Reply to the comment by Beacham and Withler on “Gene flow increases temporal stability of Chinook salmon (Oncorhynchus tshawytscha) populations in the Upper Fraser River, British Columbia, Canada”Appears in Can. J. Fish. Aquat. Sci. 66: 167–176.

2010 ◽  
Vol 67 (1) ◽  
pp. 206-208 ◽  
Author(s):  
Ryan P. Walter ◽  
J. Mark Shrimpton ◽  
Daniel D. Heath
Keyword(s):  
Temporal Variation ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Sampling Error ◽  
Fraser River ◽  
Genetic Stock ◽  
River Population ◽  
Genetic Population ◽  
Rarefaction Analysis ◽  
Temporal Variance

Beacham and Withler (2010. Can. J. Fish. Aquat. Sci. 67: 202–205) raise concerns about the experimental design and interpretation of data in the analysis of temporal genetic variation of Chinook salmon ( Oncorhynchus tshawytscha ) from the Upper Fraser River, Canada (Walter et al. 2009. Can. J. Fish. Aquat. Sci. 66: 167–176). They note that for the sampled populations, spatial genetic variance should far exceed temporal variance components based on previously published work and suggest that limited sample sizes biased our results by confounding sampling error with temporal variation. Here, we perform a rarefaction analysis by randomly removing up to 50% of the individuals from sample sites, yet the pattern of temporal versus spatial variation is similar to that reported in our original paper. We reiterate that caution should be applied to the interpretation of migration rates estimated from assignment tests, yet the absolute magnitude of our migration estimates was not central to the goals of the original paper. Although Beacham and Withler raise important points on the validation of genetic stock identification analyses, our analyses of temporal variation in genetic population structure in the Upper Fraser River population likely differ due to demographic differences between the timing of sampling of their earlier work versus our analyses.

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.

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.

Bioconcentration of Chlorophenols by Juvenile Chinook Salmon (Oncorhynchus tshawytscha) Overwintering in the Upper Fraser River: Field and Laboratory Tests

1988 ◽  
Vol 23 (1) ◽  
pp. 100-113 ◽  
Author(s):  
I. H. Rogers ◽  
J. A. Servizi ◽  
C. D. Levings
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Cold Water ◽  
Pulp Mill ◽  
Wood Preservative ◽  
Fraser River ◽  
Reference Sites ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook ◽  
River Fish

Abstract Juvenile chinook salmon were sampled from August 1986 to March 1987 at stations near Prince George and Quesnel, influenced by sewage and pulp mill discharges. Maximum densities of 0.2 fish·mࢤ2 were recorded. Salmon were collected at reference sites in November 1986 and at Agassiz in April 1987. Fingerling chinook were exposed at 0.7°C to a commercial wood preservative containing 2,3,4,6 - tetrachlorophenol (TeCP) and pentachlorophenol (PCP) in the laboratory to simulate winter conditions in the upper Fraser River. Fish exposed for 62 days to 2 ug·Lࢤ1 contained a mean of 224 ng·gࢤ1 TeCP and 431 ng·gࢤ1 PCP. Chlorophenol uptake in feral fish was low. However, 3,4,5-trichloro-guaiacol levels to 304 ng·gࢤ1 and tetrachloroguaiacol values to 136 ng·gࢤ1 were measured in March. Fish from Agassiz, 518 km downstream of Quesnel, also contained these two substances. Thus chinook salmon can bioconcentrate persistent chlorophenols and chloroguaiacols directly from cold water (< 1°C). The biological consequences are uncertain.

Extensive use of the Fraser River basin as winter habitat by juvenile chinook salmon (Oncorhynchus tshawytscha)

1991 ◽  
Vol 69 (7) ◽  
pp. 1759-1767 ◽  
Author(s):  
C. D. Levings ◽  
R. B. Lauzier
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Water Channel ◽  
Fraser River ◽  
Winter Habitat ◽  
Mean Size ◽  
System Data ◽  
The Mean ◽  
Juvenile Chinook ◽  
Stream Type

Habitat in the low-water channel of the mainstem Fraser River and larger tributaries during winter may be an unappreciated factor influencing production of stream-type chinook salmon (Oncorhynchus tshawytscha) in this system. Data from electrofishing surveys showed that shorelines were used by juvenile chinook from river km 110 to km 770. Almost the entire mainstem was therefore probably winter habitat, and major tributaries such as the Thompson, Quesnel, and Nechako rivers were also used. Estimated chinook density on the mainstem Fraser increased with distance upstream (maximum 0.30 m−2 at km 750 (Prince George)), but the highest density (0.99 m−2) in the surveys was observed on the Thompson River at Spences Bridge. The mean size of juvenile chinook decreased with distance upstream on the Fraser, ranging from 97 mm at km 110 to 65 mm at km 770. Chinook juveniles were feeding on Diptera, Trichoptera, and Plecoptera in winter. Some apparent growth was observed in the lower Fraser in early winter.

A Genetic Mixture Analysis for use with Incomplete Source Population Data

1990 ◽  
Vol 47 (3) ◽  
pp. 620-634 ◽  
Author(s):  
Peter E. Smouse ◽  
Robin S. Waples ◽  
Joseph A. Tworek
Keyword(s):  
Oncorhynchus Tshawytscha ◽  
Sampling Error ◽  
Population Data ◽  
Allele Frequencies ◽  
Composition Analysis ◽  
Source Population ◽  
Genetic Management ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Deschutes River

While anadromous salmonids reproduce in fresh water, most harvests occur at sea. Effective genetic management requires knowledge of the stock (source population) composition of the harvest. This is accomplished with genetic stock identification (GSI), which compares the genotypes of harvested fish with those of freshwater stocks, assuming that all candidate stocks are identified and that their allele frequencies are known exactly. We develop methods that: (1) allow for sampling error in allele frequencies of candidate stocks, and (2) evaluate the possibility of unsampled contributing stocks. Composition analysis for chinook salmon (Oncorhynchus tshawytscha) collected for the Bonneville Dam egg bank program in 1980 and 1981 shows that about 10% of both harvests were from the Deschutes River and about 90% from the Hanford Reach area. Contributions from lower Columbia and Snake River stocks or from unidentified sources were limited.

Cytochrome P450 1A and related measurements in juvenile chinook salmon (Oncorhynchus tshawytscha) from the Fraser River

2000 ◽  
Vol 57 (2) ◽  
pp. 405-413 ◽  
Author(s):  
J Y Wilson ◽  
R F Addison ◽  
D Martens ◽  
R Gordon ◽  
B Glickman
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Erod Activity ◽  
Dna Adduct ◽  
Clear Correlation ◽  
Fraser River ◽  
Juvenile Chinook Salmon ◽  
Liver Histopathology ◽  
Polycyclic Aromatic ◽  
Juvenile Chinook

Juvenile chinook salmon (Oncorhynchus tshawytscha) were captured at six sites on the upper Fraser, Nechako, and Thompson rivers, British Columbia, Canada. Biological responses were measured in the liver to assess the effects of contaminants on the fish before they began migration downstream. Both ethoxyresorufin-O-deethylase (EROD) activity and CYP 1A concentrations were significantly enhanced, being two- to three-fold higher in Fraser River samples compared with those fish from reference sites on the Nechako River. DNA adduct concentrations were two- to four-fold higher in Fraser River fish, although liver histopathology appeared unaffected. Polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and polychlorinated biphenyls (PCBs) in the carcasses contributed to total contaminant burdens of less than 1 pg·g-1. Polycyclic aromatic hydrocarbon (PAH) metabolites were undetectable in nearly all samples of bile. There were strong correlations between EROD activity, CYP 1A induction, and DNA adduct concentrations but no clear correlation between these responses and PCDD, PCDF, or PCB concentrations.

Identification of Farm-reared and Native Chinook Salmon (Oncorhynchus tshawytscha) on the West Coast of Vancouver Island, British Columbia, Using the Nuclear DNA probe B2-2

1994 ◽  
Vol 51 (S1) ◽  
pp. 267-276 ◽  
Author(s):  
R. E. Withler ◽  
T. D. Beacham ◽  
R. F. Watkins ◽  
T. A. Stevens
Keyword(s):  
British Columbia ◽  
Chinook Salmon ◽  
West Coast ◽  
Oncorhynchus Tshawytscha ◽  
Nuclear Dna ◽  
Vancouver Island ◽  
Band 3 ◽  
Dna Probe ◽  
The West ◽  
River Population

The chinook salmon DNA probe B2-2 was used to distinguish farm-reared (from two commercial farms) and native chinook salmon (Oncorhynchus tshawytscha) that were sampled from five populations on the west coast of Vancouver island. The Big Qualicum River population (east coast of Vancouver Island), which is believed to be the main progenitor of domesticated broodstocks used for aquaculture in British Columbia, was also sampled. The presence or absence and integrated optical densities (IODs) of three DNA fragments at 8.3 kilo base pairs (kbp) (band 1), 6.5 kbp (band 2), and 5.6 kbp (band 3) in the hybridization patterns of B2-2 on BamHI-restricted DNA were recorded for 269 chinook salmon. The frequency of occurrence of bands 2 and 3, and all seven measurements made of the relative and absolute values of the IODs of the three bands, varied significantly among populations. The IOD of band 3 provided the best discrimination among populations. The Big Qualicum and two fish farm populations were differentiated from all five west coast native populations. Discriminant analysis and a neural network were used independently to classify correctly to type an average of 97% of the native and 83% of the farm west coast DNA patterns used as test samples.

Comment on “Gene flow increases temporal stability of Chinook salmon (Oncorhynchus tshawytscha) populations in the Upper Fraser River, British Columbia, Canada”Appears in Can. J. Fish. Aquat. Sci. 66: 167–176.

2010 ◽  
Vol 67 (1) ◽  
pp. 202-205 ◽  
Author(s):  
Terry D. Beacham ◽  
Ruth E. Withler
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Pacific Salmon ◽  
Temporal Stability ◽  
Time Span ◽  
Population Variation ◽  
Stock Identification ◽  
Fraser River ◽  
Mixed Stock ◽  
Conservation And Management

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.

Juvenile Chinook Salmon (Oncorhynchus tshawytscha) Utilization of Hawks Creek, a Small and Nonnatal Tributary of the Upper Fraser River

1994 ◽  
Vol 51 (5) ◽  
pp. 1139-1146 ◽  
Author(s):  
J. Charles Scrivener ◽  
Thomas G. Brown ◽  
Bruce C. Andersen
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Sediment Load ◽  
Small Fish ◽  
Fraser River ◽  
Size Dependent ◽  
Juvenile Salmonids ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Prosopium Williamsoni ◽  
Small Tributary

Hawks Creek, a small tributary of the upper Fraser River where there is no record of spawning salmonids, was examined from May to November 1990 for the presence of juvenile salmonids. Age 0+ wild chinook salmon (Oncorhynchus tshawytscha) appeared in May, increased to peak densities of 0.76 fish∙m−2 in late August, and were absent in November. Average residence time of marked chinook juveniles was 9 d. Duration of residency was size dependent, as small fish remained longer than large fish. Rainbow trout (Oncorhynchus mykiss) and mountain whitefish (Prosopium williamsoni) also had a short residency (mean = 21 d). We suggest that unsuitable rearing conditions (e.g., sediment load) in the mainstem Fraser River during the spring and summer favour the use of small, clear, and nonnatal tributaries by juvenile salmonids. Physical and biological explanations are proposed for their temporary use. These salmonid refuge habitats need to be protected.

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