Bayesian information updating procedures for Pacific salmon run size indicators: evaluation in the presence and absence of auxiliary migration timing information

2019 ◽  
Vol 76 (10) ◽  
pp. 1719-1727
Author(s):  
Benjamin A. Staton ◽  
Matthew J. Catalano

Preseason forecasts of Pacific salmon run size are notoriously uncertain and are thus often updated using various abundance indices collected during the run. However, interpretation of these in-season indices is confounded by uncertainty in migration timing. We assessed the performance of two Bayesian information-updating procedures for Kuskokwim River Chinook salmon (Oncorhynchus tshawytscha), one that uses auxiliary run timing information and one that does not, and compared the performance with methods that did not involve updating. We found that in-season Bayesian updating provided more accurate run size estimates during the time when harvest decisions needed to be made, but that the incorporation of run timing forecasts had little utility in terms of providing more accurate run size estimates. The latter finding is conditional on the performance of the run timing forecast model we used; a more accurate timing forecast model might yield a different conclusion. The Bayesian approach we developed provided a probabilistic expression of run size beliefs, which could be useful in a transparent risk-assessment framework for setting and altering harvest targets during the season.

2013 ◽  
Vol 4 (1) ◽  
pp. 114-123 ◽  
Author(s):  
Douglas E. Olson ◽  
Michael Paiya

Abstract We evaluated growth and survival of spring Chinook salmon Oncorhynchus tshawytscha reared at varying densities at Warm Springs National Fish Hatchery, Oregon. For three consecutive brood years, density treatments consisted of low, medium, and high groups in 57.8-m3 raceways with approximately 16,000, 24,000, and 32,000 fish/raceway, respectively. Fish were volitionally released in both the autumn and spring to mimic the downstream migration timing of the endemic wild spring Chinook salmon stock. Just prior to the autumn release, the rearing density estimate was 4.24 kg/m3 for the low-density group, 6.27 kg/m3 for the medium-density group, and 8.42 kg/m3 for the high-density group. While weight gain did not differ among density treatments (P  =  0.72), significant differences were found in median fork length (P < 0.001) for fish reared at different densities. Fish reared at high density exhibited the highest on-hatchery mortality rate during two brood years; however, differences in mortality rate among densities were not significant (P  =  0.20). In one brood year, adult recovery rates appeared to support the hypothesis that lower initial densities improved postrelease survival (P < 0.01). All rearing densities utilized in this evaluation were relatively low and may partially explain why more differences were not readily apparent among density groups. In addition, the volitional release was a confounding factor in our study because we were unable to quantify the number of fish released in the autumn.


1981 ◽  
Vol 38 (12) ◽  
pp. 1636-1656 ◽  
Author(s):  
W. E. Ricker

Of the five species of Pacific salmon in British Columbia, chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) are harvested during their growing seasons, while pink salmon (O. gorbuscha), chum salmon (O. keta), and sockeye salmon (O. nerka) are taken only after practically all of their growth is completed. The size of the fish caught, of all species, has decreased, but to different degrees and over different time periods, and for the most part this results from a size decrease in the population. These decreases do not exhibit significant correlations with available ocean temperature or salinity series, except that for sockeye lower temperature is associated with larger size. Chinook salmon have decreased greatly in both size and age since the 1920s, most importantly because nonmaturing individuals are taken by the troll fishery; hence individuals that mature at older ages are harvested more intensively, which decreases the percentage of older ones available both directly and cumulatively because the spawners include an excess of younger fish. Other species have decreased in size principally since 1950, when the change to payment by the pound rather than by the piece made it profitable for the gill-netters to harvest more of the larger fish. Cohos and pinks exhibit the greatest decreases, these being almost entirely a cumulative genetic effect caused by commercial trolls and gill nets removing fish of larger than average size. However, cohos reared in the Strait of Georgia have not decreased in size, possibly because sport trolling has different selection characteristics or because of the increase in the hatchery-reared component of the catch. The mean size of chum and sockeye salmon caught has changed much less than that of the other species. Chums have the additional peculiarity that gill nets tend to take smaller individuals than seines do and that their mean age has increased, at least between 1957 and 1972. That overall mean size has nevertheless decreased somewhat may be related to the fact that younger-maturing individuals grow much faster than older-maturing ones; hence excess removal of the smaller younger fish tends to depress growth rate. Among sockeye the decrease in size has apparently been retarded by an increase in growth rate related to the gradual cooling of the ocean since 1940. However, selection has had two important effects: an increase in the percentage of age-3 "jacks" in some stocks, these being little harvested, and an increase in the difference in size between sockeye having three and four ocean growing seasons, respectively.Key words: Pacific salmon, age changes, size changes, fishery, environment, selection, heritability


1995 ◽  
Vol 52 (7) ◽  
pp. 1376-1384 ◽  
Author(s):  
Robert H. Devlin ◽  
Timothy Y. Yesaki ◽  
Edward M. Donaldson ◽  
Shao Jun Du ◽  
Choy-Leong Hew

Transgenic Pacific salmon have been produced by microinjection of a DNA construct consisting of chinook salmon (Oncorhynchus tshawytscha) growth hormone sequences driven by an ocean pout (Macrozoarces americanus) antifreeze protein promoter. This construct was retained in approximately 4% of fish derived from injected eggs, and resulted in dramatic enhancement of growth relative to controls. For coho salmon (O. kisutch) at 15 months of age, the average size of transgenic fish was more than 10-fold that of controls, with the largest fish more than 30-fold larger than nontransgenic siblings. Dramatic growth enhancement was also observed in transgenic rainbow trout (O. mykiss), cutthroat trout (O. clarki), and chinook salmon using this same gene construct. Transgenic coho salmon underwent precocious parr–smolt transformation during their first fall, approximately 6 months in advance of their nontransgenic siblings. At 2 years of age, five male transgenic coho salmon became sexually mature, and four of these transmitted the gene construct to sperm, the negative fish being transgenic in blood but not fin tissue. These results show that while some fish are mosaic for the gene construct in different tissues, most are transgenic in both germline and somatic tissue.


1987 ◽  
Vol 44 (6) ◽  
pp. 1213-1220 ◽  
Author(s):  
Robert G. Kope

A separable virtual population analysis model is developed for Pacific salmon which utilizes aged catch and spawning escapement data. This model is applied to marked chinook salmon, Oncorhynchus tshawytscha, from California's Central Valley hatcheries using weighted least squares criteria for goodness of fit. Structural inadequacies of the model apparently produce discrepancies between predicted values and observed data that are of about the same magnitude as the observational errors in estimating the recoveries of marked fish. Some of the inadequacy of the model may be due to environmentally induced variability in population parameters, but for the marked fish used in this analysis, some of the variability is probably due to year-to-year variability in hatchery practices. From this analysis it appears that although nominal fishing effort has been relatively stable or even declining in recent years, fishing mortality has been increasing with the exception of 1983 and 1984.


2010 ◽  
Vol 67 (1) ◽  
pp. 202-205 ◽  
Author(s):  
Terry D. Beacham ◽  
Ruth E. Withler

Temporally stable genetic structure among salmonid populations has been reported in many studies, although the time span evaluated in most studies is limited to 10 years or less. This result has important implications in conservation and management of Pacific salmon ( Oncorhynchus spp.) and ramifications for the construction and application of genetic databases for stock identification of fish sampled from mixed-stock fisheries. Walter et al. (2009. Can. J. Fish. Aquat. Sci. 66: 167–176) failed to consider recent studies providing evidence that their conclusion “the overall magnitude of temporal within-population variation exceeding that of among-population variation” for the populations under study may be invalid for Fraser River Chinook salmon ( Oncorhynchus tshawytscha ) populations. Their estimation of rates and patterns of migration among Chinook salmon populations also provided results that are difficult to reconcile with published information. Evaluation of the experimental designed employed by Walter et al. (2009) indicates that their sample sizes were too small to estimate reliably genetic variation among or within populations. Extrapolation of their conclusions relating temporal instability of population structure to other Chinook salmon populations or indeed other salmonid species is unwarranted.


Author(s):  
Lia Chalifour ◽  
David C Scott ◽  
Misty MacDuffee ◽  
Steven Stark ◽  
John F Dower ◽  
...  

Estuaries represent a transition zone for salmon migrating from freshwater to marine waters, yet their contribution to juvenile growth is poorly quantified. Here, we use genetic stock identification and otolith analyses to quantify estuarine habitat use by Chinook salmon (<i>Oncorhynchus tshawytscha</i>) – the Pacific salmon species considered most reliant on this habitat – in Canada’s most productive salmon river, the Fraser. Two years of sampling revealed subyearling migrant (“ocean-type”) Chinook from the Harrison River to be the estuary’s dominant salmon population throughout the emigration period. These Chinook salmon were caught predominantly in the estuary’s brackish marshes but shifted to more saline habitats as they grew. Otolith analyses indicated that these Chinook salmon have wide-ranging entry timing (from February to May), and longer estuarine residency (weeks to months, mean 41.8 days) than estimated by prior studies, but similar daily growth rates (mean 0.57 mm +/- 0.13 SD) across entry dates and residency periods, implying sufficient foraging opportunities throughout the emigration period and habitats. Together, these results suggest that estuarine habitat is more important for early marine growth of subyearling migrant Chinook salmon than previously recognized.


FACETS ◽  
2018 ◽  
Vol 3 (1) ◽  
pp. 695-721 ◽  
Author(s):  
Krishna K. Thakur ◽  
Raphaël Vanderstichel ◽  
Shaorong Li ◽  
Emilie Laurin ◽  
Strahan Tucker ◽  
...  

Infectious diseases are likely contributing to large-scale declines in chinook salmon stocks in the Pacific Northwest, but the specific agents and diseases involved, and the prevalences in migratory salmon, are mostly unknown. We applied a high-throughput microfluidics platform to screen for 45 infectious agents in 556 out-migrating juvenile chinook salmon, collected from freshwater (FW) and saltwater (SW) locations in the Cowichan River system on Vancouver Island, Canada, during 2014. Nineteen agents (5 bacterial, 2 viral, and 12 parasitic) were detected, with prevalences ranging from 0.2% to 57.6%. Co-infections between Candidatus Branchiomonas cysticola Toenshoff, Kvellestad, Mitchell, Steinum, Falk, Colquhoun & Horn, 2012, Paranucleospora theridion Nylund, Nylund, Watanabe, Arnesen & Kalrsbakk, 2010, and gill chlamydia, all associated with gill disease, were observed in SW samples. We detected agents known to cause large-scale mortalities in Pacific salmon ( Ceratonova shasta (Noble, 1950), Parvicapsula minibicornis Kent, Whitaker & Dawe, 1977), and agents only recently reported in Pacific salmon in BC ( Ca. B. cysticola, P. theridion, Facilispora margolisi Jones, Prosperi-Porta & Kim, 2012 and Parvicapsula pseudobranchicola Karlsbakk, Saether, Hostlund, Fjellsoy & Nylund, 2002). Wild and hatchery fish were most divergent in agent profiles in FW, with higher agent diversity in wild fish. Differences in prevalence largely dissipated once they converged in the marine environment, although hatchery fish may be infected by a greater diversity of agents sooner after ocean entry by virtue of their more rapid migration from nearshore to offshore environments.


1984 ◽  
Vol 41 (8) ◽  
pp. 1150-1159 ◽  
Author(s):  
Gary A. Winans

A computer oriented approach to the collection and analysis of morphometric characteristics in juvenile chinook salmon (Oncorhynchus tshawytscha) is described. A three-step data collection and storage method is used whereby X–Y coordinate data for relevant morphological features on a body form are collected with a digitizing pad and used to calculate morphometric characters. To test this method, I calculated two morphometric data sets, a conventional and a truss network, and compared them by multivariate analysis in a preliminary study of growth and development in one hatchery stock of fish, and in a survey of population differences in three naturally occurring populations of chinook salmon. Technical advantages of using a digitizing pad for collecting morphometric data are demonstrated. Hatchery-reared chinook salmon showed marked changes in body shape during the period of spring smoltification when marked changes in condition factor occurred. Multivariate differences were discerned among the three Oregon coastal stocks. Truss data provided more specific information concerning shape changes in the study of early development and produced greater between-group differences in the geographic survey. The results of these preliminary analyses can be applied to problems of identifying smolt status in hatchery fish and stock origin in mixed-stock fisheries.


2018 ◽  
Vol 75 (7) ◽  
pp. 1082-1095 ◽  
Author(s):  
Brigitte Dorner ◽  
Matthew J. Catalano ◽  
Randall M. Peterman

We expand on previous analyses of environmental factors related to productivity of Chinook salmon (Oncorhynchus tshawytscha) populations by analysing data on adult recruits per spawner from 24 wild (not hatchery) Chinook salmon stocks from Oregon through western Alaska. To determine the degree to which changes in productivity are shared and to help identify environmental variables that might be related to those changes, we estimated the magnitude and spatial characteristics of positive correlations in productivity trends among stocks separated by various distances. We used dynamic factor analysis to characterize shared time trends in productivity and found that these trends were most closely associated with the North Pacific Gyre Oscillation and, to a lesser extent, with the location of the bifurcation in the North Pacific Current as it reaches North America’s west coast. Chinook productivity patterns of separate populations have also become more synchronous in recent years, similar to results reported for other species of Pacific salmon. Such recent changes may reduce the resilience of the species to effects of climate change and habitat modification.


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