Chinook salmon (Oncorhynchus tshawytscha) undertake some of the most well-known and well-studied migrations in the animal kingdom. Following extensive migrations through riverine and marine environments, salmon in California’s Central Valley return to highly altered and spatially constrained freshwater spawning habitats. Millions of dollars are spent annually to monitor these migrations and mitigate the effects of habitat loss and hydropower operation on freshwater spawning and rearing habitat. Yet, populations remain imperiled due to increasing water temperatures, water diversions, channel alterations, high predation rates, and replacement of wild stocks with straying hatchery stocks. The Stanislaus River has one of the most comprehensive and longest running life-cycle monitoring programs in the Central Valley. Monitoring activities are designed to track the abundance, distribution, migration characteristics, and habitat use of Chinook salmon, using a variety of different sampling methods and technologies. Rotary screw trap monitoring is used to characterize juvenile downstream migration, while a fish counting weir is used to monitor upstream migration of adults. Snorkel and seining surveys document abundance and habitat use, redd and carcass surveys document spawning, collect biological samples and coded-wire-tags. These data will inform flow management and habitat enhancement to provide suitable conditions for multiple life stages of Chinook salmon.

1. Caught Between a Rock and a Hard
Place
Monitoring Chinook Salmon in California’s
Central Valley
AFS & TWS Joint Annual
Conference, Reno, Nevada
Sept 28 – Oct 3, 2019
Tyler Pilger, Dana Lee, Matt Peterson,
Andrea Fuller, Doug Demko

2. Overview
www.FISHBIO.com
• Chinook salmon life
history
• Status & management
• Regional monitoring
• Stanislaus fall-run
Chinook research &
monitoring
• Status assessment
• Summary
Food
Security and
Conservation
Management
R
esearch and Monitoring

3. www.FISHBIO.com
Background: Chinook Salmon
www.wildsalmoncenter.org

4. Background: Chinook Salmon
www.FISHBIO.com
• Metapopulation in space and time
July Jan Jun
Herbold et al 2018

5. Background: Central Valley Swimways
• Dams – historic spawning habitat inaccessible
www.FISHBIO.com
Herbold et al.
2018

6. Background: Central Valley Swimways
• Land conversion
• Water exports and introduced species
www.FISHBIO.com

7. Economically important fall-run
www.FISHBIO.com
Review of 2018 Ocean Salmon Fisheries, PFMC 2019
0
500
1,000
1,500
2,000
1985 1990 1995 2000 2005 2010 2015
Chinook
Salmon
(x1000)
Adult Escapement
In-river Harvest
Ocean harvest
Forecasted SI
Failure of 2004
and 2005 brood
year classes
(Lindley et al.
2009)

8. Economically important fall-run
• Imperfect harvest forecasts
www.FISHBIO.com
Review of 2018 Ocean Salmon Fisheries, PFMC 2019
-100%
-50%
0%
50%
100%
1985 1990 1995 2000 2005 2010 2015
(Postseason-Forecast)/Forecast

9. Management
• Doubling goal (CVPIA 1992):
• Flow and temperature “knobs”
www.FISHBIO.com

10. Management
• Increased hatchery production and off-site
releases
www.FISHBIO.com
0
0.2
0.4
0.6
0.8
1
0
10
20
30
40
50
60
1946 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005 2010
Proportion
Released
in
Estuary
Hatchery
Chinook
Released
(Millions)
Millions of Hatchery fish released Proportion Released in Estuary
Huber and Carlson 2015

11. Monitoring Pyramid
www.FISHBIO.com
Food
Security and
Conservation
Management
R
esearch and Monitoring

12. Regional Monitoring
• ~60 programs for adults and juveniles
• Federal, state & tribal agencies, organizations
• ~$10 million annually
2007 Existing Program Summary: Central Valley Salmon and Steelhead Monitoring
Programs - CDFW
www.FISHBIO.com

13. Stanislaus River Monitoring
www.FISHBIO.com
Counting
Weir
N
Spawning reach

14. Stanislaus River Monitoring - Juveniles
www.FISHBIO.com
Research:
• Comparison of RST abundance estimators
(Pilger et al. 2019)
• Predation and survival of juvenile salmon
(Ongoing)

15. Stanislaus River Monitoring - Adults
www.FISHBIO.com
Research:
• Ground-truth historical data (in prep)
• Effects of fall pulse flows on escapement
(Peterson et al. 2017)

16. Stanislaus River Monitoring
• Stock-recruit curves inform population
dynamics
www.FISHBIO.com

17. Stanislaus River Monitoring
• Fine scale surveys
www.FISHBIO.com
Research:
• Biological and environmental effects on
spawning (Peterson et al. 2020, ongoing)
• Juvenile fall-run habitat usage (ongoing)

18. Stanislaus River Monitoring
• Substantial hatchery contribution, no hatchery
on Stanislaus River
www.FISHBIO.com
Coded-wire tag data from Regional Marking Information System database (rmpc.org)

19. NOAA Status Framework
www.FISHBIO.com
Criterion
Extinction Risk
High Moderate Low
Any one of Any one of All of
Population size Ne ≤ 50
N ≤ 250
Ne = 50 – 500
N = 250 – 2,500
Ne > 500
N > 2,500
Population decline Precipitous Chronic or
depressed
No decline, stable
Catastrophic
events
Order of
magnitude decline
within 1
generation
Small but
significant decline
No apparent
decline
Hatchery
influence
High Moderate Low
Lindley et al. 2007

20. Status of Stanislaus fall-run
www.FISHBIO.com
Criterion
Extinction Risk
High Moderate Low
Any one of Any one of All of
Population size N = 14,825
SD = 11,130
Population decline +13.4% over last
10 years
Catastrophic
events
77.5% decline
from 2005 to 2008
Hatchery
influence
81% hatchery
origin 2010 to
2016

21. Summary
• Central Valley swimways
are heavily modified
• Chinook populations
highly managed, not self-
sustaining
• Non-listed runs at risk
from catastrophic events
and high hatchery
influence
www.FISHBIO.com

22. Summary
• Reduce hatchery
influence
• Focus on resilience
• Better harvest forecasts,
in-season monitoring
• Set escapement goals
based on biological
targets
• Close gaps in monitoring
www.FISHBIO.com
Food
Security and
Conservation
Management
R
esearch and Monitoring

23. Acknowledgements
Funding provided by: Oakdale and South San Joaquin Irrigation Districts
We thank the following people:
Symposium Organizers –Teresa Campbell, Erin Loury, Shaara Ainsley, Arjan Berkhuysen,
Kerry Brink, Zeb Hogan, and Herman Wanningen
FISHBIO –Michael Hellmair, Patrick Cuthbert, Ryan Cuthbert, Jeremy Pombo, John
Montgomery, Jim Inman, Chrissy Sonke, Mike Kersten, Tara Lamb, Garth Jaehnig, Rob
Fuller, Earl Fuller, Logan Douglas, Scott Stocker, Rick Biedenweg, Graham Buggs, Ian
Herzberger, Ben Griffith, Steve Clark, DeeThao, Bryce Neal, and Garret Muniain
www.FISHBIO.com

24. FISHBIO
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Vientiane Capital, Lao PDR
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Costa Rica
Questions?
Tyler Pilger
tylerpilger@fishbio.com
530.636.4698
www.FISHBIO.com