1. Application of Genetic Baseline: Aiding the Recovery of Steelhead
Scott M. Blankenship
Yakima Basin Science & Management Conference – 2011

2. Overview
Status and trends monitoring – viable salmonid population criteria
Yakima Steelhead Recovery Plan
Genetic resources available and their application

3. Viable Salmonid Population Criteria

4. VSP – What is being monitored
What are the monitoring needs associated with Recovery Plans for Pacific Northwest ESU and DPS listed under the Endangered Species Act?
Monitoring Recommendations – (Crawford and Rumsey 2009)
Address all:
Viable salmonid population criteria
Listing Factors
Threats
Threats = habitat loss, hydropower, overharvest, disease/predation, regulatory inadequacy, hatchery production, acts of nature

5. VSP – What is being monitored
VSP Adult Spawner Abundance
Unbiased sampling design with known precision and accuracy
Ratio of adipose absent/intact on spawning grounds
Calculate average coefficient of variation for natural-origin spawner estimates (per population)
Determine power to detect a significant change in abundance
Adult abundance is foundation parameter for monitoring and delisting
Juvenile abundance = freshwater production, survival, habitat use (parr)
Productivity = combines adults and juvenile abundance (adult to adult, SAR)
Overutilization = I don’t know if I would use this term, but the key is to precisely estimate harvest of wild fish, as this relates to productivity.

6. VSP – What is being monitored
VSP Adult Spawner Abundance
VSP Productivity
Develop at least 12 brood years of spawner information from cohort analysis
Recruits per spawner
Estimate juvenile migrants for at least one MPG population within each ESU/DPS
Calculate average coefficient of variation
Determine power to detect a significant change
Adult abundance is foundation parameter for monitoring and delisting
Juvenile abundance = freshwater production, survival, habitat use (parr)
Productivity = combines adults and juvenile abundance (adult to adult, SAR)
Overutilization = I don’t know if I would use this term, but the key is to precisely estimate harvest of wild fish, as this relates to productivity.

7. VSP – What is being monitored
VSP Adult Spawner Abundance
VSP Productivity
VSP Spatial Distribution
VSP Species Diversity
Short term:
Use distribution, spawn time, age structure, fecundity, and sex ratio
Long term:
Develop a genotypic and phenotypic baseline for each population within each MPG

8. Priorities and Problems

9. Problem Cases Highest: Adult Abundance in natural spawning areas
Methods:
Escapement Sampling (e.g. adjusted weir count )
Probabilistic Sampling – unbiased randomized sites
Index Spawner Survey – (e.g. expanded redd counts)
Escapement example: weir count adjusted for pre-spawn mortality
Probabilistic= unbiased randomized sites with rotational panels. Produces estimates similar to mark-recapture. Used for Wenatchee steelhead
Index surveys = used fish, redd, or carcass counts in index reaches to extrapolate to entire stream
What if you have multiple populations above count site?
What if you do not observe redds or recover carcasses poorly?

10. Yakima Steelhead Recovery Plan

11. Yakima Steelhead Recovery Plan
Landmarks:
1999 – Middle Columbia River steelhead listed a threatened

13. Yakima Steelhead Recovery Plan
Landmarks:
1999 – Middle Columbia River steelhead listed a threatened
2006 – Listing revised to cover only anadromous form of O. mykiss
2006 – Yakima Subbasin Salmon Recovery Plan adopted
2009 – Yakima Steelhead Recovery Plan (updated, revised)
2009 – YSRP incorporated into Middle Columbia Steelhead
Recovery Plan

14. Yakima Steelhead Recovery Plan
Abundance and Productivity: Ladder counts at Prosser Dam Counts at Roza Dam
Where to start? Focus on abundance and productivitiy – the critical parameters

15. Basin Map Yakima Roza Dam Prosser Dam Chandler Facility Cle Elum
Ellensburg
Roza Dam
Yakima
MPG contains four populations: Satus, Toppenish, Naches, upper Yakima
Recovery plan states that genetic information will be used to partition adult counts to population
Prosser Dam Chandler Facility

16. Basin Map Yakima Upper Yakima River Naches River Roza Dam
Cle Elum
Ellensburg
Naches River
Roza Dam
Yakima
Toppenish Creek
MPG contains four populations: Satus, Toppenish, Naches, upper Yakima
Recovery plan states that genetic information will be used to partition adult counts to population
Prosser Dam Chandler Facility
Satus Creek

17. Yakima Steelhead Genetic Resources

18. Yakima Baseline - FCA

19. Reference Collections
Initial Baseline
Additions
Satus Creek
Toppenish Creek
Ahtanum Creek
Naches River
upper Yakima River
Teanaway River
Taneum River
Skamania Hatchery
Cowiche Creek
Oat Creek
Little Rattlesnake Creek
N.F. Little Naches River
Nile Creek
Pile Up Creek
West Quartz Creek
Umtanum River
Goldendale Hatchery
Potential migrant baseline.
Structure analysis and added some collections

20. Yakima Steelhead - STRUCTURE
Yak Tea Tan Nac Oth Top Sat Gol
Purple is “other” category. Cutthroat, California redband. Ahtanum, Cowiche, Oat, Umtanum removed.
Individuals with 90% ancestry in another group than their perceived origin were removed.
Individual steelhead from baseline

21. Reference Collections
Baseline
Reporting Group
Goldendale Hatchery
Satus Creek
Toppenish Creek
Little Rattlesnake Creek
Naches River
N.F. Little Naches River
Nile Creek
Pile Up Creek
West Quartz Creek
Taneum River (residents)
Taneum River
Teanaway River (resident)
Teanaway River
upper Yakima River
Goldendale
Satus
Toppenish
Naches
upper Yakima

22. Yakima Steelhead - STRUCTURE
Yak Nac Other Top Sat Gold
Mean ancestry by collection

23. Power of reference baseline
Realistic Fishery Simulations
Reporting Group
GoldendaleH
SatusCr
ToppenishCr
NachesR
TaneumR
TeanawayR
Goldendale
1.000
0.000
Satus
0.979
0.005
0.004
0.003
Toppenish
0.002
0.990
0.001
Naches
0.006
0.982
0.007
Upper Yakima
0.013
0.014
0.993
0.994

24. Conclusions VSP criteria integral to monitoring and recovery planning
Genetic techniques offer alternative strategies for meeting monitoring requirements
Yakima Steelhead Recovery Plan adopted genetic-based metrics for estimating abundance and productivity
Genetic infrastructure in place

25. Future steps
Representative sampling of adults at Prosser Dam Partition juveniles migrants by region (traps, Chandler facility) Spatial Distribution Radio tracking and new tagging technologies What is the role of mainstem spawning to recovery scenarios? Diversity Understanding the balance between life history forms Non-native hatchery fish

26. Acknowledgements WDFW MGL Funding Norm Switzler Maureen Small
Jennifer von Bargen
Sarah Bell
Funding
Bonneville Power Administration
NOAA
Washington State Fund
Steelhead information
Yakama Nation
CRITFC

27. Questions?
Phylogenetic tree (red lines) merged with geographic position of collections (blue circles). In theory any type of similarity matrix could be displayed in this fashion. This is a very preliminary graphic, I am not sure how to refine this yet.

28. Prosser Dam Mixed Adults
Population
Location
Stage
Location (rkm)
Year
WDFW Code
SPAN
Yakima MPG
Prosser-Mixed Adults
Adult
Prosser
2007
07AJ
165
2008
08LM
228

29. Prosser Dam Mixed Adults
2007
Satus
0.07
(0.01, 0.12)
Toppenish
0.20
(0.12, 0.26)
Ahtanum
0.11
(0.03, 0.16)
Naches
0.28
(0.19, 0.34)
Upper Yakima
0.26
(0.16, 0.35)
Teanaway
0.09
(0.04, 0.20)
Skamania
0.00
(0.00, 0.00)
lower
0.38
Naches
0.28
Upper Yakima
0.34

30. Prosser Dam Mixed Adults
2008
Satus
0.10
(0.03, 0.14)
Toppenish
0.29
(0.21, 0.34)
Ahtanum
0.07
(0.03, 0.13)
Naches
(0.21, 0.37)
Upper Yakima
0.17
(0.09, 0.23)
Teanaway
0.06
(0.03, 0.18)
Taneum
0.01
(0.00, 0.03)
Skamania
0.00
(0.00, 0.00)
lower
0.46
Naches
0.29
Upper Yakima
0.24