Curtis M. Knudsen

Effects of Passive Integrated Transponder Tags on Smolt-to-Adult Recruit Survival, Growth, and Behavior of Hatchery Spring Chinook Salmon

Abstract We tagged juvenile upper Yakima River hatchery spring Chinook salmon Oncorhynchus tshawytscha with passive integrated transponder (PIT) and coded wire snout tags in a double-tag study to test the assumptions that tags are not lost and do not affect postrelease survival, behavior, or growth. The average loss of PIT tags was 2.0% (95% confidence interval [CI] = 0.7–3.2%) in juveniles before release and 18.4% in recaptures returning 6 months to 4 years after release (95% CI = 17.2–19.5%). Adult tag losses were not significantly correlated with age of return (analysis of covariance, P = 0.40), indicating that the majority of PIT tag loss had occurred within the first 6 months after release. Smolt-to-adult recruit survival (SARS) of PIT-tagged fish was significantly lower (P < 0.05) than that of non-PIT-tagged (NPT) fish because of tag loss and reduced survival, resulting in an average underestimate of SARS of 25.0%. After correcting for tag loss, we estimated PIT tag-induced mortality to be as great ...

Stock Origins of Chinook Salmon in the Area of the Japanese Mothership Salmon Fishery

Abstract The record catch of 704,000 chinook salmon Oncorhynchus tshawytscha by the Japanese mothership salmon fishery in 1980 intensified concern about the effect of high seas interceptions of salmon reared in North America. The goal of this study was to update and refine estimates of the relative proportions of Asian and North American chinook salmon stocks in the mothership fishery area in the Bering Sea and north Pacific Ocean. Linear discriminant analysis of scale pattern data was used to classify samples of immature chinook salmon aged 1.2 (one winter in fresh water, two winters at sea) from the area 46-62°N, 160°E-175°W in June and July 1975-1981 to four regions: Asia, western Alaska, central Alaska, and southeastern Alaska-British Columbia. Western Alaska, which included Canadian Yukon stocks, was further subdivided into three subregions: Yukon River, Kuskokwim district, and Bristol Bay. Overall classification accuracies averaged 74, 79, and 86%, respectively, in four-, three-, and two-category re...

Behavior and Breeding Success of Wild and First-Generation Hatchery Male Spring Chinook Salmon Spawning in an Artificial Stream

Abstract Spring Chinook salmon Oncorhynchus tshawytscha native to the upper Yakima River, Washington, were placed into an artificial stream to evaluate the effect of a single generation of hatchery culture on their spawning behavior and ability to produce offspring. From 2001 to 2005, seven independent test groups containing wild and hatchery fish were placed into the stream. The effects of body weight, spawning ground longevity, attack frequency, social dominance, courting frequency, and mate number on breeding success in hatchery and wild males were evaluated. Male breeding success increased with body weight, while spawning ground longevity was negatively associated with breeding success. Although important, body weight had a lesser effect on male breeding success than did social dominance or attack frequency. Males with high attack and courting frequencies produced the most progeny; of the traits examined, the number of female spawning partners explained the greatest amount of variation (average r 2 = ...

A Synthesis of Findings from an Integrated Hatchery Program after Three Generations of Spawning in the Natural Environment

AbstractThe Cle Elum Supplementation and Research Facility in the Yakima River basin, Washington, is an integrated spring Chinook Salmon Oncorhynchus tshawytscha hatchery program designed to test whether artificial propagation can increase natural production and harvest opportunities while keeping ecological and genetic impacts within acceptable limits. Only natural-origin (naturally spawned) fish are used for hatchery broodstock. Spawning, incubation, and early rearing occur at a central facility; presmolts are transferred for final rearing, acclimation, and volitional release at sites adjacent to natural spawning areas, where returning adults can spawn with natural-origin fish. The first wild broodstock were collected in 1997, and age-4 adults have returned to the Yakima River since 2001. An unsupplemented population in the adjacent Naches River watershed provides a reference for evaluating environmental influences. The program has been comprehensively monitored from its inception. A synthesis of findin...

Breeding success of four male life history types of spring Chinook Salmon spawning in an artificial stream

In 1997 the Cle Elum Supplementation Research Facility was established to enhance spring Chinook salmon returning to the upper Yakima River, Washington State. This effort increased spring Chinook abundance, yet conditions at the hatchery also significantly elevated the occurrence of jacks and yearling precocious males. The potential genetic effect that a large influx of early maturing males might have on the upper Yakima River spring Chinook population was examined in an artificial stream. Seven independent groups of fish were placed into the stream from 2001 through 2005. Males with four different life history strategies, large anadromous, jacks, yearling precocious, and sub-yearling precocious were used. Their breeding success or ability to produce offspring was estimated by performing DNA-based pedigree assessments. Large anadromous males spawned with the most females and produced the greatest number of offspring per mate. Jacks and yearling precocious males spawned with more females than sub-yearling precocious males. However, jacks, yearling and sub-yearling precocious males obtained similar numbers of fry per mate. In the test groups, large anadromous males produced 89%, jacks 3%, yearling precocious 7%, and sub-yearling precocious 1% of the fry. These percentages remained stable even though the proportion of large anadromous males in the test groups ranged from 48% to 88% and tertiary sex ratios varied from 1.4 to 2.4 males per female. Our data suggest that large anadromous males generate most of the fry in natural settings when half or more of the males present on a spawning ground use this life history strategy.

Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding

Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive‐reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome‐wide approaches. Genetic divergence from the source population was minimal in an integrated line, which implemented managed gene flow by using only naturally‐born adults as captive broodstock, but significant in a segregated line, which bred only captive‐origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the latter was largely attributable to genetic drift. Three independent tests for signatures of adaptive divergence also identified temporal change within the segregated line, possibly indicating domestication selection. The results empirically demonstrate that using managed gene flow for propagating a captive‐reared population reduces genetic divergence over the short term compared to one that relies solely on captive‐origin parents. These findings complement existing studies of captive breeding, which typically focus on a single management strategy and examine the fitness of one or two generations.

Genomewide association analyses of fitness traits in captive-reared Chinook salmon: Applications in evaluating conservation strategies

A novel application of genomewide association analyses is to use trait‐associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive‐ and wild‐origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus tshawytscha) and then determined how two alternative management approaches for captive rearing affected variation at these loci. Loci associated with date of return to freshwater spawning grounds (return timing), length and weight at return, age at maturity, spawn timing, and daily growth coefficient were identified using 9108 restriction site‐associated markers and random forest, an approach suitable for polygenic traits. Mapping of trait‐associated loci, gene annotations, and integration of results across multiple studies revealed candidate regions involved in several fitness‐related traits. Genotypes at trait‐associated loci were then compared between two hatchery populations that were derived from the same source but are now managed as separate lines, one integrated with and one segregated from the wild population. While no broad‐scale change was detected across four generations, there were numerous regions where trait‐associated loci overlapped with signatures of adaptive divergence previously identified in the two lines. Many regions, primarily with loci linked to return and spawn timing, were either unique to or more divergent in the segregated line, suggesting that these traits may be responding to domestication selection. This study is one of the first to utilize genomic approaches to demonstrate the effectiveness of a conservation strategy, managed gene flow, on trait‐associated—and potentially adaptive—loci. The results will promote the development of trait‐specific tools to better monitor genetic change in captive and wild populations.

What can genomics tell us about the success of enhancement programs in anadromous Chinook salmon? A comparative analysis across four generations

Population enhancement through the release of cultured organisms can be an important tool for marine restoration. However, there has been considerable debate about whether releases effectively contribute to conservation and harvest objectives, and whether cultured organisms impact the fitness of wild populations. Pacific salmonid hatcheries on the West Coast of North America represent one of the largest enhancement programs in the world. Molecular-based pedigree studies on one or two generations have contributed to our understanding of the fitness of hatchery-reared individuals relative to wild individuals, and tend to show that hatchery fish have lower reproductive success. However, interpreting the significance of these results can be challenging because the long-term genetic and ecological effects of releases on supplemented populations are unknown. Further, pedigree studies have been opportunistic, rather than hypothesis driven, and have not provided information on “best case” management scenarios. Here, we present a comparative, experimental approach based on genome-wide surveys of changes in diversity in two hatchery lines founded from the same population. We demonstrate that gene flow with wild individuals can reduce divergence from the wild source population over four generations. We also report evidence for consistent genetic changes in a closed hatchery population that can be explained by both genetic drift and domestication selection. The results of this study suggest that genetic risks can be minimized over at least four generations with appropriate actions, and provide empirical support for a decision-making framework that is relevant to the management of hatchery populations.