CVPIA Fisheries Science Integration Team Workshop€¦ · •Both groups concerned about approach...

8:30–9:00 Welcome and introductions as needed

9:00–10:00 Update progress report• Discuss proposed changes to SIT Monitoring Data Needs

document (Shelly) • Discuss floodplain habitat proposal (Mark T.)

10:00–10:20 Break

10:20–12:00 Discuss draft study plan for contact point charter (Corey)

12:00–1:00 Lunch

CVPIA Fisheries Science Integration Team Workshop

Wednesday, October 4, 08:30 to 1:00 PM

1:00–3:00 Identify who project managers are and discuss how SIT can interact with them and the work plan (Rod)

3:00–3:20 Break

3:20–4:30 Review changes to the fall run Chinook DSM as well as winter and spring run Chinook DSMs.

4:30 Adjourn


Wednesday, October 4, 08:30 to 1:00 PM

CVPIA SIT Model Outreach Results

Red Bluff, CA 7/20/17

Lodi, CA 7/24/17

Sacramento, CA 7/27/17

Initial Natural Adults

• Most recent years not included in average, so skewed lower than expected

• Red Bluff group suggested average of 2003-present GrandTab

• Lodi group not as much concern

• Does 50/50 sex ratio impact on fecundity get addressed in the model

• Sacramento group confused about “initial adults” and suggested labeling as adults at golden gate pointed upstream

• Daylight straying rate by watershed

Hatchery Allocation

• Red Bluff group mostly thought allocations too low

• Lodi group thought most allocations were too low

• Recommended using latest CWT data from the CFM program (consensus that 2012 is the most current available)

• Hatchery allocation on Feather seems reversed

• How is variability (annual) of proportion hatchery handled?

Harvest

• Red Bluff group thought rate should increase with migration distance

• Lodi group said Moke okay, but others should be lower because zero legal instream harvest

• Both recommended using latest available creel census data

Probability of Scour

• Both groups agree that heterogeneity of scour at the watershed level not represented by span of values

• Both groups confused by use of term probability

• Neither group could update values as defined

• Both groups discussed possible SIT proposal that would use a threshold flow to assign scour penalty in years that exceed the threshold (like floodplain habitat)

Limit of Anadromy

• Original SIT model scaled habitat to stream length

• Current SIT model only uses limit of anadromy to screen out areas that don’t provide of habitat, to define flow data locations, and to define flow thresholds for access and routing in some watersheds

• Consensus that lengths were off, and forks / distributaries not appropriately considered

• Resolution = individual follow-ups with identified lead to develop comprehensive mapping (digital) of limits

Diversions / Temperatures

• Both groups identified some watersheds where flow node choice should be evaluated and possibly improved

• Both groups concerned about approach used for watersheds without CalLITE nodes

• Not enough information to resolve this until CalLITE nodes are mapped with verified limits of anadromy

• Both groups questioned >25C threshold (should be lethal) – source to be provided

• Use of monthly mean temperature underestimates negative impact• Suggested reevaluating method of “temporal downscaling” of monthly

temperatures for sub-monthly exceedances of thresholds• Concern about potential for 100% diversions without 100% mortality

Spawning habitat

• Some skepticism about redd size definition (does it include superimposition and/or defense zone?)

• Some tributaries have smaller redd size requirement because of density of spawners (Battle Creek) or habitat preferences (most of San Joaquin tribs)

• Concern about scaling of IFIM study areas to true spawning regions

• Concern about use of areas from out of date studies

• Mark Gard to collect all current habitat area studies and update areas to match mapped spawning limits

Instream rearing habitat

• Concern about scaling of IFIM study areas to true rearing regions

• Some watersheds (especially SJR tribs) have “migratory only” zones

• Concern about use of areas from out of date studies

• Mark Gard to collect all current habitat area studies and update areas to match new mapped rearing regions

• Should late season temperature be “turned off” when some temperature threshold is exceeded

• Sacramento group suggested EPA Region 10 study on temperature thresholds for survival impact

Floodplain rearing habitat

• Red Bluff group noted many watersheds never activate floodplain habitat (so current SIT inputs are overestimates)

• Both groups thought many areas too high and many thresholds too low

• Lodi group questioned assumption that all available floodplain is used

• Both groups concerned about possible discrepancy between CalLITE node location and average monthly flow compared to threshold flow location based

• Suggested reevaluating method of “temporal downscaling” of monthly average flow for 14-day exceedances of floodplain thresholds

• Need to decide update on/off approach or replace with new SIT proposal?

Disease

• Consensus that temperature impact on survival appropriately incorporates disease

Predation

• Neither group could improve the probabilities of high predation• Both groups requested a better definition of how to categorize predation –

if such a categorization was available both groups seemed willing to do relative ranking

• Both groups expressed that relative categorization / ranking across regions is problematic

• Both groups strongly disliked use of contact points, but offered no replacement

• Gave both groups homework assignment to determine whether PAD database should be used at all to weight predation penalty

• Lodi group expressed interest in a simple app to help categorize predation• Sacramento group suggested describing what contact points includes

Redd dewatering / juvenile stranding

• Both groups asked how redd dewatering is handled in the model

• Neither group expressed discomfort with the number of fry produced

• Both groups asked how juvenile stranding is handled in the model

• Neither group expressed discomfort with survival of juveniles

• Expert elicited probabilities could only be improved with a refined definition of redd dewatering or scour tied directly to simulated flows used in the model

Next Steps Prioritization

• Complete limits of anadromy map including downstream limit of spawning and any “ineffective rearing regions”

• Add current diversion and temperature nodes to the map• Share with watershed experts for confirmation• Update diversion and temperature nodes where needed• Update spawning and instream habitat to match new limits of spawning

with latest habitat modeling data• Develop diversion and temperature input approach for watersheds without

CalLITE nodes• Decide on updating floodplain inputs vs. implementing new floodplain SIT

proposal• Acquire disease / survival data from Scott Foote (if it exists)

Miscellaneous Issues

• Redd size = 12.4 m2 in model, but 13.38 in the Coarse Resolution Report (Healey 1991)

• Survival less than 10% can be increased to 10% when temperature exceeds 25C

• Butte Creek routing through Sutter Bypass

• Calaveras, Cottonwood, and Stony discontinuous connection for spawning

• Disbelief in outmigration of mostly large / very large juveniles and presence of juveniles in watersheds in June / July – does Adam’s work address this?

• How is removal of “excess” spawners (Battle, Mokelumne) handled?

• Lodi group felt lower San Joaquin from Merced to Tuolumne “very different” than from Tuolumne to Delta

• Juvenile territory size requirement in Delta might be different than in watersheds (Pat Brandes)

• In-Delta fish routing could be improved based on flow split (Russ Perry paper)

• Egg to Fry survival too high (we gave example of 52% on American – experts said 5-10% max)

• Pat Brandes mentioned a recent paper showing survival in mainstem is the same as in the bypass

Changes to fall-run DSM

• Coarse resolution model.R• Added removal of natural adults by the hatchery operations• Changed the total number of hatchery origin spawners see Hatchery adult analysis.R for analysis.• Changed redd size to 13.38 square meters • Route fish from the lower Sacramento to both the north and central/south delta based on flows.• Added proposed new SIT metrics

• Juvenile survival pulse movement.R• Replaced 10% survival under 25C temps with 0% survival

• All inputs.csv• Replaced all hatchery allocation “hatch.alloc” with new values see Hatchery adult analysis.R for analysis.• Added proportion adults removed by hatchery operations “prop.nat.remov” see Hatchery adult analysis.R for

analysis.• Replaced initial number adults “init.adult” with GrandTab averages 2003-2015

Note that these were GrandTab escapement values corrected for % hatchery and % removed. see Get initial number of adults.R

• Needs• Incorporate the in channel habitat arrays and new floodplain values(?) • Run times for screw-trap data

RunTimes.xlsx

Modifications to fall-run DSM for winter-run DSM• Coarse resolution model.R

• Updated the number of hatchery returns.• Monthly dynamics for juveniles from emergence to past Chipps goes from August to March.• Use fry habitat from August to November and parr habitat from December to March.• Calculate maximum potential leaving juveniles in August, not January.• Fixed stray rate to 0.• Removed proportion stray from metrics since stray rate is 0.• Removed in-ocean harvest.

• All inputs.csv• Replaced all hatchery allocation “hatch.alloc” with 1 since it is 1 location.• Adult harvest was reduced to 0.• Updated the proportion of adults removed by hatchery operations (4%).• Updated initial number adults “init.adult” with GrandTab averages 2003-2015

• Needs• Incorporate the in channel habitat arrays and new floodplain values(?) • Need to update the “egg2fry” file for egg.tmp.eff• Average transition month (to ocean) is still February

Modifications to fall-run DSM for spring-run DSM• Coarse resolution model.R

• Updated the number of hatchery returns.• Monthly dynamics for juveniles from emergence to past Chipps goes from November to June.• Use fry habitat from November to February and parr habitat from March to June.• Calculate maximum potential leaving juveniles in November, not January.• Fixed stray rate to 0.• Removed proportion stray from metrics since stray rate is 0.• Removed in-ocean harvest.• Added the ability to make some locations inaccessible to returning adults.

• Where do we want to route the “extra” individuals when a location is inaccessible? We can also kill them.• Added holding habitat based on values supplied by Mark Gard. Note that there are not different holding habitat values for wet and

dry climates. • Adult returns are truncated to capacity if greater than what the habitat can support. Holding habitat capacity was set at 1fish/square

meter. • Yearlings

• Added the potential for juveniles to leave as yearlings the following year. Instead of fish leaving at the end of the juvenile monthly dynamics (if they survived), fish in size classes s, m, and lg in all locations except upper-mid Sac, Sutter, lower-mid Sac, Yolo, lower Sac, and SJ stick around from July to October. During this time, fish die using the habitat specific survival probabilities. Right now, yearlings do not grow. In November, yearlings are added to the new juvenile population and follow the same size-specific movement and survival rules.

• All inputs.csv• Updated all hatchery allocation.• Adult harvest was reduced to 0.• Updated the proportion of adults removed by hatchery operations (22% in the Feather).• Updated initial number adults “init.adult” with GrandTab averages 2003-2015

• Needs• Incorporate the in channel habitat arrays and new floodplain values(?) • Need to update the “egg2fry” file for egg.tmp.eff but need timing information.• Average transition month (to ocean) is still February

RunTimes.xlsx

8:30–10:00 Rod reviews FY18 process

Review objectives for fall, winter, and spring run Chinook. (cont.)

Review O. mykiss DSM

10:00–10:20 Break

10:20–12:00 Review O. mykiss DSM (cont.)

New business

12:00 Adjourn


Thursday, October 5, 08:30 to 12:00 PM

Fundamental objective Category Fundamental objective attribute

Valley Wide

Spatial structure Total no. of viable spawning populations per diversity group (NMFS def. of independent population)

Abundance

Total no. of spawning natural origin adults (across watersheds)

Naturally-spawned juvenile abundance at Chipps

Naturally produced fish in the ocean

Natural productivity

Total number of natural origin spawning adults per natural origin escapement

Nat. returning adult/natural spawner (cohort replacement)

No. natural juveniles at Chipps /Natural origin spawning adults

Life history diversityVariation (CV) of timing of peak outmigration among screwtraps

Outmigrating proportion juvenile stages (size classes) size/developmental stage at Chipps

Genetic Diversity Prop of hatchery fish that are strays

Watershed specific

AbundanceNo. of returning natural origin adultsNaturally-spawned juvenile abundance

Natural Productivity

Nat. origin returning adult/natural origin spawner prev cohort

Total number of natural origin juvenile per spawner?

Total number of natural origin spawning adults per natural origin escapement

Life history diversity

Timing of outmigration by juvenile stage (number of weeks detected per life stage and distribution shape) per watershed

Outmigrating proportion juvenile stages (fry parr smolt yearlings) size/developmental stage at location

Genetic diversity Prop of natural spawners vs hatchery

Chinook

Fundamental objective Category Fundamental objective attribute

Valley Wide

Spatial structure Total no. of viable spawning populations per diversity group (NMFS def. of independent population)

AbundanceTotal no. of spawning natural origin adults (across watersheds)

Naturally-spawned juvenile abundance at Chipps

Watershed specific

AbundanceNo. of returning natural origin adultsNaturally-spawned juvenile abundance

Naturally-spawned juvenile abundance• Juvenile biomass • Length by date – Concern: Indices will be optimal at different values based on the

watershed and the travel distance

Measuring viable populations• Escapement > 833 annually• Cohort Replacement Rate >=1• Hatchery stray rate <=10% – Concern: No population will be viable

Example output

Chinook

proposedMetrics.xlsx






10:00–10:20 Break


New business

12:00 Adjourn

# ofFry

Spawning Success

# of Females

FecunditySpawning

Habitat

IncubationTemperatures

HyporehicCondition

ReddDisturbance

Superimposition

ScouringOr

Stranding

Human(Physical)

# of Hatchery Spawners

Fish Size

Egg Size

AdultSource

SedimentSurface Fines

Water Quality

Contaminants Waste Water

Runoff

Details

../../../Steelhead/Steelhead conceptual model components and sources.xlsx

JuvenileSurvival

Juvenile Survival

BodySize

FoodAvailability

HabitatUsing

HabitatComplexity

SubstrateDiversity

CoverTemperature

SpawningDate

DischargeDisplacement Stranding

Predation

Predators

Turbidity

Diseases

ArtificialLight

Entrainment

Water Diversions

JuvenileAbundance

(Chinook and O. mykiss)WildHatchery

Water Quality

Ag Return

DO

Contaminants

JuvenileGrowth

Juvenile Growth

BodySize

FoodAvailability

HabitatUsing

HabitatComplexity

SubstrateDiversity

CoverAvg. Daily

TemperatureSpawning

Date (per day)

Discharge

JuvenileAbundance

(Chinook and O. mykiss)WildHatchery

Water Quality

Ag Return

DO

Contaminants

InchannelVs.

Side channel

PredatorAbundance

Disease

y = 0.0443x - 0.0553R² = 0.2605

0

0.2

0.4

0.6

0.8

1

1.2

5 7 9 11 13 15 17 19

Da

ily g

row

th (

mm

/d)

Average Temperature C

0

50

100

150

200

250

300

350

400

0 5 10 15 20 25 30 35 40

Fork

Length

(m

m)

Month

Resident 1/h.1s 1/1.1s

Apr Sept Feb Jul Dec May Oct Mar

O. mykiss length at age for 3 life histories (average temp)

Age-0 Age-1 Age-2

Adult Growth

Life historyResident vs. Anadromous

SalmonReturns

FoodQuality

Sex

AdultGrowth

BodySize

FoodAvailability

HabitatUsing

HabitatComplexity

SubstrateDiversity

CoverAvg. Daily

TemperatureSpawning

Date ( per Day)

Discharge

Abundance(O mykiss)

Wild

Hatchery

Water Quality

Ag Return

DO

Contaminants

InchannelVs.

Side channel

PredatorAbundance

Disease

AdultSurvival

Adult Freshwater Survival

Non HarvestAngler Mortality

Catch & Release

PoachingHatcheryCollection

FoodAvailability

Temperature

Discharge

Water Quality

DO

Contaminants

Entrainment

Predation

Disease

Colusa Draw

Dewatering

Post-spawn

Previouslya

Resident Body Size

Hatchery fish angler

mortality

AdultSurvival

Adult Ocean Survival

Bycatch

OceanConditions

FoodAvailability

Temperature

Predation

Post-spawnCondition

Body Size

MoveWithin

FW

Density ofConspecific

FoodAvailability

Age

DOY(Phenology)

Temperature

Discharge

Magnitude

HabitatAvailability

PredatorDisplacement

(Could be scale thing)

Duration ofFlow Event

Juvenile Movement

Size

Genetics

FWTo

Estuary

Genetics

FoodAvailability

Size

Age

DOY(Phenology)

Temperature

Discharge

Magnitude

Duration ofFlow Event

Juvenile Movement

SomaticGrowth t-1

SexSame when going to Ocean

Anadromous LH Hypotheses

Genetic propensity= fixed proportion based on maternal origin

Body size / somatic growth2 alternatives: faster growth = Anadromy

slower growth = Anadromy

EnvironmentalStreamflow and temperature

Variable flowsHigh temps

Influenced by location and timingcloser delta = anadromyflow and temperature triggers within decision window

Jan Mar May July Sept Oct Dec

smolting

Half poundersSpawning

smolting

Age 0

Ages 1-3

smolting

Emergence

Spawning

Ages 4+

Spawner return

Half pounders return

Emigration

Freshwater

Saltwater

Freshwater

Saltwater

Freshwater

Saltwater

Decision windows

Unresolved issues

Do juvenile (small) compete for habitat with adult (large) O. mykiss

Do we allow anadromous fish to become FW residents?after first spawning?

Do we allow FW residents that spawned to become anadromous?

Incorporation of “food” or resource availability on growth across streams?

Density dependent effects growth/LH “choice” ?






10:00–10:20 Break


New business (schedule changes)

12:00 Adjourn

CVPIA Fisheries Science Integration Team Workshop€¦ · •Both groups concerned about approach...

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