Genetic impacts of hatchery stocks on Steelhead in Lower Cowlitz tributaries

Anne Marshall, Maureen Small, and Julie Henning

Washington Department of Fish and Wildlife

“The lower Cowlitz winter steelhead historical population may have been one of the largest in the lower Columbia Basin”(Lower Columbia Salmon Recovery and Fish and Wildlife Subbasin Plan, Vol. 1, Chapter 5. 2004)

ESA-listed as threatened in 1998

-within the Lower Columbia “Distinct Population Segment” (DPS)

Major uncertainty for the DPS:

Impact of hatchery-origin steelhead on natural populations

Lower Columbia Steelhead DPS – historical populations

Lower Cowlitz winter steelhead were designated as a distinct population in recovery planning

Dams prevent access to upper Cowlitz Basin except by trapping and hauling

Cowlitz Basin perimeter

Objectives -

• Genetically characterize steelhead in lower Cowlitz tributaries

• Determine if natural-origin steelhead are genetically distinct from Cowlitz hatchery stocks

• Estimate introgression in natural population from hatchery stocks

• Investigate population structure among tributaries

• Determine if lower Cowlitz steelhead are distinct from other Lower Columbia populations

Sample adults in lower river tributaries over two years

Sample size goal of 50 natural-origin adults per tributary system

Sample any known hatchery-origin adults encountered

Sample 50 fish in each of two years from all three Cowlitz Hatchery stocks

Sampling design –

Three Steelhead stocks at Cowlitz Trout Hatchery:

- Chambers Creek (non-native, Puget Sound) early winter-run

- Cowlitz late winter-run

- Skamania (non-native, lower Columbia) summer-run

Hatchery production is mitigation for loss due to hydroelectric dams

Smolt releases of Cowlitz Hatchery steelhead stocks, 1995-2008

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100000

200000

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600000

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900000

1995

1996

1997

1998

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2008

summer-run

early-run

late-run

Lower Cowlitz tributaries – adult steelhead sampling sites

Cowlitz Trout Hatchery

Columbia River

Lower Cowlitz includes Toutle and Coweeman sub-basins, with other hatchery stock releases

3 Tributary systems sampled

Sampling Methods -Angling and dip netting, March to May - scales & fin tissue taken - careful fish handling & release

Tissue sampled from caudal fin for DNA extraction

Genetic Methods -

Statistical Analyses –

• Descriptive genetic statistics per sample

• Pair-wise differentiation tests among samples

• Factorial correspondence analysis of genotypes

• Assignment tests for population-origin

• Population structure analyses

Laboratory – Genotypes at 15 microsatellite DNA loci per fish

2008 & 2009 Sampling Results -

77 total natural-origin steelhead

8 marked hatchery fish

100 adults from each hatchery stock

2008 – 79% males; 2009 – 89% males

Tributary systems totals:

Olequa N = 44

Delemeter N = 32

Ostrander N = 1

Cowlitz Trout Hatchery

Genetic differentiation between samples – temporal and population-wide tests

Temporal samples per population were similar.

Lower Cowlitz natural-origin steelhead were differentiated from hatchery stocks.

Hatchery stocks differed from each other.

Pop 09CowHS 08CowHS 09CowHEW08CowHEW08CowHLW09CowHLW 09CowNat 08CowNat 0506Cowee

09CowHS 0.58040 0.00001 0.00001 0.00001 0.00001 0.00001 0.00001 0.00001

08CowHS 0.0010 0.00001 0.00001 0.00001 0.00001 0.00001 0.00001 0.00001

09CowHEW 0.0385 0.0322 0.00131 0.00001 0.00001 0.00001 0.00001 0.00001

08CowHEW 0.0314 0.0265 0.0072 0.00001 0.00001 0.00001 0.00001 0.00001

08CowHLW 0.0440 0.0403 0.0376 0.0298 0.00119 0.00001 0.00001 0.00001

09CowHLW 0.0421 0.0370 0.0325 0.0320 0.0071 0.00001 0.00001 0.00001

09CowNat 0.0234 0.0195 0.0242 0.0150 0.0302 0.0307 0.26797 0.00001

08CowNat 0.0205 0.0144 0.0261 0.0153 0.0299 0.0281 0.0036 0.00001

0506Cowee 0.0233 0.0195 0.0166 0.0184 0.0260 0.0225 0.0075 0.0066

Lower matrix: FST values. Upper matrix p-values for genotypic tests.Bold values not significant

Factorial correspondence analysis plot- Individual fish plotted according to genotype

Plot of centers - 08 & 09 samples

“CowClip” (orange dots) are marked hatchery-origin fish

Assignment of individuals to their population of origin

GeneClass program

Assigned fish are at least 90 times more likely to originate from one sample

Unassigned fish have similar likelihoods of originating from two or more samples

  >90% relative assignment likelihood          

Baseline Collections

  CowSum CowEWin CowLWin CowNat Assign unassigned % unassigned Total

CowSum 86 3 0 1 90 10 10.0 100

CowEWin 0 79 0 0 79 20 20.2 99

CowLWin 0 0 88 3 91 8 8.1 99

CowNat 0 3 0 44 47 21 30.9 68

CowClip 0 5 2 0 7 1 12.5 8

Total assign 90 79 91 47

correct 86 79 88 44

% correct 95.56 100 96.7 93.62        

STRUCTURE analysis – partitions data into genetic clusters using Hardy-Weinberg equilibrium

Hatchery and natural-origin steelhead in Cowlitz and Coweeman

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2

3

4

“K” (number of hypothetical populations) = 4 had highest likelihood

STRUCTURE – summary of average percentage of ancestry over all individuals for each sample, 4 genetic clusters

Cluster labels based on the dominant population in the cluster

Lower Cowlitz natural-origin steelhead – results to this point:

• As a group, were genetically distinct from Cowlitz Hatchery stocks• Ancestry estimated from hatchery stocks suggests introgression

into wild population• Average ancestry from all hatchery stocks over all natural-origin

fish was about 40%• Coweeman steelhead, a nearby population, shared similar

ancestry profile

How do Lower Cowlitz steelhead compare with other lower Columbia populations?

Other Lower Columbia Basin rivers where steelhead population samples were obtained for comparative analyses

Winter and summer-run populations

All samples from natural-origin adult steelhead

Natural-origin adults at Cowlitz barrier dam

0.01

EFLewis

CowHSumWashougal

KalamaS

Cowee

CowNat

Elochoman

KalamaW

SFToutle

NFToutle

GreenNFLewisMer

NFLewisCed

CowH E W

CowH L W

CowBarrier

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Neighbor-joining dendrogram of genetic distances among Cowlitz and lower Columbia region steelhead samples

Toutle River sub-basin in Cowlitz basin

STRUCTURE analysis: Cowlitz steelhead and other Lower Columbia steelhead at K=5 clusters

Summary of average percentage of ancestry over all individuals for each sample in 5 genetic clusters estimated by STRUCTURE

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EFLew

CowHSumWashougalKalS

CoweeCowNat

Elochoman

KalW

SFToutle

NFToutle

GreenNFLewMer

NFLewCed

CowH E W

CowH L W

CowBarrier

Results summary -

Lower Cowlitz tributaries natural-origin steelhead were genetically distinct from all Cowlitz hatchery stocks.

The three Cowlitz Hatchery stocks were genetically distinct from each other.

Lower Cowlitz steelhead showed introgression from non-native hatchery stocks, especially early winter-run stock.

Lower Cowlitz steelhead shared little ancestry with Cowlitz Hatchery native late winter-run stock.

Coweeman and Elochoman rivers winter steelhead were most similar to Lower Cowlitz steelhead.

Conclusions -

Despite large hatchery releases over many years, lower Cowlitz tributaries appear to support a distinct, native population.

The non-native, early winter-run hatchery stock appeared to have largest impact on Lower Cowlitz steelhead.

Early-winter hatchery males, present on spawning grounds several months later than expected, expanded genetic risks.

Management strategies to reduce hatchery impacts

Proposal to eliminate non-native, early winter-run stock at Cowlitz Hatchery.

Consider use of weirs in summer months to exclude hatchery summer-run stock

Revise Hatchery Genetic Management Plans (ESA “permits”)

Acknowledgements

Chris Gleizes, Mike Blankenship, Bob Gibbons and volunteer anglers conducted field sampling.

Jennifer Von Bargen conducted laboratory analyses, John Sneva interpreted scale patterns, and Steve Vanderploeg provided the lower basin map.

Genotypic data for other steelhead samples were collected by Todd Kassler and Cheryl Dean, and those samples were collected by WDFW Region 5 staff.

This project was funded in part by Tacoma Power and we thank Mark LaRiviere for project support.

Questions?