Bay-Delta Science Conference November 15 -17, 2016scienceconf2016.deltacouncil.ca.gov/sites/default/files/...2016/11/16  · November 15 -17, 2016 Flora Cordoleani, Noble Hendrix,

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Bay-Delta Science ConferenceNovember 15-17, 2016

Flora Cordoleani, Noble Hendrix, Eric Danner and Steve Lindley

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Historic vs current distribution of spring-run Chinook

Only 3 out of 19 historic independent populations of CV spring-run Chinook salmon are extant: Mill, Deer, and Butte creeks

Represent only the Northern Sierra Nevada diversity group

Listed as threatened under the federal Endangered Species Act (ESA) since 1999.

Page 3

“The status of the CV spring-run Chinook salmon ESU has probably improved on balance sincethe 2010 status review, through 2014 […].”

“The recent declines of many of the dependent populations, high pre-spawn and egg mortality, and uncertain juvenile survival during the 2012 to 2015 drought, ocean conditions, as well as the level of straying of FRFH spring-run Chinook salmon to other CV spring-run Chinook salmon populations are all causes for concern for the long-term viability of the CV spring-run Chinook salmon ESU.” [Johnson and Lindley, SR viability report (2016) and NOAA-NMFS 5 year status review report (2016)]

Central Valley spring-run Chinook viability status

Page 4

Objectives

1. Understand clearly the dynamics of Central Valley spring-run Chinook salmon in the freshwater and the ocean

2. Identify the environmental factors influencing changes in abundance of spring-run Chinook salmon populations

3. Predicting possible impacts of future water management and climate change scenarios on their dynamics

Page 5

CV spring-run Chinook salmon life cycle

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Page 6

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Page 7

76 parameters Period of model simulation: 1985 – 2008Temporal Resolution

• Annual for ocean stages• Monthly for freshwater stages

Spatial Resolution• Regional depiction of rearing habitat types into Tributaries, Sutter Bypass,

Sac. River, Yolo Bypass, Delta, and BayModel validation by fitting simulated adult abundance to historical adult

escapement abundance (Grand Tab)

Model Structure

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MarAprMayJunJulAugSepOctNovDecJanFebMarAprMayJunJulAugSepOctNovDecJanFeb

MarAprMayJunJulAugSepOctNovDecJanFebMarAprMayJunJulAugSepOctNovDecJanFeb

MarAprMayJunJulAugSepOctNov

Adult enter tributaries

Spawn

Age 3

Juvenile emergence

YoY out migration

Yearling out migration

Age 2 exit ocean

Age 2

Spawning(Age 2)

Age 4

Age 3 exit ocean

Spawning(Age 3)

Age 4 exit ocean

Spawning(Age 4)

Age 1

Spring-run aging convention

Page 9

Juvenile salmon

survival during rearing and

outmigration to the Ocean

Page 10

Young of the Year vs Yearling

Different juvenile rearing/migration strategy for spring-run Chinook

1. Young of the Year that rear for several months and migrate in the spring

2. Yearling that stays an entire year in the natal reaches before migrating to the Ocean

Page 11

Tidal Fry disperse instantaneously after emergence

TidalFry = PTF * Fry

PTF = Proportion of Tidal fry

Density independent migration of fry

Butte,Mill/Deer Cr. Fry

Tidal Fry Migrant Fry

Creek Fry

Sac River Fry

Floodplain Fry

Bay Fry

Delta Fry

Sutter Fry

Page 12

Ni,t+1 = Si 1−m Ni,t1+ ⁄Si 1−m Ni,t Ki,t

and Mi,t = Si * Ni,t – Ni,t+1

Ni,t+1 = resident fry abundanceMi,t = migrant fry abundanceSi = fry survivalm = migration rate without density dependenceKi,t = rearing capacity of habitat i

Density dependent migration of fry

Butte,Mill/Deer Cr. Fry

Tidal Fry Migrant Fry

Page 13

Habitat type Variable Habitat quality Variable rangeMainstem Velocity High <= 0.15 m/s

Low > 0.15 m/sDepth High > 0.2 m, <= 1 m

Low <= 0.2 m, > 1 mDelta Channel type High Blind channels

Low Mainstem, distributaries, open water

Depth High > 0.2 m, <= 1.5 mLow <= 0.2 m, > 1.5 m

Cover High VegetatedLow Not vegetated

Bay Shoreline type High Beaches, marshes, vegetated banks, tidal flats

Low Riprap, structures, rocky shores, exposed habitats

Depth High > 0.2 m, <= 1.5 mLow <= 0.2 m, > 1.5 m

Salinity High <= 10 pptLow > 10 ppt

Rearing Capacity estimate (C. Greene, NWFSC)

Page 14

Survival of rearing fry in the Delta

Use Newman (2003) survival rate relationship:

logit(SDelta,t)= Brearing * XRearing,i,t

Xrearing = Flow, Temperature, Exports, DCC

Page 15

Survival of sm0lt migrating to the Ocean

Survival rate in the Sutter Bypass based on acoustic tagging study:

logit(St)= B0 + B1 * Flow

Survival rate through the Delta from:1. ePTM simulations [Sridharan, V., and Byrne, B.]2. Newman equations

200 400 600 800 1000

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Page 16

Early ocean survival

Early ocean survival of smolts depends on ocean conditions in the Gulf of Farallones and the fish rearing origin

logit(Si) = (B0,i + B0-add,i )+ (B1,I + B1-add,i) * OPI

OPI = Ocean productivity indexB0-add,I = poor habitat interceptB1-add,I = poor habitat slope

Page 17

Survival of adult during holding period

Significant adult pre-spawning mortality events in 2002 and 2003 have been reported for Butte Creek population

Summer pre-spawing survival expressed as a function of water temperature [Thompson et al. (2012)] :

Sps,t = 11+𝑒𝑒−𝑏𝑏1−𝑏𝑏2𝑇𝑇

T = Temperature in holding habitat

Page 18

Mill/Deer Cr. Model sensitivity analysis

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Page 19

Mill/Deer Cr. model sensitivity analysis

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Page 20

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Butte Cr. Model sensitivity analysis

Page 21

Butte cr. model sensitivity analysis

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Butte Cr

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Page 23

Next Steps

Refine parameter values and finish model calibration- Rearing capacity in Tributaries and Sutter Bypass- Proportion of tidal fry vs rearing fry vs yearling - Evaluate relationship between egg survival and temperature in spawning

habitat

Use model for inference in evaluating water management and climate change scenarios

- Effect of increased temperature in spawning habitat?- Sutter Bypass flooding scenarios - Delta water management scenarios

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Page 25

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Page 26

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