River Hatchery Research Articles

An Assessment of Population Genetic Variation in Chinook Salmon from Seven Michigan Rivers 30 Years after Introduction

AbstractChinook salmon Oncorhynchus tshawytscha were introduced into the Lake Michigan basin from 1966 to 1968 with the transfer of fertilized eggs from the Green River Hatchery, Washington. In the more than three decades since this founding, Chinook salmon occur and are managed throughout the Great Lakes basin as a mixture of feral and supplemented populations. To evaluate the extent of genetic diversity since initial founding, we examined the pattern of variation at 18 allozyme loci among feral Chinook salmon populations in seven Michigan watersheds. We observed little divergence and low heterogeneity among the seven populations, which was consistent with the pattern expected in a single, randomly mating gene pool. We believe that the two major mechanisms contributing to the lack of among‐population heterogeneity are the relatively recent founding from a single source and the routine homogenization from annual releases of hatchery‐propagated, common‐brood‐source juveniles. We compared genetic diversity in the founded population with that of the source population to assess impacts from management activities or other events that might have caused genetic bottlenecks. Six rare alleles observed in the source stock were absent in our combined Michigan samples (N = 256), and frequencies for two of these alleles were significantly different (P ≤ 0.01) between the source and Michigan samples. Several other allele frequencies also differed significantly between the source and founded populations, providing evidence that one or more sources of genetic drift have affected allelic variation in the Michigan population. Although conservation of native genetic diversity is not a prevailing issue for Chinook salmon in Michigan waters, management approaches aimed at maintaining overall compositional and structural diversity and any recently evolved but undetected river‐specific diversity should avoid further depletion of genetic variation in this important Great Lakes recreational resource.

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SAN FRANCISCO ESTUARY & WATERSHED SCIENCE Editorial Understanding Central Valley Chinook Salmon and Steelhead: It is Time to Get off the Dime! Randy Brown, Co-Editor-in-Chief San Francisco Estuary and Watershed Science brown.randall@comcast.net BACKGROUND Chinook salmon and steelhead are important biological components of the Central Valley ecosystem. The adults spawn in many streams, the young may spend a few to several months in these streams and in the San Francisco Estuary on their way to the ocean. When the adults return to their natal streams they transfer some of the ocean derived nutrients, organic matter, and energy to the lotic foodweb. Chinook salmon and steelhead together form the basis of economically important com- mercial and recreational fisheries – both in the ocean and inland waters. Chinook salmon and steelhead also are important because they are part of the historic culture in the Central Valley and qualify as “charismatic macro- fauna” with which the public can readily identify. This identification is demonstrated by the Feather River and American River salmon festivals that annually attract thousands of adults and children. The abundances of the four Chinook salmon races (win- ter, spring, fall, late fall) and steelhead are often used to judge the ecological health of the Central Valley ecosys- tem. This judgment is in part because spring and winter Chinook are respectively listed as threatened and endan- gered under the state and federal endangered species acts and the steelhead is listed as threatened pursuant to the federal Endangered Species Act. The late fall and fall runs are federal candidate species. An important ecological objective is to restore habitat and reduce the impacts of other factors so that the two salmon races and steelhead populations recover to the point they can be delisted. To complicate matters considerably, in the Central Valley we have six hatcheries that produce and release all four races of Chinook salmon and steelhead. Five of these hatcheries are mitigation hatcheries – Coleman, Feather River, Nimbus, Mokelumne, and Merced. Two of the hatcheries, Feather River and Mokelumne, also rear and release “enhancement” salmon that are grown specifically to increase the numbers of salmon available to the ocean fisheries. The other hatchery, Livingston Stone National Fish Hatchery, supplements the winter Chinook run. These hatcheries collectively produce and release impres- sive numbers of fish each year: Fall Chinook – 30 million, mostly smolt sized fish, from the five mitigation hatcheries; Spring Chinook – About two million smolts from the Feather River Hatchery; Late fall Chinook – About one million advanced smolts from Coleman National Fish Hatchery; Winter Chinook – About 250,000 advanced smolts from Livingston Stone National Fish Hatchery; Steelhead – About 1.5 million yearlings from Cole- man, Feather River, Nimbus and Mokelumne hatch- eries. Release strategies vary with the race and the hatchery. However, most fall Chinook from the Feather River and Nimbus hatcheries are released off-site in San Pablo Bay,

Incidence of Phenotypic Female Chinook Salmon Positive for the Male Y-Chromosome-Specific MarkerOtY1in the Central Valley, California

Abstract Fall-run chinook salmon Oncorhynchus tshawytscha collected during 1999 carcass surveys of seven locations within the Sacramento River basin and six locations within the San Joaquin River basin, California, were screened using the Y-chromosome-specific marker OtY1 to evaluate inconsistencies between sexual genotype and phenotype. Of 287 phenotypic females screened, 46 (16% overall) tested positive for the Y-chromosome marker. Stream populations had higher frequencies of sex-reversed males (American River, 20%; Battle Creek, 35%; Feather River, 20%; Merced River, 24%; Mokelumne River, 38%; and Yuba River, 25%) than hatchery populations (Feather River Hatchery, 0%; Nimbus Hatchery, 12%; Merced River Hatchery, 14%; and Mokelumne River Hatchery, 4%), and several other streams had intermediate frequencies. All 150 male fall-run chinook salmon from the sampling locations tested positive for the Y-chromosome marker. These results present evidence that some genetic males have been sex reversed and have th...

Genetic Characterization of Naturally Spawned Snake River Fall-Run Chinook Salmon

We sampled juvenile Snake River chinook salmon Oncorhynchus tshawytscha to genetically characterize the endangered Snake River fall-run population. Juveniles from fall and spring–summer lineages coexisted in our sampling areas but were differentiated by large allozyme allele frequency differences. We sorted juveniles by multilocus genotypes into putative fall and spring lineage subsamples and determined lineage composition using maximum likelihood estimation methods. Paired sMEP-1* and PGK-2* genotypes—encoding malic enzyme (NADP+) and phosphoglycerate kinase, respectively—were very effective for sorting juveniles by lineage, and subsamples estimated to be 100% fall lineage were obtained in four annual samples. We examined genetic relationships of these fall lineage juveniles with adjacent populations from the Columbia River and from Lyons Ferry Hatchery, which was established to perpetuate the Snake River fall-run population. Our samples of naturally produced Snake River fall lineage juveniles were most closely aligned with Lyons Ferry Hatchery samples. Although fall-run strays of Columbia River hatchery origin found on spawning grounds threaten the genetic integrity of the Snake River population, juvenile samples (a) showed distinctive patterns of allelic diversity, (b) were differentiated from Columbia River populations, and (c) substantiate earlier conclusions that this population is an important genetic resource. This first characterization of naturally produced Snake River fall chinook salmon provides a baseline for monitoring and recovery planning.

Prevalence ofRenibacterium salmoninarumin Juvenile Spring Chinook Salmon at Columbia and Snake River Hatcheries, 1993–1996

Abstract We monitored the prevalence and severity of Renibacterium salmoninarum (RS) infections in juvenile hatchery spring chinook salmon Oncorhynchus tshawytscha at eight Columbia and Snake river hatcheries from 1993 through 1996. This study followed a prior study that monitored RS in the same hatcheries from 1988 through 1992. In the current study, we found that the prevalence of RS-positive fish declined at two hatcheries relative to the preceding 5 years. Prevalence dropped from near 90% in 1992 to below 50% at both sites by 1993 and was less than 20% at three locations in 1995. In contrast, prevalence increased at four of seven sites in 1993 and six of seven sites in 1994. This indicated that previously reported declines in RS prevalence at these locations might have been temporary. Our results showed that in 1993 the majority of fish at all monitored hatcheries had low RS-antigen levels and remained that way at most locations through 1996. These results suggest that certain hatchery practices may l...

Adult Returns of Subyearling and Yearling Fall Chinook Salmon Released from a Snake River Hatchery or Transported Downstream

Abstract We compared the release-to-adult returns of coded-wire-tagged groups of fall chinook salmon Oncorhynchus tshawytscha in a 2 × 2 factorial experimental design: subyearlings and yearlings released directly from a hatchery versus those barged below two main-stem hydroelectric dams on the Snake River, Washington. Releases comprised six brood years over a 6-year period. In every release year, chinook salmon released as yearlings performed better than subyearlings; this was true both for returns to the Snake River and for their contribution to Pacific Ocean and lower Columbia River fisheries. We found no significantly consistent differences in rates of return between transported and on-station releases for either age-class. Return rates of both subyearlings and yearlings varied significantly with year of release. Median migration speeds of branded chinook salmon released on-station varied directly with Snake River flows. However, there was no general relation between flow (and attendant spill) in the S...

Incidence ofRenibacterium salmoninarumInfections in Juvenile Hatchery Spring Chinook Salmon in the Columbia and Snake Rivers

From 1988 through 1992, we assessed the prevalence (frequency of occurrence) and severity (degree of infection) of Renibacterium salmoninarum (RS) among fish in marked groups of Columbia River basin and Snake River basin hatchery spring chinook salmon Oncorhynchus tshawytscha before release and during their seaward migration. During the study, prevalence of RS infection decreased (from >90% to <65%) in six of the eight hatchery groups. We attributed this decrease to changes in hatchery practices that reduced vertical and horizontal transmission. Fish from Snake River hatcheries had a higher prevalence of infection when sampled at dams (mean >90%) than in the hatchery (mean <70%), but there were no differences in similar comparisons of Columbia River fish. Although prevalence and severity of RS infection were not correlated in the groups studied, it appears that fish from the Snake River were more severely infected than those from the Columbia River. Some groups of Snake River fish had higher severity of infection at dams than in the hatchery, but infection in fish from Columbia River hatcheries did not change. These differences between Snake River and Columbia River fish might have resulted from differences in river conditions and the distances from hatcheries to dams.

Factors Affecting the Homing of Fall Chinook Salmon from Columbia River Hatcheries

Abstract Straying results in an exchange of individuals between wild and hatchery salmon populations and is important because it could affect their genetic differences. Understanding what factors affect straying could help in the development of procedures for controlling the influence of specific stocks on nearby populations. We explore the effects of release date and the transportation of juvenile Chinook salmon Oncorhynchus tshawytscha on straying by adults from two Columbia River hatcheries. Early and late releases from Washougal Hatchery produced much higher straying levels than intermediate release dates, and this pattern was consistent among brood years. Fish reared at Grays River Hatchery and released from Washougal Hatchery strayed significantly more than local (i.e., Washougal) fish of the same brood year and release date. Our results and those from previous studies indicate that the sequence of imprinting events is characterized by the combination of the time at which the fish experience given l...

Effect of Hatchery Lighting on Smolting, Migration, and Survival of Steelhead

Abstract Summer steelhead (Oncorhynchus mykiss) were reared at South Santiam Hatchery, Oregon, under different lighting conditions for about 2 months prior to release. Groups of about 40,000 steelhead were reared under constant lighting from mercury-vapor lights (“lighted” fish) and compared with groups of fish that were covered with black plastic each night at dusk (“covered” fish). These groups were also compared with groups of the same strain reared at Roaring River Hatchery, Oregon, which had no nighttime lighting around the ponds (“unlighted” fish). At the time fish were released from their hatcheries, gill ATPase activity was significantly higher in the unlighted group at Roaring River Hatchery than in both groups at South Santiam Hatchery, where ATPase activity did not differ between lighted and covered groups. The lighted group was more silvery than covered or unlighted groups. The covered group was slightly smaller than the other two groups and showed decreased migration downstream. Timing of migration was similar in all three groups. Fish less than 17 cm were not recaptured in the migrant trap. The return of adults from the covered group was not significantly different from returns from the other two groups. Differences in fish physiology and behavior were associated with the lighting treatment, but whether or not low-level hatchery lighting benefits steelhead fitness remains ambiguous.

Manifestation of Proliferative Kidney Disease in Chinook Salmon (Oncorhynchus tshawytscha) Following Transfer of Infected Smolts to Sea Water.

For 4 consecutive years, the prevalence and severity of proliferative kidney disease (PKD), caused by the PKX myxosporean, in chinook salmon (Oncorhynchus tshawytscha) from the Puntledge River Hatchery, Vancouver Island, British Columbia, Canada was investigated after the fish were transferred to sea water. In the spring of 1991 through 1994, smolts were transferred from the hatchery to the Pacific Biological Station (PBS), Nanaimo, British Columbia at about the same time that their cohorts were released for seaward migration. In 1991, fish were maintained in PKX-free fresh water, and in 1992 fish were maintained in a seawater neetpen. In 1993 and 1994 fish were maintained in seawater tanks maintained at 15-17°C. In all years, virtually all the fish were subclinically infected with PKX at the time of transfer from the hatchery, and a prevalence of almost 100% was eventually observed in the fish after they were transferred to PBS. This study demonstrates that PKD can occur in sea water in post smolts originating from watersheds where the PKX parasite is present. It is, therefore, possible that PKD may impact ocean survival of salmon originating from PKX enzootic watershed, particularly because the disease causes osmoregulatory imbalances and anemia.

Behavioral and physiological changes in yearling chinook salmon during hatchery residence and downstream migration

Swimming stamina, buoyancy, and gill Na +K + ATPase activity were measured in yearling spring chinook salmon before and after release from Dworshak National Fish Hatchery and Rapid River Hatchery from 1986 to 1988. Behavioral and physiological indices remained constant during the 3 months prior to release in early April. Following release, freeze-branded smolts were sampled at Lower Granite Dam, 118 and 279 km downstream from the respective hatcheries. These smolts exhibited swimming stamina and gill Na +K + ATPase levels that were significantly higher than those measured at the time of release. Buoyancy decreased among the same fish (significantly for one group). Migration rates to Lower Granite Dam were slow, but increased as smolts migrated further downstream. Experimental manipulation of water temperatures in the laboratory, using Little White Salmon National Fish Hatchery stock, produced smolts with behavioral and physiological responses similar in magnitude to those measured in actively migrating smolts from the Idaho hatcheries. The commonly held premise that, as a result of smoltification, migrating fish exhibit decreased swimming stamina and increased buoyancy during migration, is not supported by this study. Furthermore, the results indicate that the general hatchery population of yearling chinook salmon received insufficient environmental cues necessary for full smolt development, prior to release.

Physiological changes related to migration tendency in rainbow trout ( Oncorhynchus mykiss)

Rainbow trout allowed to undergo volitional release at Roaring River Hatchery, Oregon, were separated into migrant and non-migrant populations. In two of the three years of the study, the extent of migration from the raceway was similar to the extent of migration from the area of stocking in a nearby reservoir. Each population in the hatchery was examined for 11 different physiological measurements. Differences between migrant and non-migrant trout were found in condition factor, gill Na +K +-ATPase activity, plasma thyroxine concentrations and muscle and liver glycogen. These results suggest that physiological changes were occurring during the migration of the trout from the raceways. No genetic basis for migration tendency or the physiological changes could be demonstrated.

Geographical patterns of straying of fall chinook salmon, Oncorhynchus tshawytscha (Walbaum), from Columbia River (USA) hatcheries

The large-scale spatial patterns of straying of marked chinook salmon, Oncorhynchus tshawytscha (Walbaum), produced at hatcheries in the Columbia River (north-west USA) are described. Straying rates were extremely variable among hatcheries (from 1% to 95%). Fish produced near the mouth of the river strayed more commonly than those produced farther upriver. While the large-scale straying patterns were well explained by the distance between the hatchery of origin and alternative destinations, substantial deviations from this pattern were observed at smaller scales. Three distinct areas of origin were identified and most straying occurred between hatcheries and natural spawning grounds within each area. The location of the stream where the hatchery of origin is located affects the patterns of straying. Fish reared at hatcheries in the main stem of the river did not stray into tributaries as often as predicted by a model based exclusively on linear distance between alternative locations. Likewise, fish released from large tributaries strayed to main stem hatcheries less often than predicted by the model. Fish produced at hatcheries on north bank tributaries appeared to stray less into southern streams than fish released from southern streams. These findings indicate that salmon are more likely to stray to spawning areas similar to their natal site than to dissimilar sites, in addition to the tendency to stray to nearly sites. In addition to the general patterns, examination of data from two types of transplants indicated that there is a genetic component to homing/straying behaviour within the watershed. However, salmon transplanted into the Columbia River watershed from elsewhere showed homing precision comparable to that of local fish, although they retained their ancestral marine distribution.

Genetic Variation in Naturalized Rainbow Trout ( Oncorhynchus mykiss) from Minnesota Tributaries to Lake Superior

Genetic variation at 27 polymorphic loci that code allozymes was compared among collections of naturalized, anadromous-form rainbow trout ( Oncorhynchus mykiss) from Lake Superior tributaries in Minnesota and among four hatchery strains. Genetic differences were observed among collections from naturalized populations from tributary streams and among hatchery strains (P < 0.01). In naturalized populations, most genetic variation observed occurred among individuals within samples (95.5%) and was comparable to values reported for other naturalized Lake Superior populations of rainbow trout. Cluster analysis of genetic distance coefficients revealed two main groups. One group included a subgroup of samples from heavily stocked streams (Devil Track, Flute Reed, and Baptism rivers) and the Michigan hatchery strain which had been used to stock these streams. The second group included collections from the Knife River drainage and Knife River hatchery fish. Collections from Indian Camp Creek and of the “kam-loops” hatchery strain were the most differentiated of the samples and showed little genetic affinity to each other or the two main groups. The “kamloops” strain did not exhibit allelic frequencies expected for rainbow trout derived from the Kamloops region of the upper Fraser River of British Columbia. No evidence was found to support the contention that the “kamloops” hatchery strain had interbred with wild populations. Widespread stocking of Michigan strain fish may have reduced genetic differences among naturalized, wild populations along Minnesota's Lake Superior shoreline. Population-specific management of rainbow trout by tributary is a justifiable approach to consider. If maintenance of the genetic differences among the wild, naturalized populations is desired, “kamloops” and the Michigan hatchery strains should not be stocked. Stocking programs instead should use gametes from returning adults of a river for subsequent juvenile propagation and stocking back into the same river.

Overview of the interactions and environmental impacts of hatchery practices on natural and artificial stocks of salmonids

Artificial propagation of Pacific salmon has been carried out for over a century. Salmonid stocks used in hatcheries were made homogeneous to be more easily manipulated. The stocks that form the basis for most coastal net and troll fisheries are currently of hatchery origin, and a 3–5% escapement of hatchery stock is considered adequate for reproduction. During the period 1960–1980, although numbers and average sizes of coho released from Columbia River hatcheries increased, returning adults declined between 1970 and 1980. Massive efforts were made to improve the efficiency of production in salmon hatcheries. Adult biomass potential decreased where there was a proportional increase in precociousness, resulting in a decrease in older mature individuals. Fisheries based upon enhancement have consistently fostered the over-fishing of naturally reproduced stock. For reasons never satisfactorily explained, salmonids have been released for decades in upstream areas without a basic understanding of instream ecological requirements of the salmonids, a knowledge of what resources these released salmonids are being superimposed upon, or a concern for the ecological devastation caused by these practices. A policy based on artificial propagation served as an accomplice in reducing wild salmonid stock genetic diversity among wild salmonid stocks and average size and age of returning adults. Fishery policy-makers were provided a convenient excuse for the worst possible resource use practices, and used hatcheries to affect wild salmonid stocks profoundly.

Individual downstream swimming speed during the natural smolting period among young of Baltic salmon (Salmo salar)

The individual downstream swimming behaviour of two-summer-old salmon from the Ume River hatchery stock was monitored throughout the natural smolting period in May–June. The experiment was performed in an artificial-stream tank (diameter 11 m) equipped with a passive integrated transponder (PIT) tag monitoring system. The swimming speed of individual fish in relation to water velocity and the porportion of time during which an individual fish showed active versus passive displacement were investigated using a total of 224 sexually immature fish and previously mature males, individually PIT tagged. At peak migration fish swam downstream at an average speed of about double the water velocity, indicating active downstream migration. No differences in downstream swimming speed between migratory and nonmigratory fish were observed. However, migratory and nonmigratory fish used considerably different proportions of the total time swimming faster than the water current, 10% for migratory fish but only 0.1% for nonmigratory fish. Migratory smolts covered about 25% of their total downstream displacement by means of active downstream swimming: 3.3 km out of 13.5 km in 24 h. Thus, the study clearly shows that active downstream swimming is an important part of the migratory repertoire of salmon smolts.

Unusual eosinophilic granule cell proliferation in coho salmon ( Oncorhynchus kisutch)

Whitish, opaque, coalescing masses were observed coating the visceral organs of numerous adult coho salmon when they were dissected for artificial spawning in the autumn of 1983 at the Puntledge River hatchery, British Columbia. One affected fish was observed in November 1991. Histological examination of 10 of these fish (nine in 1983 and one in 1991) revealed that the lesions consisted of unusual proliferations of eosinophilic granule cells (EGCs) with some characteristics of neoplasia. The proliferative lesions extended throughout the gastrointestinal tract and infiltrated through all layers of the gut. Pancreatic tissue and adipose tissues associated with the pyloric caeca were also infiltrated and replaced by the proliferating EGCs. A mild diffuse infiltration was also observed in the spleen, liver and kidney. Histochemical analysis and ultrastructural examination showed the proliferating cells to be essentially identical with the EGCs which are usually concentrated in the stratum granulosum of the intestine in normal salmonid fishes.

Returns of Hatchery Steelhead Relative to Site of Release below an Upper-River Hatchery

Steelhead smolts Oncorhynchus mykiss reared at the Chilliwack River Hatchery in southwestern British Columbia were tagged, transported, and released at four (1982) or six (1983, 1984) locations along the Chilliwack River. Returning adults were recovered from the sport fishery within three 10-km reaches (lower, middle, and upper) situated downstream of the upper-river hatchery. Percent recoveries were highly correlated with mean smolt size at stocking (range, 61–115 g), and most returning adults were caught within the lower river. There were small but significant effects of release location on the distribution of adult steelhead recoveries in two of three reaches. Within the lower-river catch of adults, the percentage of all lower-release recoveries was 10.3 percentage points higher than the percentage of all middle-release recoveries and 10.7 points higher than the percentage of all upper-release recoveries. In the upper-river catch, the percentage of all upper-release recoveries was 5.5 and 11.4 points higher than the percentage of all middle- and lower-release recoveries, respectively. Middle-river recoveries were not disproportionately higher for any release-reach group. Similarly, among adults that returned to the hatchery channels in the upper river, on average, 43% were from the upper, 30% from the middle, and 27% from the lower reaches of release; thus, homing was strongly influenced by the rearing location. In a steelhead fishery associated with an upper-river hatchery and dependent on wild and hatchery-reared fish, transport and release of smolts affected homing of adults, but there was substantial dispersal of lower-river fish to the upper river. These findings have implications for selective management of augmented steelhead stocks.

Evidence for Inheritance of Age of Maturity in Chinook Salmon (Oncorhynchus tshawytscha)

We report results of age-specific mating experiments carried out with chinook salmon (Oncorhynchus tshawytscha) at Elk River Hatchery, Oregon. Our analysis of returns from these experiments includes assessment of the marine growth of progeny, and we also account for the negative bias on mean age of returning mature progeny that is a consequence of troll fishery harvest of immature salmon. Results suggest that (a) heritability of age of maturity is relatively high in this species (calculated h2 were 0.49–0.57 and 0.39–0.41 for males and females, respectively), (b) inheritance of age of maturity of females appears to be independent of age of male parent, and (c) for a given parental age, "faster-growing" progeny generally mature at younger ages, but (d) progeny from older parents are not generally smaller at age than progeny from younger parents. Inheritance of age of maturity therefore cannot be a simple reflection of inheritance of growth rate. We tentatively propose the existence of heritable minimum threshold lengths that differentially trigger maturation according to age and sex of parents. We also consider the significance of these experiments for artificial propagation of this species.

Comparsion of selected strains of infectious hematopoietic necrosis virus (IHNV) using neutralizing trout antisera

Comparsion of selected strains of infectious hematopoietic necrosis virus (IHNV) using neutralizing trout antisera