# Presentation: 185701

## 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, IDFG
- 		Shawn Narum, CRITFC
- 		Paul Moran, NOAA-Fisheries
- 		Scott 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

**Notes:**
I stayed general so as not to bore people... do we need more?

## 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.

**Notes:**
Since we went over this last year, do we need more methods info. than this?

## Genetic Stock Identification/Stock Composition Estimation Schematic

**Notes:**
This is to show the interaction of the baseline and the actual sampling program at LGR

## Lower Granite Dam Fish LadderChinook 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)

**Notes:**
>90% Accuracy on aging for a new lab

## 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	

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

- 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.

**Notes:**
 2) GSI is a general term that can mean
 3) Two different things: MSA and IA
 4) It is easier to estimate proportions than individual origin.

## Genetic Mixture Analysis

- 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.

**Notes:**
 2) GSI is a general term that can mean
 3) Two different things: MSA and IA
 4) It is easier to estimate proportions than individual origin.

## 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

## Neighbor-joining dendrogram of 38 baseline collections

- 0.1

**4**

**1**

**7**

**6**

**8**

**65**

**65**

- 68

- 35

**22**

**23**

**21**

**28**

- 96

**33**

**34**

- 83

- 51

- 21

- 30

**24**

**36**

- 32

- 17

- 2

**2**

**3**

**5**

- 52

**38**

**10**

**15**

- 100

- 53

- 5

**12**

**11**

**35**

**9**

**13**

**14**

- 61

- 30

- 13

- 4

- 9

- 7

- 31

**16**

**17**

- 100

**27**

**37**

- 51

- 45

**25**

**26**

**29**

- 98

- 90

- 74

**18**

**20**

- 100

**19**

**31**

- 40

**30**

**32**

- 44

- 14

- 46

- 20

- 2

- Lostine

- Tucannon

- Fall Chinook

- Imnaha

- MiddleForkSalmon

- SouthForkSalmon

- Upper Salmon

- Grande Ronde

- Rapid River Hat.

- Clearwater

## 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?

## Individual assignment of baseline fish

## Proportional assignment of simulated fish

## 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

- Percent of Individuals sampled multiple times

- 2x
- 3x

- (N=934)		                    (n=1522)

## Hatchery and wild returns to reporting group in 2005 and 2006

- 2005:

- 2006:

- wild
- hatchery

## Wild returns to LGD assigned by scale age and return year

## 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 | GSI
Estimate | 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).**

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

| Reporting Group | GSI
Estimate  | 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

- Age composition estimates were very precise and accurate using scales from live fish at Lower Granite Dam
- 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.
- ~_<_1% of fish sampled at LGD are duplicates
- Proportional assignment of hatchery and wild fish was consistent over the two years for which samples were examined.
- Qualitative differences in age structure of fish assigned to different reporting groups were noted, but none were statistically significant.

## Further Questions and Discussion Topics

- What is the required resolution for managers in the Snake River Basin?
- Can we achieve that resolution in Snake River baseline?
- We need to develop variance estimators..?
- Using scales patterns can we further refine the Hatchery/Wild estimation at LGR (work is in progress at IDFG Nampa Research?
- We are close to completing the Steelhead baseline... do we want to continue this work on Steelhead?