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Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures
at Lower Granite Dam
Tim CopelandMatthew Campbell, Christine Kozfkay, and Bill Schrader
Idaho Department of Fish and Game
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Viable Salmonid Population Parameters
• AbundanceAbundance• How many of them are there?How many of them are there?
• ProductivityProductivity• How well do they reproduce & How well do they reproduce &
survive?survive?• Spatial structureSpatial structure
• Where are they?Where are they?• DiversityDiversity
• What are they like?What are they like?
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•Abundance is a primary status metric•Salmon/steelhead = number of spawning adults
•Productivity = abundance x age comp. through time•Combination measures population resiliency
•Necessary for sustainable harvest•Necessary for conservation of weak stocks & biodiversity
Abundance & Productivity
Productivity (geomean R/S)
5% extinction risk
25% extinction riskA
B
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•Data collection during spawning is very difficult•Status assessments used aggregate data & habitat models from outside DPS
Challenges for Snake River Steelhead
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“A-run” versus “B-run”
Stock Ocean
ResidenceTiming over Bonneville
Size at return Distribution
A-run Usually 1 yr June - Aug < 78 cmTucannon, Grand Ronde, Imnaha, low elevation tribs of Clearwater
& Salmon, upper Salmon
B-run Usually 2 yrs Sept - Oct > 79 cmNorth & South Fk Clearwater, Lochsa , Selway, SFSR, MFSR
“A-run” steelhead Grand Ronde River
“B-run” steelhead S.F. Clearwater
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•Characterize allele frequencies from contributing stocks•Genotype mixed sample•Estimate stock proportions from genetic baseline
Genetic Stock Identification
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Strategy• Sample aggregate at Lower Granite Dam
(numbers & age composition)• Use genetic stock identification• Develop data suitable for VSP assessments
(abundance & productivity)• Address A vs B dichotomy
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METHODS
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GENETIC BASELINE
•66 sample collections
•9 geographic groups
1) Elk Creek (Joseph)2) Snake/Lower Clearwater3) South Fk Clearwater4) Upper Clearwater5) Imnaha6) Lower Salmon7) South Fk Salmon8) Middle Fk Salmon9) Upper Salmon
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Wild steelhead only!
•Aug 24 – Nov 25•Scales taken, length recorded•13 microsatellite loci from standard set•Genetic sex marker
2008 Adult Sampling at Lower Granite Dam
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•Proportion by group estimated with ONCOR
For the entire wild run (all samples)
By sex (male and female)
By size (fork length <78 cm or >78 cm)
By run-timing (early, middle, late)
By total age (3, 4, and 5 year olds)
• 95% bootstrap confidence interval
Mixture Analyses
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RESULTS
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Lower Granite Dam Sampling• Sample period missed first 13% of run• 46% unclipped fish were hatchery-origin• 20,078 wild fish• 992 aged, 1,076 genotyped• 65.7% genetically female
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Age composition(n = 992)
Ocean Age
Freshwater age
X 1 2 3 4 5
1 13 5 180 204 27 1
2 35 2 286 168 25 0
3 5 0 20 20 1 0
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Genetic Stock CompositionN = 20,078
AB
A
AA AB
B B
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1.0%
35.7%
8.2%
15.9%
8.6%
15.8%
3.5%5.0% 6.4%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
0.0%
37.2%
6.4%
14.5%11.0% 10.8%
1.1%
5.5%
13.7%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
By Sex
Female
Male
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By Length
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0.24%
46.90%
0.59%4.26%
21.58%
7.80%
1.07%2.36%
15.19%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
By Total Age (3 or less)
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0.61%
41.37%
8.29%
15.03%9.51%
11.71%
0.22%4.58%
8.65%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
By Total Age (4)
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0.74%
19.74%
11.14%
22.96%
3.27%
19.54%
8.20% 9.88%4.52%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
By Total Age (5 or greater)
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0.74%
19.74%
11.14%
22.96%
3.27%
19.54%
8.20% 9.88%4.52%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
By Total Age (5 or greater)
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0.7%
34.3%
2.9%
10.2% 10.8%
18.1%
2.8%
9.6% 10.7%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
By Run-Timing (Early)
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0.7%
35.2%
9.8%
17.2%
8.8%13.2%
3.0% 3.3%
8.8%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
By Run-Timing (Middle)
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0.0%
43.5%
14.0%
24.6%
8.8%1.8%
0.0% 1.9%5.4%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
By Run-Timing (Late)
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0.7%
34.3%
2.9%
10.2% 10.8%
18.1%
2.8%
9.6% 10.7%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
By Run-Timing (Early)
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0.7%
35.2%
9.8%
17.2%
8.8%13.2%
3.0% 3.3%
8.8%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
By Run-Timing (Middle)
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0.0%
43.5%
14.0%
24.6%
8.8%1.8%
0.0% 1.9%5.4%
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
By Run-Timing (Late)
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MAJOR FINDINGS
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•Genetic groups did not conform with TRT population structure
•Majority from 3 stocks (65%):
•Snake/Lower Clearwater, Upper Clearwater, Lower Salmon
•Grand Ronde likely lumped with Snake/Lower Clearwater
•Two large areas of good habitat have poor representation
•Middle Fk Salmon & South Fk Salmon
Stock Contribution
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•Females comprise 2/3 of adult steelhead
•Female-biased sex ratios may result from:
1. Males residualize more than females
2. Females may be more iteroparous
•Dams & long migration reduces successful iteroparity
•No population effects = widespread male residualization?
Sex Composition
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•Length conformed with A/B expectations
•Salmon River B stocks return over Lower Granite earlier
•Lower Salmon stock has older age comp than other A-runs
•All stocks produce smaller/younger & larger/older adults
•A/B dichotomy masks important diversity for conservation
“A-run” versus “B-run”
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Summary
First time Snake River steelhead abundance estimated at the stock/population level
This approach provides information relevant to VSP criteria
Abundance
Age composition
Sex ratio
Genetic diversity
Life history diversity
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Future•Improve baseline
•Better resolution within some groups (e.g., Lemhi R)•Coverage needed in some areas (e.g., Grand Ronde) •Resolve differences with TRT population structure?•Annual maintenance sampling
•Sample entire adult run•Transition to SNPs•Include smolt sampling at Lower Granite Dam
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