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  • Pacific Rim Population Structure of Chinook Salmon as Determined 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 (F ST

    ) 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: beachamt@pac.dfo-mpo.gc.ca

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

    1604

    Transactions of the American Fisheries Society 135:1604–1621, 2006 � Copyright by the American Fisheries Society 2006 DOI: 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

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