Ogo2, Ogo4 (Olsen et al. 1998), Oke4(Buchholz et al. 2001), Omy325 (O’Connell et al.

1997), Oki100 (K. M. Miller, unpublished data), and

Ots2, Ots9 (Banks et al. 1999) were size-fractionated

on denaturing polyacrylamide gels and allele sizes

were determined with Genescan 3.1 and Genotyper 2.5

software (PE Biosystems, Foster City, California).

The six loci previously analyzed on nondenaturing

polyacrylamide gels stained with ethidium bromide

have been analyzed since 1998 on automated DNA

sequencers. However, estimated allele sizes at these

loci differed between the two laboratory techniques. As

outlined by Beacham et al. (2003), in order to convert

allele sizes between the two techniques, we analyzed

approximately 600 fish using both techniques and

determined the distributions of allele frequencies. By

inspection of the allele frequencies, we were able to

match specific allele sizes obtained from the sequenc-

TABLE 1.—Summary of the number of sampling sites or Chinook salmon populations within each geographic region outlined

in Figure 1 (N¼number of populations sampled within regions). A complete list of the populations is outlined by Beacham et al.

(2006a) in Table 1 of the Appendix. The range of annual and population samples sizes within regions is in parentheses.

Region N Mean annual sample size Mean population sample size

Russia 13 59 (12, 150) 64 (19, 150)Upper Yukon River, Canada 4 51 (4, 113) 129 (47, 241)Teslin River 2 17 (8, 38) 42 (29, 55)Yukon–Carmacks 3 64 (27, 200) 191 (94, 369)Yukon River–main stem 3 36 (8, 106) 48 (11, 106)Pelly River 6 46 (7, 138) 76 (24, 161)Stewart River 2 62 (13, 129) 156 (112, 199)Lower Yukon River, Canada 2 76 (5, 201) 340 (113, 567)Kluane River 1 32 32Upper Yukon River, Alaska 2 69 (4, 112) 104 (91, 116)Tanana River 3 84 (19, 180) 84 (19, 180)Middle Yukon River, Alaska 2 237 (27, 447) 237 (27, 447)Koyukuk River 4 104 (19, 196) 104 (19, 196)Lower Yukon River, Alaska 4 73 (17, 207) 91 (17, 113)Alsek River 4 93 (14, 238) 255 (24, 432)Taku River 5 89 (13, 204) 124 (72, 204)Stikine River 7 110 (5, 224) 250 (24, 606)Southeast Alaska 3 122 (57, 192) 122 (57, 192)Queen Charlotte Islands 1 50 (27, 80) 201Nass River 10 66 (3, 239) 178 (31, 299)Upper Skeena River 3 70 (25, 200) 209 (34, 416)Babine River 1 89 (27, 192) 266Bulkley River 3 103 (13, 213) 275 (13, 585)Middle Skeena River 3 50 (19, 99) 166 (46, 288)Lower Skeena River 6 70 (17, 116) 187 (21, 457)Northern British Columbia 22 74 (3, 260) 175 (30, 507)Southern British Columbia 10 82 (2, 214) 156 (20, 402)East Vancouver Island 16 112 (11, 201) 309 (22, 901)West Vancouver Island 19 84 (6, 215) 260 (33, 518)Upper Fraser River 25 47 (1, 208) 135 (18, 453)Middle Fraser River 20 69 (2, 326) 208 (22, 584)Lower Fraser River 7 65 (3, 184) 307 (104, 548)North Thompson River 8 50 (2, 257) 119 (19, 262)South Thompson River 11 55 (3, 201) 154 (13, 366)Lower Thompson River 9 82 (15, 306) 265 (131, 553)Boundary Bay 2 69 (46, 91) 69 (46, 91)Puget Sound 7 88 (50, 100) 114 (50, 282)Strait of Juan de Fuca 1 100 100Coastal Washington 4 40 (11, 98) 70 (59, 98)Lower Columbia River 3 90 (77, 100) 90 (77, 100)Willamette River 3 64 (12, 99) 64 (12, 99)Middle Columbia River 5 33 (20, 40) 33 (20, 40)Upper Columbia River (spring) 4 91 (64, 100) 91 (64, 100)Upper Columbia River (summer/fall) 5 83 (13, 100) 83 (13, 100)Snake River (spring/summer) 14 57 (17, 100) 77 (17, 220)Snake River (fall) 1 56 (20, 91) 111North and Central Oregon 7 57 (23, 100) 65 (37, 100)South Oregon 5 76 (48, 100) 76 (48, 100)Klamath River 5 67 (15, 100) 67 (15, 100)California Central Valley (spring) 4 35 (15, 52) 43 (15, 82)California Central Valley (fall) 11 66 (25, 120) 84 (25, 200)

1606 BEACHAM ET AL.

ers to specific allele sizes from the manual gels, and

then convert the sizing in the manual gel data set to

match that obtained from the automated sequencers.

Estimated allele sizes from both systems were very

highly correlated, and r2 exceeded 0.987 for all loci. In

general, sizes for the same allele from the sequencers

were larger than those estimated from manual gels,

with the difference increasing with allele size. The

initial technique used in our laboratory to survey

microsatellite variation, which incorporated four 20-

base pair (bp) size ladders on a gel, lacked the

resolution to differentiate between alleles differing by 2

bp in size when allele sizes were greater than about 180

bp. Although alleles differing by 2 bp in size were

observed with the automated sequencers at some of the

six loci initially surveyed, adjacent alleles were

combined in order to conform to the 4-bp resolution

obtained during application of the manual gel tech-

nique. The practical effect of merging the two data sets

at these loci was to forgo some of the resolution among

populations that would have been provided by the

identification of additional alleles.

Data analysis.—All annual samples available for a

location were combined to estimate population allele

frequencies, as recommended by Waples (1990). Each

population at each locus was tested for departure from

Hardy–Weinberg equilibrium (HWE) by using Genetic

Data Analysis (GDA) software (Lewis and Zaykin

2001). Critical significance levels for simultaneous

tests were evaluated using sequential Bonferroni

adjustment (Rice 1989). Weir and Cockerham’s

(1984) genetic differentiation index (FST

) estimates

for each locus over all populations were calculated with

FSTAT version 2.9.3.2 (Goudet 1995). The signifi-

cance of the multilocus FST

value over all samples was

determined by jackknifing over loci. Populations were

combined into 16 regional groups in order to display

mean pairwise FST

values between regions. Cavalli-

Sforza and Edwards (CSE) (1967) chord distance was

used to estimate genetic distances among all popula-

tions. An unrooted neighbor-joining tree based upon

CSE was generated using NJPLOT (Perriere and Gouy

1996). Bootstrap support for the major nodes in the tree

was evaluated with the CONSENSE program from

PHYLIP based upon 1,000 replicate trees (Felsenstein

FIGURE 1.—Geographic regions where Chinook salmon from over 320 populations or sampling sites were surveyed for

microsatellite variation. A complete list of the populations surveyed within each region was outlined by Beacham et al. (2006a).


1993). The software program FSTAT was used to

measure the allelic richness (allelic diversity standard-

ized to a sample size of 121 fish) for each group of

populations evaluated. Computation of the number of

alleles observed per locus was carried out with GDA.

The distribution of genetic variation in Chinook salmon

was evaluated among river drainages or regions,

among populations within drainages or regions, and

among sampling years within populations. In order to

maintain a balanced design, river drainages or regions

included in the analysis required two or more

populations each with two or more years of samples

available. Accordingly, river drainages or regions had a

North American distribution and they were (specific

populations in parentheses): Yukon River (Chandindu,

Tozitna rivers), Alsek River (Blanchard, Klukshu

rivers), Stikine River (Little Tahltan, Verrett rivers),

Nass River (Damdochax, Owegee rivers), Skeena

River (Bulkley, Morice, Sustut rivers), northern British

Columbia (Kitimat, Wannock rivers), Vancouver

Island east coast (Quinsam River, Nanaimo River fall

run), Vancouver Island west coast (Robertson, Nitinat

rivers), upper Fraser River (Dome, Tete Jaune rivers),

middle Fraser River (Quesnel, Nechako rivers), lower

Fraser River (Harrison River, Maria Slough), South

Thompson River (Louis, Deadman rivers), Snake River

spring run (Marsh, Upper Salmon rivers), and Cal-

ifornia Central Valley fall run (Sacramento, Merced,

Feather rivers). Estimation of variance components of

river drainage or region differentiation, among popu-

lations within drainages or regions, and among years

within populations was determined with GDA. Allele

frequencies for all location samples surveyed in this

study are available at the Molecular Genetics Labora-

tory web site (http://www-sci.pac.dfo-mpo.gc.ca/mgl/

default_e.htm).

Results

Variation within Populations

Considerable variation was observed in the number

of alleles recognized at each locus, ranging from 15

(Ots9) to 60 alleles (Ots102) (Table 2). As expected,

lower heterozygosity was observed at those loci with

fewer alleles. Observed and expected heterozygosities

were in close agreement for those loci analyzed solely

on the automated sequencers. Observed heterozygos-

ities were less than expected heterozygosities for all

loci partly screened on the manual gels. Unequal

amplification of alleles may have resulted in failure to

detect large alleles in some individuals under ethidium

bromide staining. One locus (Ots102) was clearly not

in HWE, with observed genotypic frequencies in about

70% of populations examined not conforming to those

expected under HWE. More homozygous individuals

were observed than expected at this locus, indicative of

either a null allele or marked differential amplification

of alleles.

The number of alleles observed displayed consider-

able variation across regional groups of Chinook

salmon. Chinook salmon from the Alsek River in

northern British Columbia and the Klamath River in

California displayed the fewest number of alleles

compared with Chinook salmon in other regions

surveyed (Table 3). The most genetically diverse

Chinook salmon were observed from northern British

Columbia, Washington (Puget Sound and coastal

populations), and the spring run in upper Columbia

River basin, with an average of over 300 alleles

observed in total for salmon from these regions.

Chinook salmon from these regions displayed approx-

imately 50% more alleles than did Chinook salmon

from the Alsek and Klamath rivers, two regions of low

genetic diversity. There was no difference in genetic

TABLE 2.—Number of alleles, expected heterozygosity (He), observed heterozygosity (H

o), percent significant Hardy–

Weinberg equilibrium tests (HWE; n ¼ 325 tests), and FST

among 325 Chinook salmon samples (SD in parentheses) for 13

microsatellite loci.

Locus Alleles He

Ho

HWE FST

Ots9 15 0.53 0.52 1.5 0.094 (0.006)Oke4 17 0.64 0.63 1.2 0.117 (0.005)Ogo4 23 0.75 0.75 3.0 0.113 (0.005)Ots2 28 0.64 0.63 3.9 0.110 (0.007)Ogo2 30 0.71 0.71 0.6 0.095 (0.006)Omy325 43 0.75 0.74 6.0 0.130 (0.006)Ssa197 45 0.92 0.91 4.2 0.036 (0.002)Ots104 45 0.93 0.91 3.9 0.030 (0.002)Ots107 47 0.91 0.89 5.9 0.051 (0.003)Oki100 47 0.93 0.92 3.0 0.031 (0.002)Ots101 50 0.91 0.88 12.8 0.036 (0.002)Ots100 58 0.93 0.91 10.1 0.026 (0.002)Ots102 60 0.92 0.66 69.6 0.045 (0.002)All loci 0.063 (0.010)

1608 BEACHAM ET AL.

diversity of the stream-type and ocean-type life

histories. For example, the ocean-type life history

predominates in the Klamath River, and the stream-

type life history type comprises all of the returning

Chinook salmon to the Alsek River, yet Chinook

salmon from both of these rivers displayed lower

diversity than Chinook salmon from other areas

sampled. The greatest differentiation in terms of allelic

diversity among regions was observed at those loci

with larger numbers of total observed alleles.

Distribution of Genetic Variation

Gene diversity analysis of the 13 loci surveyed was

used to evaluate the distribution of genetic variation

among river drainages or regions, among populations

within river drainages or regions, and among years

within populations. For 14 river drainages or regions

with a North American geographic distribution, the

amount of variation within populations ranged from

88% (Oke4) to 97% (Oki100) and the average for an

individual locus was 93% (Table 4). Variation among

the 14 river drainages or regions accounted for 3.9% of

total observed variation. Variation among populations

within river drainages or geographic regions accounted

for 2.6% of observed variation. The variation among

sampling years within populations was the smallest

source of variation observed, accounting for 0.5% of all

variation. Differentiation among river drainages and

populations within river drainages was approximately

13 times greater than that of annual variation within

populations. For the time intervals surveyed in our

study, annual variation in microsatellite allele frequen-

cies was relatively minor compared with differences

among populations within river drainages and among

river drainages on a geographically diverse scale of

distribution.

Population Structure

Clear genetic differentiation was evident among

Chinook salmon populations sampled in the different

geographic regions surveyed. The FST

value over all

populations and loci was 0.063, with individual locus

values ranging from 0.026 (Ots100) to 0.130 (Omy325)

(Table 2). Chinook salmon from southern Oregon and

California were among the most distinct regional

groups of stocks included in the survey (Table 5).

Substantial within-group differentiation was observed

within the lower and mid-Columbia River grouping,

with average differentiation among populations within

the group similar to the level of differentiation

observed among groups (Table 5). Differentiation

between populations in the Willamette River drainage

and those in the lower Columbia River accounted for

the observed within-group differentiation in the lower

Columbia River region. Lesser regional average

differentiation was observed among populations in

the transboundary rivers (Alsek, Stikine, and Taku

rivers) than among populations in the Nass River,

Skeena River, and Queen Charlotte Islands in northern

British Columbia.

TABLE 3.—Mean number of alleles observed per locus at 13 microsatellite loci for Chinook salmon from 22 regions

standardized to a sample size of 121 fish per region. Region codes are as follows: QCI ¼ Queen Charlotte Islands, SEAK ¼southeast Alaska, NBC ¼ northern British Columbia, ECVI ¼ east coast Vancouver Island, WCVI ¼ west coast Vancouver

Island, SBC¼ southern British Columbia.

Region Ots9 Oke4 Ogo2 Ots2 Ogo4 Omy325 Ots101 Ots104 Oki100 Ssa197 Ots107 Ots100 Ots102 Total

Russia 3.7 3.2 9.9 3.3 8.4 11.1 30.4 31.2 24.6 29.7 27.1 31.9 37.9 252.3Yukon 4.0 4.2 8.5 3.0 9.8 10.6 32.6 26.9 29.5 32.4 24.3 25.9 38.6 250.4Alsek 2.7 3.5 6.2 3.1 8.3 7.8 26.7 22.6 23.2 15.3 18.0 28.8 27.1 193.1Taku, Stikine Rivers 5.3 5.0 12.4 8.8 13.6 19.8 32.8 28.5 29.8 29.6 34.8 34.9 38.7 294.1QCI, SEAK 4.7 5.0 9.6 12.4 14.0 16.9 26.4 25.8 26.9 27.9 29.0 29.9 28.6 257.2Nass River 5.6 6.2 10.1 10.7 11.4 16.8 26.8 29.1 29.6 29.6 30.1 32.7 31.9 270.5Skeena River 5.5 5.7 13.4 12.6 13.1 18.2 30.1 28.8 28.8 31.5 30.8 33.3 38.7 290.4NBC 6.2 5.7 13.6 14.3 14.5 17.8 29.4 29.5 28.6 32.6 35.4 37.9 41.3 306.8Fraser River 5.4 6.5 11.4 12.3 13.8 14.8 27.8 28.0 27.9 27.9 32.5 32.8 32.9 274.2Thompson River 4.7 6.7 12.3 10.6 12.4 15.1 27.5 27.1 28.2 28.9 30.5 31.1 38.3 273.5ECVI 5.6 6.6 9.8 16.2 15.5 11.0 24.0 27.4 26.4 26.4 26.4 42.0 33.5 271.0WCVI 5.1 5.8 10.7 11.8 14.4 10.9 25.4 29.3 33.8 29.9 28.8 39.0 35.0 279.7SBC 5.2 5.9 11.1 13.9 11.8 17.9 28.3 26.5 29.1 29.6 28.3 35.4 41.5 284.5Washington 6.4 8.1 14.4 17.7 17.1 16.4 31.0 31.9 30.8 34.1 32.2 37.9 42.7 320.6Lower and middle Columbia River 4.5 8.3 13.6 14.0 10.5 11.2 28.4 30.8 29.6 29.6 26.6 34.4 42.5 284.0Upper Columbia River–spring 5.3 7.6 14.7 15.6 15.6 13.4 26.3 32.8 30.2 28.7 35.0 41.3 42.4 309.0Snake River–spring 4.8 6.8 10.8 8.1 11.2 10.6 25.4 30.4 22.0 23.0 28.6 34.6 37.1 253.5North and Central Oregon 4.1 5.9 12.8 11.6 14.4 13.4 30.2 30.4 29.6 25.8 33.0 42.0 34.9 288.2South Oregon 4.8 6.0 13.4 11.4 10.7 13.8 27.8 23.8 30.1 27.4 28.2 33.9 35.1 266.4Klamath, Trinity rivers 3.0 3.0 6.9 8.7 7.5 6.6 26.3 20.0 23.3 19.5 19.7 22.9 24.9 192.3California Central Valley 3.9 5.0 11.5 13.6 9.9 14.6 33.4 24.3 32.5 28.9 27.7 39.1 35.0 279.4


The general pattern observed in our survey was a

regional structuring of populations. Chinook salmon

spawning in different tributaries within a major river

drainage or spawning in smaller rivers in a geographic

area were generally more similar to each other than to

populations in different major river drainages or

geographic areas. For example, in northern locations,

the 13 Russian populations surveyed clustered together

in 98% of dendrograms evaluated, and the 37

populations sampled in the Yukon River drainage

TABLE 4.—Hierarchical gene diversity analysis for 13 microsatellite loci of 32 Chinnok salmon populations within 14 river

drainages or regions (*P , 0.05; **P , 0.01). River drainages or regions and lakes within drainages or regions had a North

American distribution (specific populations in parentheses): Yukon River (Chandindu, Tozitna rivers), Alsek River (Blanchard,

Klukshu rivers), Stikine River (Little Tahltan, Verrett rivers), Nass River (Damdochax, Owegee rivers), Skeena River (Bulkley,

Morice, Sustut rivers), Northern British Columbia (Kitimat, Wannock rivers), Vancouver Island east coast (Quinsam River,

Nanaimo River fall run), Vancouver Island west coast (Robertson, Nitinat rivers), upper Fraser River (Dome, Tete Jaune rivers),

middle Fraser River (Quesnel, Nechako rivers), lower Fraser River (Harrison River, Maria Slough rivers), South Thompson

River (Louis, Deadman rivers), Snake River spring run (Marsh, Upper Salmon rivers), and California Central Valley fall run

(Sacramento, Merced, Feather rivers). Sampling years within populations were outlined by Beacham et al. (2006a). The last

column shows the ratio of the sum of the among-population and among-drainage variance components divided by the among-

year variance component.

Locus Within populationsAmong years

within populationsAmong populations

within drainages Among drainages Ratio

Ogo2 0.8903 0.0022** 0.0404** 0.0671** 48.9Ogo4 0.8936 0.0041** 0.0281** 0.0742** 25.0Oke4 0.8766 0.0027** 0.0273** 0.0934** 44.7Omy325 0.8781 0.0030** 0.0327** 0.0862** 39.6Oki100 0.9686 0.0024** 0.0202** 0.0088 12.1Ots2 0.8798 0.0034** 0.0413** 0.0755** 34.4Ots9 0.9237 0.0033** 0.0237** 0.0493** 22.1Ots100 0.9644 0.0153** 0.0098** 0.0105* 1.3Ots101 0.9604 0.0038** 0.0229** 0.0129 9.4Ots102 0.9456 0.0090** 0.0282** 0.0172* 5.0Ots104 0.9644 0.0042** 0.0219** 0.0095 7.5Ots107 0.9441 0.0038** 0.0270** 0.0251** 13.7Ssa197 0.9620 0.0057** 0.0166** 0.0157* 5.7All 0.9306 0.0050** 0.0255** 0.0389** 12.9

TABLE 5.—Mean pairwise FST

values averaged over 12 microsatellite loci from 16 regional groups of Chinook salmon that were

sampled at 325 locations across the Pacific Rim. Comparisons were conducted between individual populations in each region.

Values in bold italic (diagonal) are comparisons among populations within each region. The FST

values are listed below the

diagonal; SDs are above the diagonal. Some of the regions listed in Table 1 were combined to facilitate analysis. Region codes

(RC) are as follows: (1) Russia, (2) Yukon River, (3) Alsek, Taku, and Stikine rivers and southeast Alaska, (4) Nass and Skeena

rivers and Queen Charlotte Islands, (5) northern and central British Columbia mainland, (6) southern British Columbia mainland,

(7) Fraser River, (8) Vancouver Island east coast, (9) Vancouver Island west coast, (10) Washington (includes Boundary Bay,

Puget Sound, and Strait of Juan de Fuca), (11) lower and middle Columbia River and Willamette River, (12) upper Columbia and

Snake River, summer and fall runs, (13) upper Columbia and Snake River, spring run, (14) coastal Washington, northern and

central coastal Oregon, (15) southern coastal Oregon and Klamath River, and (16) California’s Central Valley.

RC 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

1 0.018 0.023 0.015 0.031 0.037 0.011 0.014 0.025 0.019 0.012 0.022 0.034 0.012 0.016 0.025 0.0142 0.083 0.038 0.023 0.032 0.038 0.017 0.017 0.030 0.020 0.015 0.019 0.041 0.019 0.020 0.024 0.0183 0.052 0.064 0.030 0.036 0.046 0.025 0.024 0.032 0.026 0.019 0.020 0.038 0.016 0.021 0.029 0.0214 0.070 0.073 0.058 0.051 0.043 0.020 0.016 0.022 0.024 0.021 0.024 0.039 0.026 0.025 0.030 0.0245 0.075 0.075 0.052 0.047 0.057 0.033 0.036 0.035 0.038 0.033 0.039 0.047 0.041 0.035 0.039 0.0366 0.068 0.068 0.050 0.050 0.050 0.054 0.012 0.020 0.022 0.014 0.014 0.033 0.014 0.013 0.018 0.0117 0.077 0.084 0.064 0.057 0.060 0.062 0.041 0.019 0.024 0.013 0.015 0.045 0.015 0.019 0.023 0.0188 0.100 0.099 0.080 0.067 0.061 0.058 0.070 0.058 0.025 0.025 0.025 0.037 0.026 0.027 0.024 0.0239 0.084 0.085 0.071 0.064 0.070 0.063 0.063 0.068 0.056 0.016 0.017 0.031 0.020 0.020 0.024 0.014

10 0.094 0.086 0.063 0.066 0.059 0.043 0.062 0.055 0.059 0.031 0.016 0.030 0.012 0.017 0.018 0.01511 0.092 0.090 0.064 0.071 0.066 0.053 0.069 0.071 0.068 0.055 0.055 0.032 0.010 0.012 0.017 0.03612 0.099 0.101 0.075 0.078 0.076 0.055 0.072 0.070 0.068 0.053 0.057 0.062 0.029 0.024 0.034 0.04413 0.062 0.089 0.062 0.074 0.075 0.070 0.067 0.094 0.083 0.082 0.063 0.071 0.066 0.016 0.022 0.01714 0.078 0.087 0.058 0.065 0.061 0.046 0.066 0.066 0.065 0.053 0.034 0.066 0.076 0.035 0.035 0.02115 0.128 0.124 0.101 0.103 0.097 0.071 0.101 0.092 0.093 0.074 0.063 0.096 0.110 0.053 0.039 0.03316 0.133 0.116 0.090 0.093 0.085 0.061 0.090 0.074 0.077 0.064 0.078 0.082 0.105 0.061 0.089 0.010

1610 BEACHAM ET AL.

clustered together in 92% of the dendrograms (Figure

2). Farther south, 20 west coast Vancouver Island

populations clustered together in 70% of dendrograms

evaluated. Puget Sound (including Boundary Bay)

populations clustered together, as did populations from

coastal Washington. California Central Valley popula-

tions were a distinct group of populations, clustering

together in 100% of dendrograms evaluated, and were

well differentiated from coastal populations in Oregon.

Although the general pattern was clustering of

populations within a river drainage, there were some

exceptions to a strict cluster. In the Fraser River

drainage, the majority of populations clustered togeth-

er: middle Fraser, upper Fraser, and all Thompson

River populations clustered with strong bootstrap

support (87%) (Figure 2). However, populations in

the lower Fraser River were distinct from those in the

rest of the drainage. Fall-run populations in the

Harrison and Chilliwack rivers, as well as populations

from tributaries on the north side of the lower river,

clustered separately from other Fraser River popula-

tions. They were more similar to populations from the

southern British Columbia mainland than they were to

other Fraser River populations, but the relationship

between lower Fraser River populations and those in

adjacent regions is uncertain, given the low bootstrap

support for the cluster with southern mainland

populations (Figure 2).

Population structure in the Columbia River drainage

was dependent both upon run timing and geographical

discreteness. Spring-run populations from the mid and

upper portions of the drainage, including the Snake

River, were distinct from later-returning runs in the

drainage, with the spring-run populations clustering

together in 92% of dendrograms evaluated (Figure 2).

Fall-run populations in the upper Columbia and Snake

rivers were distinct from but similar to populations in

the lower Columbia River drainage, including the

Willamette River drainage. Lower Columbia River

populations were distinct from coastal Washington

populations to the north and coastal Oregon popula-

tions to the south (Figure 2).

The widespread geographic distribution of popula-

tions included in the survey allowed a determination of

major lineages of Chinook salmon. One major group of

populations included those surveyed in Russia, the

Yukon River, and the Alsek River (Figure 2). Within

this group, there was clear distinction among popula-

tions from these three geographic regions, and also

evidence of geographic structuring within regions. For

example, populations from the Pahacha River and

Olutorksy Bay clustered together and were separate

from other Russian populations. The Pahacha River

and Olutorksy Bay populations are located in the very

northeast of the Kamchatka Peninsula, and were

geographically distinct from other Russian populations.

In the Yukon River, two major groups of populations

were observed, which roughly corresponded to popu-

lations located in the Yukon Territory and Alaskan

portions of the drainage. The two most downstream

populations located within the Yukon Territory, and

hence geographically the closest to Alaska, were the

Chandindu and Klondike rivers, and these populations

clustered with the Alaskan group of populations

(Figure 2). They were most similar to the Chandalar

River population, which was the most upstream

population of the Alaskan populations surveyed.

A major lineage of Chinook salmon was observed in

populations sampled in southeast Alaska: the Taku,

Stikine, Nass, and Skeena rivers. There was geographic

structuring of populations within this major lineage

generally corresponding to river drainage, although

there was some discontinuity between populations in

the lower portions of the Nass and Skeena rivers and

those in the middle and upper portions of the drainage

(Figure 2). Populations in the Taku and Stikine rivers

were more similar to each other than to populations in

the Nass and Skeena rivers, but they also clustered by

drainage.

Genetic variation was observed among Chinook

salmon populations sampled in the central coast of

British Columbia, with the Wannock River population,

which spawns in the outflow river (Wannock River)

draining Owikeno Lake in the central coast, distinct

from other populations in the region. Wannock River

Chinook salmon are known for their large body size,

and form a very important component of the well-

known recreational fishery in Rivers Inlet. Within the

region, populations in tributary streams to Owikeno

Lake (Sheemahant, Ashlulm, and Neechanze rivers)

were distinct from those in other locations. Populations

in more northern areas of the central coast (Hirsch,

Kitimat, Kateen, and Kildala rivers) clustered sepa-

rately from those in more southern areas of the central

coast (Dean, Atnarko, Nusatsum, and Takia rivers), but

there was only a weak association between the two sets

of populations (Figure 2).

Chinook salmon populations sampled on Vancouver

Island were distinct from other populations surveyed in

British Columbia, and indeed there was a clear

demarcation between populations sampled on the east

and west coasts of the island. West coast Vancouver

Island populations were most similar to Chinook

salmon from other regions in British Columbia,

whereas east coast Vancouver Island populations were

most similar to Puget Sound populations in Wash-

ington (Figure 2). For the west coast Vancouver Island

region, populations north of Brooks Peninsula (a


FIGURE 2.

1612 BEACHAM ET AL.

FIGURE 2.—(Continued.) Neighbor-joining dendrogram of Cavalli-Sforza and Edwards (1967) chord distance for over 320

populations of Chinook salmon surveyed at 12 microsatellite loci. The locus Ots102 was not included in the analysis because of

the level of Hardy–Weinberg equilibrium observed. Bootstrap values at major tree nodes indicate the percentage of 1,000 trees

where populations beyond the node clustered together.


FIGURE 2.—Continued.

1614 BEACHAM ET AL.

possible glacial refuge on northwest Vancouver

Island), such as those from Colonial Creek and Marble

River, were quite distinct from those in more southern

locations in the regions. Populations associated with

the Stamp River and Robertson Creek hatchery, either

through transplants from the hatchery or by straying,

were distinct from other populations in the region. For

the east coast of Vancouver Island, populations from

the northeast coast (Nimpkish River, Woss Lake,

Quatse River) were distinct from those along the

central and southern areas of the east coast.

In Washington, there were clear genetic differences

between populations surveyed in Puget Sound, and

those surveyed on the Pacific Coast. The single

FIGURE 2.—Continued.


population surveyed from the Strait of Juan de Fuca,

the Elwha River population, was more similar to, but

distinct from, the Puget Sound populations. Pacific

coastal populations were more similar to coastal

populations in Oregon than they were to populations

surveyed in Puget Sound (Figure 2).

Spring-run Chinook salmon returning to the middle

and upper portions of the Columbia River drainage

were quite unlike any other group of populations

sampled south of the border between Canada and the

United States. This lineage was most similar to

populations surveyed in northern British Columbia

and areas farther north (Figure 2). Summer-run and

fall-run populations in the Columbia River drainage

were similar to each other, but there was clear

geographic structuring, with lower river populations

distinct from populations returning to the upper

portions of the drainage. Populations spawning in the

Willamette River drainage, although relatively close to

lower Columbia River populations geographically,

were distinct from those in the lower Columbia River.

The only exception was the Sandy River spring-run

population, which likely reflected transplantation

history of the population.

Oregon coast populations tended to be grouped into

a northern and central coastal region, and a southern

coastal region, but consistent differentiation was

limited. Both groups of populations clustered with

populations from the coastal Washington region

(Figure 2). In California, geographic structuring of

the populations surveyed was observed. Klamath River

populations were distinct from those returning farther

south to the Sacramento River drainage. The Klamath

River populations were most similar to populations

returning to the Oregon coast, but Central Valley

populations were most similar to upper Columbia River

populations (Figure 2).

Discussion

The survey of microsatellite variation included an

examination of variation at 13 loci encompassing

approximately 510 alleles, with 15–60 alleles recog-

nized per locus. The number of fish surveyed per

population ranged from about 10 to 700 individuals

(Beacham et al. 2006a). With a variable number of

individuals surveyed per population, there was a

potential for sampling error in estimated allele

frequencies obscuring genetic relationships among

related populations, particularly if sample sizes were

small for some populations in a lineage. For example,

in the Yukon River drainage, population sample sizes

ranged from about 10 to 567 individuals, and it was

potentially possible that estimates of genetic distances

among populations were not determined satisfactorily

for populations of smaller sample size, particularly for

those loci with larger numbers of alleles. However,

Kalinowski (2005) reported that, through simulation

studies, loci with larger numbers of alleles (higher

mutation rates) produced estimates of genetic distance

with lower coefficients of variation than loci with fewer

numbers of alleles without requiring larger sample

sizes from each population. Kalinowski (2005) report-

ed that when FST

is greater than 0.05 between

populations, sampling fewer than 20 individuals per

population should be sufficient for estimation of

genetic distance. For the Yukon River drainage

example, the average FST

value between populations

was 0.04, so that relative genetic differences among

populations should have been accurately determined.

Population structuring based upon geographic differ-

ences with the drainage was observed, and the drainage

clustering of all populations sampled received strong

bootstrap support (92%). Therefore, it seems likely that

variation in the number of individuals surveyed within

a population in our study did not generally result in

misidentification of genetic relationships among pop-

ulations.

Inferences concerning the genetic relationships of

populations surveyed in our study were dependent

upon accurate determination of population allele

frequencies. Microsatellite alleles differ in size, but

alleles of the same size at a locus in geographically

disparate populations may not be identical in descent as

a result of size homoplasy. Convergent mutations in

different lineages may produce alleles of the same size,

with the result that greater differentiation among

lineages may exist than is otherwise revealed by

analysis of size variation. However, phylogenetic

analyses among related populations may not be

affected significantly by size homoplasy, as the large

amount of variation present at highly polymorphic

microsatellite loci largely compensates for size homo-

plasy (Estoup et al. 2002).

Obtaining a tissue sample for DNA extraction can

frequently be challenging if the collection program is

directed toward sampling adults, and if populations

spawn in remote areas opportunities to collect samples

may be limited. It would not be unusual to have smaller

numbers of fish sampled over a number of years in

order to obtain samples for genetic characterization of

the population. In our study, all samples available for a

specific sampling site or population were combined in

order to estimate genetic differentiation among popu-

lations. Annual variation in allele frequencies within a

population were estimated to be 13 times less than the

geographic and population differences observed, so

pooling of annual samples over time is a reasonable

approach to estimate population allele frequencies.

1616 BEACHAM ET AL.

Relative annual stability of microsatellite allele fre-

quencies has been demonstrated previously for Chi-

nook salmon (Beacham et al. 2003) and is a general

feature of microsatellite loci in salmonids (Tessier and

Bernatchez 1999; Beacham et al. 2006b).

Life history variation and genetic differentiation

have been proposed to be linked in Chinook salmon.

Juvenile life history, based upon whether the juveniles

displayed stream-type or ocean-type life history

patterns, was proposed as a method to define races of

Chinook salmon (Healey 1983, 1991). In a study of

allozyme variation of Chinook salmon in British

Columbia, Teel et al. (2000) reported that two major

groups of populations existed. The first group was

coastal and included populations from the central coast

region of British Columbia, Vancouver Island, and the

lower Fraser River. The second group was interior and

included the Nass and Skeena rivers and the upper

portion of the Fraser River drainage. Teel et al. (2000)

concluded that the geographic distribution of the

coastal and inland groups largely coincided with the

geographic distribution of stream-type and ocean-type

life history forms, and that the geographic population

structuring observed may have reflected postglacial

dispersal by two lineages from distinct refugia. In an

allozyme-based study that evaluated population struc-

ture over a larger geographic area (British Columbia to

California) than that of Teel et al. (2000), Waples et al.

(2004) suggested that proposing two major lineages to

account for the observed genetic structure and juvenile

life history characteristics in British Columbia may

have been too simplistic.

Is Chinook salmon population structure concordant

when evaluated with different classes of genetic

markers? For example, Allendorf and Seeb (2000)

reported that a concordant pattern of population

structure in sockeye salmon was observed when

comparing population structure based upon allozyme

and microsatellite variation. For Chinook salmon, the

broad-scale population structure observed from surveys

of allozyme variation (Waples et al. 2004) generally

conformed to those observed in the survey of

microsatellite variation. For example, regional groups

of populations were observed in the Central Valley of

California, coastal Oregon, the Columbia River, coastal

Washington, Puget Sound, and the Fraser River. Some

discrepancies in population structure occurred between

the two marker classes, but these were largely restricted

to regions in British Columbia where allozyme-based

surveys had not been as extensive as in the microsat-

ellite survey. For example, unlike the results reported

by Teel et al. (2000), our study populations surveyed in

the central coastal region of British Columbia were

more similar to populations in northern British

Columbia, such as the Nass, Skeena, Stikine, and

Taku rivers, than they were to populations in southern

British Columbia located on Vancouver Island or the

lower Fraser River drainage. Secondly, the close

affinity between the Nass, Skeena, upper Fraser, and

Thompson River populations reported by Teel et al.

(2000) was not observed in our study. The survey of

microsatellite variation revealed strong separation of

Nass and Skeena River populations from populations

surveyed in the interior portion of Fraser River

drainage. Microsatellite variation generally revealed a

drainage-based population structure when populations

in major river drainages in British Columbia were

surveyed.

The microsatellite-based survey of population struc-

ture in British Columbia Chinook salmon did not

provide supporting evidence for two major lineages of

Chinook salmon that were strongly correlated with

juvenile life history characteristics. This was apparent

in the Thompson River drainage, where both life

history types can occur. Specifically, ocean-type

populations sampled in our study included the lower

Shuswap, the middle Shuswap, Little, lower Adams,

South Thompson, and lower Thompson rivers (Candy

et al. 2002). These populations did not cluster together

in a manner that was completely separate from other

stream-type populations in the drainage. Although the

lower Thompson, South Thompson, Little, and lower

Adams River populations formed a small branch on the

dendrogram, they were separate from the lower and

middle Shuswap River populations, which were most

similar to stream-type populations in the South

Thompson River drainage. These ocean-type popula-

tions likely originated from stream-type progenitors

and thus reflect adaptation to environmental conditions

that promote faster-growing juveniles capable of

smolting during their first year of life. In the lower

Fraser River drainage, the Upper Pitt, Birkenhead, and

Big Silver River populations all display stream-type

juvenile life history (Candy et al. 2002), but they were

most similar to Harrison and Chilliwack River fish, two

ocean-type populations in the lower portion of the

drainage, rather than to stream-type populations in the

middle and upper portions of the Fraser River drainage.

The ocean-type lower Fraser River populations were

distinct from ocean-type populations in the Thompson

River drainage. It seems likely that, as suggested by

Brannon et al. (2004), stream-type and ocean-type

juvenile life histories are not genetically based, but

rather reflect environmental conditions experienced

during early juvenile rearing in freshwater.

The most pronounced genetic differences associated

with life history characteristics (either juvenile life

history or adult run timing) have been observed in


Columbia River Chinook salmon. Spring-run popula-

tions in the upper Columbia and Snake River drainages

are strongly genetically differentiated from summer-run

and fall-run populations in the same portion of the

drainages, regardless of whether the genetic loci

surveyed are allozymes (Waples et al. 2004), mito-

chondrial DNA (Brannon et al. 2004), or microsatel-

lites (Rasmussen et al. 2003; present study). However,

outside of the Columbia River drainage, run time is not

a key factor in accounting for differentiation among

populations. Waples et al. (2004) suggested that all

spring-run populations in the upper Columbia River

basin probably had a single common lineage, and

present-day populations reflect radiation from this

single lineage. The results from the microsatellite

survey support this perspective, but evolution of a

specific run-time or juvenile life history from a single

genetic lineage is likely restricted to only the upper

Columbia River basin populations. In other areas,

variation in run timing or juvenile life history can be

observed in a variety of genetic lineages (Utter et al.

1989), which as Waples et al. (2004) suggested, would

be exactly the pattern expected from repeated periods

of parallel evolution of life history characters.

Population structure of Chinook salmon in North

America has been influenced to some degree by

transplantations within the species natural range. For

example, in southern British Columbia, Harrison River

Chinook salmon in the lower Fraser River have been

transplanted to the Chilliwack River, which is also in

the lower Fraser River drainage, as well as to the

Capilano River in the southern British Columbia

mainland. The Capilano River population was ob-

served to be more similar genetically to those from the

Harrison River than to other southern mainland

populations, probably reflecting the transplantation

history of the populations. Big Qualicum River

Chinook salmon have been transplanted to Lang Creek

on the southern British Columbia mainland, and this

population is more similar to east coast of Vancouver

Island populations than to other populations on the

southern British Columbia mainland. In the Columbia

River drainage, the genetically distinctive spring-run

Willamette River populations (Waples et al. 2004) have

been transplanted to the Sandy River in the lower

Columbia River basin. Microsatellite variation again

indicated the distinctive nature of the spring-run

Willamette River populations, but the spring-run Sandy

River population was more similar to other Willamette

River populations rather than to populations in the

lower Columbia River drainage. Allozyme variation

indicated that the fall-run Sandy River population was

more similar to other populations in the lower

Columbia River than to spring-run populations in the

Willamette River drainage (Waples et al. 2004). The

Willamette River populations included in our survey

corresponded well to the Willamette River metapopu-

lation proposed by Brannon et al. (2004).

Population structure of Chinook salmon on a Pacific

Rim basis derived from microsatellite analysis would

support the concept of at least a Bering Sea refuge in the

north and a Columbia River refuge in the south as

suggested by McPhail and Lindsey (1970). In the south,

recolonization of the upper Fraser and Thompson River

drainages may have occurred from source populations

in the upper Columbia and Snake River drainages (Utter

et al. 1989; Reisenbichler et al. 2003). In our study,

some relationship was observed between upper Fraser

and Thompson River populations and spring-run

populations in the Columbia and Snake rivers. Howev-

er, summer- and fall-run populations from these

drainages were more similar to California Central

Valley populations than to Fraser River populations.

Existing populations from Vancouver Island, the lower

Fraser River, Puget Sound, coastal Washington, the

Columbia River (summer and fall runs only), Oregon,

and California were most similar, and may be a result of

dispersal from a common southern refuge.

The Chinook salmon populations surveyed from

Russia and the Yukon and Alsek rivers were distinct

from populations surveyed in more southern locations

in North America. The Alsek River populations were

notable for their greater similarity to Russian and

Yukon River populations some thousands of kilome-

ters distant than they were to other transboundary rivers

(Taku and Stikine rivers) in the same general

geographic location. In sockeye salmon, very distinct

differences in Alsek River populations were observed

compared with populations in the Taku and Stikine

rivers (Beacham et al. 2006b). Kluane Lake, situated in

the southwest Yukon Territory in Canada, is now part

of the Yukon River drainage. However, Bostock

(1969) suggested that Kluane Lake used to be part of

the Alsek River drainage until the advance of the

Kaskawulsh glacier about 400 years ago. (The Alsek

River populations, while distinct, were more similar to

Russian populations than they were to present-day

upper Yukon River populations. The low allelic

diversity observed in Alsek River populations may

reflect recent population bottlenecks and restricted

gene flow. Although Ford (1998) may have questioned

whether there was a northern glacial refugium for

Chinook salmon, the microsatellite evidence is consis-

tent with a least one northern refugium, and given the

very distinct genetic profiles of sockeye and Chinook

salmon from the Alsek River, there may have been

more than one northern refugium for salmon.

Microsatellites have been effective in allowing an

1618 BEACHAM ET AL.

evaluation of the population structure of Chinook

salmon on a wide geographic basis. The ease of

laboratory processing enabled large numbers of fish to

be surveyed, and supported a technique that is powerful

in elucidating population structure, as well as providing

the capability of accurate stock identification in fishery

management applications (Beacham et al. 2006a).

Surveys of microsatellite variation in Chinook salmon,

currently conducted in a number of laboratories along

the Pacific Coast of North America, will probably

become increasingly applied in assessment of popula-

tion structure, determination of management units, and

the management of mixed-stock fisheries.

Acknowledgments

A substantial effort was undertaken to obtain

samples from Chinook salmon in this study. Starting

from the south, we thank C. Garza of the National

Marine Fisheries Service (NMFS) Southwest Fisheries

Center for samples from some California populations.

D. Teel of the NMFS Northwest Fisheries Science

Center provided samples from California, Oregon, and

the Columbia River. J. B. Shaklee of the Washington

Department of Fish and Wildlife provided samples

from Washington and the Columbia River. In southern

British Columbia, we thank various field staff of the

Canada Department of Fisheries and Oceans (CDFO)

for baseline sample collection, as well as First Nations

staff. In northern British Columbia and the central

coast, the Kitasoo Fisheries Program is acknowledged

for some central coast populations. We thank northern

CDFO staff, who collected and supervised collections

in Skeena River and central coast drainages. We also

acknowledge the various agencies, organizations, and

companies who collected samples in British Columbia.

For the Nass River, these included LGL, Ltd.,

Environmental Research Associates and the Gitxsan

Watershed Authority in the Skeena River drainage. We

are also highly appreciative to W. Heard of the NMFS

Auke Bay Laboratory for providing samples from

southeast Alaska. S. Johnston and P. Milligan of the

CDFO Whitehorse office supervised collections of the

Canadian portion of the Yukon River drainage, and P.

Etherton and I. Boyce supervised collections in the

transboundary rivers. J. Wenburg of the U.S. Fish and

Wildlife Service Anchorage genetics laboratory pro-

vided samples from the Alaskan portion of the Yukon

River drainage. L. Fitzpatrick drafted the map. C.

Wallace assisted in the analysis. Funding for the study

was provided by the CDFO.

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