CVPIA Science Integration Team Meeting

CVPIA Science Integration Team Meeting

June 23, 2021

Welcome!

Some Logistics• Please keep yourself muted when not speaking• Please identify yourself when you do speak• If you didn’t receive a direct calendar invite for this meeting and would

like to be added to the SIT email list, please contact [email protected]

CVPIA SIT Meeting June 23, 2021

Agenda• 10:00-10:05 Welcome, Agenda Review – Megan Cook (FWS)

• 10:05-10:15 Upcoming in SIT for 2021 – Megan Cook (FWS)

• 10:15-10:45 Model Updates: Late-fall-run Chinook salmon DSM – Jim Peterson (OSU/USGS), Adam Duarte (USFS)

• 10:45-11:05 SIT Proposal: CalSim Update – Mark Tompkins (FlowWest)

• 11:05-11:15 CVPIA Data Guidance Update – Erin Cain (FlowWest)

• 11:15-11:20 CVPIA Funding Update – Rod Wittler (USBR)

• 11:20-12:00 Trawl Efficiency Project Updates and Discussion – Russ Perry (USGS)• Integrating acoustic tag, coded wire tag, and DNA data to estimate trawl efficiency and

abundance of genetic winter Chinook Salmon at Chipps Island


Final NTRS is online!

http://cvpia.scienceintegrationteam.com/about/

Something to Celebrate

http://cvpia.scienceintegrationteam.com/about/

Overview of SIT 2021 Schedule• NTRS Communications Plan

• Habitat Restoration Coordinators and CVPIA staff will be presenting to partners in various forums (e.g., watershed groups)

• Completion and Release of new Version of SIT Chinook Salmon DSMs• Review calibration and sensitivity analysis results• Review updated simulation results based on existing strategies• Future discussion: SIT model use by other groups

• SIT Determines whether Priorities Need Revision • Threshold for changing priorities is high – has our fundamental understanding

of the system changed?• Combined FY20/FY21 Adaptive Management Update

• Draft for review by early November


SIT 2021 Overview

NTRS PrioritiesRestoration Actions

and Info Needs Prototype Model ChangesBased on proposals accepted by the SIT

SIT discusses and affirms model changesIs the model improved?

Model Calibration / Sensitivity AnalysisDoes the model still

make sense?

Run existing Priorities through updated Model

Assess revised outputAre existing priorities

still supported?

SIT Prioritization? Develop new

candidate strategies, update priorities

New Release of Model

Aug SIT Call

Oct SIT Meeting

NEW: SIT Background Workshop (Aug 18, 1-3pm)• Topics: Refresher on SIT process, DSMs, and NTRS development;

forum to ask questions and understand how we got here• Who should attend: New SIT members, anyone who wants a refresher• Email [email protected] with questions

August 25 SIT Call (9am-1:30pm *TIME UPDATED)• Topics: review updated model calibration and sensitivity analysis

results, review simulation results of existing strategies from updated model, SIT input on next steps to Science Coordinator

• Expect email with updated model output ~2 weeks prior

SIT 2021 Schedule

mailto:[email protected]

September 15 SIT Call (10am-12pm)• Topics: Regular SIT updates, Subgroup updates (email

[email protected] with items for New Business)October 13-14 SIT Meeting (9am-4pm)

• Topics: Final review of results of simulated strategies from updated model; SIT input on Adaptive Management Update to Science Coordinator; Regular SIT updates (time allowing)

• Expect draft of Adaptive Management Update ~2 weeks laterDecember 15 SIT Call (10am-12pm)

• Topics: FY20 and FY21 Adaptive Management Update, regular SIT updates

SIT 2021 Schedule


Summary of Updates • Edits to be consistent with Near-term Restoration Strategy• Update and clarify process for proposing changes to DSMs • Clarify pre-proposal and full proposal templates• Add in flexibility to annual memo review timeline

Additional comments/edits welcome until July 15(email [email protected])

http://cvpia.scienceintegrationteam.com/meetings/

Revised SIT Guidelines



Late-fall-run Chinook Salmon DSM Results from Expert Meeting

Jim Peterson (OSU/USGS)Adam Duarte (USFS)


SIT Proposal, 2018

Approved: May 23-24, 2018

Late Fall Chinook expert meetingsMay 20 & 24

ParticipantsP. Bratcher (CDFW), M. Brown (FWS), C. Chamberlain (FWS), M. L. Earley (FWS), D. Killam (CDFW), K. Niemala (FWS)

Model overviewLate – fall discussion

Model inputsTributary populationsTimingLife-history

Conceptual models

Late Fall Chinook Salmon model inputs

Habitat • Only late fall-specific habitat available: spawning habitat in

upper Sacramento• Use fall run habitat for remaining tributaries

Other inputs same as fall run

Late-fall-run Chinook extent

Battle CreekClear Creek

Adult late-fall Chinook can stray to other tributaries

adult returns

Timing Chinook Salmonjuvenile rearing/outmigrating

adult returns

spawning

Late fall adult returns

spawning

adult returns Battle/ClearUpper Sacramento

Outmigrant timing at Red Bluff, 2010-2019

0.00

0.05

0.10

0.15

0.20

Date

Pro

porti

on p

assi

ng

Apr-1 May-1 Jun-1 Jul-1 Aug-1 Sep-1 Oct-1 Nov-1 Dec-1 Jan-1 Feb-1 Mar-1

Subyearling “Yearling”

Timing and life historyHypotheses1) Majority leave as fry. Stick around upper Sacramento down to GCID2) Evidence of majority holding above RBDD3) Movement could be genetic where a certain portion juveniles holding4) Water temp influences movement

– Could be related to thermal block ~18-20 C [might compare GCID fish to temps]– Unnatural cold water upstream hold fish

Tisdale Weir Rotary Screw Traps

Knights Landing Rotary Screw Traps

Sacramento Beach Seines Combined

Sacramento Trawls (Sherwood Harbor)

Modeling alternative hypotheses

Alternative juvenile dynamics1) Fry leave natal tributaries and rear in the Sacramento and delta using

habitat filling rules identical to fall run.2) Fry leave natal tributaries and rear in the Sacramento with 25% migrating

below RBBD rear in Sacramento and delta.3) Fry leave natal tributaries and rear in the Sacramento and delta but they

do not pass an downstream segment is temperatures > 18 C.

- Give each equal weight and average- Sensitivity analysis

Timing and life historyAge at return

CWT: SATTERTHWAITE ET AL. 2017. TAFS 146:594–610

0

10

20

30

40

50

60

70

1-2 3 4 5+

Perc

ent c

ompo

sitio

n

Age

Central Valley Fall (CWT) Late Fall, 2006-2019 CDFW

Calibration dataGrandTab

Sacramento River 2000-2019 above and below RBBDClear Creek 2002-2019Battle Creek, 2000- 2019 above CNFH (marking error adjustment, K. Niemela)

Spawning ground surveys:Sacramento River, CDFW 2000- 2019Clear Creek, USFWS 2007-2018

SIT Proposal: Update CALSIM flow inputs to DSMs

Mark Tompkins, FlowWest


• Issue of Concern: The current DSM monthly flow inputs are from an older (~2009-2015) version of the CALSIM model run of Central Valley water system operations. Therefore, DSM simulations do not reflect the most current set of operational rules and may not capture the most likely future flow conditions in CVPIA watersheds.

• Proposed Change: This proposal would replace the flow inputs from the older CALSIM model run with new flow inputs from the most current (2019) CALSIM model run that incorporates expected future operational rules. *Note – DSM calibration will still use CALSIM flows generated with operational rules representative of the period that aligns with GrandTabescapement data used in calibration.

• Rationale: Monthly flow inputs to the DSM are used to generate habitat and temperature inputs and therefore influence both survival and growth. DSM simulations should use flows based on water system operations modeling expected to be the most representative of future conditions.

• Timing: Next DSM update cycle (2022)


CVPIA Data Guidance Update

Erin Cain, FlowWest


Data Guidance ImplementationHosting CVPIA data on EDI

Finding CVPIA Data Packages on EDI

What is EDI?

Data packages on EDI store datasets and metadata

To create data packages to upload to EDI you must use EML (extensible markup language)

EDI (Environmental Data Initiative)

https://portal.edirepository.org/nis/home.jsp

Excel Workbook- personnel, title, keyword set, license, funding, maintenance, coverage (geographic, temporal, taxonomic) ,

attributes, code definitions

Word Docs- abstract- Methods

Example

EMLaide FACILITATING DATA UPLOADS TO EDI

Template Materials

- Enables users to create valid EML documents with high metadata standards

- Uses template materials with a well known data entry interface (excel, word)

- Detailed documentation and instructions

EMLaide - R package developed by FlowWest

https://cvpia-osc.github.io/EMLaide/articles/template-doc.html

https://cvpia-osc.github.io/EMLaide/index.html

For R Users:

Step by step guide to generating EML document using EMLaide and template materials

CVPIA data in the queue

Stanislaus O. mykiss life-cycle monitoring (FISHBIO - Michael Hellmair) - Weir monitoring data- PIT monitoring and trapping data

Juvenile salmon growth and lower foodweb experiment in the Sutter Bypass and lower Sacramento and Feather Rivers (Flora Cordoleani and Carson Jeffers)

- Hydrology data- Food web structure data - Fish growth data

Thank you to everyone who has worked with us so far to get data uploaded to EDI!

CVPIA Funding Update

Rod Wittler, USBR


FY2021 WRR Supplemental Funds & SIT Info Needs

• SIT Subgroups• Habitat Assessment (Wittler & Tompkins)

• FY2022 Updated Charter• Funded - Stage 2 – Upper Sac & Clear Creek

• Salmon Demographics (Beakes & Matthias)• FY2022 Updated Charter

• Permitting• Study Design

Model Segment Status Use 1 Use 2 Use 3 Use 4Clear Creek - Reading Bar to Confluence(RM 0 to RM 8.37)8.37 miles

Planned (TSC) on behalf of NCAO

Spawning Gravel Injection Design

Rearing Habitat Design

Spawning Habitat Assessment

Rearing Habitat Assessment

Sacramento River - Keswick to Clear Creek(RM 302 to RM 289)13 miles

Complete (TSC) Spawning Gravel Injection Design

Spawning Habitat Assessment


Use of Constructed Habitat by Juvenile Salmonids

Sacramento River - Clear Creek to Red Bluff Diversion Dam(RM 289 to RM 243)46 miles

Planned for FY 2021 and 2022 (TSC) – Dependent upon 2021 Supplemental SDM Funding


Spawning Gravel Injection Design


Rockwad design

Use of Constructed Habitat by Juvenile Salmonids

Sacramento River – Red Bluff Diversion Dam to Wilkins Slough(RM 243 to RM 118)125 miles

Planned. Dependent upon 2022 and beyond Supplemental SDM Funding

Food for Fish Prey Tracking



Rockwad design

Sacramento River – Wilkins Slough to Freeport(RM 118 to RM 46)72 miles

Complete (TSC) Fremont Weir Notch Design

Food for Fish Prey Tracking


Rockwad design


Summary of 2D Hydrodynamic Modeling Activities on the Sacramento River and Clear Creek

Integrating acoustic tag, coded wire tag, and DNA data to estimate trawl efficiency and abundance of genetic winter Chinook

Salmon at Chipps IslandRuss Perry, USGS


Russell W. PerryUSGS, Western Fisheries Research [email protected]

Brian Pyper, Arnold J. Ammann, Bryan G. Mathias , Joshua A, Israel, Rachel C. Johnson, and Patricial L. Brandes

Counting the needles in the haystack: Estimating abundance of endangered winter run Chinook salmon leaving the Delta

Acknowledgements

CVPIACAMTCADFWIEPUSGS Pacific RegionField staff

Winter RunMonitoring Network

(Johnson et al. 2017 SFEWS)

1) Genetic run ID 2) Abundance

3) Survival 4) Diversity

5) Condition 6) Data access

6 System-wide Recommendations

12 miles

12 km

SacramentoTrawl Site

ChippsIsland

Trawl Site

Long-Term Trawl Monitoring in The Delta• >40 years of juvenile salmon catch data (1976 – present)• Coded Wire Tag recoveries• Index of survival and abundance• Genetic and otolith sampling (recent years)

What Can we Infer from Catch Data?

Chipps Islanddaily trawl catch

2017

• Timing? Maybe• Index of abundance? Only if capture probability is constant• Run composition? No.

Why is Abundance at Chipps Important?• Monitor status of endangered population

• Early indicator of year-class strength• Take action if low abundance

• Critical nexus between freshwater and ocean• Partition freshwater from ocean survival

• Inform life cycle models• Calibrated and validated with abundance data• SIT’s DSMs

• Used only spawner data for calibration

The Needle in the Haystack

What are the Challenges?What is the trawl’s capture probability?

Trawl efficiency: proportion caught of those available during sampling

What are the Challenges?Who are we looking at?

Hatchery origin? Naturally produced?

Which hatchery?

Which population?• Fall or Late-fall

harvestable• Spring Run

threatened• Winter

endangeredThe tool:Codes Wire Tags25% mark rate

The tool:Genetic Stock ID

Photo credit: USFWS, Steve Martarano

5-Year Study (2017 – 2021)3 Parts:

1) Acoustic telemetry+

2) CWT Catch & Trawl efficiency

+

3) Trawl catch & Genetic ID

=Estimate of

run-specific abundance

Releaselocation

Trawllocation

RAT

p1 p2 pD…

Ψ1 Ψ2 ΨD

time

Part 1: Acoustic TelemetryMultistate Mark-Recapture Model

• “States” are daily time periods.• S = Probability of surviving to trawl site.• Ψd = Fraction arriving on day d.• pd = Daily detection probability.

S

Dual JSATS Telemetry Array Chipps Island

Part 2: Trawl Data and CWT Catch• Ten 20-minute tows per day• 3 – 7 days per week

• 5 days/week in 2019• Samples 5% – 14% of the time

• Trawl efficiency = fraction of fish captured during sampling.• Capture probability = fraction of all fish captured.

Hybrid AT-CWT ModelReleaselocation

Trawllocation

RAT

p1 p2 pD…

Ψ1 Ψ2 ΨD

S

RCWT

N1 N2 ND…

Ψ1 Ψ2 ΨD

S

Acoustic Tags Coded Wire Tags

E1,j

• Nd = Daily CWTs passing trawl site • Cd,j = CWT caught on day d, tow j• fd,j = fraction of day sampled• Ed,j = trawl efficiency

C1,jf1,j Trawl catch data

E1,j = f1,jN1

C1,j

Factors Affecting Trawl Efficiency• Release-group level

• Random effect – variance among release groups

• Daily level• Mean daily Delta outflow

• Tow level• Tow direction (Upstream, Downstream)• Tidal velocity (instantaneous – mean velocity)• Interaction: Outflow x tidal velocity• Overdispersion

• Fit model in a Bayesian framework in JAGS

2017-2019 Paired Release Summary• 22 Paired Release Groups• 6,348 AT fish released• 8,345,444 CWT fish released

• 1,292 AT fish detected at Chipps• 1,428 CWT fish captured at Chipps

• 2020-2021 data not yet analyzed

Part 3:Genetics Data and Abundance Model

Trawl Genetic Sampling

• Unmarked fish classified by length-at-date (LAD)

• Genetic tissue samples• All LAD late-fall and winter run• Up to 10 spring run LAD• Up to 25 fall run LAD

• Genetic assignment to true winter run• Near 100% assignment accuracy

Genetic Data from 2019 at Chipps

0

2

4

6

8

10

Jan Feb Mar Apr May

2019

Number of true winter run in DNA samples

Winter LADSpring LAD

LAD Group

Catch

Genetic Analysis

True Winter Run

Winter 98 94 (96%) 35 (37%)Spring 1,80

4267 (15%) 4 (1.5%)

* No true winter run in late-fall or fall LAD, 2017 - 2019

Model StructureTW_win[d] ~ Poisson(Ntot * arr_prob[d] * p[d] * p_dna_win[d] * qw)TW_spr[d] ~ Poisson(Ntot * arr_prob[d] * p[d] * p_dna_spr[d] * (1 – qw))

Data:TW_x[d] = Daily number of true winter run in DNA samples from winter and spring LAD groups

Biological parameters:Ntot = Total abundance of true winter runarr_prob[d] = Daily arrival probability

Sampling / nuisance parameters:p[d] = Daily capture probability = f(trawl efficiency, number of tows, tow duration)p_dna_x[d] = Daily fraction of each LAD group subsampled for DNA analysisqw = proportion of true winter run that fall into LAD winter group

- Fitted in JAGS simultaneously with paired-release data and efficiency model

Run Timing Modelf(lognormal kernel | µ, σ) + εdεd = autocorrelated process errorKey features:• Flexible shape to match data• Borrows information across days• Accommodates missing data (days with no trawling)

Model Testing withSimulated Data

Model Fitted to Simulated Catch Data

Day of Year

30 True Winter Run Identified

Day of Year

Total Abundance

Many Simulations over Range of Abundances

True Abundance (thousands)

EstimatedAbundance(thousands)

0.75% Trawl Efficiency

80% Credible Intervals

Application to Real Data

Preliminary Abundance Estimates2017

2018

2019

Dai

ly A

bund

ance

of T

rue

Win

ter R

un (8

0% C

I)

Winter Run JuvenileProduction Estimate

Comparison with Red BluffJuvenile Production Estimates (JPE)

Red Bluff JPE (millions)

Chipps JPE (thousands)

2017

2018

2019

4.4% survival

Summary

• Paired-release study design effective for estimating efficiency

• Able to estimate abundance with little bias

• Estimates of daily abundance and run timing

• Techniques applicable to other runs

• Abundance estimates are preliminary!

Potential Uses of A Trawl Efficiency Model

• Abundance and Composition• Natural vs Hatchery Origin• By race (using genetics)

• Spring run (funded for FY22 – 24)• By population

• Survival• Hatchery groups – Release to Chipps, Chipps to hatchery• Natural groups – Spawner to Chipps, Chipps to return

• Retrospective analysis• 40 years of trawling data with CWT captures• Long-term patterns of freshwater and ocean survival

Otolith-based population assignment

Slide provided courtesy of Anna Sturrock

Questions?

Photo credit: USFWS, Steve Martarano

Huge THANK YOU to…all of our speakers today

all of you for attending and participatingour diligent notetaker Priscilla Liang

Aug 18, 1-3pm: SIT Background Workshop (NEW)• Topics: Refresher on SIT process, DSMs, and NTRS development; forum to ask

questions and understand how we got hereAug 25, 9am-1:30pm: SIT Call (UPDATED)• Topics: review updated model calibration and sensitivity analysis results,

review simulation results of existing strategies from updated model, SIT input on next steps to Science Coordinator

• Expect email with updated model output ~2 weeks priorSept 15, 10am-12pm: SIT Call• Topic: Regular SIT updates Oct 13-14, 9am-4pm: SIT Meeting• Topic: Final review of results of simulated strategies from updated model; SIT

input on Adaptive Management Update to Science Coordinator; Regular SIT updates

Dec 15, 10am-12pm: SIT Call• Topic: FY20/FY21 Adaptive Management Update


SIT 2021 Schedule


CVPIA Science Integration Team Meeting

Documents

Transcript of CVPIA Science Integration Team Meeting