Conference Call

September 16, 2020 Slides

By phone:

Bernard Aguilar, Mandy Banet, Denise Barnard, Mike Beakes, Matt Brown, Felipe Carrillo, Megan Cook, Flora Cordoleani, John Dealy, Lauren Diaz, Adam Duarte, Brian Ellrott, Sadie Gill, Eric Ginney, Chris Hammersmark, John Hannon, Brett Harvey, Jason Hassrick, Travis Hinkelman, John Kelly, Priscilla Liang, Erin Lunda, Bruce McLaughlin, John McManus, Erica Meyers, Cyril Michel, Mike Mimeo, Jim Peterson, Corey Phillis, Dick Pool, Mike Prowatzke, Emanuel Rodriguez, Derek Rupert, Alicia Seesholtz, Tanya Sheya, Kate Spear, Susan Strachan, Pamela Taber, Mark Tompkins, Mike Urkov, Bill Vanderwaal, Page Vick, Heidi Williams, Rod Wittler, Mike Wright

Summary of Action Items


  1. Review final NTRS. Document Submit addenda as appropriate to and by October 2.
  2. Review proposed NTRS adaptation schedule. Document Submit comments to by October 2.
  3. Review proposals for model changes.
  4. Review Data Guidance. Document

Mike Urkov

Make responses to the previous comments on NTRS available

Megan Cook

Coordinate independent science review of SIT process in the near future

10:00-10:10 AM

Intro to Megan Cook, CVPIA Science Coordinator (FWS)

  • Grew up in the Central Valley (Stockton)
  • B.S. Ecology, Behavior, Evolution (UC San Diego) and M.S. Wildlife Science (Oregon State)
  • With FWS for 9 years
  • Experience in collaborative science planning, landscape-scale partnerships, data management

10:10-10:25 AM

Near Term Restoration Strategy (NTSR)–Mike Urkov (FlowWest)

  • Oct 2 deadline for submitting addenda to NTRS
  • Text is finalized, by our agreements for engagement, acting members of SIT have until 102 (2 weeks) to review, if there are any comments or addenda suggested for NTRS, will append to document. For all intents and purposes, finalized now
  • Where is it? Document in the agenda for today’s meeting on the SIT website
  • Strategy is finalized. The SIT has till October 2nd to provide any addenda if necessary. Moving to a 5 year implementation window with annual adaptive management updates. The responses to the previous comments are documented and will be made available by Mike Urkov.

Updates and Primary Edits

  1. Emphasis on SDM and process
  2. Executive Summary
  3. Clean up of terminology/consistency
  4. Focused description of single overarching Strategy:
    • Restoration Actions (9 salmon only)
    • Information Needs (9 salmon / 7 O. mykiss / 5 sturgeon)
  5. Glossary!
  • No changes to conclusions/priorities/information needs

Process for Strategy Review and Revision

  1. Five-year implementation window
  2. Annual Adaptive Management Updates
  3. SIT will review the current prioritizations and assess whether they remain applicable
  4. Possible that large-scale changes in the understanding could necessitate an update to the prioritization and a revision to this Strategy
  • October 2 deadline for submitting addenda to NTRS (send to and

Next Steps

  1. 508 compliance for official posting to web
  2. Begin five-year cycle
  3. Consider changes to DSMs
  4. Update information needs

10:25-10:40 AM

5-year Schedule for NTRS adaptation–Megan Cook (FWS)

  • Slow the process down to match work schedules, including implementation of actions in real world. Rod brought up concerns associated with the timing of priorities, noting that they need to be make available by March at the latest to feed into the funding cycle. This will be reviewed again during the October meeting. Brian Ellrott brought up the initiation of an independent science review. Megan will coordinate that in the near future. Brian suggest reassembling the same group of people, if possible, that put together the 2008 Listen to the River report.

Purpose of NTRS Schedule

  • Intentionally slow the SIT process down, particularly for the modeling work
  • Account for realistic timelines in obtaining new or updated information for the decision support models (maybe not annual)
  • Acknowledge the potentially limited value in changing priorities every single year
  • Improve capacity to operate in adaptive management framework

Year Zero (2020): Finalize NTRS for FY21-25

  1. SIT October meeting
    • Finalize NTRS, including addenda from SIT members
    • Decide on direction for proposed model changes

Year One: Model Development Year

  • Modelers (winter): Refactor models based on model changes, continue to make models transparent and online for people to reference
  • SIT March meeting: Present prototype model changes to SIT, discuss
  • Modelers (spring/summer):
    • Integrate model updates, calibrate model,do sensitivity analysis
    • Subgroup reviews Model Calibration/Sensitivity Analysis (is model still sound given changes?). Jim- For reviewing results, anyone in SIT can participate, not exclusionary.
    • Run existing 13+ strategies through revised model (how might output change?)
  • SIT Oct meeting:
    • Hear results of the review of Model Calibration/Sensitivity Analysis,
    • Discuss results of running current strategies through the model–determine whether existing priorities should remain or be altered,
    • Start developing ideas on new candidate strategies
  • SIT members (winter): Use new web tool (planned) to explore candidate strategy ideas and model output

Year Two: Recommendations Year

  • SIT Jan call: Further develop candidate strategies that we want to consider together
  • Modelers (winter): Draft model run of candidate strategies
  • SIT March meeting:
    • Review results of candidate strategies
    • Determine revised set of priorities
  • Modelers (spring): revise model based on feedback and do final model run
  • SIT calls (summer):
    • Finalize updates to priorities,
    • Present proposed model changes
  • SIT Oct meeting: Decide on direction for proposed model changes

Year Three: Model Development Year

Same as Year 1

Year Four (2024): Recommendations Year

Same as Year 2; revised recommendations basis for next NTRS

Year Five (2025): Complete Next NTRS (FY26-30)

Complete the next version of the NTRS with recommended priorities for restoration actions and information needs

10:40-11:20 AM

Proposals for Model Changes–Jim Peterson (USGS), and Adam Duarte (USFS)

  • Provide overview. Decisions to be make at next meeting.

Food 4 Fish, (Rod Wittler and Mike Beakes, BOR) Proposal

  • Could be used to update the growth submodel in the SIT’s current Chinook salmon DSMs. This is a longer term SIT model change. Probably not this iteration.
  • Point source for prey for outmigrating salmonids, initial mixing (point source or adjacent wetland). Dark blue is dilution of augmented food supply, decay of augmented food supply, and consumption of augmented food supply. Hydrologics that control mixing, transport, dilution
  • 2 methods for models that have been done. Calculate area of dark blue triangle and consider that has a different/higher growth rate than background level of growth rates associated with instream perennial habitat. Latter assigned in the model to have higher growth rate. Temporarily assigning that habitat to floodplain/other. Haven’t figured out all the mechanics yet.
  • The Tisdale weir (upstream boundary of SRH2-D Model) has been made available to us, going all the way to Freeport. Don’t have to build this model, can just use this one.
  • Adam- Is plan to get a written proposal for next meeting, or update for next model change?
  • Rod- more of the latter. Changes not ready by timeframe for next cycle. Will be a year from now before we’re ready to talk about what we want to do for this.

Habitat Inputs (Mark Tompkins, FlowWest) Proposal

  • SIT Proposal drafted, ready for review. Has been through habitat subgroup, incorporated comments.
  • Authors- Rod Wittler, John Hannon, Rene Henery, Mark Tompkins, Chris Hammersmark
    • Supported by the habitat subgroup- Mark Gard, Lisa Hunt, Matt Brown, Derek Rupert
  • Submodels Affected
    1. Juvenile Survival
    2. Adult In-river Survival
    3. Reproductive Success
    4. Juvenile Migration Success
  • Submodel Parameters Affected
    1. Spawning habitat
    2. In-channel rearing habitat
    3. Floodplain rearing habitat
  • Overarching Objective- take a bowl of fruit, turning that into a consistent bowl of apples (similar methodology, accuracy behind it)
  • Hypotheses:
    1. More accurate and consistent habitat inputs across all watersheds included in the life cycle models will improve model performance and reduce model uncertainty
    2. Certainty of expected effectiveness of restoration actions (as determined by the life cycle models) will be improved with more accurate and consistent habitat inputs across all watersheds
  • Current Inputs
    1. WUA based (mostly)
    2. Variable age
    3. Variable extent
      • Different scales of how representative they are, some detailed, some not
    4. Variable hydrologic range
      • Some high flows, some low flows
    5. Proportional (Suitable Area= f (area* depth suitability * velocity suitability)
    6. Subsampled (representative reaches)
  • Proposed Inputs
    1. Driven by 2-D modeling, becoming more available and easier and easier to develop
    2. Instead of proportional suitability, will have range of suitable conditions, captures where habitat is suitable and scaling proportionally for floodplain rearing
  • Hammersmark- Different areas produce food in a different way
  • Duration optimal for first 9 days, falls after that
  • One of the reasons why we don’t have an exact approach- timestep, not daily. Could be model upgrade, would add inundation duration as factor
  • Tools built now require a flow input and are run through a processor to get at what the spatial habitat value is. If we followed exactly where we’re at now, would have to take flow time series, input it, and generate habitat time series separate of SIT model, would be input of SIT model
  • Integration Instructions
    1. Watersheds with 2D models 2020-2022
      • Tuolumne, Mokelumne, American, Yuba, Deer, maybe Stanislaus
    2. Watersheds in charter 2022-2025
      • American, Yuba, Lower-mid Sac, Upper Sac, Clear, Upper-mid Sac, Feather, Butte, Stanislaus, Lower San Joaquin
    3. Other watersheds 2025 and beyond…
    4. Life cycle model must accommodate old and new habitat inputs
    5. Conduct sensitivity analysis on old vs. new habitat inputs
    6. Output from sensitivity analyses should guide future habitat input updates
  • SIT proposal is filled out and available on the SIT website. The proposal focuses on trying to come up with a consistent more accurate way of quantifying habitat inputs for the DSMs. Jim asked if these would be dynamic to include operations in future iterations. Chris H. said that is part of the challenge now. Because of how the habitat inputs are created and then fed into the DSMs.

Survival in the Delta (Cyril Michel, NMFS) Proposal, Supporting Manuscript

  • As temp increasing, energy of predators need to increase as well
  • With increase with water temp, more predator activity
  • Strong relationship in water temp and predation rate
  • Temp/survival model
  • Temperature/survival relationship is currently implemented in the model, maybe not capturing everything and more focused on physiological limits on juvenile salmon, didn’t incorporate predator/prey relationship. Pretty straightforward change
  • Jim noted that this proposal is a straightforward change to the model if approved.

Survival in Sac River (Cyril Michel, NMFS) Proposal, Supporting Manuscript

  • Flow vs. survival relationship for the Sacramento River
  • Proposing change in flows to survival relationship. Worked with Jim a few years ago to implement flow/survival relationship back then.
  • Survival should vary in response to flow with a step function. When river flows are below 4300 cfs, we see survival around 3% at Wilkins Slough
  • 18.9% survival for flows between 4,259 and 10,712 cfs
  • 50.8% for flows above 10,712 cfs
  • Past studies have found a strong relationship between flow and juvenile survival during outmigration in the Sacramento River
  • Assembled a bunch of different telemetry groups from 2013-2019. Mostly comprised of spring/fall-run fish
  • Preliminary look at how survival changed in relationship to flow. 5% quantile flow bins
  • Survival plateaued around 50%
  • Promising not a linear relationship
  • Flow drives, or is strongly correlated with, many other covariates
    • 10700 cfs threshold: turbidity? Behavioral response of predators?
  • Matt Brown- are flow rates daily averages? How to incorporate to monthly timestep of model? Cyril- haven’t thought too much about it, has occurred to me, will talk to Jim and Adam about this. Jim- we can figure out something to do about this
  • Brett Harvey- mechanisms very important for how info is used. Is there any sort of step-change in measured velocities? Velocity is what fish experience in terms of transport. Cyril- looking into that soon
  • Cyril noted new evidence that suggests survival associated with flow should be a step function.

11:20-11:35 AM

Data Guidance/EDI Demonstration (Sadie Gill, FlowWest) Document

  • Data Guidance for CVPIA Funded and/or Authorized Work: “Practitioners awarded funds for projects by CVPIA should designate a ‘data steward’ on their project team. Data stewards manage the project data to ensure CVPIA data requirements are met.
  • Metadata Schema
    1. Ecological Metadata Language schema maps to federally approved metadata standards
    2. EML documents are formatted using XML
    3. Encoding that are human- and machine-readable’
  • Data Steward will fill out template and share with CVPIA data manager
  • R package EDIutils enables users to create valid EML documents with CVPIA best practices baked in
  • CVPIA data manager will upload data package to EDI’s repository
  • Sadie discussed the EDI repository and her role in ensuring data meet certain standards. Folks can do this themselves, but she is here and willing to help them through this process. During the October meeting she will be giving a more in-depth demonstration with a real-world example.
  • For the Oct meeting, hope to go through and create a data object uploaded to the repository, show what pieces go into it, what was the template. Will be working John Hannon’s dataset, ask how he thinks it went

11:35-11:50 AM

Update on Butte/Sutter Bypass Survival Studies (Flora Cordoloeani, NOAA) Slides, Supporting Report

  • Sacramento Valley
    1. Few remaining historic wetlands
    2. Remnant off-channel habitat in flood bypass system
    3. Sutter Basin = uppermost flood bypass in the Sacramento Valley
    4. Managed wetland for migratory birds and farming
  • Ecological role of the Sutter Basin?
    1. Most abundant spring-run Chinook population
    2. Large juveniles produced
  • What are the growth benefits to juvenile Chinook Salmon rearing in Butte Sink and Sutter bypass?
  • Cage experiment- 5 regions (butte Sink, Upper Bypass, Lower Bypass, Sac River, Feather River), 3 habitat types (channel, off-channel wetland, off-channel agriculture), 26 cages (5 individually PIT tagged salmon per cage, from 2/19/2019-4/3/2019)
  • Sampling steps
    1. Salmon measurement
    2. Water quality
    3. Lower trophic sampling
    4. Wild fish sampling
    5. Stomach contents
  • Water conditions driving productivity
  • Fish growth correlated to zooplankton densities
    1. Mixed effect model: FL Growth rate = f(water quality & lower food web) + habitat type
  • Multiple salmon runs & similar diet
  • Next steps: use for the SIT model
    1. How can we incorporate this information into a salmon life cycle model such as the SIT model?
      • Ratkowsky temperature-dependent growth model
  • Flora presented some of her work on fish growth and is looking for ways to integrate this information into life cycle models, like the SIT’s DSMs.

11:50 AM-12:00PM

Prep for October SIT Meeting (Megan Cook- FWS, Jim Peterson- USGS, Adam Duarte- USFS)

Agenda Overview

  1. SIT Business

    • NTRS finalization with addenda
    • Schedule for NTRS, revisions incorporated
    • Subgroup Reports/Model Change Proposals
    • Comparison of NTRS Priorities with Currently Funded Actions
  2. Relevant Information Sharing

    • Briefing from NMFS – elements in BiOp good candidate for CVPIA
    • Briefing on CVPIA Long-term Operation (LTO) from USBR Bay-Delta Office
    • SIT and Other Science Partnerships
      1. Sacramento River Science Partnership briefing?
      2. Coordinated Salmonid Science Plan briefing?
  3. Focus on Monitoring and Data

    • Monitoring Requirements Overview
    • Data Guidance / EDI Demonstration
    • Project Updates Requested (Monitoring and Data Focus)
      1. Clear Creek Phase 2A & 3C – Derek Rupert (USBR)
      2. Yuba Hallwood – Paul Cadrett (FWS)
      3. Upper Sac – John Hannon (USBR)
      4. Stanislaus – JD Wikert (FWS)
      5. Stanislaus gravel – John Hannon (USBR)
      6. American River – John Hannon (USBR)
    • Monitoring and Data Synthesis Discussion

Meeting Decisions

  • Final version of NTRS and Addenda
  • Revisions to 5-year schedule for NTRS
  • Direction for proposed model changes

Summary of Pre-work

  1. Review final NTRS. Document Submit addenda as appropriate to and by October 2.
  2. Review proposed NTRS adaptation schedule. Document Submit comments to by October 2.
  3. Review proposals for model changes.
  4. Review Data Guidance. Document

12:00 PM

  • Adjourn