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Use of microsatellite DNA markers to determine the reproductive success of hatchery and natural origin chinook
salmon in a supplemented Idaho stream
Brian Leth –Idaho Dept. of Fish and Game
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Acknowledgements
• Dr. Madison Powell (University of Idaho)• Jeffrey Lutch (IDFG)• Pahsimeroi Hatchery staff • Matt Campbell, Chris Cegelski, and Bruce Barnett • Bonneville Power Administration (Funding)
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ISS Study• Large-scale statewide study to evaluate effects
of supplementation• Monitor and evaluate the production and
productivity of supplementation and natural origin chinook spawning in treatment and control streams– Adult escapement (rack returns, redd counts)
– Juvenile production (juvenile emigrant traps)
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Rationale for Small Scale Study
• Relative Reproductive Fitness?– Supplementation vs. natural adults
• Supplementation and Natural Adult Spawning Distribution?– Temporal and Spatial Distribution– Random Mating
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Pahsimeroi River Study
Determine the reproductive success of naturally spawning supplementation and natural origin chinook in the Pahsimeroi River
Goal:
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Study Area
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Research Objectives
1. Determine the contribution of naturally spawning supplementation and natural origin adults to F1 smolt production
2. Determine if the proportional contribution varies among the parr, presmolt and smolt life stages
3. Determine the spawn timing and distribution of the supplementation and natural adults
4. Determine the contribution of supplementation and natural adults to the returning F1 Adults
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Research Objectives
1. Determine the contribution of naturally spawning supplementation and natural origin adults to F1 smolt production
2. Determine if the proportional contribution varies among the parr, presmolt and smolt life stages
3. Determine the spawn timing and distribution of the supplementation and natural adults
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FryPresmolt
Smolt
Egg
Adult
What F1 Life Stage to Sample for Contribution
Parr
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FryPresmolt
Smolt
Egg
Adult
What F1 Life Stage to Sample for Contribution
Parr
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BY 2000 Juvenile Chinook Expanded Trap NumbersPahsimeroi River, Idaho
0
100
200
300
400
500
Mar-01
Apr-01
May-01
Jun-01
Jul-0
1
Aug
-01
Sep
-01
Oct-01
Nov-01
Dec-01
Jan-02
Feb
-02
Mar-02
Apr-02
May-02
Date
Em
igra
nts
Parr (37.9%) Presmolts (31.4%) Smolts (30.7%)
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BY 2000 Juvenile Chinook Expanded Trap NumbersPahsimeroi River, Idaho
0
100
200
300
400
500
3/11
/01
4/11
/01
5/11
/01
6/11
/01
7/11
/01
8/11
/01
9/11
/01
10/11/01
11/11/01
12/11/01
1/11
/02
2/11
/02
3/11
/02
4/11
/02
5/11
/02
Date
Nu
mb
er o
f Em
igra
nts
Parr (37.9%) Presmolts (31.4%) Smolts (30.7%)
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Research Objectives
1. Determine the contribution of naturally spawning supplementation and natural origin adults to F1 smolt production
2. Determine if the proportional contribution varies among the parr, presmolt and smolt stages
3. Determine the spawn timing and distribution of the supplementation and natural adults
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BY 2000 Juvenile Chinook Expanded Trap NumbersPahsimeroi River, Idaho
0
100
200
300
400
500
Mar-01
Apr-01
May-01
Jun-01
Jul-0
1
Aug
-01
Sep
-01
Oct-01
Nov-01
Dec-01
Jan-02
Feb
-02
Mar-02
Apr-02
May-02
Date
Em
igra
nts
Parr (37.9%) Presmolts (31.4%) Smolts (30.7%)
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Methods-Objectives 1&2
• Genetic Contribution– Collect tissue samples from all adults
released released above the weir– Collect tissue samples from emigrating
juveniles across the entire emigration period
– Use Microsatellite DNA markers to conduct parental exclusion analyses
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Methods-Objectives 1&2 Parental Exclusion
124 132 152 136
Female 1 Male 1 Male 2
144 152
124 136 152132
Male 2 Excluded No Parents Excluded
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Statistical Analysis• Objective 1- Determine the contribution of naturally spawning supplementation and natural
origin adults to F1 smolt production
- Observed vs. expected contributionX2 Goodness of fit test
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Statistical Analysis- Objective 1 • Genetic Contribution
– Compare expected vs. observed contribution to smolt production from adults released upstream
• Released Adults
-Females
40% Natural
60% Supplementation
-Males
66% Natural
34% Supplementation
• Possible Crosses from random matings
Nf x Nm=(0.4x0.66)= .26
Sf x Sm=(0.6x0.34)= .20
Nf x Sm=(0.34x0.4)= .14
Sf x Nm=(0.66x0.6)= .40
1.00
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Statistical Analysis- Objective 1 • Genetic Contribution
– Compare expected vs. observed contribution to smolt production from adults released upstream
• Released Adults
-Females
40% Natural
60% Supplementation
-Males
66% Natural
34% Supplementation
• Possible Crosses from random matings
Nf x Nm=(0.4x0.66)= .26
Sf x Sm=(0.6x0.34)= .20
Nf x Sm=(0.34x0.4)= .14
Sf x Nm=(0.66x0.6)= .40
1.00
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Statistical Analysis
Objective 2 – Differences in contribution among three juvenile life stages
- paired t-tests between groups (parr, presmolt, smolt)
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Research Objectives
1. Determine the contribution of naturally spawning supplementation and natural origin adults to F1 smolt production
2. Determine if the proportional contribution varies among the parr, presmolt and smolt life stages
3. Determine the spawn timing and distribution of the supplementation and natural adults
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Methods-Objective 3 Spawn Timing and Distribution
• 25% of all adults released upstream in 2002 were tagged with 7/8” disc tags.
• Spawning area was divided into three strata (lower, middle, and upper).
• One transect from each strata was walked every three days
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Methods-Objective 3
• Spawn Timing
-Determined from the observation of spawning behaviors
-Proportion of each group observed actively spawning each survey will result in a spawn timing distribution
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Methods-Objective 3
• Spawning Distribution
-During spawning surveys, GPS locations of all known origin adults observed were recorded
-Will compare distributions of both groups throughout the spawning period
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Status of Study
• Tissue Sample Collection
• DNA extraction
• Microsatellite marker selection
• Genotyping
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Timeline for Remainder of Study
• Conduct exclusion analysis during Fall 2004
• Complete report and submit by January 2005
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QUESTIONS?