Conference Call

January 12, 2022 Slides

Meeting Summary

The SIT held its first meeting of the year on January 12, 2022. The Science Coordinator provided an overview of the SIT’s objectives and major milestones for 2022. Objectives include providing a forum for Central Valley anadromous fish science, developing additional improvements to the Chinook salmon decision support models (DSMs), making progress on the steelhead and sturgeon DSMs, learning from our existing monitoring data and improving upon our monitoring enterprise. The SIT also reviewed the current list of SIT Subgroups, points of contact, members, and current tasks. SIT members interested in joining a SIT subgroup should contact Megan (subgroups include Climate Change, Habitat, Monitoring, and Salmon Demographics/Movement/Growth. Mark Tompkins provided an update of the Habitat Subgroup activities and two related proposals (Updated Flow Inputs and Spawning Habitat Decay). Adam Duarte led the first discussion on the Chinook salmon juvenile movement hypotheses. The SIT reviewed the existing movement hypotheses in the DSMs, discussed why incorporating multiple hypotheses is important, how multiple hypotheses could be incorporated into the DSMs, how we could test the hypotheses, and discussed the tools that would assist the SIT in evaluating different hypotheses. As homework, SIT members are asked to continue thinking about additional juvenile movement hypotheses for Chinook salmon and to send ideas to Megan to compile for discussion during the Feb SIT call (please send by Feb 1).

Action Items

(1) Review the written proposals for the Updated Flow Inputs and Spawning Habitat Decay and be prepared to discuss during Feb SIT call.

(2) Please contact to sign up for SIT Subgroups (Climate Change, Habitat, Monitoring, Salmon Demographics/Movement/Growth)

(3) Please contact or to sign up to present a science talk, project update, or suggest a presentation on other program to the SIT during 2022.

(4) Continue thinking about what hypotheses should be included in future versions of Chinook salmon DSMs and the monitoring data needed to test them. Please send a short description to Megan to compile to discuss during the next SIT call (by Feb 1 if possible).

Detailed Meeting Notes


Bernard Aguilar, Mike Beakes, Thad Bettner, Erica Bishop, Tricia Bratcher, Matt Brown, Erin Cain, Heather Casillas, Charles Chamberlain, Megan Cook, Flora Cordoleani, Holly Dawley, Carl Dealy, Adam Duarte, Brian Ellrott, Sadie Gill, Harmony Gugino, Chris Hammersmark, John Hannon, Michael Harris, Brett Harvey, Rene Henery, Cyril Michel, Jason Hassrick, Jensena1 (name unknown), John Kelly, Bryan Matthias, Priscilla Liang, Duane Linander, Erin Lunda, Amy Lyons, Todd Manley, Keith Marine, Mike Memeo, Erica Meyers, Kirk Nelson, James Pearson, Jim Peterson, Corey Phillis, Emanuel Rodriguez, Derek Rupert, Will Satterthwaite, Ian Smith, Nicholas Som, Kate Spear, Erin Strange, Steve Thomas, Mark Tompkins, Annalisa Tuel, Mike Urkov, Rod Wittler, Mike Wright

10:00: Introductions / Agenda Review (Megan Cook)

10:05: 2022 SIT Objectives and Schedule (Megan Cook, Jim Peterson, Rod Wittler)

  1. Provide a forum to communicate new science for anadromous fish in the Central Valley
  2. Finalize the release of Chinook salmon DSM v2.0 (model documentation and publishing)
  3. Develop/improve tools for SIT model visualization and exploration
  4. Develop additional improvements to the Chinook salmon DSMs and finalize proposals to be ready for next round of Chinook salmon model updates (by Oct 2022) Develop approach to better consider climate change in modeling/prioritization Improve habitat estimates where possible (including habitat change and updated flow inputs) Improve Chinook salmon demographic, movement, and growth parameters/rulesets where possible Re-analyze Chinook salmon CWT data to include newly released data
  5. Make progress in improving the steelhead and sturgeon decision support models Information needs gap analysis with existing work Develop plan and milestones
  6. Learn from our existing monitoring data and improve monitoring coordination, guidance, and implementation Initiate process for analysis of existing monitoring data Solidify process to accept, process, store, and use effectiveness monitoring data
  7. Continue making CVPIA-funded data available on EDI website
  8. Produce Adaptive Management Update by end of the year

Overview of 2022 Calendar

  • Ongoing: Science talks, project updates, updates/discussions with other programs
  • Feb: Finalize FY20/FY21 Adaptive Management Update
  • Jan-March: Discuss Chinook salmon juvenile movement rulesets
  • Approximately Spring: Deeper dive into monitoring topics
  • April: Deadline for submitting new pre-proposals
  • Sept: Deadline for full proposal approval
  • Oct: Next round of prototyping model changes begins (so model proposals and related work must be complete and ready)
    • Last chance for changes prior to next NTRS
  • Nov: FY22 Adaptive Management Update released for SIT review

Look Ahead to Next NTRS

  • 2022: Identify and propose desired model changes, make progress on info needs
  • Winter 2022 / 2023: Incorporate model changes
  • 2023: Revisit objectives, candidate restoration strategies
  • 2024: Finalize New Recommendations (priority actions and info needs) for Chinook salmon, steelhead, sturgeon
  • By 2025: Publish next Near-term Restoration Strategy

  • Rod: Timing the next NTRS with the following NOFO is an important overarching goal. We really need to have an updated set of priorities in NTRS v. 2 ready for the next NOFO.Desirable timing to pursue.

10:20: FY20/FY21 Adaptive Management Update Revised Schedule (Megan Cook)

  • Circulate draft to SIT by Jan 287 for review and comment
  • Feb 9: Monthly SIT meeting with Q&A time
  • Feb 11: SIT comments due
  • Science Coordinator will finalize document by Feb 18
  • Addenda due by Feb 25

  • Target dates, will not get less than 2 weeks to review draft

10:30: SIT Subgroups (Megan Cook)

  • Habitat
  • Monitoring
  • Climate Change (new)
  • Salmon Demographics, Movement, and Growth (restructured)
    • Bioenergetics
    • Food for fish
  • (Steelhead PWT)
  • (Sturgeon PWT)

  • Anyone welcome on any subgroup, reach out to any subgroup if you’d like to be involved

  • Rene Henery: would be great to have subgroup about reorienting to recovery project

  • Rod: There are two organizations that are focusing on floodplain dynamics- accessing/building new floodplains, idea is to get fish out on floodplains to grow faster. Not sure if included in salmon demographics committee, would be a good place to include

Monitoring Subgroup

  • Point of contact: Megan Cook (
  • Members: Mike Beakes USBR, Tricia Bratcher CDFW, Matt Brown FWS, Charlie Chamberlain FWS, Megan Cook FWS, Adam Duarte USFS, Jim Earley FWS, Sadie Gill FW, Jason Hassrick ICF, Bryan Matthias FWS, Jim Peterson OSU, Mark Tompkins FW, Mike Urkov, JD Wikert FWS, Rod Wittler USBR
  • Current tasks:
    • Update Monitoring Guidance
    • Develop guidance on project characteristics that warrant higher level monitoring
    • Address additional effectiveness monitoring consideration s
    • Respond to requests for input on monitoring design
  • Next meeting: target before Feb SIT meeting
  • New volunteers during meeting: Keith Marine

Climate Change Subgroup (new)

  • Point of contact: Brian Ellrott (
  • Members (to be invited): Tricia Bratcher CDFW, Megan Cook FWS, Adam Duarte USFS, Brian Ellrott NMFS, Kirk Nelson USBR, Jim Peterson USGS/OSU, Corey Phillis MWD, Kevin Thielen USBR, Mark Tompkins FlowWest, Rod Wittler USBR, Mike Wright USBR
  • Current tasks:
    • Brian drafted pre-proposal to begin conversation Determine goal/expected outcome for addressing climate change in the DSM
  • Consider potential methods to address
  • Next meeting: Megan to send poll to schedule for late Jan

Salmon Demographics, Movement, and Growth Subgroup (restructured)

  • Point of contact: TBD
  • Members (to be confirmed): Mike Beakes, Megan Cook, Adam Duarte, Brian ellrott, Brett Harvey, Bryan Matthias, Cyril Michel, Jim Peterson, Russ Perry, Corey Phillis, Rod Wittler
  • Current tasks:
    • Convene and agree on subgroup structure and tasks: coordination on salmon demographics info needs, bioenergetics proposal, food for fish data
  • Next meeting: target before Feb SIT meeting
  • New volunteers during meeting: Keith Marine, Rene Henery, Ian Smith (submitted by Mike Beakes), Charlie Chamberlain (and/or Jim Earley)

Habitat Subgroup

  • Point of contact: Mark Tompkins (
  • Members: Matt Brown FWS, Charlie Chamberlain FWS, Blair Greimann USBR, Chris Hammersmark cbec, John Hannon USBR, Rene Henery TU, Mark Gard CDFW, Mike Memeo DWR, Samuel Provins FWS, Derek Rupert USBR, Mark Tompkins FW, Rod Wittler USBR
  • Current tasks:
    • Habitat inputs modeling
    • Spawning habitat decay proposal
    • Consider/advise SIT on other habitat related improvements
  • Next meeting: late Jan
  • New volunteers during meeting: Keith Marine

Habitat Subgroup Meeting Summary

  • Topics
    • Inventory of 2D hydraulic models in CVPIA reaches
    • Status of Habitat Assessment Charter
    • Review and discussion of spawning habitat decay SIT proposal
    • Clarification of participation/points of contact
    • Preliminary discussion of potential new off channel habitat data
  • Action items
    • Clarify habitat input needs with hydraulic modelers
    • Acquire Clear Creek gravel augmentation data from Matt Brown
    • Summarize current spawning habitat “carrying capacity”
    • Get criteria/details on new off channel habitat data
    • Set next meeting (later January)

Updated Flow Inputs Proposal Updates

  • Note: previously referred to as CalSim or Operations Proposal. Updated proposal name more directly communicates what’s being done
  • Summary: Use latest (2019) CALSIM model run that incorporates expected future operational rules
  • Full proposal has been available and will be reposted with Jan meeting notes on SIT website
  • Final step: final review/thumbs up at Feb meeting

Spawning Habitat Decay Proposal

  • Summary: Updates method for calculating spawning habitat decay based on modeled sediment transport rates and tied to the flow inputs to the DSMs
  • Full proposal will be available with Jan meeting notes on SIT website
  • Next step: review/thumbs up at Feb meeting

SIT Action Item: Review the written proposals for the Updated Flow Inputs Proposal and the Spawning Habitat decay Proposals and be prepared to discuss during Feb SIT call

10:45: Juvenile Fish Movement Rule Sets – Part 1 (Adam Duarte)

Chinook Salmon Movement Hypotheses: Background

  • Current fall, winter, and spring run DSMs

Chinook Salmon Movement Hypotheses: Goals for today

  1. Review how fish currently move in the DSMs to refamiliarize everyone
  2. Review why incorporating multiple movement hypotheses is likely beneficial
  3. Discuss how these hypotheses could be incorporated into existing DSMs
  4. Discuss how we might test each of these hypotheses
  5. Identify what tools/exercises would be useful for the group to evaluate the different movement hypotheses
  6. Get SIT members thinking about what hypotheses should be included in future versions of Chinook salmon DSMs
  • Rene Henery: Opens up meta questions about the modeling process. The ruleset we have for fish movement is because we have a bunch of similar hypotheses why fish move. There was one effort that quantified that and laid that out numerically that we could lift and apply. Feels like we could come up with alternate hypotheses but the one that was used was based on empirical data from fish (already ground-truthed in a particular system). Feels like there’s some kind of sequencing where we come up with hypotheses, experiment with how they could affect results, test hypotheses, but happens before we add them to the model. Wondering about sequence and timeline.
  • Adam Duarte: Other hypotheses not shown here. Weighing hypotheses differently.
  • Mike Beakes: connection with salmon demographic work
  • Complexity for the sake of complexity doesn’t make things better

Fish Habitat Use and Movement Out of Tributaries, Reaches, Bypasses, and Delta

  1. Rule set used
  2. Once a fish grows to size class 3: move out of tributary to mainstem
  3. Once a fish reaches size class 4: leaves the system
  4. No habitat: send downstream
  5. Downstream movement also related to pulse flows
  6. Bypass rules: % fish movement into = % discharge entering bypass
  7. Mainstem rules: % fish from each trib = % fish rearing section


  • Keith: How does pulse flow operate across size classes? Jim: depends on time of year and size class
  • Rod: Mainstem rules: re-explain?
  • Adam: 3 tributaries coming in, have to decide (tracking fish coming back to natal tributaries), which get priority? Currently the decision that was made in 2015 was that we would allocate the same proportion
  • Mike Beakes: Initial steps in demographic work is to review study plan with this group. Most likely a mark recapture effort (active sampling of fish and passive sampling). Will be able to confront/create new hypotheses
  • Rene: implications for slicing time further? - issue is monthly timestep of CalSim (long running limitation)
  • Mike Beakes: I will work with our CalSim modelers to see what limitations/opportunities there are on this topic.
  • Sadie Gill: daily valley-wide water temperature estimates is another limiter

Why incorporating multiple movement hypotheses is likely needed

  • Currently cannot directly evaluate how it influences our results (though likely huge)
  • Literature supports alternative hypotheses
  • For example: “movers” vs “stayers” life histories

Questions on why incorporating multiple hypotheses beneficial?

  • Brian Ellrott: awesome idea
  • Keith Marine: this question about how fish move has significant influence on outputs. When we get into monitoring discussions should pay some priority attention to this one to try to get you some data to try to calibrate/test whatever hypothetical strategies try to incorporate
  • Jim suggests revisiting previous work - Adam developed an integrated model for estimating a variety of parameters using spawning ground surveys and screw trap data. Intent was to use monitoring data to update some of these parameters values in this sort of integrated Bayesian framework.

How these hypotheses could be incorporated into existing DSMs

Example from late-fall-run DSM

  1. Majority leave as fry. Stick around upper Sacramento down to GCID
  2. Evidence of majority holding above RBDD
  3. Movement could be genetic where a certain portion juveniles holding
  4. Water temp influences movement
  5. Could be related to thermal block, approximately 18-20 C [might compare GCID fish to temps]
  6. Unnatural cold water upstream hold fish


  • Rene: how do we prioritize weighting the different hypotheses vs. looking at the success of the hypotheses at creating an outcome that more closely is reality.
  • Adam: if we have evidence to support one hypothesis more, can develop expert elicitation process to change those weights. Once we have those weights, through adaptive management process, we update those weights using monitoring data. Maybe we have 80% of weight on first hypothesis and then after 2-3 years of monitoring it seems like hypothesis 3 is better at predicting what we’re seeing in system.
  • Jim: smart thing would be to use existing data to do starting weights but then evolve through time to adjust.
  • Adam: waterfowl found that as system changes across 20 years, a hypothesis will ramp up and be more supported as it shifts to a different ecological state. So a hypothesis could be weighted around 0 but then become more accurate in future years.

How we might test each of these hypotheses

  • At least two potential options
    • Directed studies (faster, but narrower in scope [spatially])
    • Adaptive management (slower, but generalizable at least at two different scales)

Adaptive management

  • Number of juveniles produced -> implement management action or do nothing -> distribution and abundance of juveniles downstream
  • Models, management, and monitoring are all important to effective decision making

Useful monitoring data for this specific effort

  • Number of spawners
  • Prespawn mortality
  • Sex ratio
  • Habitat amounts
  • Temperature and flow
  • Food availability
  • Juvenile outmigrants per tributaries by month and size class (RST)
  • Juvenile outmigrants across tributaries by month and size class (Chipps Trawl)

What tools/exercises would be useful for the SIT to evaluate the different movement rulesets?

  • Sadie showed an example of graphs that showed juveniles per tributary at Chipps by month and size class. Feedback was this was useful and also helpful to group for Central Valley wide metrics.
  • Showing median most interpretable
  • Rene: also clumped by some kind of category - like regional water year type or total water year type
  • Nick Som: It’s also possible to have differences between run types (like spring vs. fall run) resolve as emergent properties of the model based on how the submodels are parameterized.
  • Brian Ellrott: Wonder if there’s a way to use eye lens and otolith chemistry info here
  • Jim: run reconstruction would be very useful

SIT Homework

Continue thinking about what hypotheses should be included in future versions of Chinook salmon DSMs…and the monitoring data needed to test them

SIT Action Item: Please send short description to Megan to compile to discuss during next SIT call (by Feb 1 if possible)

11:30: Call for 2022 SIT Presentations (Megan Cook)

  • Science Talks – new study plans, field reports, data summaries/analyses
  • Project Updates – new restoration plans, progress reports, restoration outcomes
  • Other Programs – who do you want to hear from?
  • SIT Action Item: Please reach out to with ideas!

11:45: New Business? (All)

12:00: Adjourn