1. Factors affecting the
marine survival of
Puget Sound steelhead
Northwest
Fisheries
Science Center
Barry Berejikian and Megan Moore
Environmental and Fisheries Sciences Division
Manchester Research Station

2. Salish Sea Marine Survival Project
(Steelhead Workgroup)
Puget Sound Steelhead Marine Survival
Workgroup Participants
• Neala Kendall, WDFW
• Megan Moore, NWFSC
• Barry Berejikian, NWFSC
• Scott Pearson, WDFW
• Ken Warheit, WDFW
• Erik Neatherlin, WDFW
• Chris Ellings, Nisqually Indian Tribe*
• Sandie O’Neill, WDFW
• Mike Crewson, Tulalip Tribes*
• Ed Connor, Seattle City Light
U.S. Department of Commerce | National Oceanic and Atmospheric Administration | NOAA Fisheries | Page 2
Contributing Experts
• Steve Jeffries, WDFW
• Bruce Stewart, NWIFC
• Paul Hershberger, USGS
• John Kerwin, WDFW
• Dave Beauchamp, UW
• Linda Rhodes, NWFSC
• Lyndal Johnson, NWFSC
• Gina Yitalo, NWFSC
• Penny Swanson, NWFSC
• Brian Beckman, NWFSC
• Andy Goodwin, U.S. Fish and Wildlife Service
• Joy Evered, U.S. Fish and Wildlife Service
• Kym Jacobson, NWFSC
• Mary Arkoosh, NWFSC
• Joe Dietrich, NWFSC
Project Management and Facilitation
• Michael Schmidt, Long Live the Kings
• Iris Kemp, Long Live the Kings

3. Outline
• Puget Sound steelhead life history and abundance
trends
• Factors that may affect marine survival
• Freshwater
• Marine
• Salish Sea Marine Survival Project (wrt steelhead) –
next steps
3

4. Puget Sound Steelhead
• Very popular sport and important tribal fisheries
• Predominantly winter-run populations (late fall – spring)
• Roughly 1.5 M hatchery-reared fish released annually
• PS steelhead listed ‘Threatened’ in 2007
• Factors in listing decision
• Declines in abundance and productivity
• Habitat (dams, urbanization, water quality)
• Artificial propagation

5. Oncorhynchus mykiss life history
Egg
Parr
Maturation in
freshwater
Smolt (age 1 -3)
Estuary/early marine (2 weeks)
Ocean (1 – 3 years)
Maturation and
spawning Rainbow trout
(resident form)
Steelhead
(anadromous form)

6. Abundance of Puget Sound and WA coast
populations
0
5000
10000
15000
20000
25000
1980 1985 1990 1995 2000 2005 2010 2015
Skagit
Green
Puyallup
Nisqually
Queets
Quinault
Hoh
Quillayute

7. Abundance trends
0%
10%
20%
30%
40%
50%
60%
70%
80%
Nisqually Puyallup Green Skagit Quinault Queets Hoh Quillayute
Puget Sound Washington Coast
South North South North
Mean(2005-2010)/Mean(1984-1989)

8. Marine (smolt-to-adult) survival
0%
2%
4%
6%
8%
10%
SAR
Lower Columbia Coast Puget Sound
0%
2%
4%
6%
8%
10%
1970 1975 1980 1985 1990 1995 2000 2005 2010
SAR
Brood year
Summer-run
Winter-run
Source: Puget Sound Steelhead Marine Survival Draft Workplan

9. Where does this lead us?….
• Abundance and SAR trends point to:
 Strong marine signal
 Different signal within Puget Sound than elsewhere (lower survival), particularly
since early1990’s
 Possibly worse conditions in ‘the deep south’
• What is different about Puget Sound that might reduce marine survival relative to
other regions?
 Puget Sound freshwater stream effects on smolt characteristics
 Migration routes in the Pacific Ocean
 Puget Sound marine conditions

10. Freshwater effects
(on subsequent marine survival)
• Some hypotheses:
Reduced diversity (‘Portfolio effect’: e.g., Schindler et al. 2012. Nature)
Hatchery effects (genetic or ecological)
Water quality (e.g., toxics)
Disease

11. 11
Hood Canal Steelhead

12. Freshwater: Spawn timing
DewattoRiver
TahuyaRiver
UnionRiver
NFSkokomishRiver
SFSkokomishRiver
HammaHamma
Duckabush
DosewallipsRiver
LittleQuilceneRiver
BigBeefCreek
0.00
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0.80
0.90
Proportionofredds
Source: WDFW SGS Database & Hood Canal Steelhead Project
0.00
0.10
0.20
0.30
0.40
0.50
Proportionofredds
Kitsap
Peninsula
Olympic
Peninsula

13. Freshwater: Spawn timing and size at age
13
R² = 0.8836
80
90
100
110
120
130
140
50 100 150
Meanforklength(mm)atage-1(spring)
Mean spawning date (days from Jan 1)
0
20
40
60
80
100
120
140
160
180
200
220
Age-1 Age-2 Age-3Forklength(mm)

14. Source: Hood Canal Steelhead Project 14
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Age
1 2 3 4
Freshwater: Age-at-smoltification

15. Source: Hood Canal Steelhead Project
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
20-Mar 3-Apr 17-Apr 1-May 15-May 29-May 12-Jun 26-Jun
Cumulativeproportionofsmolts
Date
Big Beef
Dewatto
Tahuya
Little Quilcene
Duckabush
Hamma Hamma
Skokomish
Freshwater: Smolt migration timing
L. Quilcene
Duckabush
Hamma
Hamma SF Skokomish
TahuyaDewatto
Big Beef
R² = 0.6455
110
115
120
125
130
135
360 410 460 510 560 610
MeanCalendardayofoutmigration
Accumulated winter temperature units ( C)

16. 16
Other freshwater effects
Hatcheries may have both ecological and genetic effects:
 Notably, no steelhead released into the Nisqually River since 1980
Water Quality/toxics:
Toxic contaminant exposure data for steelhead is lacking
Nisqually considered most pristine in main basin of Puget Sound
Disease:
 Nanophyetus: more prevalent in south than north Puget Sound
 Rapid infections; can affect swimming performance
0%
10%
20%
30%
40%
50%
60%
70%
80%
Nisqually Puyallup Green Skagit Quinault Queets Hoh Quillayute
Mean(2005-2010)/Mean(1984-1989)
Puget Sound Washington Coast
Mean annual hatchery smolt releases
1986-2007
0K 203K 207K 329K

17. Steelhead in the marine environment
• Pacific Ocean migratory patterns and distribution
• Puget Sound migratory behavior and survival

18. Steelhead Ocean migratory behavior
McMichael et al. Animal Biotelemetry 2013, 1:14 (Figures 2 and 4)

19. Steelhead Ocean Distribution (spring/summer)
Atcheson et al. 2010. Trans. Am. Fish. Soc. 141 (4)
19

20. Steelhead in the marine environment
• Pacific Ocean migratory patterns and distribution
• Puget Sound migratory behavior and survival

21. 21
TABLE 2. Fish taxa captured by surface trawls at 52 sites in greater Puget
Sound during May–August 2003; taxa are ranked in order based on highest
to lowest frequency of occurrence. (Rice et al. 2012. Marine and Coastal
Fisheries 4: 117-128)
SPECIES % frequency
1. Chinook salmon Oncorhynchus tshawytscha 65.6
2. Pacific herring Clupea pallasii 57.6
3. Threespine stickleback Gasterosteus aculeatus 51.5
4. Surf smelt Hypomesus pretiosus 50.0
5. Chum salmon O. keta 35.4
6. River lamprey Lampetra ayresii 25.4
7. Pacific sand lance Ammodytes hexapterus 22.4
8. Coho salmon O. kisutch 11.7
9. Bay pipefish Syngnathus leptorhynchus 11.2
10. Pacific sandfish Trichodon trichodon 9.0
11. Starry flounder Platichthys stellatus 8.8
12. Shiner perch Cymatogaster aggregata 6.1
13. Steelhead O. mykiss 3.7
**species ranked 14-33 not shown

22. Acoustic telemetry
Vemco 7mm and 9 mm pingers
@ 69kHz, 136 db

23. Limitations/considerations for acoustic telemetry
• Handling and tag effects never fully known (some
negative effects on growth)
• Tag loss in seawater 2% (V7) - 12% (V9), but not
until after outmigration
• Seals can hear them (Cunningham et al. in review)
• Detection range of receivers varies depending on
currents, noise, water quality etc.
• Expected to under-estimate natural survival rates

24. Steelhead telemetry in Hood Canal
Moore et al. 2010a. TAFS
Moore et al. 2010b. PLOS One
Moore et al. 2012. PLOS One
Moore et al. 2013. PLOS One

25. Moore et al. 2010a. Trans. Am. Fish. Soc. 25

26. Moore M, Berejikian BA, Tezak EP (2013) A Floating Bridge Disrupts Seaward Migration and Increases Mortality of Steelhead Smolts in Hood Canal, Washington
State. PLoS ONE 8(9): e73427. doi:10.1371/journal.pone.0073427
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073427
Known survivors
Presumed mortalities
Telemetry useful for identifying hotspots
Possible mortalities
Undetermined

27. Puget Sound Telemetry ‘Study’
Hood Canal Rivers: 2006-2010
Moore, Berejikian, et al. (NWFSC)
Green River: 2006-2009
Fred Goetz, Tom Quinn et al (UW, ACOE)
Puyallup River: 2006, 2008-2009
Andrew Berger et al. (Puyallup Tribe)
Nisqually River: 2006-2009
Sayre Hodgson et al. (Nisqually Tribe)
Skagit River: 2006-2009
Ed Conner et al. (Seattle City Light)

28. Telemetry array
Migration Segments
Hood Canal Puget Sound Skagit
1st segment River Mouth - HCB River Mouth - CPS River Mouth - DP
2nd segment HCB – ADM CPS – ADM
3rd segment ADM – JDF ADM – JDF DP - JDF

29. 2006 -2009 Puget Sound Telemetry Study
Population
N2006 N2007 N2008 N2009
W H W H W H W H
Hood canal 73 33 123 47 67 42 105 59
Green 100 50 39 50 48 50 50 -
Nisqually 55 - 49 - 14 - 69 -
Puyallup 25 25 - - - 90 - 66
Skagit 23 - 47 - 50 50 25 55
TOTAL 334 355 411 293

30. Cumulative travel times
0
2
4
6
8
10
12
14
16
18
20
RM-HCB RM-ADM RM-JDF
Hood CanalSkok
BBC
0
2
4
6
8
10
12
14
16
18
20
RM-NAR RM-CPS/DP RM-ADM RM-JDF
Traveltime(days)
Puget Sound
Nisqually
Puyallup
Green
Skagit

31. Travel rates
0
5
10
15
20
25
30
35
40
45
50
RM-NAR/CPS/DP NAR-CPS CPS-ADM ADM/DP-JDF
Travelrate(km/d)
Puget SoundNisqually
Puyallup
Green
Skagit
0
5
10
15
20
25
30
35
40
45
50
RM-HCB HCB-ADM ADM-JDF
Hood Canal
Skok
BBC

32. Mark-Recapture Survival Estimates: Cormack-Jolly-Seber
Population
N2006 N2007 N2008 N2009
W H W H W H W H
Hood canal 73 33 123 47 67 42 105 59
Green 100 50 39 50 48 50 50 -
Nisqually 55 - 49 - 14 - 69 -
Puyallup 25 25 - - - 90 - 66
Skagit 23 - 47 - 50 50 25 55
TOTAL 334 355 411 293
Categorical variables
Population
Region (HC, SS, Skagit)
Rear type (H/W)
Migration Segment
Year
Tag Type
Continuous variables
Distance travelled
Body Length
Model with lowest AICc = ~(Segment x population)+ (year)+ (rear type H/W)
N=1393

33. Early marine survival in Hood Canal and Puget Sound steelhead
0%
5%
10%
15%
20%
25%
30%
35%
40%
Skokomish (W) Skokomish (H) Hamma (H) BBC (W)
AverageRM-JDFSurvival
Hood Canal
0%
5%
10%
15%
20%
25%
30%
35%
40%
Nisqually (W)Puyallup (W) Puyallup (H) Green (W) Green (H) Skagit (W) Skagit (H)
Puget Sound
W = Wild H = Hatchery
Combined early marine survival estimate = 17% (hatchery = 12% , wild = 20%)

34. Source: Welch et al. PNAS 108: 8708-8713
Strait of Georgia and Johnstone Strait
steelhead survival estimates

35. 35
0
1000
2000
3000
4000
5000
6000
1
31
61
91
121
151
181
211
241
271
301
331
361
391
421
451
481
511
541
571
601
631
661
691
721
Numberofsurvivors
Days after seawater entry
River mouth to Pacific Ocean (21 days)
Adult return at 3% SAR (720 days)
Instantaneous daily mortality rates:
River mouth to Pacific Ocean (M = 0.086)
Pacific Ocean entry to adult return (M = 0.003)

36. Distance from Juan de Fuca Strait (km)
050100150200250
Survival(%)
0
20
40
60
80
100
Big Beef
Green
Nisqually
Puyallup
Skagit
Skokomish
Can we identify mortality ‘hot spots’?
NAR
CPS
HCB
DP
ADM
NAR = Tacoma Narrows
CPS = Central Puget Sound
ADM = Admiralty Inlet
HCB = Hood Canal Bridge
DP = Deception Pass

37. Comparing Puget Sound to Hood Canal
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
RM-HCB/CPS HCB/CPS-ADM ADM-JDF RM-JDF
2008
SurvivalProbability
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
RM-HCB/CPS HCB/CPS-ADM ADM-JDF RM-JDF
2009
(Skokomish RM-HCB = 66 km)
(Nisqually RM – CPS = 67 km)

38. Telemetry Summary
 Low early marine survival rates consistent with SARs and abundance of Puget Sound steelhead
 Instantaneous daily mortality rates are high (i.e., mortality occurs very quickly)
 Rapid travel times (1 – 3 weeks from river mouths to ocean entry)
Puget sound may serve more a migratory corridor than a rearing environment
Has it always been this way, or is that part of the problem?
 Hood Canal and Puget Sound steelhead exhibit different patterns
 Central Puget Sound may represent a mortality hotspot

39. Steelhead dying
at high rate in PS
Predation IS proximate/
direct cause of mortality
Predation IS NOT proximate/
direct cause of mortality
Poor fish condition and/or altered behavior:
freshwater (F) or marine (M) effect (ranked)
1. Disease (M/F)
2. Poor water quality/toxics (M/F)
3. Genetic fitness loss (F)
4. HABs (M)
5. Foraging/Starvation (M)
6. Portfolio (outmigrant size or timing -F)
7. Structural changes in marine habitats (M)
Predator-prey interactions
1. Depensation
2. Increase in key predator populations
3. Decrease abundance of other prey

40. 2013-2015 Steelhead Marine Survival Study
Activities
2013
September
October
November
December
2014
January
February
March
April
May
June
July
August
September
October
November
December
2015
January
February
March
April
May
June
Permitting
Upgrade telemetry receivers
Studies
1: Complete retro telemetry data
analysis
2: Complete SAR trend analysis
3: Fish characteristics vs. SARs
4. Enviro. data vs. SARs & telemetry
5: Predator review
6: Genome-wide association study
7: Juvenile fish health assessment
8: Reciprocal transplant
9. Harbor seal interactions
10: Dinner bell effect
11: Modeling (affiliated)
Legend for study work
Preparation
Field Work
Analysis
Reporting
Tech Memo Due

41. 8. Reciprocal transplant
Test following effects on marine survival
 Population
 Location
 1st segment
 2nd segment
 Translocation (nuisance)
41
B1
C
B2
D
E
A2
A1

42. Predator-prey interactions
42
Avian predators (S. Pearson, WDFW, review in prep)
cormorants (most abundant)
Caspian terns
common mergansers
loons
rhinoceros auklets (feed on smaller prey)
Mammalian predators
Harbor porpoise
Harbor seals
Identifying potentially important predators on steelhead smolts
Criteria:
1. Spatial and temporal overlap,
2. Known to eat steelhead
3. Known to eat similarly sized salmon or other fish
4. Increasing or stable abundance,

43. Predator-prey interactions (harbor porpoise)
(J. Evenson, WDFW, 2013, unpublished data)
43
1993-1998 1999-2004 2005-2011

44. Predator-prey interactions (harbor seals)
44
Harbor seal counts
Jeffries et al. 2003 J. Wildlife Manage.

45. 9. Harbor seal/steelhead
interactions
45
B1
C
B2
D
E
A2
A1
Quantify
 core foraging areas of harbor seals
during the steelhead smolt outmigration;
 spatial and temporal overlap of harbor
seals and steelhead smolts in specific
areas of Puget Sound;
 predation events by seals on tagged
steelhead smolts
GPS, acoustic tag/receiver, VHF

46. 10. Dinner Bell effect
Do smolts with pinging
transmitters experience
similar mortality to those
with temporarily silent
transmitters?

47. 10. Dinner Bell effect
Do smolts with pinging
transmitters experience
similar mortality to those
with temporarily silent
transmitters?
~ 5 days

48. More Acknowledgements…..
Telemetry study funding provided through NOAA, USACE (Seattle District), UW, Steelhead Trout
Club of Washington, Pacific Ocean Shelf Tracking Network (POST)
Survival Modeling Support
Mike Melnychuk (UW)
Jeff Laake (NOAA SWFSC)
Field/Logistic Support
Long Live the Kings ▪ Hood Canal Salmon Enhancement Group ▪
Mat Gillam ▪ R2 Resource Consultants ▪ Bob Leland ▪ Kelly Kiyohara ▪ Pat
Michael Brody Antipa ▪ Pete Topping ▪ Deborah Feldman ▪ Kelly Andrews ▪
John Blaine ▪ Jim Deveraux ▪ Skip Tezak Correigh Greene ▪ Anna Kagley ▪ Shawn Larson ▪ Jeff
Christiansen ▪ John Rupp ▪ Chuck Ebel ▪ Jose Reyes-Tomassini ▪ Jennifer Scheurell ▪ Chris Ewing
Dawn Pucci ▪ Kurt Dobszinsky ▪ Paul Winchell ▪ David Welch ▪ Debbie Goetz ▪ Jose
Gimenez ▪ Aswea Porter ▪ Emiliano Perez ▪ Craig Smith ▪ Tim Wilson ▪ Florian
Leischner ▪ Christopher Ellings ▪ Scott Steltzner

49. • Figure 2. Survival estimates for smolts migrating through fresh- and saltwater migration segments.
Moore M, Berejikian BA, Tezak EP (2012) Variation in the Early Marine Survival and Behavior of Natural and Hatchery-Reared Hood Canal Steelhead. PLoS One
7(11): e49645. doi:10.1371/journal.pone.0049645
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049645
Telemetry useful for estimating survival (especially relative survival)
-Release to river mouth
-River mouth to HC bridge
-HC bridge to Admiralty Inlet
-Admiralty Inlet to Pillar Point

50. Comparing Puget Sound to Hood Canal
SurvivalProbability
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
RM-HCB/CPS HCB/CPS-ADM ADM-JDF RM-JDF
2008
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
RM-HCB/CPS HCB/CPS-ADM ADM-JDF RM-JDF
2009
(Big Beef RM-HCB = 25 km)
(Green River RM-CPS = 11 km)

51. Quantifying encounter and predation rates
• Spatial overlap: seal and steelhead detections on same
receivers
• Temporal and spatial overlap: concurrent pings on same fixed
(moored) receivers
• Potential encounters: pings detected on mobile (seal-mounted)
receivers
• Putative predation events:
• recurring continuous pings on seal-mounted receivers,
perhaps followed by...
• Stationary tags (defacated tags) connected to seal
movements/locations

52. Puget Sound Chinook salmon
• Residency in Puget Sound = weeks to years.
• Very abundant in Puget Sound spring through
summer (Beauchamp and Duffy 2011, Rice et al. 2012)
• Spring/summer growth rate and body size strongly
correlated with survival (in hatchery stocks: Duffy and Beauchamp
2011)
• Foraging opportunities, diet composition, and
competition (including comp. with hatchery Chinook salmon) likely
influence survival.

53. 6/3/2014 53
20 fish were released and 6 were detected at the Point Reyes Array. That’s 30%
survival over 137 km
12 (60%) were detected traveling from the river mouth through San Pablo Bay
and through San Francisco Bay (77 Km), 2 went south of the Bay Bridge Array,
and 10 that entered the ocean were detected at point reyes.
Sundstrom et al 2013
Oregon estuaries, lose about 50% in < 20 km or even shorter distances. Steepest
losses in areas where there’s been documented high predation rates
San Francisco Bay

54. 6/3/2014 54
Species Year Release
date
Release
size
(mm)
Duration
(weeks)
Detected (Chinook)
Survival est (Sthd)
Instantaneous
daily mortality
Chinook
(Hatch)
2008 May 9 190-233 ~14 43% M = 0.008
Sthd
(Wild)
2008 April 16 –
May 27
170-190 ~ 2
~ 1
~ 3
89% RM to HCB
18% HCB to JDF
16.5% RM to JDF
M = 0.008
M = 0.242
M = 0.086
Is the estimate 20% EMS high or low?
Chamberlain et al. 2011 TAFS and Moore et al. 2012 PLOS One