Estimating the Age and Origin of Spring/Summer Chinook Salmon at

Lower Granite Dam

Christian Smith USFWS Abernathy Lab, Longview, WA

Jody White Quantitative Consultants, Inc. Boise, ID

Cooperators: Matt Campbell and Tim Copeland, IDFGShawn Narum, CRITFCPaul Moran, NOAA-FisheriesScott Marshall, LSRCP

Objectives

• Estimate the age composition of Snake River Spring/Summer Chinook Salmon migrating upstream of Lower Granite Dam

• Determine the power and sensitivity of the Snake River Chinook baseline to allocate unknown individuals to reporting groups

• Estimate the stock composition using genetic mixture analysis of the Snake River Spring/Summer Chinook Salmon migrating upstream of Lower Granite Dam

General Methods• 2005 (8%) and 2006 (10%) Chinook migrating upstream

from April 1 – August 15 were sampled systematic/random) at LGR fish ladder (Jerry Harmon, NOAA fisheries)

• All fish were measured, scales sampled, external tags and marks noted, and scanned for PIT and CWT.

• All wild fish scales were read by IDFG technicians at Nampa Research, Nampa Idaho.

• All wild fish and a subsample of hatchery fish were genotyped at the USFWS Abernathy and IDFG Eagle Genetics Labs.

Genetic Stock Identification/Stock Composition Estimation Schematic

Systematic Random Sampleof Chinook/Steelhead Adults

(Run Year)

Lower Granite DamLadder Trap

Wild/HatcheryTags/Scale Patterns/Marks

Take Scales from each fish

Age

Genotype

Sample All Watersheds

Baseline Development

Hatchery Populations

Population Identification

NaturalPopulations

Temporal/SpatialStability

(Periodic Sampling)

Estimate where they are from

Lower Granite Dam Fish LadderChinook Samples

• 2005 (8% sample)– 1,573 (74%) hatchery

• adipose clip, CWT or known PIT tag present

– 544 (26%) wild/natural• adipose fin present, no associated marks or tags

• 2006 (10% sample)– 1,821 (71%) hatchery– 739 (29%) wild/natural

Lower Granite Spring/Summer Chinook Aggregate Age Composition (error bars = 1 SD)

-10.0%

0.0%

10.0%

20.0%

30.0%

40.0%

50.0%

60.0%

70.0%

80.0%

Age 1 Age 2 Age 3 Age 4

Perc

ent o

f Tot

al

Ocean Age

2005

2006

2007

Lower Granite Wild Chinook Age Composition 2007 Early vs. Late Run Timing

Lower Granite Wild Chinook Age Composition 2007 Early vs. Late Run Timing

Genetics overview

1. Asses the power of standardized genetic baseline to infer origin of Chinook salmon in the Snake River

2. Use the baseline to allocate Chinook salmon sampled at LGD to Snake River reporting groups based on origin (hatchery vs wild) and age.

Genetic Mixture Analysis

1) proportional assignment (mixture analysis): Stock proportions of a mixture are estimated. E.g., 15% belong to pop 1

30% belong to pop 2 55% belong to pop 3

2) individual assignment (assignment tests): Stock assignments of individual fish are estimated. E.g., fish 1 is from pop 2

fish 2 is from pop 3 etc.

Genetic Mixture Analysis

1) Assignment / allocation to populations: Fish are assigned or proportions are allocated to

baseline populations.

2) Assignment / allocation to reporting groups: Genetically similar populations are pooled into

aggregates called “reporting groups” Fish are assigned or proportions are allocated to these

reporting groups.

Used updated version of the published Snake River microsatellite baseline:

Narum SR, Stephenson JJ, Campbell MR. 2007. Genetic variation and structure of Chinook salmon life history types in the Snake River. Transactions of the American Fisheries Society 136:1252-1262.

13 microsatellite markers in 38 collections

Collection Sample size1 Tucannon 1612 Imnaha 1373 Minam 1384 Lostine 1015 CatherineCr 1246 LyonsFerryH(Fall) 1377 ClearwaterR(Fall) 1108 NezPerceTribalH(Fall) 1349 LoloCr 10910 NewsomeCr 10911 DworshakH. 9212 RedRiver 8613 Powell(Lochsa) 13814 S.ForkClearwater 18715 RapidRiverH 14116 BigCr(upper'01) 15617 BigCr(upper'02'03) 6918 JohnsonCr 14319 Secesh 13720 JohnsonCr(suppl.) 10521 SawtoothH 18122 W.ForkYankeeFork 5923 E.ForkSalmonR 14124 Pahsimeroi 10525 Marsh 14126 BearValley('98'01) 9927 BigCr(lower'98'02) 7728 DeckerFlats 8229 ElkCr 3630 KnoxBridge 9231 PovertyFlats 9132 StolleMeadows 9133 ValleyCr(lower) 9434 ValleyCr(upper) 9535 CrookedF 10036 Lemhi 4737 CamasCreek 4638 Wenaha 46

4137

RapidRHat/CW/GR

0.1

41

768

6565

68

35

2223

2128

96

3334

83

51

21

30

2436

32

17

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552

38

1015

100

53

5

1211

359

1314

6130

13

4

9

7

31

1617

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2737

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2526

2998

90

74

1820

100

1931

40

3032

44

14

46

20

2

LostineTucannon

Fall Chinook

Imnaha

MiddleForkSalmon

SouthForkSalmon

Upper Salmon

Grande Ronde

Rapid River Hat.

Clearwater

Neighbor-joining dendrogram of 38 baseline collections

MPGs vs genetic reporting groups

• MPGs combine spring and summer Chinook salmon, genetics separates all spring from summer, but is not able to distinguish among summer stocks.

• Grand Ronde / Clearwater / Imnaha / Rapid River grouping.– GR+Imn, Clear, Rapid or GR+Clear+Rapid, Imn

• Insufficient sampling of some MPGs?

0%

10%

20%

30%

40%

50%

60%

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80%

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MPG RG

Genetic RG

Individual assignment of baseline fish

0%

10%

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40%

50%

60%

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MPG RG

Genetic RG

Proportional assignment of simulated fish

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0.70

TucS

T

Imna

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Lost

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Snake

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ESTIMATE

Proportional assignment of tagged fish

Genetic samples

Rapid / Clearwater

Salmon

Fall Chinook

Genetic samples

Rapid / Clearwater

Salmon

Fall Chinook

Proportion of fish sampled more than once(samples exhibiting identical genotypes)

2005 2006

1.0%

0.8%

0.6%

0.4%

0.2%

0.0%

Year

Per

cen

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Ind

ivid

uals

sam

pled

mul

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es

2x3x

(N=934) (n=1522)

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0.70

0.80

TucST Imnaha RapCWST LostST SnakeOT MFSalST SFSalST upSalST

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

TucST Imnaha RapCWST LostST SnakeOT MFSalST SFSalST upSalST

Hatchery and wild returns to reporting group in 2005 and 2006

2005:

2006:

wildhatchery

Population Sample size reporting groupTucannon 161 TucSTImnaha 137 ImnahaMinam 138 RapCWSTCatherineCr 124 RapCWSTLoloCr 109 RapCWSTNewsomeCr 109 RapCWSTDworshakH. 92 RapCWSTRedRiver 86 RapCWSTPowell(Lochsa) 138 RapCWSTS.ForkClearwater 187 RapCWSTRapidRiverH 141 RapCWSTCrookedF 100 RapCWSTWenaha 46 RapCWSTLostine 101 LostSTLyonsFerryH(Fall) 137 SnakeOTClearwaterR(Fall) 110 SnakeOTNezPerceTribalH(Fall) 134 SnakeOTCamasCreek 46 MFSalSTBigCr(upper'01) 156 MFSalSTBigCr(upper'02'03) 69 MFSalSTMarsh 141 MFSalSTBearValley('98'01) 99 MFSalSTBigCr(lower'98'02) 77 MFSalSTElkCr 36 MFSalSTJohnsonCr 143 SFSalSTSecesh 137 SFSalSTJohnsonCr(suppl.) 105 SFSalSTKnoxBridge 92 SFSalSTPovertyFlats 91 SFSalSTStolleMeadows 91 SFSalSTSawtoothH 181 upSalSTW.ForkYankeeFork 59 upSalSTE.ForkSalmonR 141 upSalSTPahsimeroi 105 upSalSTDeckerFlats 82 upSalSTValleyCr(lower) 94 upSalSTValleyCr(upper) 95 upSalSTLemhi 47 upSalST

2569

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

TucST Imnaha RapCWST LostST SnakeOT MFSalST SFSalST upSalST

1yr 2005

2yr 2005

3yr 2005

1yr 2006

2yr 2006

3yr 2006

Wild returns to LGD assigned by scale age and return year

Reporting Group GSIEstimate

95% CI (very preliminary)

ODFW Estimate

Tucannon River 108 11 - 2245

Imnaha River 451 203 – 704 311

Rapid River/Clearwater/Grande Ronde

3477 3067 – 4121 993*

Lostine River 14 0 – 76 219

Middle Fk Salmon 894 491-1140

South Fk Salmon 1794 1315 – 2192

Upper Salmon 1778 1403 – 2192

Snake Falls 254 140 – 438

2005 reporting group escapement estimates Lower Granite Dam. Confidence intervals are ?. ODFW Estimates are from a mix of weir mark-recaptures and redd expansions. * = only for Grande Ronde not Rapid River or Clearwater River tributaries (see next slide).

Reporting Group GSIEstimate

95% CI (very preliminary)

ODFW Grande Ronde Estimate

Rapid River/Clearwater/Grande Ronde.

3477 3067 – 4121 993*

Example: How do we break down a large reporting unit into management areas?

Use the known escapement (esc.) estimates:Clearwater Esc. = Reporting Group - Grande Ronde Esc. – Rapid River Esc.

- Additional data from weirs in the Clearwater R.can be used to further partition the estimate.

Conclusions

1. Age composition estimates were very precise and accurate using scales from live fish at Lower Granite Dam

2. Baseline used here allows allocation to genetic reporting groups with ~90% accuracy. Allocation to MPGs and populations is generally less accurate. Baseline provides resolution for individual assignment for stream-type vs ocean-type Chinook.

3. ~<1% of fish sampled at LGD are duplicates4. Proportional assignment of hatchery and wild fish was consistent

over the two years for which samples were examined.5. Qualitative differences in age structure of fish assigned to

different reporting groups were noted, but none were statistically significant.

Further Questions and Discussion Topics

1. What is the required resolution for managers in the Snake River Basin?

2. Can we achieve that resolution in Snake River baseline?3. We need to develop variance estimators..? 4. Using scales patterns can we further refine the Hatchery/Wild

estimation at LGR (work is in progress at IDFG Nampa Research?5. We are close to completing the Steelhead baseline… do we want

to continue this work on Steelhead?