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Letter to Irma Largomarcino,  Supervisor National Marine Fishery Service Arcata Area Office, and California Biodiversity Council, from Siskiyou County Supervisor Marcia Armstrong regarding coho genetics in the Klamath.

8/14/12

Irma, pursuant to our conversation at today's Board of Supervior's meeting, I find it difficult to believe that you are unaware of the issue of coho genetics in the Klamath. I have pointed this out at length in my formal coho comments over the years.


Here is that report I mentioned
 

Marcia Armstrong
 

[ http://www.nwfsc.noaa.gov/publications/techmemos/tm17/papers/moran2.htm
http://www.nwfsc.noaa.gov/publications/techmemos/tm17/figures/bermfig2.htm ]
 

Figure 2 from NOAA Technical Memorandum 17, Application of DNA Tecnology to the management of Pacific Salmon - Phylogeographic Structure of Coho Salmon Populations Assessed by Mitochondial DNA by Paul Moran and Eldredge Bermingham, indicates that Klamath River Iron Gate Hatchery stocks are genetically related to coho of South Puget Sound, North Oregon and Washington Coast cluster. (Ironically, the same biological kinship group as that of the Alsea decision.) Iron Gate Hatchery (IGH) coho were determined to be of an entirely different genetic cluster than the Rogue River and Cowlitz coho, which are in the SONCC biological ESU.


Here are excerpts from some of my prior comments:
 

These were among my 1995 comments in the coho status review. The citations are to the Klamath River Basin Fisheries Task Force Long Range Plan

Chapter 5, pg. 2 History - "Upper basin stocking programs were begun in 1890 by the U.S. Bureau of Fisheries (Fortune et al. 1966). No hatchery was established at this time...Coho salmon were stocked in 1895..." (Note: it appears from the text that these were of Sacramento River origin as were chinook fry stocked during this period.)

Chapter 5, pg. 2 - "The U.S. Fisheries Bureau set up a fish trapping facility at Klamathon in 1910. The Klamathon Racks blocked upstream migration of chinooks and coho into the upper Klamath drainage. Finally the Fisheries Bureau established a hatchery at Hornbrook in 1912, and by 1914 chinook and coho salmon of Klamath River origin were being raised and planted by this facility. Operation ceased in 1919."

Chapter 5, pg. 5 Iron Gate Hatchery Returns - "Coho returns from 1979-1988 have ranged widely from a low of 289 in 1983 to a high of 2,893 in 1987. Average run size has been 1,851...Coho from Cole River Hatchery on the Rogue sometimes return to Iron Gate."

Chapter 5, pg. 6 Iron Gate Hatchery Planting Procedures, Stock Transfer - "Coho yearlings have been released in March and April. From 1986 to 1988 40% of the Coho yearlings were planted at the hatchery. The remainder were transplanted into Indian Creek, Elk Creek and Beaver Creek. Iron Gate coho were planted in the salmon River in 1985. 450,000 and 850,000 surplus coho eggs were shipped to the Mad River Hatchery in 1986 and 1987, respectively."

Chapter 5, pg. 13 "Iron Gate Hatchery Coho were outplanted in Elk, Grider, and Beaver creeks in the Middle Klamath region from 1986-88. Smith et al. (1985) said similar programs in Oregon "lacked biological benefit." Although stocked streams reared more juveniles, researchers observed that native juveniles were displaced by hatchery fish. Further, when hatchery adults returned to spawn with native fish, juvenile recruitment was greatly reduced due to less well-adapted offspring (Smith et al. 1985)."

Chapter 5, pg. 14 The Use of Non-Native Broodstocks - "Riesenbichler (1988) found that the survival of transplanted coho salmon decreased in a linear fashion with the distance planted from their native watershed (Figure 5-2). The original coho broodstocks at both major hatcheries in the Klamath Basin were from Cascade Hatchery stocks in Oregon. The distance between their stream of origin, the Columbia River, and the Klamath River is over 800 km. The productivity of the stock is thus predicted to be very low (Figure 5-2). Problems with low productivity and erratic patterns of return of hatchery coho after introduction may have been attributable to the inappropriate adaptations of this stock. Recent improved performance of this stock may reflect adaptations to the hatchery environment (or domestication) allowing better survival under these artificial conditions. Problems with interaction with native populations may still occur, however."

Chapter 5, pg. 15 "Oregon hatchery programs used coho salmon large central facilities for all of the Oregon Coast. As these hatchery coho, lacking adaptations to local conditions, strayed back to spawn with wild stocks, fewer viable smolts were produced (Solazzi et al. 1983). The program of outplanting coho fingerlings and yearlings in Elk, Beaver and Indian Creeks may have had a negative impact on any wild stocks still remaining in those basins. While this program is still being monitored to determine if the planting has led to increased self-sustaining coho production, Withler (1982), in a review of the literature, found that the introductions of Pacific anadromous salmonids, using non-native broodstock, have been unsuccessful in producing new self-reproducing populations anywhere on the West Coast."

Chapter 5, pg. 15 The Use of Non-Native Broodstocks - "The Klamath River has periodic high levels of the protazoan disease organism Ceratomyxa shasta. Marsh areas and lakes are thought to be optimal conditions for this protazoan although the lifecycle of the organism remains unknown. All stocks of rainbow trout in the areas above Iron Gate Dam are resistant to this disease (Buchanan in press). Locally adapted steelhead stocks in the vicinity of Iron Gate Hatchery should also have evolved almost total resistance. Studies at the Nehalem River in Oregon found that introductions of Trask River coho decreased the viability of native Nehalem coho stock substantially because the introduced Trask fish lacked resistance to Ceratomyxa shasta (Kapuscinski 1984)..."

Chapter 5, pg. 6 Iron Gate Hatchery Broodstock - ..."Insufficient numbers of native coho were returning to the hatchery site when Iron Gate Dam was completed, so coho stocks were founded with eggs imported from the Trinity River Hatchery [from Cascade Hatchery stock], Cascade Hatchery in Oregon, and Mt. Shasta Hatchery (CH2M Hill 1985). Since Mt. Shasta Hatchery is on the Sacramento, which does not have coho salmon, the coho from this source may have been from another California stream, such as the Noyo River (Bob Corn personal communication)..."

Chapter 5, pg. 8 Trinity River Hatchery - ..."From 1979 to 1988 the average number of coho juveniles planted was 670,531 annually. Plants ranged from a high of 1,198,696 in 1981 to a low of 156,150 in 1984..."

Chapter 5, pg. 10 Trinity River Hatchery Planting Procedures, Stock Transfers - "Coho and steelhead were widely transplanted prior to 1984 in the Trinity Basin as far down as Weitchpec and in Hayfork and South Fork of the Trinity drainage. All releases of both species now are made only at the hatchery. Coho are released in March and steelhead are released in March and April. Prior to 1984, plants of both species were a mixture of fingerlings and yearlings. Now steelhead and coho are raised to yearling size before release..."

Chapter 5, pg. 10 Trinity River Hatchery Broodstock - "Coho stocks were derived from Cascade Hatchery in Oregon..."

Chapter 5, pg. 11 Trinity River Hatchery Disease and Operational Problems - "Diseases present at Trinity River Hatchery include enteric red mouth which is caused by the bacteria Yersinia rickeri, bacterial kidney disease (BKD), white spot and infectious necrosis (IHN), a viral disease. Seven million coho eggs were found to be at risk to IHN in 1985 and destroyed as a precautionary measure (Bob Corn personal communication)..."

"Bartley and Gall (1990) recently reported that crosses between chinook and coho salmon ("conooks") were occurring in the Klamath River Basin and particularly at or below Trinity River Hatchery. Chevassus (1979), in a review of the literature, found natural crossing of chinook and coho to be extremely rare. The earlier run timing of the hatchery strain of coho versus original native coho stocks, the large runs of both coho and fall chinook in recent years, and the limited amount of spawning area below the hatchery may be the combination of factors that led to this occurrence.

"Hendrick et al. (1987) also noted the crosses occurring at the Trinity River Hatchery and described changes in resistance to disease that may be related to the hybridization. They noted that coho were not susceptible to IHN at the hatchery or anywhere in their range. Experiments were conducted by Hendrick et al. (1987) and it was discovered that while pure coho were resistant to IHN, chinook had some susceptibility, and the hybrid conooks had almost no resistance to IHN. Hybridization could lead to increased loss of fish at Trinity River Hatchery due to IHN. Bartley (personal communication) indicates that hybrids may retain external characteristics of chinook or coho but sometimes have mixes of both. Thus, the problem of intermixing hybrids into broodstocks could elude graders and continue to exacerbate the problem."

Chapter 5, pg. 17 Disease Introductions a Side Effect of Large Scale Fish Culture - "The introduction of broodstock or eggs from outside the basin represents an increased threat of introduction of non-endemic disease organisms (PNFHPC 1989). Because native fish are not resistant to such diseases, introductions can be potentially devastating. CDFG guidelines so longer allow fish from outside to be introduced into the Klamath drainage."
____________________
 

from the attached rept APPENDIX D.
HISTORICAL OCCURRENCE OF COHO SALMON IN THE UPPER KLAMATH, SHASTA, AND SCOTT RIVERS.
California Department of Fish and Game
Northern California and North Coast Region
February 2002


Early Stocking History
The earliest record of coho salmon being stocked in the Klamath Basin was of a plant
made in 1895. Fortune et al. (1966) reports that 460,000 coho salmon were stocked in the
Klamath River (300,000 fry and 160,000 yearlings). Further examination of the original records
from the U.S. Commission on Fish and Fisheries (1895) revealed those fish were raised in the Ft.
Gaston facility in Hoopa and were stocked in the Trinity River and in Supply Creek, a tributary
to the Trinity River. Those fish were reared from eggs taken at a facility in Redwood Creek (a
substation of the Ft. Gaston facility) and also from eggs shipped from another facility not
identified in the report (but were likely from out of the basin). Insight as to the purpose of this
1895 coho salmon plant may be found in the U.S. Commission on Fish and Fisheries (1895)
report that states; “Most of the salmon and steelhead eggs were taken at the [Redwood Creek]
substation, as there was no run of either kind in the Trinity, all the fish having been taken at the
cannery at the mouth of Klamath River”. Although the Ft. Gaston facility operated until 1898,
1895 was the only year coho salmon were stocked into the Klamath Basin prior to 1911 (Cobb
1931).

In anticipation of the construction of Copco Dam, the “Klamathon Racks”, a fish egg
taking station located near the old town of Klamathon, was built in 1910 and began operating
that same year (Leitritz 1970). These racks extended across the Klamath River, effectively
blocking the salmon runs. The Klamathon Racks were, “necessary that the supply of salmon
may be maintained in the Klamath River...” (CFGC 1918). Fish trapping records beginning in
the 1910-1911 season indicate that coho salmon were migrating upriver through that area,
making it clear that their upstream migration encompassed areas upriver from where the Iron
Gate and Copco dams now reside (Cobb 1931).
Although the construction of the Klamathon Racks began in 1910, the racks were not
completed on time. The Fiscal Year 1911 report (July 1, 1910 to June 30, 1911) of the U.S. Fish
Commissioner states that: “....the racks were not completed in time to intercept the run of
chinook salmon. Later in the season, before the completion of the silver salmon work, they were
carried away, but not before satisfactory collections of eggs had been made”. The actual
number of coho salmon eggs taken during the 1910-1911 season at the Klamathon Racks was
not given in the records, however, 2,109,000 coho salmon eggs collected there were transferred
to the California Fish Commission’s Sisson (Mt. Shasta) Hatchery (CFGC 1913). The resultant
fry were subsequently stocked back into the Klamath and Sacramento rivers (CFGC 1913).
This
was the first effort made by the State of California to increase the runs of coho salmon (CFGC
1913). Beginning with the 1912-1913 season, coho salmon eggs taken at the Klamathon Racks
were mostly reared and released from the US Bureau of Fisheries’ Hornbrook Hatchery on the
Klamath River.
Apparently, no coho salmon eggs were collected at the Klamathon Racks during the
1911-1912 and 1917-1918 seasons as coho salmon are not mentioned in the available federal and
state records. However, coho salmon eggs were taken during the five consecutive seasons
beginning with the 1912-1913 season (Cobb 1931). With two exceptions (1913-1914 and 1915-
1916), the numbers of coho salmon eggs collected each season at the Klamathon Racks are not
available, however, the number of fry reared at the Hornbrook Hatchery from coho salmon eggs
taken at the Klamathon Racks are provided (Cobb 1931, Fortune et al. 1966). Number of eggs
collected and number of coho salmon produced from 1910 through 1917 are summarized in
Appendix Table D-1.

Klamathon Racks, we used the average number of eggs per female coho salmon (2,394 - see
Coho Salmon Status Review, Chapter III, Biology - Life History and Unique Characteristics).
Based on this, an estimated 881 females would have been required to obtain the number of eggs
collected at the Klamathon Racks that were transferred to Sisson Hatchery during the 1910-1911
season. Greater numbers of females were required in subsequent seasons (1913-1914 through
1915-1916) (Appendix Table D-1). The 1912 -1913 and 1916-1917 seasons were drought years
in which the take of salmon eggs, both chinook and coho salmon, was greatly reduced (Fiscal
Year 1913 report of the U.S. Fish Commissioner, CFGC 1918). The relatively large numbers of
coho salmon females required to yield the reported egg take and hatchery production indicates
that significant numbers of coho salmon were in the Klamath River in the vicinity of the
Klamathon Racks during those years.
The Klamathon Racks were rebuilt during the fall of 1918 and ownership of the facility
was granted to the State of California by the U.S. Bureau of Fisheries. It began supplying most
of the eggs utilized by the State because production from other stations, such as the Baird Station
on the McCloud River, was seriously curtailed due to impacts from ocean harvest, irrigation
diversions and dam building (CFGC 1921). At this time, fish culture emphasis for the State
focused on the production of chinook salmon and trout, and although many coho salmon were
caught at the Klamathon Racks, it was the larger chinook salmon that were selected (Bryant
1923). Since the Hornbrook Hatchery was considered by the State to be ill-equipped to rear fry
and because it had an unreliable water supply, the facility was abandoned in 1919 in favor of the
new Fall Creek Hatchery (CFGC 1921).
Appendix D Page 4
Fortune et al. (1966) indicates that hatchery coho salmon were stocked in the Klamath
River on only four occasions between 1919 and 1959. Totals of 178,000, 73,380, 20,000 and
20,000 fry and fingerlings were planted in 1919, 1934, 1940 and 1941, respectively. A review of
California Fish and Game Commission Biennial Reports for the years 1930 through 1950 reveals
that additional plants totaling 476,000 coho salmon were made to the Klamath River (Siskiyou
County) between 1930 and 1932 (CFGC 1932).
These fish were reared at the Fall Creek
Hatchery (CFGC 1932) and presumably originated from the Klamathon Racks, as was the
practice of the day.
Hatchery Stocks
Historically, the practice of importing non-native fish was common, especially in systems
where native fish had been extirpated or were in low abundance (also see Status Review,
Chapter VII, Influence of Existing Management Efforts). Following completion of Iron Gate
Hatchery in 1966, adult coho salmon returns were less than 500 fish. After the completion of
Trinity River Hatchery in 1963, adult coho salmon returns at this facility rarely exceeded 1,000
fish prior to 1971. In an effort to increase returns to Iron Gate Hatchery, coho salmon from the
Cascade River in Oregon were stocked in 1966, 1967 and 1969 (CDFG 1994). The first
significant transfer of coho salmon to Trinity River Hatchery occurred in 1964 when Eel River
coho salmon stock were brought in. This was followed by plantings of coho salmon originating
from the Cascade River, Oregon in 1966, 1967 and 1969. Noyo River stock was also planted in
1969 and Alsea River stock was planted in the Trinity in 1970 (CDFG 1994). It appears the
intent of these out-of-basin transfers was to augment already existing, albeit dwindling, natural
coho salmon populations. Current California Fish and Game Commission policy now essentially
prohibits all out-of-basin fish transfers.

--------------------
http://www.nwfsc.noaa.gov/publications/techmemos/tm17/

http://www.nwfsc.noaa.gov/publications/techmemos/tm17/papers/moran2.htm

_________________________
http://genome-lab.ucdavis.edu/people/Israel/pc_finalgenetics.pdf
PacifiCorp
Klamath Hydroelectric Project
FERC Project No. 2082
 February 2004 PacifiCorp
Fish Resources FTR.DOC Fish Resources FTR Page 9-13

9.7.4 Review of Hatchery-Related Genetic Information on Klamath Salmonids
9.7.4.1 Coho Salmon Broodstock Practices
Three significant genetic concerns remain for hatchery populations of coho salmon in the
Klamath basins. First, the potential for domestication selection in hatchery populations, such as
the Trinity River fish hatchery where there is no or little infusion of wild genes. Also, concern
exists about out-of-basin straying by large numbers of hatchery coho. However, hatchery
production of coho salmon at the Mad River and Rowdy Creek facilities was ceased after the
1999 brood year, thereby eliminating potential genetic introgression associated with hatchery
releases from these facilities (NOAA Fisheries, 2003).
The NOAA Fisheries is concerned about
the origins of the current coho stocks in the Klamath River. The NOAA Fisheries (NOAA
Fisheries, 2003) stated that there is evidence that several of the large river basins in the SONCCESU,
including the Rogue, Klamath, and Trinity rivers, are heavily influenced by hatchery
releases of coho salmon. Historical and reciprocal transfers of stocks between SONCC and the
Central California ESU streams were common (see below), and SONCC streams also have
received inter-basin plants from hatchery stocks in the Lower Columbia River/Southwest
Washington, Puget Sound/Strait of Georgia, and Oregon Coast ESUs.
Two of the four hatcheries
still producing and releasing coho salmon in the SONCC ESU are Iron Gate fish hatchery and
Trinity River fish hatchery.
Iron Gate fish hatchery was founded in 1965 from Klamath River coho salmon returning to the
hatchery. Cascade Hatchery (Columbia River) coho salmon stock were released in 4 of the first 5
years of the hatchery’s operation via Trinity River fish hatchery and Mt. Shasta fish hatchery. In
1977, two-thirds of the coho released from Iron Gate fish hatchery were planted from the Trinity
River (Rushton, pers. comm., 2003).
Since 1977, only Klamath River basin fish have been
released from Iron Gate fish hatchery. Adult returns averaged 1,120 fish between 1991 and 2000,
and an average of 161 females have been spawned at Iron Gate fish hatchery annually during the
same period (NOAA Fisheries, 2003).
Accurate estimates of the relative contributions of wild and hatchery-produced fish are not
available for the Klamath River (CDFG, 2001). Beginning in 1995, Iron Gate fish hatchery coho
salmon have been marked with left maxillary clips. Data on hatchery returns, which have only
been published for 2000, indicate that 80 percent of the 1,353 adults returning to Iron Gate fish
hatchery were marked as hatchery fish. Of those fish, 98 percent were Iron Gate fish hatchery
releases and the remaining were from the Trinity and Cole River (Rogue River, Oregon) fish
hatcheries. Fish from the Trinity River fish hatchery have right maxillary clips, while those from
the Cole Hatchery have had their adipose fin clipped. Cole River fish have been verified by
recovered pit tags (Iron Gate fish hatchery staff, personal communication in Hedgecock et al.
2002). Since Iron Gate fish hatchery is located near the upper end of accessible habitat, the
significance of the high percentage of hatchery fish with respect to the total production in the
Klamath basin is uncertain (NOAA Fisheries, 2003).
Trinity River fish hatchery began releasing coho salmon in 1960. Originally, Trinity River fish
were used as broodstock, although coho salmon from the Eel River (1965), Cascade River
(1966-7, 1969), Alsea River (1970), and Noyo River (1970) have been reared and released at the
hatchery as well as elsewhere in the Trinity basin. Outmigrant trapping on the lower Trinity
River indicates that marked Trinity River fish hatchery fish comprised 65 to 97 percent of the
catch between 1998 and 2000. In addition, an estimated 85 to 95 percent of the estimated coho
salmon run upstream of Willow Creek weir between 1997 and 2001 were of Trinity River fish
hatchery origin (Wade Sinnen, personal communication cited in CDFG, 2002). Additional
analysis of carcass data suggests that straying of Trinity River fish hatchery coho is high and a
large percentage of in-river spawners are of Trinity River fish hatchery origin.

9.7.4.2 Hybridization of Chinook and Coho Salmon at Trinity River Hatchery
Bartley et al. (1990) identified Chinook and coho salmon hybrids from Deadwood Creek, a
tributary to the Trinity River, and from rearing ponds at Camp Creek, a tributary to the Lower
Klamath River. Forty alleged juvenile out-migrant (smolt) coho salmon were collected in August
1984 from Deadwood Creek. A sub-sample of 120 putative juvenile Chinook salmon was
collected from rearing ponds at Camp Creek. Juveniles from the rearing ponds were the progeny
of presumable Chinook salmon that had been captured at Camp Creek. The spawning location of
the broodstock of these fish is unclear. Bartley et al. (1990) reported fish were spawned at Iron
Gate hatchery and transported back to Camp Creek to be reared. Hatchery personnel reported
that all Camp Creek broodstock were spawned at Camp Creek from 1986 to 1990 (Rushton, pers.
comm., (2003). Previous analysis of populations of Chinook and coho salmon in California
(Bartley, 1987; Bartley and Gall, 1990) revealed seven allozyme loci whose allelic products
could be used to distinguish between the two species. Electrophoretic analysis of 21 allozymes
was performed and the likelihood of hybridization for individuals expressing alleles of both
parental species was evaluated using the hybrid index described by Campton and Utter (1985).
Genotypes and hybrid index scores of the 40 juvenile salmon from Deadwood Creek suggested
that 11 were Chinook salmon, 26 were coho salmon, and three were presumptive Chinook-coho
hybrids. The hybrids were heterozygous for the common alleles of both Chinook and coho
salmon at five out of seven distinguishing allozyme loci. Fourteen of 120 fish from the Camp
Creek rearing ponds were heterozygous for the common alleles of both species at all seven
distinguishing loci.
Observed hybrids were considered to be first generation because all of the
distinguishing loci, with the exception of one locus in a single individual, were heterozygous,
containing one allele from Chinook salmon and the other allele from coho salmon.
While a quantitative estimate of the level of Chinook-coho hybridization in California was not
possible because of the non-random sampling of fish within populations, the Deadwood Creek
and Camp Creek samples represented the only occurrences of putative hybridization revealed in
an analysis of 36 Chinook populations and 27 coho populations from northern California
(Bartley, 1987; Bartley and Gall, 1990). Moreover, no evidence of Chinook-coho hybridization
was reported in a study of 86 populations of Chinook between the Babine River, British
Columbia, and the Sacramento River, California (Utter et al. 1989).
Bartley et al. (1990) suggest that the 14 hybrids from the Camp Creek rearing ponds were the
result of hatchery personnel inadvertently crossing pure Chinook and coho salmon during
spawning operations and hybrid offspring were placed with pure Chinook in the rearing ponds.
Hatcheries designed to offset losses of salmon spawning habitat through artificial spawning
could contribute to the erosion of the genetic resource of Chinook and coho salmon through
direct or indirect production of hybrid salmon. All fish, including alleged hybrid individuals,
held at the Camp Creek rearing ponds were released into the Klamath River system under the
presumption they were pure Chinook salmon. If hybrid Chinook-coho salmon return to spawn,
genetic resources within naturally spawning populations of both species may erode in the
Klamath River system.
Disruption of the natural spawning environment and crowded spawning sites may result in
hybridization of fish (Hubbs, 1955). When interspecific mating occurs between coho and
Chinook salmon, gametes (genetic information passed on to the next generation in one particular
species or the other) and/or spawning sites are no longer available for other population members
for each species (Utter, 1989). Since mating between coho and Chinook produce offspring that
are sterile (Johnson, 1988), the genes those parents carried (that component of genetic diversity
for the population as well as the species as a whole) are no longer perpetuated in generations
subsequent to the sterile offspring produced. In addition, as the rate of hybridization between the
two species increases, there will be fewer individuals in the population who will pass their
genetic information further than one generation. Interspecific hybridization, when the hybrid
offspring are sterile, lowers the numbers of successfully reproducing fish (individuals that
produce offspring that return to reproduce successfully themselves) in the population. As the
number of successfully reproducing fish relative to all breeding members (not necessarily
reproductively successful) of the population decreases, the proportion of the entire gamut of
genetic diversity harbored by that population and that is passed onto the next generation also
decreases. This phenomenon is called genetic drift and may contribute to erosion of genetic
resources of small, fluctuating populations like Pacific salmonids.
_____________________
 

Excerpts from my Feb 21, 2002 comments on Federal Register Feb. 11 Vol. 67, No. 28, Proposed Rules, Page 6215-6220 :
 

Historic Decline and Current Status of Coho Salmon in California, Larry R. Brown, Peter B. Moyle and Ronald Yoshiyama, North American Journal of Fisheries Management, Vol. 14, No. 2, May 1994:

"Except in the Eel River, coho salmon stocks in the larger rivers of California are now dominated by hatchery production, and even several small coastal streams receive regular plants of hatchery fish. These hatchery stocks are of diverse origin, but all have included fish derived from outside the river system receiving the plantings and often from outside California. Hatchery stocks have also been used to reestablish extirpated populations or to supplelment depeleted runs, which may partly explain the overall lack of genetic differentiation among coho salmon from different California streams (Bartley et. al 1992.)..." (Emphasis mine.)

From the final listing determination of SONCC coho (Federal Register Vol. 62, No. 87, Rules and Regulations May 6, 1997 pgs. 24588-24609):

"Stock transfers of coho salmon have been (and continue to be) common throughout the West Coast; the nature and magnitude of these transfers varies by geographic region. Compared to areas farther north, hatcheries in central California and southern Oregon/northern California are relatively small and widely dispersed, given the size of both areas. In recent years, large hatcheries in southern Oregon/northern California (e.g., Mad and Trinity Hatcheries) have produced 400,000 to 500,000 juveniles annually, while smaller hatcheries, and most hatcheries in central California, produce no more than 100,000 to 200,000 juveniles each year. There has been considerable transfer of coho salmon among hatcheries or egg-taking stations in central and northern California, with the fish eventually outplanted in either area. Northern California hatcheries have also received fairly large transplants of coho salmon from hatcheries in Washington and Oregon, which have spread to central California through stock transfers. Because of the predominance of hatchery stocks in the Klamath River Basin, stock transfers into Trinity and Iron Gate Hatcheries may have had a substantial impact on natural populations in the basin. In contrast, Cole Rivers Hatchery (on the Rogue River) appears to have relied almost exclusively on native stocks..." [at 24601]

NMFS-NWFSC-24: Status Review of Coho Salmon from Washington, Oregon, and California - Laurie A. Weitkamp, Thomas C. Wainwright, Gregory J. Bryant, George B. Milner, David J. Teel, Robert G. Kope, and Robin S. Waples:

"Southern Oregon/northern California coasts ESU--Hatchery production of coho salmon in the southern Oregon/northern California coasts ESU is greater than in the central California coast ESU, but considerably less than in more northerly ESUs. Large hatcheries within this ESU (e.g., Mad, Trinity) have released 400,000-600,000 coho salmon annually in recent years, with total annual production at approximately 1.4 million coho salmon between 1987 and 1991 . Aside from considerable movement of coho salmon between hatcheries or egg-taking stations in central and northern California, northern California hatcheries have also received fairly large transplants of coho salmon from hatcheries in areas outside the ESU, including the Oregon coast, lower Columbia River/southwest Washington coast [Cascade and Klaskanine], and Puget Sound/Strait of Georgia (Fig. 35)...."

[ http://www.nwfsc.noaa.gov/publications/techmemos/tm17/figures/bermfig2.htm ]
 

Figure 2 from NOAA Technical Memorandum 17, Application of DNA Tecnology to the management of Pacific Salmon - Phylogeographic Structure of Coho Salmon Populations Assessed by Mitochondial DNA by Paul Moran and Eldredge Bermingham, indicates that Klamath River Iron Gate Hatchery stocks are genetically related to coho of South Puget Sound, North Oregon and Washington Coast cluster. (Ironically, the same biological kinship group as that of the Alsea decision.) Iron Gate Hatchery (IGH) coho were determined to be of an entirely different genetic cluster than the Rogue River and Cowlitz coho, which are in the SONCC biological ESU.

This exclusion of the IGH coho from the SONCC biological ESU is consistent with numerous narratives that indicate IGH coho broodstock originated from the Cascade hatchery in the Columbia River Gorge.

Chapter 4, pg. 13 of the Long Range Plan For The Klamath River Basin Conservation Area Fishery Restoration Program (William M. Kier Assoc. 1991):

states: "The hatchery runs of coho for both Iron Gate and Trinity River hatcheries were created from broodstock from the Cascade Hatchery in the Columbia River Basin. This stock returns to the lower river in September and October, with the peak generally occurring in the second week of October (Hubbell 1979)…"

Chapter 5, pg. 6 Iron Gate Hatchery Broodstock states - ..."Insufficient numbers of native coho were returning to the hatchery site when Iron Gate Dam was completed, so coho stocks were founded with eggs imported from the Trinity River Hatchery, Cascade Hatchery in Oregon, and Mt. Shasta Hatchery (CH2M Hill 1985). Since Mt. Shasta Hatchery is on the Sacramento, which does not have coho salmon, the coho from this source may have been from another California stream, such as the Noyo River (Bob Corn personal communication)..."

Apparently, IGH coho stocks were also subsequently fortified with stocks of Columbia River origin . Historic Decline and Current Status of Coho Salmon in California, Larry R.

Brown, Peter B. Moyle and Ronald Yoshiyama, North American Journal of Fisheries Management, Vol. 14, No. 2, May 1994 states:

"...During 1963-1968, adult returns to the Iron Gate Hatchery in the headwaters of the Klamath River never exceeded 500 fish (data in Brown and Moyle 1991a. App.) Following an intensive stocking program begun in 1966 (and continued in 1967 and 1969) with Cascade River (Oregon) fish, adult returns to the hatchery were over 1,000 fish in seven spawning seasons and exceeded 2,200 fish twice, most recently in 1987; numbers typically have ranged between 400 and 1,500 (Hiser 1991.) This hatchery run, therefore, is composed basically of an imported stock."

STATUS OF "NATURALIZED" IGH COHO or "OUTPLANTS" ?

Chapter 5, pg. 2 of the Long Range Plan For The Klamath River Basin Conservation Area Fishery Restoration Program (William M. Kier Assoc. 1991) or LRP establishes that nonindigenous stocking programs commenced more than a century ago:

"Upper basin stocking programs were begun in 1890 by the U.S. Bureau of Fisheries (Fortune et al. 1966). No hatchery was established at this time...Coho salmon were stocked in 1895..." [Note: it appears from the text that these were of Mt. Shasta hatchery origin as were chinook fry stocked during this period. This is coho from the Sacramento system.]

IGH records show that at least 40% of the juveniles released from IGH in the following years were outplanted directly into the tributaries of the Klamath River. Total juvenile releases 1986-87= 205,000; 1987-88=135,000; 1988-89=143,400. (Klamath River Fisheries Resource Plan, CH2M Hill, for USDOI, Feb 1985 ) We know that from 1979-1988, an average 119,796 coho yearlings were outplanted from the IGH annually.

The LRP Chapter 4, pg. 13 states;

" Coho yearlings from Iron Gate Hatchery were transplanted to Indian Creek, Beaver Creek, and Elk Creek between 1985 and 1989 and have resulted in at least some spawning activity in Indian Creek (Dennis Maria personal communication.)"

Chapter 5, pg. 6 Iron Gate Hatchery Planting Procedures, Stock Transfer states:

 

"Coho yearlings have been released in March and April. From 1986 to 1988 - 40% of the Coho yearlings were planted at the hatchery. The remainder were transplanted into Indian Creek, Elk Creek and Beaver Creek. Iron Gate coho were planted in the Salmon River in 1985."

From the USFS report "Evaluation of Fish Habitat Condition and Utilization in Salmon, Scott, Shasta, and Mid-Klamath Sub-Basin Tributaries 1988/1989" states:

 

"The CDF&G and Karuk Tribe have cooperatively operated rearing ponds on Indian Creek since 1980. Current rearing activities include one facility utilizing Iron Gate Hatchery chinook fingerlings that has a capacity to produce 80,000 yearlings for release into Indian Creek. Other releases include 24,000 to 48,000 juvenile coho salmon from Iron Gate Hatchery planted yearly between 1986 and 1989, and 8,000 steelhead fingerlings planted in 1983.)

In addition the Klamath River Basin Fisheries Resource Plan CH2MHill Feb., 1985 states:

"Iron Gate Hatchery fish have been planted periodically in the Scott Subbasin (CDFG, Iron Gate Hatchery annual reports). Surplus adult coho salmon (50 fish) were planted in Shackleford Creek in 1971. Surplus adult steelhead were planted in the East Fork Scott River (130 fish) in 1972; Mill Creek (108 fish), Etna Creek (68 fish), and Shackleford Creek (50 fish) in 1978; Etna Creek (100 fish) in 1982; and Canyon Creek (53 fish) and Mill Creek (163 fish) in 1983..."

 

There is ample evidence that IGH coho, (descended from imported OCH coho,) were widely naturalized or outplanted in the mid-Klamath and its tributaries. It is highly probable that they returned to spawn and that their progeny populate the system. It is uncertain whether these fish are considered part of the biological ESU or the listed ESU. It is also uncertain how one can tell these progeny apart from any "wild" coho or naturally spawning Trinity River coho or their progeny.

 

STATUS OF IGH DRIFT?

There is evidence to point to the a possibility of a significant drift in hatchery coho spawners. Historic Decline and Current Status of Coho Salmon in California, Larry R. Brown, Peter B. Moyle and Ronald Yoshiyama, North American Journal of Fisheries Management, Vol. 14, No. 2, May 1994, references a study of Trinity River hatchery (TRH) coho by (Rogers, D.W. CA DFG Anadromous Fish Branch, Admin. Rept. 73-10.).

that determined "Significant numbers of fish (about 40% of adult escapement) apparently spawned naturally in the Trinity River or in the tributaries above the North Fork confluence during 1969 and 1970, mainly in the area between Lewiston Dam and Douglas City."

The Federal Register Notice Vol. 62. No. 87, Tuesday, May 6, 1997 "Rules and Regulations" pg. 24588-24609 announcing the final determination of the Southern Oregon Northern Coastal Coho Salmon ESU as "threatened" states:

..." However, large hatchery programs, particularly in the Klamath/Trinity basin, raise serious concerns about effects on, and sustainability of, natural populations. For example, available information indicates that virtually all of the naturally spawning fish in the Trinity River are first-generation hatchery fish...." [at 24590]

(Note, there is little information coho populations in the Klamath and its tributaries because fish weirs are inoperable and fish counts are not conducted during peak spawning times due to typically high flows at that time. Also, the IGH did not consistently tag its fish.)

 

TRH COHO ARE DESCENDED FROM EXEMPTED COHO -A CONUNDRUM

As previously quoted from Chapter 4, pg. 13 of the Long Range Plan For The Klamath River Basin Conservation Area Fishery Restoration Program (William M. Kier Assoc. 1991):

"The hatchery runs of coho for both Iron Gate and Trinity River hatcheries were created from broodstock from the Cascade Hatchery in the Columbia River Basin. This stock returns to the lower river in September and October, with the peak generally occurring in the second week of October (Hubbell 1979)…"

Chapter 5, pg. 10 Trinity River Hatchery Broodstock states - "Coho stocks were derived from Cascade Hatchery in Oregon..."

 

TRH COHO WERE WIDELY NATURALIZED OR OUTPLANTED

Historic Decline and Current Status of Coho Salmon in California, Larry R. Brown, Peter B. Moyle and Ronald Yoshiyama, North American Journal of Fisheries Management, Vol. 14, No. 2, May 1994:

"Like the Iron Gate stock, the Trinity River stock is primarily of nonnative origin. The first significant planting was of Eel River stock in 1964, followed by Cascade River (Oregon) stocks in 1966, 1967, and 1970. Noyo River (California) stock was planted along with Cascade River fish in 1970, and Alsea River (Oregon) stock was planted along with Cascade River fish in 1970…"

Chapter 5, pg. 8 of the Long Range Plan For The Klamath River Basin Conservation Area Fishery Restoration Program (William M. Kier Assoc. 1991) states:

..."From 1979 to 1988 the average number of coho juveniles planted was 670,531 annually. Plants ranged from a high of 1,198,696 in 1981 to a low of 156,150 in 1984..."

Chapter 5, pg. 10 Trinity River Hatchery Planting Procedures, Stock Transfers states –

"Coho and steelhead were widely transplanted prior to 1984 in the Trinity Basin as far down as Weitchpec and in Hayfork and South Fork of the Trinity drainage. All releases of both species now are made only at the hatchery. Coho are released in March and steelhead are released in March and April. Prior to 1984, plants of both species were a mixture of fingerlings and yearlings. Now steelhead and coho are raised to yearling size before release..."

 

TRH COHO EXHIBIT EXCEPTIONAL INCIDENCE OF DRIFT

(See above subsection entitled "STATUS OF IGH DRIFT?")

Historic Decline and Current Status of Coho Salmon in California, Larry R. Brown, Peter B. Moyle and Ronald Yoshiyama, North American Journal of Fisheries Management, Vol. 14, No. 2, May 1994:

Klamath-Trinity entire system to mouth: 93 streams; 1,860 native and naturalized; 16,265 hatchery (Includes Iron Gate and Trinity hatcheries, as well as hatchery fish spawning below Trinity Hatchery based on the assumption that 60% of returning hatchery fish actually enter the hatchery, with the remainder spawning outside (Rogers 1973)

The Federal Register Notice Vol. 62. No. 87, Tuesday, May 6, 1997 "Rules and Regulations" pg. 24588-24609 announcing the final determination of the Southern Oregon Northern Coastal Coho Salmon ESU as "threatened" states:

..." However, large hatchery programs, particularly in the Klamath/Trinity basin, raise serious concerns about effects on, and sustainability of, natural populations. For example, available information indicates that virtually all of the naturally spawning fish in the Trinity River are first-generation hatchery fish. Several hatcheries in the California portion of this ESU have used exotic stocks extensively in the past..." [at 24590]

NOAA Technical Memorandum NMFS-NWFSC-24: Status Review of Coho Salmon from Washington, Oregon, and California - Laurie A. Weitkamp, Thomas C. Wainwright, Gregory J. Bryant, George B. Milner, David J. Teel, Robert G. Kope, and Robin S. Waples:

"Southern Oregon/northern California coasts ESU--Hatchery production of coho salmon completely eliminates the Trinity River system as derived totally from hatchery fish. (Rogers, D.W. 1973.)

California Department of Fish and Game, National Marine Fisheries Service Southwest Region Joint Hatchery Review Committee Final Report on Anadromous Salmonid Fish Hatcheries in California (Review Draft) June 27, 2001:

"…Coho returning to the Trinity River are overwhelmingly of hatchery origin. The hatchery stock is considered part of the Southern Oregon/Northern California coho ESU but is not listed…"

 

KLAMATH -TRINITY METAPOPULATION?

From Salmon and Steelhead populations of the Klamath-Trinity Basin, California - Roger Barnhart, California Cooperative Fishery Research Unit April 1994 (Presented at the Klamath Basin Fisheries Symposium, March 24, 1994:

"Coho salmon were placed in one metapopulation."

"The status of wild coho populations in the Klamath River Basin is unknown; there may still be pure strains in tributaries of the lower Klamath River such as Hunter and Terwer creeks. The hatchery runs of coho for both Iron Gate and Trinity River hatcheries were created from broodstock from Cascade Hatchery in the Columbia River Basin (Hubbell 1979). Coho juveniles from both hatcheries have been outplanted to many other portions of the basin, notably the Salmon River and the South Fork Trinity River.

"Based on the history of hatchery introductions and intrabasin transfers of coho the Committee categorized Klamath Basin coho as one metapopulation. The Committee did not attempt to define breeding populations due to lack of information..."

 

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