Kelt Steelhead Studies: Evaluating Reconditioning and

Reproductive Success in the Columbia River Basin Douglas R. Hatch, Ryan Branstetter, John Whiteaker, Shawn Narum,Jeff StephensonColumbia River Inter-Tribal Fish Commission

Dave Fast, Joe Blodgett, Bill Bosch, Todd NewsomeYakama Nation Fisheries

Devin Best, Confederated Tribes of the Warm Springs Reservation of Oregon

Chris Fisher, Rhonda DasherConfederated Tribes of the Colville Reservation

Tracy HauserBonneville Power Administration

• Initiated in 2000, just started our 3rd year following the rolling provincial review.• This project’s proposal included geographic replication, but between the

recommendation stage in the rolling provincial review process and final budget agreement between NPCC and Bonneville, the project budget was reduced by $155,000. This resulted in the geographic replication being dropped.

• Proposed in the 07-09 Project Solicitation with Yakima River and Snake River components.

Kelt Reconditioning Research in the Columbia Basin 2000-017-00

Evaluate Relative Reproductive Success of Natural-Origin, Hatchery-Origin, and Reconditioned Kelt Steelhead 2003-062-00

• Response to the Bonneville Request for Studies (RFS).• Project started in February 2004, we will begin our 3rd year on April 1, 2006.• Proposed in the 07-09 Project Solicitation with similar scope.

1. Evaluate effects of directly transporting steelhead kelts around the hydro system on enhancement of iteroparity.

2. Evaluate effects of short-term kelt reconditioning and subsequent transportation of kelts around the hydro system on enhancement of iteroparity. Short-term reconditioning will be performed using fish from collection facilities within the Yakima, Umatilla, Grande Ronde, and Imnaha river basins.

3. Evaluate effects of long-term kelt reconditioning and subsequent release for natural spawning on enhancement of iteroparity.

4. Evaluate effects of long-term kelt reconditioning and captive spawning on: a) gamete and progeny viability; and b) enhancement of iteroparity.

Objectives: Kelt Steelhead Reconditioning Study

Prosser Hatchery Operation

Management Scenarios

• In-river release – Capture kelt PIT tag & release.• No-term- Capture kelt, tag, transport below

Bonneville Dam and release.• Short-term -- Capture kelt, tag, feed for 6 weeks,

transport below Bonneville Dam and release.• Long-term – Capture kelt, tag, feed for

~7months; determine maturation level, and release in river.

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Receiver Locations

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RM 85 RM 0RM 85 RM 25RM 60

In-river Estuary Ocean

-No-term and Short-term migration evaluations.

-Detection patterns in 2005 based on hydro-acoustic tags.

-pooled results from all treatment groups.

-n=120

Median travel time from Bonneville to ocean entry

2004 2005

No-term 115hr 126hr

Short-term

140hr 78hr

Final detection location for no-term (NT) and short-term (ST) treatments in 2004 and 2005. Receivers were located only in the estuary and ocean in 2004.

Final Detection Location

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2004 NT 2004 ST 2005 NT 2005 ST

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Short-term Long-term

Survival to release of reconditioned kelt steelhead from the Yakima River

1. Identify specific streams where reproductive success of natural-origin, hatchery-origin, and reconditioned kelt steelhead can be tested.

2. Evaluate reproductive success of natural-origin, hatchery-origin, and reconditioned kelt steelhead and adult resident O.mykiss at a variety of streams in the Upper Columbia, Mid-Columbia, and Snake River ESUs using pedigree analysis.

3. Apply kelt steelhead reconditioning techniques at selected streams to post-spawners for release back into study streams.

Objectives: Reproductive Success Study

•Rationale

•We have established that kelt reconditioning is possible and have demonstrated successful spawning migrations and redd construction (BPA Project 200001700).

•However, the reproductive success of reconditioned kelts needs to be explored to assess the net benefit of this program. In addition, comparisons to natural origin first time spawners can be used to evaluate reconditioned kelt contributions relative to a first time spawner baseline, and comparisons with hatchery origin steelhead is important to evaluate if kelt reconditioning is a viable alternative to more traditional hatchery supplementation.

•Technological advances in DNA-typing make direct measurement of reproductive success using pedigree analysis practical. Employing these new techniques, our study will directly measure the reproductive success of natural-origin, hatchery-origin, and reconditioned kelt steelhead in natural stream settings. This will yield quantitative data replicated geographically and temporally that will add resolution to the issue.

• Chose 3 or more replicate streams.

• Within each stream genotype all possible O. mykiss spawners (including anadromous and resident fish).

• Collect representative sample of juvenile O. mykiss and using parentage analysis match them with parents.

• Hypothesis: The composition of spawners (hatchery-origin, natural-origin, reconditioned kelt) is the same as the composition of parents of a representative sample of juveniles.

General Scheme

•Conceptual Model

Maiden adult steelhead Kelt steelhead Resident O. mykiss spawners

Juvenile steelhead

Kelt steelhead

Fed and reconditioned ~8mo

Release

d back in

strea

m if matu

re

Interrogate

d for P

IT;

DNA if new

fish

DNA Collected

PIT tagged Released

DNA Collected

PIT tagged Released

Spawning Population C omposition

Hatchery

steelhead

Wild

steelhead

Resident

mykiss

Reconditioned

Kelt

J uvenile Parent C omposition

Hatchery

steelhead

Wild

steelhead

Resident

mykiss

Reconditioned

Kelt

H o

DNA CollectedCounted & released

A relatively low (but not too low) abundance of adult steelhead in the stream (~200).

The stream must have hydrological conditions that are favorable to using a weir during the steelhead migration.

The stream must also have a suitable location for a rotary screw trap or some other juvenile trap.

Prefer a stream with low abundance of resident O. mykiss.

Stream location should be relatively close to a hatchery facility for reconditioning.

Study Stream Selection Criteria

• Shitike Creek – Deschutes River tributary.• Omak Creek – Okanogan River tributary.• Bonaparte Creek – Okanogan River tributary.• Ahtanum Creek – Yakima River.• Section Corner Creek – Tributary to Satus Creek/Yakima

River. Field laboratory

Streams selected

Shitike Creek

Omak Creek

Section Corner Creek

• Low water in 2005

• Low fish abundance

• Inexperience in reconditioning

• Incomplete sampling

• Brook Trout sampling

Challenges

Kelt Reproductive Success

Genetic Results

Sample Numbers

• 759 samples genotyped with 17 microsatellites– 32 known Brook Trout– 1 parr identified as a brook trout– 17 unknown source samples– 7 duplicate samples– 43 poor quality samples

• 659 samples included in statistical analysis

Genetic Tests

• Diversity Statistics– Expected and Observed Heterozygosity– Number of Alleles and Allelic Richness

• Hardy-Weinberg equilibrium• Genotypic Linkage Disequilibrium• Pairwise FST Values / Genic differentiation rates• Pairwise genetic distances / Neighbor joining

tree• Parentage Analysis

Diversity statisticsn = sample size HE = expected heterozygosity HO = observed heterozygosityA = Average number of alleles per locus AR = Allelic richness

Population n H E H O A AR

Omak Adult Steelhead 95 0.8155 0.797 13.12 8.22

Omak Residents Above MF 21 0.8326 0.7785 9.94 8.29

Omak Residents Below MF 78 0.8277 0.7996 12.18 8.05

Shitike Adult Steelhead 55 0.8242 0.8099 14.18 9.17

Shitike Resident RBT 146 0.7027 0.7006 13.29 7.25

Shitike Juveniles 61 0.6973 0.7044 11.65 7.17

Satus Creek Adult Steelhead 31 0.7864 0.7779 9.94 7.47

Yakima River Kelts (Prosser) 13 0.821 0.767 8.41 8.27

Section Corner Creek Juv. 159 0.7411 0.7903 7.06 5.85

Hardy Weinberg Equilibrium

• 161 Total Tests• 16 significant• 12 In Section Corner Creek juveniles• 2 in Omak Creek residents below Mission Falls• 1 in Omak Creek adult steelhead• 1 in Yakima River kelt steelhead

Linkage Disequilibrium

• 1168 pairwise tests• 250 were significant• 128 in Section Corner Creek juveniles• 83 in Omak Creek residents below Mission Falls• 39 in Omak Creek steelhead

Pairwise FST Values / Genic differentiation rates

 

Omak Omak Omak Shitike Shitike Shitike Satus Yakima Section

Adult Res 1 Res 2 Adult Res Juv Adu Kelt Juv

Omak Adu ---

Omak Res1 0.0256 ---

Omak Res2 0.0294 0.0077 ---

Shitike Adu 0.0158 0.0275 0.0313 ---

Shitike Res 0.0817 0.1060 0.1046 0.0497 ---

Shitike Juv 0.0849 0.1083 0.1054 0.0555 0.0021 ---

Satus Adu 0.0225 0.0348 0.0410 0.0176 0.0781 0.0820 ---

Yakima Kelt 0.0276 0.0162 0.0283 0.0114 0.0957 0.1020 0.0168 ---

Section Juv 0.0501 0.0691 0.0754 0.0432 0.0953 0.1017 0.0127 0.0518 ---

* NOT significant at adjusted critical level =.05 / 36 tests = 0.0014

Neighbor joining dendrogram Cavalli-Sforza Edwards genetic distance

Shitike Creek Adult Steelhead

Shitike Creek Resident RBT

Shitike Creek Juveniles

100

99

Yakima River Kelt Steelhead

Section Corner Creek Juveniles

Satus Creek Adult Steelhead

10095

86

Omak Creek Adult Steelhead

Omak Creek Resident RBT Above Mission Falls

Omak Creek Resident RBT Below Mission Falls

99

Parentage Analysis:Section Corner Creek

• 5 males from Satus Creek• 6 females from Satus Creek• 5 female kelts from Yakima River

• Assigned all 159 juveniles back to a single parental cross.

Parentage Assignment Matrix: Section Corner Creek

  Male 1 Male 2 Male 3 Male 4 Male 5 Sum

Female 1 41 41 (1)

Female 2 6 7 13 (2)

Female 3 9 15 6 1 2 33 (6)

Female 4 1 3 2 7 13 (4)

Female 5 27 11 38 (3)

Female 6 10 1 10 21 (3)

Kelt 1

Kelt 2

Kelt 3

Kelt 4

Kelt 5

Sum 51 (3) 61 (5) 6 (1) 11 (3) 30 (4)

Overripe

Partially Blind

Parentage Analysis: Shitike Creek

• Adult Steelhead from Shitike Creek• Resident Rainbow Trout from Shitike Creek

• Limited results in assigning juveniles back to potential parents

Parentage Analysis:Shitike Creek

• Shitike Creek juveniles grouped closest to Shitike Creek resident rainbow trout on the neighbor joining tree.

• Shitike Creek Juveniles and Shitike Creek resident rainbow trout had an insignificant FST Value.

• Many residents unsampled.

• The fall migration of juveniles sampled in 2005 were comprised of progeny from unsampled resident rainbow trout.

Summary

• Average survival in long-term reconditioning experiments = 46%.

• Two movement patterns have been detected in the estuary.• Kelts appear to not reside in the estuary. • Reproductive success experiment sites have been chosen and

tests are in progress.• Kelts placed into Section Corner Creek did not contribute to the

progeny collected.• Overripe• Blind

• Parentage assignment worked well (159 of 159 Section Corner Creek juveniles).