scholarly journals Modelling salmon migration as a mixture problem

2019 ◽  
Vol 76 (6) ◽  
pp. 856-870 ◽  
Author(s):  
Skip McKinnell
Keyword(s):  
Chinook Salmon ◽  
Sockeye Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Simulated Data ◽  
Columbia River ◽  
Single Pulse ◽  
Model Complexity ◽  
Fraser River ◽  
The Individual ◽  
Large Adult

Pulses of abundance in salmon migrations can arise from single populations arriving at different times, from multiple populations with different timing characteristics, or as a combination of these. Daily observations typically record an aggregate measure of abundance passing some location rather than the abundances of the individual components. An objective method is described that partitions a compound migration into its component parts by exploiting differences in the characteristics of each pulse. Simulated data were used to demonstrate when greater model complexity may be desirable. Three case studies of increasing complexity (Chilko Lake sockeye salmon smolts (Oncorhynchus nerka), large adult Columbia River Chinook salmon (Oncorhynchus tshawytscha), Fraser River salmon test fishery) demonstrate how the model can be applied in practice. Results indicated that Chilko Lake smolts rarely emigrate to sea as a single pulse, that the dates used to distinguish the spring run of Chinook salmon in the Columbia River may be overestimating its abundance, and that pulses of sockeye salmon abundance in a Fraser River ocean test fishery in 2014 may have arisen from some factor other than population composition.

Ceratomyxa shasta (Myxozoa: Myxosporea) in juvenile chinook salmon (Oncorhynchus tshawytscha): experimental transmission and natural infections in the Fraser River, British Columbia

1985 ◽  
Vol 63 (7) ◽  
pp. 1737-1740 ◽  
Author(s):  
Susan M. Bower
Keyword(s):  
Chinook Salmon ◽  
Sockeye Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Developmental Stages ◽  
River Estuary ◽  
Fraser River ◽  
Experimental Transmission ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook ◽  
Intraperitoneal Inoculation

Ceratomyxa shasta (mainly trophozoites) from the intestinal tract of a naturally infected juvenile chinook salmon (Oncorhynchus tshawytscha) developed in the coelom of laboratory-reared chinook salmon when inoculated intraperitoneally. All developmental stages were observed. Successful subpassages were accomplished by intraperitoneal inoculation of trophozoites and sporoblasts, but an infection did not develop when these stages were pipetted into the esophagus of susceptible fish. Heavy infections, including the presence of C. shasta sporoblasts or spores, were observed in 2 of 28 feral juvenile chinook salmon seined from the Fraser River estuary in late July and early August. Trophozoite-like cells were observed in six other chinook salmon from this group. No C. shasta were observed in 15 juvenile sockeye salmon (Oncorhynchus nerka) caught in the estuary along with the chinook salmon.

Route selection in a large river during the homing migration of Chinook salmon (Oncorhynchus tshawytscha)

2006 ◽  
Vol 63 (8) ◽  
pp. 1752-1762 ◽  
Author(s):  
Matthew L Keefer ◽  
Christopher C Caudill ◽  
Christopher A Peery ◽  
Theodore C Bjornn
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Columbia River ◽  
Large River ◽  
Migration Route ◽  
Route Selection ◽  
Behavioral Differences ◽  
Long Distance ◽  
Selection Decisions ◽  
Efficient Route

Upstream-migrating adult salmon must make a series of correct navigation and route-selection decisions to successfully locate natal streams. In this field study, we examined factors influencing migration route selections early in the migration of 4361 radio-tagged adult Chinook salmon (Oncorhynchus tshawytscha) as they moved upstream past dams in the large (~1 km wide) Columbia River. Substantial behavioral differences were observed among 11 conspecific populations, despite largely concurrent migrations. At dams, Chinook salmon generally preferred ladder passage routes adjacent to the shoreline where their natal tributaries entered, and the degree of preference increased as salmon proximity to natal tributaries increased. Columbia River discharge also influenced route choices, explaining some route selection variability. We suggest that salmon detect lateral gradients in orientation cues across the Columbia River channel that are entrained within tributary plumes and that these gradients in cues can persist downstream for tens to hundreds of kilometres. Detection of tributary plumes in large river systems, using olfactory or other navigation cues, may facilitate efficient route selection and optimize energy conservation by long-distance migrants.

Assessing covariability among populations in the presence of intraseries correlation: Columbia River spring-summer chinook salmon (Oncorhynchus tshawytscha) stocks

2000 ◽  
Vol 57 (3) ◽  
pp. 616-627 ◽  
Author(s):  
Louis W Botsford ◽  
Charles M Paulsen
Keyword(s):  
Chinook Salmon ◽  
Degrees Of Freedom ◽  
Oncorhynchus Tshawytscha ◽  
Columbia River ◽  
Data Types ◽  
Natural Logarithm ◽  
Different Types ◽  
John Day River ◽  
One Year ◽  
John Day

We assessed covariability among a number of spawning populations of spring-summer run chinook salmon (Oncorhynchus tshawytscha) in the Columbia River basin by computing correlations among several different types of spawner and recruit data. We accounted for intraseries correlation explicitly in judging the significance of correlations. To reduce the errors involved in computing effective degrees of freedom, we computed a generic effective degrees of freedom for each data type. In spite of the fact that several of these stocks have declined, covariability among locations using several different combinations of spawner and recruitment data indicated no basinwide covariability. There was, however, significant covariability among index populations within the three main subbasins: the Snake River, the mid-Columbia River, and the John Day River. This covariability was much stronger and more consistent in data types reflecting survival (e.g., the natural logarithm of recruits per spawner) than in data reflecting abundance (e.g., spawning escapement). We also tested a measure of survival that did not require knowing the age structure of spawners, the ratio of spawners in one year to spawners 4 years earlier. It displayed a similar spatial pattern.

Changes in adult Chinook salmon (Oncorhynchus tshawytscha) survival within the lower Columbia River amid increasing pinniped abundance

2019 ◽  
Vol 76 (10) ◽  
pp. 1862-1873 ◽  
Author(s):  
A. Michelle Wargo Rub ◽  
Nicholas A. Som ◽  
Mark J. Henderson ◽  
Benjamin P. Sandford ◽  
Donald M. Van Doornik ◽  
...  
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Columbia River ◽  
Mixed Effects ◽  
Eumetopias Jubatus ◽  
Considerable Effort ◽  
Alosa Sapidissima ◽  
Sea Lions ◽  
Regression Modelling ◽  
Passive Integrated Transponder Tags

Considerable effort towards conservation has contributed to the recovery of historically depleted pinniped populations worldwide. However, in several locations where pinnipeds have increased, they have been blamed for preventing the recovery of commercially valuable fish species through predation. Prompted by increasing pinniped abundance within the Columbia River (CR), USA, over a 6-year period, we used passive integrated transponder tags to measure the survival of adult spring-run Chinook salmon (Oncorhynchus tshawytscha) through the estuary and lower CR to Bonneville Dam (river kilometre 234). We estimated 51 751 – 224 705 salmon died annually within this reach from sources other than harvest. Mixed-effects logistic regression modelling identified pinniped predation as the most likely source of this mortality. The odds of survival was estimated to decrease by 32% (95% CI: 6%–51%) for every additional 467 sea lions (Zalophus californianus and Eumetopias jubatus) present within the CR and to increase by 32% (95% CI: 8%–61%) for every increase of 1.5 in the log of American shad (Alosa sapidissima), a potential prey item for sea lions.

Roles of Olfaction and Vision in Choice of Spawning Site by Homing Adult Chinook Salmon (Oncorhynchus tshawytscha)

1968 ◽  
Vol 25 (5) ◽  
pp. 867-876 ◽  
Author(s):  
Alan B. Groves ◽  
Gerald B. Collins ◽  
Parker S. Trefethen
Keyword(s):  
Chinook Salmon ◽  
Untreated Control ◽  
Sexual Maturity ◽  
Oncorhynchus Tshawytscha ◽  
Columbia River ◽  
Control Fish ◽  
Male Fish ◽  
Fish Hatchery ◽  
Spawning Site

An experiment was conducted to examine the roles of olfaction and vision in directing the choice of spawning site by homing adult chinook salmon (Oncorhynchus tshawytscha) on the lower Columbia River. Male fish that voluntarily entered the Spring Creek National Fish Hatchery were treated to occlude their olfactory or visual senses or both. Treated and untreated (control) fish were released upstream and downstream in the river, more than 19 km from the hatchery. Effects were assessed by analyzing returns to the hatchery and to other points.Of 866 fish released, 348 or 40% were recovered; about half of them, or 176 returned to Spring Creek. Three per cent of the olfactory occluded, 23% of the visually occluded, and 46% of the control fish returned to Spring Creek. Of the fish recovered elsewhere, 77% were recovered at hatcheries and spawn-taking sites along the lower Columbia; 23% were recovered from sources unrelated to spawn taking.Olfaction appeared to be the key sense that directed the return of these fish to Spring Creek; vision was held to be less important. Olfactory occlusion also reduced the recoveries at other spawn-taking sites, where blinded fish were recovered in appreciable numbers. Recovery of the control fish, especially the smaller ones, at other spawn-taking sites was associated with advancing sexual maturity.

Changes in the Average Size and Average Age of Pacific Salmon

1981 ◽  
Vol 38 (12) ◽  
pp. 1636-1656 ◽  
Author(s):  
W. E. Ricker
Keyword(s):  
Growth Rate ◽  
Chinook Salmon ◽  
Sockeye Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Gill Nets ◽  
Growing Seasons ◽  
Mean Size ◽  
Average Size

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

Individual variation in dispersal behaviour of newly emerged chinook salmon (Oncorhynchus tshawytscha) from the Upper Fraser River, British Columbia

1997 ◽  
Vol 54 (7) ◽  
pp. 1585-1592 ◽  
Author(s):  
M J Bradford ◽  
G C Taylor
Keyword(s):  
British Columbia ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Population Variation ◽  
Fraser River ◽  
Movement Behaviour ◽  
Spawning Areas ◽  
Dispersal Distances ◽  
Stream Type ◽  
Downstream Movement

Immediately after emergence from spawning gravels, fry of stream-type chinook salmon (Oncorhynchus tshawytscha) populations from tributaries of the upper Fraser River, British Columbia, distribute themselves downstream from the spawning areas, throughout the natal stream, and into the Fraser River. We tested the hypothesis that this range in dispersal distances is caused by innate differences in nocturnal migratory tendency among individuals. Using an experimental stream channel, we found repeatable differences in downstream movement behaviour among newly emerged chinook fry. Fish that moved downstream were larger than those that held position in the channel. However, the incidence of downstream movement behaviours decreased over the first 2 weeks after emergence. We propose that the variation among individuals in downstream movement behaviour we observed leads to the dispersal of newly emerged fry throughout all available rearing habitats. Thus, between- and within-population variation in the freshwater life history observed in these populations may be caused by small differences in the behaviour of individuals.

A multiple-reach model describing the migratory behavior of Snake River yearling chinook salmon (Oncorhynchus tshawytscha)

1998 ◽  
Vol 55 (3) ◽  
pp. 658-667 ◽  
Author(s):  
Richard W Zabel ◽  
James J Anderson ◽  
Pamela A Shaw
Keyword(s):  
Chinook Salmon ◽  
Migration Rate ◽  
River Flow ◽  
Oncorhynchus Tshawytscha ◽  
Nonlinear Models ◽  
Columbia River ◽  
River System ◽  
Snake River ◽  
Migration Route ◽  
Time Step

A multiple-reach model was developed to describe the downstream migration of juvenile salmonids in the Columbia River system. Migration rate for cohorts of fish was allowed to vary by reach and time step. A nested sequence of linear and nonlinear models related the variation in migration rates to river flow, date in season, and experience in the river. By comparing predicted with observed travel times at multiple observation sites along the migration route, the relative performance of the migration rate models was assessed. The analysis was applied to cohorts of yearling chinook salmon (Oncorhynchus tshawytscha) captured at the Snake River Trap near Lewiston, Idaho, and fitted with passive integrated transponder (PIT) tags over the 8-year period 1989-1996. The fish were observed at Lower Granite and Little Goose dams on the Snake River and McNary Dam on the Columbia River covering a migration distance of 277 km. The data supported a model containing two behavioral components: a flow term related to season where fish spend more time in regions of higher river velocity later in the season and a flow-independent experience effect where the fish migrate faster the longer they have been in the river.

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