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

Acknowledgements

• Dr. Madison Powell (University of Idaho)• Jeffrey Lutch (IDFG)• Pahsimeroi Hatchery staff • Matt Campbell, Chris Cegelski, and Bruce Barnett • Bonneville Power Administration (Funding)

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)

Rationale for Small Scale Study

• Relative Reproductive Fitness?– Supplementation vs. natural adults

• Supplementation and Natural Adult Spawning Distribution?– Temporal and Spatial Distribution– Random Mating

Pahsimeroi River Study

Determine the reproductive success of naturally spawning supplementation and natural origin chinook in the Pahsimeroi River

Goal:

Study Area

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

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

FryPresmolt

Smolt

Egg

Adult

What F1 Life Stage to Sample for Contribution

Parr

FryPresmolt

Smolt

Egg

Adult

What F1 Life Stage to Sample for Contribution

Parr

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%)

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%)

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

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%)

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

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

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

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

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

Statistical Analysis

Objective 2 – Differences in contribution among three juvenile life stages

- paired t-tests between groups (parr, presmolt, smolt)

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

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

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

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

Status of Study

• Tissue Sample Collection

• DNA extraction

• Microsatellite marker selection

• Genotyping

Timeline for Remainder of Study

• Conduct exclusion analysis during Fall 2004

• Complete report and submit by January 2005

QUESTIONS?