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STATUS REVIEW FOR LOWER COLUMBIA RIVER COHO SALMON

by

Orlay W. Johnson

Thomas A. Flagg

Desmond J. Maynard

George B. Milner

F. William Waknitz

National Marine Fisheries Service

Northwest Fisheries Center

Coastal Zone and Estuarine Studies Division

2725 Montlake Boulevard East

Seattle, WA 98112

June 1991
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This document is available to the public through:

National Technical Information Service

U.S. Department of Commerce

5285 Port Royal Road

Springfield, VA 22161
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SUMMARY

This report summarizes biological information on coho salmon (Oncorhynchus

kisutch) from the lower Columbia River* (LCR) gathered in conjunction with a U.S.

Endangered Species Act (ESA) status review. Under the ESA, any “distinct

population segment” of fishes qualifies as a “species” and is eligible for protection if

it is threatened or endangered. National Marine Fisheries Service (NMFS) policy is

that a population will be considered “distinct” for purposes of the ESA if it represents

an evolutionarily significant unit (ESU) of the species as a whole (Waples 1991). The

ESA evaluation of coho salmon is complicated because the LCR has sustained intense

human perturbation in the last century. Commercial exploitation of coho salmon and

degradation of salmon spawning habitat reduced coho salmon numbers to near

extinction around the middle of this century. The advent of extensive artificial

propagation of the species in hatcheries has “rebuilt” the runs to at or above historic

levels. However, this process has changed the coho salmon runs in the LCR from

predominantly naturally spawning fish to predominantly hatchery-maintained fish.

Native runs, if they persist, would exist only as small remnant populations.

Life History

Coho salmon represent one of five species of anadromous Pacific salmon

native to North America. Throughout their range, native coho salmon populations

return to their natal streams to spawn from early fall to late spring. Fry emerge from

*LCR is defined in this document as the Columbia River and its tributaries

below Bonneville Dam, exclusive of the Willamette River. The mid Columbia River

is defined as the area from Bonneville Dam to the confluence of the Snake and

Columbia Rivers. The upper Columbia River is the area above this confluence,

including the area above Grand Coulee Dam.
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egg nests (redds) between early March and July, rear in fresh water for a year, migrate

to sea the next season, and return to spawn after 5 to 20 months of feeding in the open

ocean.

The NMFS Northwest Region Biological Review Team (BRT) evaluated

studies on natural history of coho salmon to determine if there are distinct differences

between populations. The BRT also evaluated whether the characteristics of the life

history of coho salmon might indicate that native populations could persist,

considering the extensive hatchery releases, outplantings, overharvest, and habitat

destruction in the LCR over the last 100 years.

Fidelity of homing in coho salmon under natural conditions is similar to that

demonstrated for other species of Pacific salmon and appears sufficient to maintain

populations with a similar level of distinctiveness. Different coho salmon populations

show timing differences from fry emergence to time of adult spawner returns. Coho

salmon show freshwater, estuarine, and ocean migratory patterns apparently

determined by the geographic area of their natal streams. Homing and spawning

behavior is complex and would suggest a selection mechanism that appears sufficient

to reduce gene flow from nonnative populations. However, the BRT determined, from

the available evidence, that the massive and extensive disruptions documented in coho

salmon populations in the LCR have depleted native populations enough that

population differences have been largely eliminated.

Historical and Current Abundance

Prior to the 1900s, naturally produced coho salmon were widespread in the

Columbia River Basin, with a historical center of abundance in the LCR. There were

also large runs of coho salmon in the middle and upper reaches of the Columbia River

and in the Snake River. All upper, middle, and Snake River runs were drastically
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reduced or destroyed by various factors prior to the 1950s, including overharvest and

habitat destruction or blockage (Cramer et al. 1991).

It is impossible to accurately estimate the decline in LCR stocks of coho

salmon, but the BRT estimated that the runs may have been reduced to less than 5%

of historic levels by the late 1950s.

The drastic decline in coho salmon abundance initiated a widespread hatchery

enhancement program after 1960 (ODFW 1990a,b; VTDF 1991a). This program

increased coho salmon populations in the Columbia River to or above historic levels.

The total return to the river often exceeded 400,000 fish in recent years (Howell et al.

1985, CBFWA 1990, PFMC 1991).

The causes of the original decline in coho salmon were not eliminated by this

extensive hatchery production. Overharvest, habitat blockage and destruction, and

other activities detrimental to natural production continued. The result was a

continued decline in naturally spawning runs while exploitation of hatchery fish

continued at increased levels. The Columbia River is now managed almost entirely for

commercial exploitation of hatchery fish.

In the early 1980s, it was estimated that less than 25,000 coho salmon were

spawning naturally in the Columbia River Basin (Wahle and Pearson 1987; CBFWA

1990). These fish were thought to have been mainly feral hatchery fish and returns

from hatchery outplants in streams away from hatcheries, although some were

naturally produced fish. The BRT found no data to suggest these numbers have

changed significantly to the present.

It is believed that the majority of naturally produced coho salmon return to the

LCR to spawn between early December and March (ODFW 1990b, 1991a,b; Cramer

et al. 1991). The Oregon Department of Fish and Wildlife (ODFW) estimates there

may be less than 195 of these fish in Oregon and that they may exist only as small,
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isolated populations in the Lewis and Clark and Sandy River systems (ODFW 1991c).

No detailed information was available from the Washington Department of Fisheries

(WDF) on possible locations where natural spawning may occur or on numbers of

nonhatchery origin coho salmon that may spawn. The BRT estimated there may be

only about 100 post-December spawning coho salmon in lower Columbia River

tributaries in Washington.

There is a post-December run of naturally spawning fish that return to the

North Fork of the Clackamas River in Oregon (Cramer 1991). Counts over the North

Fork Dam fluctuated substantially between 1957 and 1989, but there is no apparent

trend in abundance. This run was not part of the original petition for lower Columbia

River coho salmon, but was reviewed by the BRT as a special case. Computer

modeling indicates this population has less than a 0.1% chance of extinction during

the next 100 years assuming no change to population parameters.

Effects of Artificial Propagation

The BRT evaluated the outplanting history of hatchery populations in the LCR

to determine if these populations could represent the historical ESU. The BRT

determined that the history of hatchery populations shows an infusion of stocks from

throughout the basin and coastal regions in Oregon and Washington (ODFW 1990a,b;

1991c; VTDF 1991a,d). Most hatcheries in the basin manage their hatchery

populations for stocks which have either a predominately northern or southern ocean

distribution from the mouth of the Columbia River (Cramer et al. 1991; VTDF

1991a). These stocl-,s themselves are a mixture of populations, and the BRT was

unable to determine if any LCR hatchery stocks represent historically distinct LCR

populations.
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Genetic Analysis

The NMFS Northwest Fisheries Center collected coho salmon samples from t

LCR for electrophoretic analysis. The BRT analysis and a review of the scientific

literature of other genetic studies on LCR coho salmon were inconclusive in

determining whether distinct coho salmon populations existed in the LCR.

Effects of Parasitism

Ceratomyxa shasta is a protozoan parasite of coho salmon which can cause

large losses of adult fish. Stocks of coho salmon in the LCR, and some populations in

coastal Oregon and Washington, are presumed to have an inherited resistance to the

parasite. Studies suggest the presence of C. shasta may act to reduce introgression in

LCR stocks from populations that lack resistance to the parasite.

Conclusions

The BRT concluded that the available data fail to identify an existing

evolutionarily significant unit in the lower Columbia River. If one or more coho

salmon ESUs are present in the Columbia River, fishery management actions and

research studies have inadequately documented these populations.
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ACKNOWLEDGMENTS

The status review for the lower Columbia River coho salmon was conducted by

the NMFS Northwest Region Biological Review Team (BRT). The extensive public

record developed pursuant to this review and discussions of that record by the ESA

Technical Committee formed the basis for this report. Members of the BRT for LCR

coho salmon were David Damkaer, Thomas Flagg, Elizabeth Gaar, Lee Harrell, Orlay

Johnson, Robert Jones, Conrad Mahnken, Gene Matthews, Desmond Maynard,

George Milner, Gerald Monan, Ben Sandford, Michael Schiewe, Grant Thompson,

Merritt Tuttle, William Waknitz, Robin Waples, John Williams, and Gary Winans.
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INTRODUCTION

Coho salmon (Oncorhynchus kisutch) are native to the Columbia River Basin

and its tributaries (Fig. 1). They once were abundant throughout most of this large,

complex drainage, with naturally spawning populations of over 600,000 fish. Twothirds of the historical Columbia River coho salmon production may have originated

in the lower Columbia River and its tributaries (LCR) (Mullan 1984). Present

population estimates of “wild,”1 naturally spawning fish in the LCR are around

25,000. The majority of these are feral hatchery fish, and only 600 may be of nonhatchery origin. This situation prompted Oregon Trout, Oregon Natural Resources

Council, Northwest Environmental Defense Center, American Rivers, and the

Oregon and Idaho Chapters of the American Fisheries Society to petition the National

Marine Fisheries Service (NMFS) to list LCR coho salmon as threatened or

endangered “species” under the Endangered Species Act (ESA). This report

summarizes the review of the status of these fish conducted by the NMFS Northwest

Regional Biological Review Team (BRT).

KEY QUESTIONS IN ESA EVALUATIONS

Two questions must be addressed in a determination of whether a listing for a

petitioned group of fish is appropriate under the ESA: 1) Is the petitioned stock a

“species” as defined by the ESA? 2) If so, is the “species” threatened or endangered?

The “Species” Question

The ESA of 1973 was designed to identify and protect plant and animal

species whose numbers and habitats had become sufficiently depleted to critically

1 As used in this report and in common usage on the LCR, “wild” fish are progeny of

naturally spawning fish. In other regions of the Columbia and Snake Rivers, “wild”

usually refers only to indigenous fish unaffected by artificial propagation.
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threaten their survival. The Act as amended in 1978 allows protection of three

biological categories: species, subspecies, and “distinct population segments” of

vertebrates. However, the Act provides no guidance for determining what constitutes

a distinct population. To clarify the issue for Pacific salmon, NMFS published an

interim policy describing how the definition of “species” in the Act will be applied to

anadromous salmonids (Federal Register Docket No. 910248-1048; 13 March 1991).

A more detailed description of this topic appears in the NMFS “Definition of

Species” paper (Waples 1991).

NMFS policy for Pacific salmon stipulates that a salmon population or group

of populations will be considered “distinct” for purposes of the Act if it represents an

evolutionarily significant unit (ESU) of the biological species. There are two criteria

a population must meet to be considered an ESU. The first is that the population must

demonstrate reproductive isolation from other conspecific populations. The second is

that the population represents an important component in the evolutionary legacy of

the biological species.

Types of information that can be useful in determining the degree of

reproductive isolation include incidence of straying, rates of recolonization, degree of

genetic differentiation, and the existence of barriers to migration. Insight into

evolutionary significance can be provided by data on phenotypic, life-history, and

protein or DNA characteristics; habitat differences; and the effects of stock transfers

or supplementation efforts.

Hatchery Fish

In the ESA evaluation of LCR coho salmon, the question of whether hatchery

fish should be included in the species and threshold determinations must be

addressed. Abundance levels of coho salmon in the LCR are probably at or above
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historical levels, but these coho salmon are largely fish of hatchery origin. The ESA

has as its first stated purpose “to provide a means whereby the ecosystems upon

which endangered and threatened species depend may be conserved.” The

Department of Commerce is mandated to conserve endangered and threatened

species in their natural habitats. Therefore, NMFS policy is to consider only

naturally- spawning populations in determining whether a population is a “species”

for the purposes of the Act (Waples 1991).

The decision to focus on wild fish is based entirely on ecosystem

considerations; the question of the relative merits of hatchery and wild fish is a

separate issue. Fish are not excluded from ESA consideration simply because some of

their direct ancestors may have spent time in a fish hatchery, nor does identifying a

group of fish as “wild” as defined here automatically mean that they are part of an

ESU.

Once a wild component of a population has been identified, the next step is to

determine whether this population component is “distinct” for purposes of the ESA.

In making this determination, we used guidelines in the NMFS “Definition of

Species” paper (Waples 1991). We considered factors outlined in Section IIIC

(Effects of supplementation and other human activities) to determine the extent to

which artificial propagation may have affected the wild fish, through either direct

supplementation or straying of hatchery fish. Thus, although naturally spawning fish

may meet the definition of “wild” adopted here, they may be excluded from ESA

considerations for any of several reasons.

Threshold determinations also focused on wild fish, on the premise that an

ESU is not viable unless a population exists in the natural habitat. In developing

recovery plans for “species” listed as threatened or endangered, the use of artificial

propagation may be considered. If an existing hatchery is associated with the listed

11 species,” an important question to address in formulating a recovery plan is
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whether the hatchery population is similar enough to the wild population that it can

be considered part of an ESU. Factors to consider in this regard include origin of

donor stock(s), brood-stock practices, evidence for domestication or artificial

selection, population size, and the number of generations the stock has been cultured.

In general, hatchery populations that have been substantially changed as a result of

these factors should not be considered part of an ESU.

Thresholds for Threatened or Endangered Status

Neither the National Marine Fisheries Service nor the U.S. Fish and Wildlife

Service (USFWS), which share authority for administering the ESA, has an official

policy regarding thresholds for considering ESA “species” as threatened or

endangered. The Northwest Region of NMFS has published a Technical

Memorandum on this topic (Thompson 1991). Written comments received by NMFS

and extensive discussions in ESA Technical Committee meetings stressed the

importance of incorporating the concepts of Population Viability Analysis (PVA) into

threshold considerations. However, the field is rapidly evolving and a definitive

policy position on this issue is not expected in the near future. Furthermore, most of

the PVA models developed to date require. substantial life-history information that

often will not be available for Pacific salmon populations.

Therefore, instead of using a single, numerical threshold value, we used a

variety of information in evaluating the level of risk faced by an ESU. Important

factors considered included 1) absolute numbers of fish and their spatial and temporal

distribution; 2) current abundance in relation to historical abundance and current

carrying capacity of the habitat; 3) trends in abundance, based on indices such as dam

or redd counts or on estimates of spawner-recruit ratios; 4) natural and

human-influenced factors that cause variability in survival and abundance;
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5) possible threats to genetic integrity (e.g., from strays or outplants from hatchery

programs); and 6) recent events (e.g., a drought or improvements in main-stem

passage) that have predictable short-term consequences for abundance of an ESU. In

addition, until a more comprehensive PVA model becomes available for Pacific

salmon, we used the stochastic extinction model of Dennis et al. (1991) to provide

some idea of the likely status of the population in the future. This model is useful for

identifying outcomes that are likely if no protective measures are taken because it

assumes that future fluctuations in population abundance are determined by

parameters of the population measured in the recent past.

GEOGRAPHIC AREA

The BRT’s status review focused on populations of coho salmon in the LCR.

Preliminary reviews were conducted on other stocks of coho salmon from the entire

Columbia River and its tributaries. Under time constraints imposed by the ESA, it

was impossible to evaluate the potential for ESA status of any non-LCR populations.

The petition for listing coho salmon explicitly defined the stocks as “coho

populations spawning in tributaries below Bonneville Dam, except the Willamette

River” (Petition, 30 May 1990, ESA record II.B.1).
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BIOLOGICAL INFORMATION

Life History

Coho salmon are native to North America and range throughout temperate

waters of the northern Pacific Ocean. They are anadromous and return to spawn in

natal streams beginning in early fall. Historically, the Columbia River probably

represented one of the major centers of naturally produced coho salmon.

Throughout their range, local populations of coho salmon emerge from redds

(gravel nests) over a 3-week period between early March and late July, rear in fresh

water for a year, migrate to sea the next season, and return in 5 to 20 months to

spawn (Godfrey 1965). Although early and late emerging populations often exist

sympatrically within a stream system, proper timing of emergence has distinct

survival advantages. Within a week of emergence, coho salmon fry become

aggressive and territorial (Hoar 1951, Chapman 1962, Mason 1966). As prior

residents are always dominant in territorial disputes (Chapman 1962), later emerging

fry are forced to establish and defend territories in vacant habitat. Many

later-emerging fry, finding no vacant territory, form schools of subordinate fish that

survive either by swamping territory holders or drifting downstream in search of

vacant habitat. As no returning adult coho salmon have been observed without a

freshwater annulus (scale mark), it appears that all coho salmon fi-Y must find some

freshwater habitat for their first year of life or perish (Shapovalov and Taft 1954;

Mason 1975).

Outmigration of coho salmon in the Columbia River peaks in May, but

extends from early April through June (Niska and Willis 1963, Willis 1962, Dawley

et al. 1986). As smolts outmigrate, they cluster in large schools and demonstrate a

variety of survival behaviors. In the Columbia River estuary, most coho salmon
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smolts spend midmorning to late afternoon near shore, and they are found in midriver

areas at dawn and dusk. Schools intermingle as they cross paths during the smolt

outmigration, but apparently resegregate once in the ocean, as less than 10% of the

marine juveniles caught with purse seines come from different freshwater rearing

areas (Emlen et al. 1990).

Coho salmon from different geographic areas appear to have their own

migration patterns (Brannon 1984, Quinn and Tallman 1987). Columbia River

juveniles apparently remain in coastal water (within about 35 km of shore) (Pearcy

1984, Pearey and Fisher 1988) and travel as far north as the northernmost tip of

Vancouver Island and as far south as Eureka, California (Wright 1968).

A major factor in population cohesiveness is the fidelity with which adult salmon are

able to home to their natal streams. Although ocean homing mechanisms are poorly

understood, once near shore, salmon are guided to their natal stream by following a

series of imprinted scents (see reviews by Hasler and Scholz 1983, Smith 1985, and

Quinn and Tallman 1987).

Straying in coho salmon is well documented when access to natal streams is

obstructed or damaged (Allen 1956, Martin 1984), but homing under normal

conditions is fairly accurate (between 73 and 100% as reviewed by Quinn and

Tallman 1987). Researchers reported no straying between populations of northern

California coastal coho salmon when stream mouths were separated by about 32 km

and only moderate straying between populations when the stream mouths were

separated by 8 km (Taft and Shapovalov 1938). Ricker (1972) reviewed a study with

Toutle River coho salmon outplanted on-station and at a site 80 km away in the

Columbia River. All 377 returning adults from the on-station outplant entered only

the Toutle Hatchery; however, large numbers of the outplanted fish returned to the

Toutle Hatchery and other hatcheries.
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Salo and Bayliff (1958) were the first to demonstrate that coho salmon inherit

their adult return time. Hager and Hopley (1981) demonstrated the inheritance of

adult timing within Columbia River coho salmon stocks.

Coho salmon in the LCR have a wide range of run times. Historically, coho

salmon began their spawning migration by entering the river in early September and

continued at least through February (reviewed in Cramer et al. 1991). Hirose (1983)

observed coho salmon of apparent wild origin that returned to Gnat Creek in the

Columbia River from mid-September to mid-February, with the peak of the run near

the end of October. He suggested the actual spawning season for nonhatchery coho

salmon in the LCR ranged from late November through early January. A run of

naturally spawning fish to the North Fork of the Clackamas River returns from

November through March (Cramer 1991).

Recent coho salmon runs in the LCR were primarily managed for hatchery

fish with only two run-times. An early group or “S-Type” has a southerly marine

distribution from the mouth of the Columbia River. It returns to the river in August

and September and is the principal stock reared by the Oregon Department of Fish

and Wildlife (ODFW) (Cramer et al. 1991). The late group or “N-Type” has a

northerly marine distribution from the Columbia River. It returns to the river in

October and November. This stock was first cultured at the Cowlitz Hatchery by the

Washington Department of Fisheries (VVDF) in 1967 (Hager and Hopley 1981).

Since the 1970s, it has been introduced into all WDF hatcheries of the LCR, although

some VVDF hatcheries also culture early-run coho salmon (VTDF 1991d).

If populations of nonhatchery origin fish still exist in the LCR, they would

probably spawn before or after the influx of returning hatchery fish. Unfortunately,

little data are available on early and late spawning coho salmon. ODFW and VMF

have conducted spawning ground surveys, but no surveys have been over the entire
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spawning period nor were they always consistent from year to year. WDF’s surveys

have been conducted since 1945, but before winter 1990-91, only occurred at the

peak of the expected hatchery run and primarily on streams known to be influenced

by hatchery fish. ODFWs surveys began in 1949 and cover 10 streams with little

hatchery influence; however, in general, they only observe spawners once or twice

during late November to late December.

In the winter of 1990-91, ODFW and VVDF expanded the number of streams

they surveyed and extended the survey time to include post-December 15 spawners.

Wild spawners were surveyed by ODFW from October to February, while WDF

surveyed streams with suspected wild spawners only in January and February. During

this time, ODFW surveyed 87 streams and found 514 coho salmon of which 57 were

counted after 15 December. The post-December 15 spawners were counted in 11

streams (13% of streams surveyed). WDF surveyed 40 streams beginning 2 January

and found 11 live and 10 dead coho salmon in 12 streams (30% of streams surveyed).

ODFW also counted 121 redds in their post-December 15 counts, while WDF found

54 redds (ODFW 1991a, WDF 1991c).

WDF also conducted scale analysis on coho salmon harvested in October and

on carcasses collected in the January-February stream surveys. WDF found that

1325% of the October fishery samples exhibited wild/natural scale patterns as did

100% (N = 5) of the stream-surveyed post-December fish (VVDF 1991e).

ODFW concluded that their surveys indicated distinct and well-separated

populations of coho salmon on the spawning grounds only in the Lewis and Clark

River and Skipanon River. The early runs peaked about the first week of November,

whereas the late runs peaked about the middle of January. There was a 6-week

separation between the two runs during which no fish were observed on the spawning
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grounds. This temporal separation should preclude gene flow between the early and

late runs.

WDF drew no conclusions regarding whether their surveys identified distinct

wild spawning populations, but a supplemental document (WDF 1991d, p. 13)

concluded:

Whether there are still small pockets of self-sustaining wild populations that

have never been impacted by hatchery production in any Washington tributary

is an unknown. To assume there are, given the record, would seem to be a

most notable defiance of the odds.

A naturally spawning population of coho salmon occurs in the North Fork of

the Clackamas River. The Clackamas River is a tributary of the Willamette River and

was specifically excluded from the original ESA petition for LCR coho salmon.

However, the BRT considered the Clackamas River coho salmon a “population of

special concern,” in part because this run may be the “last substantial remaining

native coho stock in the Columbia River basin” (Nehlsen et al. 1991).

The adult coho salmon runs at North Fork Dam on the Clackamas River peak

in September and again in January (Cramer 1991). The late-run coho salmon are

presumed to be the progeny of naturally spawning adults, since no known hatcheries

propagate coho salmon with this late run-timing. This run of late fish has shifted from

November, during 1958 to 1963, to January, during 1985 to 1989 (Howell et al. 1985,

Cramer 1991). The two runs overlap, but reportedly there is a break of several weeks

between the time spawning ends in the early group and begins in the late group

(Cramer 1991). However, the Clackamas River system has experienced extensive

coho salmon outplantings, and genetic studies indicate that the juvenile portions of

the run have electrophoretic patterns similar to those from hatchery fish outplanted

into the river in previous years (see “Genetics” section).
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Dam counts of returning coho salmon on the Clackamas River also present a

pattern which is common throughout the LCR and which demonstrates the difficulty

in determining the evolutionary lineage of late-run fish. Dam counts of coho salmon

returning to the North Fork of the Clackamas River have been compiled since the

1950s (Cramer 1991). Table 1 presents these data in 3-year blocks as percent per

period per month of fish over the dam. This reveals that the early run and the late run

have both experienced reductions in the mid-part of their runs with consequent

increases in the tails. In the time period 1987-89, over 5% of the early-run hatchery

fish returned in August (in previous years this was less than 0.1%) and almost 9% of

the late-run “wild” fish returned in March (in previous years this was 0.2% or less).

Presumably the early-run hatchery fish demonstrate a similar tail in December and

January. Thus, unless tagging data are available on differences in actual spawning

times between the runs, it is difficult not to speculate that a major portion of the

late-run is the tail of the early-run hatchery fish, forced later and later by fishery

management practices during the October to November harvest season.

Historical and Current Abundance

Until the early 1900s, naturally produced coho salmon were widespread

throughout the Columbia River Basin. Historical abundance is believed to have

centered in the LCR; however, some stocks migrated to the Spokane River, over 435

km upriver (Mullan 1984).

Most estimates of the historical population size of the Columbia River coho

salmon rely on commercial catch data. Mullan (1984) suggested early harvest

amounted to between 300,000 and 400,000 fish annually. Beiningen (1976) indicated

the catch between 1894 and 1920 averaged 476,000 fish annually. More accurate
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estimates of historical abundance combine commercial catch data with theoretical

harvest rate and fish size to project total population size. Chapman (1986) suggested

an average fish size of 3.18 kg, adjusted the estimated catch by a (theoretical)

optimum sustained yield (harvest) of 77%, and estimated a peak (5-year average)

pre-1900 abundance of 618,000 adult coho salmon entering the Columbia River

system annually.

The inriver harvest of Columbia River coho salmon reached a peak of

3,599,550 kg (about 880,000 fish) in 1925, after which the fishery experienced an

almost-continuous decline to the 1960s (Fig. 2) (Beiningen 1976, Mullan 1984,

PFMC 1991). The decline in production was widespread throughout the river system

and was, undoubtedly, attributable to combinations of overharvest and habitat loss.

All middle and upper Columbia River stocks of coho salmon were drastically

reduced or destroyed by construction of impassable mill dams, unscreened irrigation

diversions, habitat loss, and overharvest prior to completion of Grand Coulee Dam in

1941 (Mullan 1984). All coho salmon stocks spawning above Grand Coulee Dam

were eliminated with the completion of the dam as no facilities were provided for fish

passage. The extent that the middle and upper Columbia River stocks declined during

the early part of the century is indicated by counts at the first Columbia River

main-stem dam (Rock Island Dam) of 183, 69, 10, 0, 58, 78, 13, 12, 29, 1, and 22,

from 1933 to 1943, respectively (Mullan 1984).

Counts of coho salmon passing Bonneville Dam after its completion in 1938

indicated a total minimum upstream run of 12,000 to 18,000 fish annually between

1938 and 1942 (Fig. 3) (COE 1990). Coho salmon passing Bonneville Dam

continued to decline, reaching lows of under 3,000 fish in the late 1950s. Between the

1940s and late 1950s, many of the fish migrating above Bonneville Dam were lower
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river stock (Bonneville Hatchery) produced at the U.S. Fish and Wildlife

Leavenworth National Fish Hatchery on the Wenatchee River (Mullan 1984).

The abundance of coho salmon in the Snake River was also drastically

reduced (to about 3,000 fish) by the time upstream adult counts were available at Ice

Harbor Dam in 1962 (COE 1990). The last known coho salmon stocks were

eliminated from the Snake River system by 1986 (COE 1990).

Mullan (1984) indicated that two-thirds of the historical Columbia River coho

salmon production may have originated in the LCR, with a likely historic peak

abundance of over 400,000 coho salmon originating in the LCR prior to the 1920s.

It is impossible to accurately estimate the decline in LCR stocks of coho

salmon below Bonneville Dam. Dam counts and spawning surveys are only available

for a few tributaries. However, river harvest reached a low of 15,000 to 19,000 fish

annually from 1958 to 1960 (CBFWA 1990). This suggests the decline in LCR stocks

followed a pattern similar to stocks in the middle and upper parts of the Columbia

River Basin.

The BRT developed an estimate of the minimum returns of coho salmon to the

Columbia River from peak harvest in 1925 to the present (Fig. 2 and Table 2). For the

period 1925 to 1960, we used total inriver harvest (Beiningen 1976) adjusted for

harvest rate and average fish size. For the period 1925 to 1950, we used a (perhaps

conservative) harvest rate of 77% as suggested by Chapman (1986). From 1950 to

1960, we used actual harvest rates (ODFW 1990b). We used an estimate (probably

optimistic) of 4.08 kg average fish size for this entire period as suggested by the

Oregon Fish Commission (1975). From 1938 to 1959, Bonneville Dam counts were

added to the estimate. For the period 1960 to 1990, we used a population estimate

that accounted for river commercial and sport harvest, hatchery returns, and

Bonneville Dam and lower river tributary dam counts (PFMC 1991).
14

The BRT estimate indicates the numbers of coho salmon returning to the

Columbia River may have been reduced to fewer than 25,000 fish by the late 1950s

(Fig. 2 and Table 2). This suggests that by the late 1950s, the abundance of returning

coho salmon produced from the Columbia River had been reduced to less than 5% of

historic levels (25,000/618,000).

The BRT used a computer model developed by Dennis et al. (1991), to

simulate the population dynamics of the annual Columbia River coho salmon runs.

The model estimates the probability of extinction during the next 100 years assuming

continuation of population abundance trends and parameters from the period modeled

to the future. Using this model, there was a 39.2% probability of extinction from the

period of peak harvest in 1925 to the (first) population low in 1943 (Table 2). The run

temporarily stabilized in the mid-1940s (Fig. 2 and Table 2). However, overall, the

run continued to decline from 1943 to 1959, with the chance of extinction increasing

to 73.3% (Table 3). There was some production of coho salmon at state and federal

fish hatcheries in the Columbia River Basin from the 1940s through the 1950s

(Mullan 1984, ODFV 1990a). This hatchery production may have contributed to

stabilization of the run.

The drastic decline in abundance of LCR coho salmon initiated a widespread

hatchery enhancement program after 1960 (ODFW 1990a,b; WDF 1991a). This

program included increased production of coho salmon at existing fish hatcheries and

construction of new facilities. Since the 1960s, the vast majority of coho salmon

returning to the Columbia River have been of hatchery origin (CBFWA 1990). BRT

computer modeling suggests the current (hatchery-based) population of coho salmon

in the Columbia River is stable (it has less than 0.1% probability of extinction in the

next 100 years) (Table 3).
15

The hatchery enhancement program built a population of historic proportions

(Fig. 2 and Table 2). Returns of coho salmon to the Columbia River increased

quickly after the 1960s. The total return to the river often exceeded 400,000 fish in

recent years (Howell et al. 1985, CBFWA 1990, PFMC 1991). During the 1980s, the

run ranged from 138,000 to 501,000 fish between 1980 and 1984, and from 382,000

to a historic high of 1,553,000 fish between 1985 and 1989 (CBFWA 1990). These

fluctuations in run size were attributed to variations in hatchery smolt production,

smolt quality, juvenile-to-adult survival, and harvest (CBFWA 1990).

The majority (about 85%) of hatchery production of coho salmon in the

Columbia River system has centered in the LCR (CBFWA 1990). However, there are

hatcheries on the Bonneville Dam pool that produce coho salmon. Counts of coho

salmon passing Bonneville Dam have exceeded 12,000 annually since 1962 and

averaged 46,530 annually during the 1980s (Fig. 3) (COE 1990).

The hatchery-based coho salmon enhancement program for the LCR has

allowed development of large-scale sport, commercial, and tribal fisheries. However,

the dynamics and structure of the population have been altered dramatically. Almost

the entire population of (perhaps 500,000) coho salmon now returning annually to the

Columbia River system are hatchery fish. The number of naturally spawning coho

salmon returning to the LCR is limited.

Wahle and Pearson (1987) indicated that in the early 1980s, less than 25,000

coho salmon were spawning naturally in the Columbia River Basin (Tables 4-8).

CBFWA (1990) indicated the number of naturally spawning coho salmon in the

Columbia River Basin continued to exceed 23,000 during the late 1980s (Tables 4-8).

These fish include feral hatchery fish spawning in streams near hatcheries, returns

from hatchery outplants in streams away from hatcheries, and naturally produced
16

fish. The BRT has found no data to suggest these numbers have changed significantly

to the present.

It appears that the current number of coho salmon spawning in streams in the

LCR is less than 6% of historic abundance (<25,000/400,000). The BRT believes

there are two important components of naturally spawning coho salmon in the LCR:

fish of first generation hatchery origin and fish from naturally spawning parents

(which may include both hatchery and nonhatchery origin fish).

Up to 30,000,000 hatchery reared juvenile coho salmon are released annually

on the Washington side of the LCR (Table 4) (VVDF 1991a). Appro3dmately twothirds of this production is released into streams near hatcheries, and the remainder is

released into tributaries away from hatcheries (mostly as fry outplants). WDF

maintains in excess of 70,000 adult coho salmon returning to their LCR fish

hatcheries (WDF 1991a) (Table 4). It is common for VVDF to release in excess of

15,000 of these adult hatchery fish to spawn naturally in streams near the hatcheries

(these are fish counted over hatchery weirs or released from adult collection ponds)

(Table 4).

Typically, less than 10,000,000 hatchery reared juvenile coho salmon were

released annually on the Oregon side of the LCR during the 1980s (Howell et al.

1985, Cramer and Chapman 1990, ODFW 1991a). Most coho salmon reared in

hatcheries in Oregon are now released as smolts into streams near hatcheries.

However, ODFW has a long history of off-station outplanting of fry, juveniles, and

prespawning adults to streams away from hatcheries (ODFW 1991a). The BRT does

not have information to indicate the number of Oregon hatchery fish allowed to

spawn naturally in streams near hatcheries; however, the number may exceed 4,000

(Wahle and Pearson 1987).
17

A primary concern is that surveys of small tributary index spawning areas

indicated continued decline in natural production of coho salmon in the LCR in areas

away from hatcheries (Cramer and Chapman 1990, ODFW 1990b, WDF 1991a). The

BRT developed a comparison of average spawners/km from 1951 to 1990 for 10

Oregon and 13 Washington index streams. The BRT selected 1951 to coincide with

data presented by ODFW (1990b) and because few streams were surveyed in

Washington prior to that date (WDF 1991b). We averaged WDF index area counts

for pre- and post-December surveys. The BRT also reviewed 1990-91 spawning

ground surveys of 87 ODFW index streams and 40 VTDF index streams in the LCR

basin (ODFW 1991a, WDF 1991c).

Most adult coho salmon of first generation hatchery origin return to spawn

between early October and late November each year. WDF surveys indicate the

October to December segment of coho salmon spawning in streams away from

hatcheries has been in decline for the past 40 years (VVDF 1991b). From the 1950s

to the present, this run segment has been reduced from between 31 to 62 fish/km to

about 6 fish/km. However, the actual magnitude of decline from historic levels is

undoubtedly greater since the early spawning ground surveys coincide with periods

of historic low returns of coho salmon to the Columbia River. Computer modeling

suggests this run segment of coho salmon spawning in the LCR away from hatcheries

in October to December has a 12.9% chance of extinction in the next 100 years if

population parameters remain stable. This run segment may be somewhat stabilized

through hatchery outplants.

The BRT does not have long-term information concerning the number of fish

spawning naturally away from hatcheries in October to December in Oregon.

However, in 1990, ODFW counted 3 fish/km in surveys of 10 standard index streams

during this time period (Table 9) (ODFW 1991a).
18

The BRT used data from Fulton (1970) and estimated there are about 544 km

of coho salmon spawning habitat on the Washington side of the LCR and about 402

km on the Oregon side. However, ODFW (1991a) indicated there may be up to 944

km of coho salmon spawning habitat on the Oregon side of the LCR. As previously

indicated, VIDF surveys averaged 6 spawners/km while similar ODFW surveys

averaged 3 spawners/km. Therefore, it is possible that there are approximately 3,000

coho salmon spawning between October and December in the LCR away from

hatcheries in Washington and between 1,100 and 2,600 in Oregon.

Another important run component consists of coho salmon returning to the

Columbia River between early December and March. These fish return after the

major influx of the hatchery-based (October to November spawning) population. This

run component may consist mainly of fish of nonhatchery origin (Cramer and

Chapman 1990; ODFW 1990b, 1991a,b; Cramer 1991).

WDF (1991b) and ODFW (1990b, 1991a) surveys indicate this

post-December component of coho salmon spawning in the LCR away from

hatcheries has also been in a steady decline for the past 40 years (Fig. 4). From the

1950s to the present, this component had been reduced from between 31 to 50 fish/

km to under 0.6 fish/km. VIDF and ODFW 1990-91 surveys of post-December

spawning coho salmon suggested that there are currently 0.3 spawners/km on the

Oregon side of the LCR and 0.2 spawners/km on the Washington side (ODFW

1991a, VTDF 1991c). Computer modeling suggests this post-December spawning

run segment of coho salmon in Washington tributaries of the LCR has, almost a 90%

chance of extinction in the next 100 years (Table 3). Computer modeling indicates

this post-December spawning run segment of coho salmon in Oregon tributaries of

the LCR has a 100% chance of extinction during the next 100 years (Table 3).
19

ODFW (1991c) estimated that there are now less than 195 post-December

spawning coho salmon on the Oregon side of the LCR excluding the Willamette

River system. The majority of these fish may exist as small populations in the Lewis

and Clark River and Sandy River or in other small tributaries (ODFW 1991c).

The BRT does not have detailed population information for LCR

post-December spawning coho salmon in Washington. However, based on the BRT

estimate of 544 km of spawning habitat in Washington and the current 0.2 spawner/

km estimate, it is possible there are now only about 100 post-December spawning

coho salmon in the LCR in Washington.

A late-returning (post-December) component of the coho salmon run in the

North Fork of the Clackamas River may also be of nonhatchery origin (ODFW

1990b, Cramer 1991, Nehlsen et al. 1991). Computer modeling indicates this

population has less than a 0.1% chance of extinction during the next 100 years, if

population parameters remain stable (Table 3). However, the 1991 return of postDecember spawning coho salmon to the North Fork of the Clackamas River is

projected to be at a recent low of only about 300 fish (Cramer 1991). Therefore, this

population deserves continued monitoring.

In summary, even though there is a large hatchery-based population averaging

about 500,000 coho salmon returning yearly to the LCR, all information indicates a

steady decline (to present lows) in natural production away from hatcheries. The BRT

identified from the literature several components of the current coho salmon

population spawning in the LCR. In October to December, about 20,000 feral

hatchery fish spawn in streams near hatcheries. Also at this time, about 6,000 fish

spawn in streams away from hatcheries, and post-December, after the hatchery runs

have passed, about 600 fish spawn in tributaries away from hatcheries.
20

It has been suggested that these declines in natural production are coincident

with high harvest rates on abundant hatchery stocks (Cramer and Chapman 1990;

ODFW 1990b, 1991a). However, declines may also be influenced by outplants of

large numbers of hatchery fry (ODFW 1991a) or by continued habitat degradation.

History of Hatchery Stocks and Outplantings

One of the major issues the BRT considered in determining whether a coho

salmon ESU remains in the LCR is the extent of hatchery programs in the lower river

basin. The BRT considered three principal points: 1) history and numbers of hatchery

releases, 2) composition of hatchery stocks, and 3) geographic areas of hatchery

releases. This brief summary only focuses on reports from a few hatchery programs,

but it is representative of the extensive documentation of hatchery practices in the

Columbia River reviewed by members of the BRT.

Coho salmon hatcheries have operated on the Columbia River since the 1890s

(WDF 1991d). In the early years, hatcheries mined wild runs for eggs, but little

success was realized in juvenile production. Beginning in the 1930s, hatcheries

improved juvenile survival, and by the 1960s, the success of juvenile rearing was

greatly increased. Coho salmon smolt production in Washington increased from

about 2.5 million in 1960 to 23.5 million in 1987. There are now 16 hatcheries

rearing coho salmon in the LCR (Table 10).

Hatcheries not only release fish at the hatchery (on-station releases), but also

outplant them to other tributaries and even other drainages (off-station outplants).

This has occurred since the 1890s when there was no knowledge of genetic

population integrity. Salmon eggs were transferred into the LCR from coastal rivers

(ODFW 1990a, WDF 1991d) and moved from the lower- and mid-river sites to

upriver locations (WDFG 1902).
21

Currently, tens of millions of juvenile coho salmon are released each year into

the LCR (Tables 11-13). If these hatchery stocks were derived directly from local

indigenous wild stocks, could they represent the only remaining LCR ESU, if distinct

populations have been eliminated in the wild? Unfortunately, coho salmon outplanted

into the LCR are the progeny of numerous previous stock transfers over multiple

generations and may carry the genetic material of a broad spectrum of ancestral

stocks, often from different watersheds; some were not even of Columbia River

origin.

In Oregon, stock composition of the major hatchery complexes includes

coastal (e.g., Coos Bay, Yaquina River), Washington LCR (e.g., Lewis, Toutle,

Grays, Elokomin, and Kalama Rivers), and native runs of coho salmon (Table 14).

Stocks of coho salmon in Washington hatcheries are of a similarly mixed lineage

(WDF 1991d).

These mixtures of hatchery stocks were not simply released at hatcheries and

into adjacent tributaries, but were scattered throughout the Columbia River Basin

(even to upriver hatcheries). The recent outplanting history of Oregon LCR streams is

presented in Table 15. Often, a single stream will receive fish from two, three, or

more hatcheries in any given year. In addition, excess hatchery adults were

occasionally released into nonhatchery streams in the region (Table 16). Data for

specific stock movements on the Washington side are not presented here, but closely

resemble those in Oregon (WDF 1991d).

Transplantation was extensive even in river systems with tributaries now

managed for “natural spawners.” Histories of “wild” coho salmon streams in Oregon

during the 1980s (Table 17) reveal extensive outplants as late as 1987 in two of five

streams investigated. Even the Clackamas River, the one system in the entire river

which is regarded as having a remnant “wild” run of coho salmon (Nehlsen et al.
22

1991), received smolts and presmolts in 1987 (Table 18). An examination of the

stocking histories, depicted as a likely “family tree” of two of these Oregon streams

the Clackamas River and Still Creek, emphasizes this amalgamation of coho salmon

stocks (Figs. 5 and 6) (ODFW 1991a).

Although returns to tributaries outplanted with hatchery fish are often

poor (Tables 19-20), this practice is extensive and has occurred for decades.

The BRT compared outplanting records of VTDF and ODFW with

topographical maps of the area and determined that many streams/tributaries below

Bonneville Dam have no recorded outplants of hatchery coho salmon since 1980

(Table 21). Few of these streams have been monitored for adult coho salmon (Table

22), and no reliable scientific data exist that could confirm whether or not adults, if

present, are genetically distinct from hatchery stocks.

Genetics

Background

Several protein electrophoretic studies have demonstrated distinct population

structure between some coho salmon populations. In early genetic studies focusing on

single loci, the transferrin locus was found to be polymorphic; several studies found a

significantly lower frequency of the B allele of transferrin in Fraser River and

Columbia River coho salmon compared to all other sampled populations (Utter et al.

1970, 1973, 1980; May 1975; Allendorf and Utter 1979). Suzumoto et al. (1977) and

Winter et al. (1980) reported differential resistance to bacterial kidney disease among

transferrin genotypes. Also, Pratschner (1978) showed differential mortality from

vibriosis, cold-water disease, and furunculosis between transferrin genotypes. Thus,

transferrin polymorphisms may be maintained by a selective mechanism and may

reflect adaptive properties of the different genotypes rather than ancestral

relationships.
23

Most other loci examined in coho salmon have been less informative. May

(1975) reported a variant allele of lactate dehydrogenase (LDH-4, now called

LDH-B2*) which showed a clear separation between south Puget Sound (including

Hood Canal) and north Puget Sound coho salmon stocks. Utter et al. (1980) reported

data from several studies on unusual allelic variants in coho salmon from the Feather

River Hatchery, California, and suggested that these variants occur widely in the

southern part of the coho salmon range. On the Oregon coast, Olin (1984) identified

four distinct allelic groupings. Wehrhahn and Powell (1987) found distinct allelic

frequency differences between fish from the lower coastal mainland of British

Columbia and Oregon.

Hjort and Schreck (1982) studied electrophoretic, morphological, and life

history characteristics of coho salmon in Washington, Oregon, and California. In

general, they found that 1) stocks geographically close were similar; 2) stocks in

large rivers were more similar to each other than to stocks from smaller stream

systems, independent of geographic proximity; 3) hatchery stocks were more similar

to each other than to wild stocks, and wild stocks were more similar to each other

than to hatchery stocks.

Solazzi (1986) used electrophoretic data from a study at the University of

California (Davis) to assist fisheries managers with decisions related to stock

transfers. Solazzi identified five groups of coho salmon in Oregon and California.

Columbia River fish clustered with those from the Rogue and Klamath Rivers. Two

California streams also clustered with this group of large-river populations. All other

Oregon coho salmon populations were contained in the other four groups.
24

BRT Analysis of LCR Coho Salmon Populations

Several problems became evident during the BRT’s literature review of

genetic studies on coho salmon. First, and most significant, was the paucity of studies

using naturally spawning fish. Funding and research priorities in the Columbia River

Basin have emphasized hatchery production to the exclusion of naturally spawning

stocks (VTDF 1991a). Second, in comparison to other Pacific salmon, coho salmon

showed less genetic variability at protein coding loci (Allendorf and Utter 1979, Utter

et al. 1980) and in restriction fragment analysis of mitochondrial DNA (Moran 1987).

Thus, without genetic baselines for historical native coho salmon, and hampered by

the genetic peculiarities of coho salmon, it is difficult to determine the evolutionary

heritage of any present-day naturally spawning populations.

Therefore, to help evaluate the genetic status of LCR coho salmon, the NMFS

Northwest Fisheries Center collected fish samples from LCR streams and hatcheries

for allozyme analysis. These new data were analyzed and compared with published

and unpublished genetic data from a variety of sources2.

Materials and methods--Sixteen samples of juvenile salmon were collected in

January and February 1991 from populations of both naturally spawning and

hatchery fish from the LCR (Fig. 7 and Table 23), including whole body collections

from nine hatcheries and from presumably natural spawning parents (wild fish) at

seven locations recommended by biologists from ODFW and WDF. Fish from the

Lewis and Clark River (n = 6) and Grays River (n = 10) were processed

electrophoretically but were not used in the analyses because of the small numbers.

The collections were made by staff from NMFS, ODFW, and WDF under the

coordination of William Waknitz (NMFS; Manchester, Washington), Richard

2 This study will be described in the NOAA Technical Memorandum series.
25

Ledgerwood (NMFS; Hammond, Oregon), and Robert Jones (NMFS; Portland,

Oregon).

In the field, whole blood was withdrawn from the dorsal aorta after caudal

amputation. Blood was held on ice until the plasma was separated by centrifugation

(3-6 hours later). The plasma was then frozen with the whole fish (on dry ice) and

transported to the NMFS Montlake Laboratory, Seattle, Washington, where the

samples were held at -85°C until processing.

Electrophoretic analyses followed Aebersold et al. (1987). Thirty-seven

enzymes encoded by 80 loci were screened for each fish (Table 24). In addition,

transferrin was resolved on a modified Ridgway et al. (1970) starch gel using a

general stain for proteins. Comparisons among samples were made using Nei’s

(1972) measure of genetic similarity and the log likelihood ratio test (g-test) (Sokal

and Rohlf 1969).

Dendrograms were constructed from the matrices of genetic similarities using

an unweighted average linkage method (Sneath and Sokal 1973). Data also were

analyzed from the literature (Utter et al. 1970, 1973, 1979; May 1975; Hjort and

Schreck 1982; Olin 1984; Bartley 1987; Reisenbichler and Phelps 1987), from

unpublished data, and from results of electrophoresis on new samples collected

specifically for the ESA status review. The unpublished studies were from 17 NMFS

samples and 20 University of California (Davis) (Gall 1991) samples.

Transferrin data were treated separately because these polymorphic loci may

be maintained by a selective mechanism. The rest of the electrophoretic loci of this

survey were assumed to be selectively neutral. The allozyme data from the various

sources were collated into a master set consisting of 68 samples having, as a

minimum requirement, data at the 18 polymorphic loci (Table 25). This minimally

sufficient set of loci was used as a starting point to examine as broad a geographic

range as possible. In addition to the master set itself, two of its subsets were 26
26

analyzed. One subset included 31 populations with data for 38 polymorphic loci

(Table 26). This subset, chosen for maximum genetic resolution, included samples

from British Columbia (4), Puget Sound (8), LCR (15), Washington and Oregon

coasts (3), and California (1). The second subset, chosen to examine genetic

relationships among samples within the LCR, consisted of the 14 samples collected

in 1991 and analyzed using 19 polymorphic loci (Table 27).

Results--The distribution of transferrin allele frequencies in samples from the

LCR were different from all other geographic regions (Fig. 8). Lower Columbia

River samples typically showed higher frequencies of the A allele and lower

frequencies of the B and C alleles than found in samples from the other geographical

regions. The difference was even more striking if only the data for brood years prior

to 1980 were considered: B allele frequency prior to 1980 was 0.003 compared to a

frequency of 0.035 after 1980. However, even after this tenfold increase in frequency,

the LCR frequency was about half that of other regions.

Cluster analysis of transferrin similarities showed that the LCR samples were

most similar to those from California and very different from Oregon coastal samples

(Fig. 9). The first three clusters from the top contained all of the LCR (n = 22) and

California (n = 14) samples. Only 3 of 29 Oregon coastal samples group with the

LCR and California samples. In comparison, the lower four clusters contained most

of the Oregon coastal samples (26 of 29) and the only sample from Puget Sound.

Little structuring either geographically or temporally of genetic similarities

based on transferrin areles within the LCR was apparent from cluster analysis (Fig.

10). The upper cluster included 25 of 33 samples and contained 5 of 6 wild samples.

The middle cluster (7 samples) included the other wild sample along with 4 lower
27

LCR, 1 Willamette, and 1 upper LCR hatchery samples. The lower cluster was

represented by 1 of 2 samples from Eagle Creek National Fish Hatchery. Very low

frequencies of both the transferrin B and C allele characterized the upper cluster. Low

transferrin B and high (around 0.20) transferrin C allele frequencies were typical of

the middle cluster. High frequencies of transferrin B and C alleles (about 0.20)

described the monotypic lower cluster.

In most cases, samples replicated over time fell into the same cluster of the

transferrin dendrogram. However, there were three exceptions. The 1991 Eagle Creek

sample was the sole representative of the lower cluster, but the samples from the late

1970s or early 1980s fell into the middle cluster. Also, early 1980s samples from

Bonneville Hatchery3 were located in the middle cluster, but the 1991 samples

(Cascade) were found in the upper cluster. Finally, the 1991 sample of naturally

spawning Clackamas River coho salmon fell into the upper cluster, whereas the early

1980s samples were found in the middle cluster.

Samples from the LCR were not electrophoretically differentiated from most

of the other samples in a cluster analysis of genetic similarities for 68 samples using

the minimally acceptable set of 18 polymorphic loci (Fig. 11). Fifteen of 18 LCR

samples occurred in the second cluster along with 14 of 27 Oregon coastal, 3 of 9

California, and 8 of 9 Puget Sound samples. One LCR sample in the first cluster was

in company with 1 California and 9 Oregon coastal samples. The other 2 LCR

samples fell into the sixth cluster along with at least 1 sample from all of the regions

represented in the 68-sample set. The mix of Oregon coastal samples occurring in

clusters with LCR was 50% from both northern and southern drainages (dividing line

was Florence, Oregon).

3 Cascade, Oxbow, and Bonneville Hatcheries form the Bonneville Hatchery

complex.
28

Results of a cluster analysis of a 31-sample subset of the 68-sample set using

38 polymorphic loci are shown in the dendrogram of Figure 12. Nine clusters are

apparent. LCR samples were distinct from British Columbia and Puget Sound

samples with the exception of 1 Puget Sound sample from Green River Hatchery.

The only California sample formed a cluster of its own. Although the I Oregon and 2

Washington coastal samples showed genetic similarities to some LCR samples, these

were statistically distinct (P < 0.0005) from their nearest LCR neighbors in the

dendrogram.

Finally, results of a cluster analysis of 14 samples (a subset of the 31-sample

set) using 19 polymorphic loci are shown in Figure 13. These samples were presmolts

collected in 1991. There was no apparent geographical or temporal structuring or

separation between hatchery and wild stocks among the eight clusters.

An interesting observation was the high genetic similarity between the coho

salmon samples from the Clackamas River and two other samples, the Cowlitz

Hatchery late-run stock and the Cascade Hatchery stock. Unsmolted fish of the

Cowlitz and Bonneville Hatchery stocks were outplanted into the Clackamas River in

1984 and 1987, respectively (Table 18). These fish would have been the correct

brood years (1983 and 1986) to represent the grandparents and parents of the 1989

brood fish from the Clackamas River sampled in 1991. This information may explain

why Clackamas River samples showed the highest genetic similarity to the Cascade

Hatchery sample and the next highest genetic similarity to the Cowlitz Hatchery

late-run sample.
29

Discussion--Genetic differences between the LCR and Washington or Oregon

coastal coho salmon were seen in the analyses of the transferrin and the 38

polymorphic loci data sets. Transferrin allele frequencies in the LCR were different

from the Oregon coast prior to the 1980s. This might suggest reproductive isolation

and/or unique selection pressure. Although the degree of LCR-Oregon coast

differentiation decreased after early 1980, mostly due to an increase in transferrin B

frequencies, LCR samples still remained distinct from Oregon coastal samples.

The reason for the increase in the frequency of transferrin B in the LCR is

unclear. The increase could indicate introgression of coastal alleles through straying

or transplanting of Oregon coastal stocks, or perhaps this allele was present at low

frequencies in populations of the LCR prior to the 1980s and has increased in

response to changing selection pressures. Note that only two of the pre-1980s

samples were nonhatchery, and one of these harbored the B allele at low frequency

(May 1975).

The reason for the high degree of similarity observed between many California

and LCR samples based on the transferrin locus is also unclear. There may be similar

selective regimes acting on transferrin genotypes, or there may have been stock

transplants. Straying would not be very likely over such distances. Very little

evidence of reproductive isolation was apparent from the analysis of the 68-sample

data set. Although all except 3 of the LCR samples fell into one cluster, this cluster

also included about 50% of the Oregon coastal (27), 33% of the California (9), and

89% of the Puget Sound (8) samples. It is possible that the set of 18 loci used to

analyze this set of samples was not adequate to define any existing genetic

structuring.

Genetic differences as well as similarities between populations can be

generated much more quickly by introductions of new genetic material than by 30
30

reproductive isolation. The introduction of new genetic material from Cascade

Hatchery might explain the higher genetic similarity of the 1991 Clackamas sample

with the Cascade Hatchery stock than with an earlier sample from the Clackamas.

This suggests that there was gene flow between this hatchery transplant and naturally

spawning Clackamas River coho salmon. Similar studies on the relationship between

genetic similarities in LCR coho salmon and stocking histories might provide further

insight into the evolutionary legacy of petitioned coho salmon populations.

Effects of Parasitism

Ceratomyxa shasta is a protozoan parasite of chinook and coho salmon and

occurs in locations associated with lakes or reservoirs (Amos 1985). The parasite has

caused large losses of adult fish in several LCR hatcheries (Wood 1979). In a survey

of coho salmon in Oregon, Sanders et al. (1970) found that the parasite was present

only in populations within the Columbia River or near its mouth. Ching and Munday

(1984) reported C. shasta in the Fraser River, a large river system in British

Columbia.

Hemmingsen et al. (1986) demonstrated that resistance to C. shasta in coho

salmon is a heritable trait. When progeny of pure Big Creek (LCR), pure Soleduck

and Smith Rivers (coastal), and hybrid crosses between the Columbia River and

coastal river stocks were exposed to C. shasta in the laboratory, the Big Creek fish

showed the highest resistance. The hybrid cross showed intermediate resistance, and

the pure coastal fish had the lowest resistance. Based on this information, the

investigators suggested that the prevalence of C. shasta within the LCR may exert

strong selective pressure against introgression from fish that lack resistance to the

parasite. This pressure could reduce gene flow between the LCR and coastal river

populations.
31

LCR coho salmon may also exhibit an inherited resistance to other parasites or

diseases (Suzumoto et al. 1977, Pratschner 1978) which might act to reduce gene

flow between this region and other areas.

CONCLUSIONS

In keeping with the guidelines established by NMFS (Waples 1991) for

species determination under ESA, the BRT evaluated whether LCR coho salmon

represent a “distinct population segment” that is reproductively isolated and

“represents an important component in the evolutionary legacy of the species.”

During the status review of LCR coho salmon, the BRT considered the following

information on reproductive isolation particularly significant:

1) Few studies of distinct populations of naturally spawning fish in the LCR were

identified. No recent studies concerning the genetics, morphology, behavior, or

other aspects of LCR wild fish populations were identified which would delineate

reproductively isolated groups.

2) Hatcheries in the LCR rear coho salmon that are products of multitudes of stocks

from throughout the region, including the coast. In recent years, the emphasis in

hatchery production has focused on fish derived from the LCR, but the lineage of

even these stocks involves interhatchery transfers.

3) The LCR has been managed for hatchery production, not wild salmon, for over 30

years. Hatcheries have released fish in virtually every major tributary throughout

the LCR. In these releases, the carrying capacities of tributaries were often

exceeded by hundreds of thousands of hatchery fry or smolts. The extent and

duration of the releases suggest that naturally spawning populations in these

streams are mixtures of the native and introduced hatchery stocks.
32

4) Numerous studies have determined that fidelity of homing in coho salmon (one of

the most important factors necessary for reproductive isolation) occurs at a rate

similar to that found in other anadromous salmon (usually well over 90%).

However, coho salmon stray at a high rate when access to natal streams is blocked

or imprinting is inadequate. Within the LCR, extensive blockage of natal

spawning areas has occurred and many fish released from hatcheries have not

been properly imprinted.

5) Differential resistance to the parasite Ceratomyxa shasta, prevalent in the

Columbia River, may reduce gene flow between coho salmon populations in the

LCR and other regions.

6) Time of return to the LCR is different between early and late spawners. Hatchery

fish have been selected for early- to mid-season spawning. It has been proposed

that coho salmon spawning from mid-December to March may represent native

nonhatchery populations. However, the BRT found no published studies on

genetic, morphological, behavioral, or other characteristics of these fish which

would indicate whether these late-spawning stocks are feral-hatchery fish or

isolated remnants of historical populations.

7) Numerous studies indicate that naturally spawning populations of coho salmon

have a complex stock structure that could survive a series of natural or manmade

disruptions. Whether the extent of hatchery releases, overharvest, and extensive

habitat destruction on the Columbia River is beyond the capability of these

populations to survive is unknown.

8) Electrophoretic surveys of naturally spawning coho salmon in the LCR have been

extremely limited, and available information is inconclusive.

9) Hatchery releases and outplants have been extensive and of over 30 years

duration. It is unlikely that any naturally spawning populations e2dst in the LCR
33

that do not have some introgression from hatchery stocks. The extent of this

introgression is unknown.

10) There has been little attempt to maintain habitat in the LCR; consequently, many

streams can no longer maintain sizeable spawning populations or successfully rear

juveniles.

11) For decades, harvest of LCR coho salmon has often exceeded 90%. It is likely

populations of naturally spawning fish were depleted below levels necessary for

survival, especially when these same populations were spawning in poorly

maintained habitat and mixed with extensive hatchery releases and/or outplants.

12) There is at least one well-documented naturally spawning coho salmon

population--the late, post-December run in the Clackamas River. However, only a

preliminary investigation was carried out on this stock as it was not part of the

initial ESA petition. This run has a complex history of human disruption and

requires further investigation.

13) Observations of naturally spawning coho salmon in the Columbia River are in the

ESA record (e.g., Sandy River, Lewis and Clark River, Washougal River, and

Hood River). However, the BRT was unable to find any published genetic,

morphological, or other specific studies on these stocks.

From the information developed during the status review, the BRT concluded

that at one time, coho salmon spawning in the LCR were probably reproductively

isolated from other coho salmon populations. However, human intervention during

the last century has lessened this isolation; the evidence evaluated by the BRT was

insufficient to determine the extent or significance of this reduction.
34

The BRT concluded that the available data fail to identify an existing

evolutionarily significant unit in the lower Columbia River. If one or more coho

salmon ESUs are present in the Columbia River, fishery management actions and

research studies have inadequately documented these populations.
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