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

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?

• 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

• Data collection during spawning is very difficult• Status assessments used aggregate data &

habitat models from outside DPS

Challenges for Snake River Steelhead

“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

• Characterize allele frequencies from contributing stocks• Genotype mixed sample• Estimate stock proportions from genetic baseline

Genetic Stock Identification

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

METHODS

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

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

• 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

RESULTS

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

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

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

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

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

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

MAJOR FINDINGS

• 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

• 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

•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”

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

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