Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock...
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![Page 1: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/1.jpg)
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
![Page 2: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/2.jpg)
Viable Salmonid Population Parameters
• Abundance• How many of them are there?
• Productivity• How well do they reproduce &
survive?• Spatial structure
• Where are they?• Diversity
• What are they like?
![Page 3: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/3.jpg)
• 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
Ab
un
dan
ce (
10 y
r g
eom
ean
)
Productivity (geomean R/S)
5% extinction risk
25% extinction riskA
B
![Page 4: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/4.jpg)
• Data collection during spawning is very difficult• Status assessments used aggregate data &
habitat models from outside DPS
Challenges for Snake River Steelhead
![Page 5: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/5.jpg)
“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
![Page 6: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/6.jpg)
• Characterize allele frequencies from contributing stocks• Genotype mixed sample• Estimate stock proportions from genetic baseline
Genetic Stock Identification
![Page 7: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/7.jpg)
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
![Page 8: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/8.jpg)
METHODS
![Page 9: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/9.jpg)
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
![Page 10: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/10.jpg)
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
![Page 11: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/11.jpg)
• 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
![Page 12: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/12.jpg)
RESULTS
![Page 13: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/13.jpg)
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
![Page 14: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/14.jpg)
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
![Page 15: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/15.jpg)
Grand
e Ron
de (E
lk Cr.)
Snake
/Low
er C
lear
water
SF Cle
arwat
er
Upper
Cle
arwat
er
Imna
ha
Lower
Sal
mon
SF Sal
mon
MF S
alm
on
Upper
Sal
mon
0.0%
5.0%
10.0%
15.0%
20.0%
25.0%
30.0%
35.0%
40.0%
45.0%
50.0%
0.5% (95)
36.1%(7,256)
7.6%(1,520)
15.4%(3,092)
9.5%(1,911)
13.9%(2,793)
2.7%(544)
5.1%(1,028)
9.2%(1,841)
Genetic Stock CompositionN = 20,078
AB
A
AA AB
B B
![Page 16: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/16.jpg)
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
![Page 17: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/17.jpg)
Grande
Ronde (E
lk C
r.)
Snake/
Lower C
lear
water
SF Cle
arwat
er
Upper C
lear
water
Imnah
a
Lower S
alm
on
SF Sal
mon
MF S
alm
on
Upper S
alm
on
0.0%10.0%20.0%30.0%40.0%50.0%
0.66%
42.63%
2.37%8.81%
12.39% 14.69%
2.18% 4.56%11.72%
A-run (78 cm or less)
SF Cle
arwat
er0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
B-run (79 cm or greater)
By Length
![Page 18: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/18.jpg)
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)
![Page 19: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/19.jpg)
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)
![Page 20: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/20.jpg)
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)
![Page 21: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/21.jpg)
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)
![Page 22: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/22.jpg)
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)
![Page 23: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/23.jpg)
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)
![Page 24: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/24.jpg)
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)
![Page 25: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/25.jpg)
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)
![Page 26: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/26.jpg)
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)
![Page 27: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/27.jpg)
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)
![Page 28: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/28.jpg)
MAJOR FINDINGS
![Page 29: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/29.jpg)
• 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
![Page 30: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/30.jpg)
• 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
![Page 31: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/31.jpg)
•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”
![Page 32: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/32.jpg)
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
![Page 33: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/33.jpg)
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
![Page 34: Estimating Viable Salmonid Population Parameters for Snake River Steelhead using Genetic Stock Identification of Adult Mixtures at Lower Granite Dam Tim.](https://reader035.fdocuments.us/reader035/viewer/2022062519/5697bfde1a28abf838cb1fb3/html5/thumbnails/34.jpg)