Conference Call

March 24, 2021 Slides

By phone:

Bernard Aguilar, Mandy Banet, Mike Beakes, Tricia Bratcher, Matt Brown, Felipe Carrillo, Megan Cook, Matthew Dekar, Lauren Diaz, Adam Duarte, Stephanie Durkacz, James Earley, Laurie Earley, Sadie Gill, Ryan Greathouse, Chris Hammersmark, John Hannon, Michael Harris, Rene Henery, Elizabeth Jackson, John Kelly, Morgan Kilgour, Priscilla Liang, Duane Linander, Erin Lunda, Todd Manley, Cyril Michel, Kirk Nelson, Reid Nelson, Jim Peterson, Richard Pool, Michael Prowatzke, Derek Rupert, Ian Smith, Kate Spear, Alexander Tasoff, Mark Tompkins, Mike Urkov, Bill Vanderwaal, Page Vick, JD Wikert, Rod Wittler

Meeting Summary

The Science Coordinator announced that the final formatted version of the Near-term Restoration Strategy was complete and posted to the SIT website. A broader communications strategy still being planned.

The Science Coordinator solicited feedback on updated SIT Guidance and Templates for Proposing changes to DSMs. Please provide comments and edits on the following documents to by April 2.

The SIT heard the results of prototyping model changes based on proposals the SIT previously reviewed and accepted. All changes received thumbs up to proceed with the understanding that the SIT will have additional opportunity to provide feedback when the changes are incorporated into the model and model calibration and sensitivity analysis occurs. The specific input from SIT was to:

  • Incorporate the updated survival estimates in the Sacramento River and the north delta based on data provided from Cyril Michel. Consider incorporating adjustments for size classes smaller than the fish in Cyril’s dataset.
  • Proceed with the updated habitat input approach in Deer Creek
  • Proceed with updating the model with habitat estimates for winter-run Chinook salmon in Battle Creek

The SIT provided initial feedback on how to proceed with developing the late-fall-run Chinook salmon DSM and provided suggestions for the appropriate subject matter experts to invite to a late-fall-run Chinook salmon expert meeting.

The SIT began to discuss the topic of integrating the Chinook salmon runs into a single DSM and provided initial ideas about pros, cons, and the timing. SIT members were invited to contact the Science Coordinator if they are interested in potentially serving on a subgroup to develop a plan for how this would proceed. Additional discussion on this topic will be part of future SIT meetings.

Corey Phyllis (MWD) provided an update regarding the Growth/Bioenergetics Proposal, which would update the growth transition matrices in the DSMs with mass-specific growth rates. Expected next steps are to provide the SIT with an updated proposal by June 2021, develop a request for prey density data, and present the results of bioenergetics sensitivity analysis by the fall.

Mike Beakes (USBR) presented a summary of the San Joaquin Steelhead Monitoring Workshop that took place in Feb 2021. Planned next steps include the development of a monitoring plan and the SIT will have the opportunity to participate and collaborate in its development. A few topics were left in the parking lot for future discussion, O. mykiss habitat size classes.

Detailed Meeting Notes


Welcome, Agenda Review–Megan Cook (FWS)

  • Final NTRS is online on the SIT website!
  • A broader NTRS communications plan is forthcoming


FY20 Memo, Updated SIT Guidance, Review SIT 2021 Process-Megan

  • Document for review coming soon
  • Other documents developed in past: Salmon demographics subgroup, habitat modeling priorities input needs, SIT critical monitoring needs
  • NTRS and memo are most up to date SIT documentation/priorities
  • SIT will have two weeks to provide comments on draft
  • Revised of SIT guidelines ready for review, posted on meeting portion of the SIT website
  • Nothing surprising or major, some language editing so we’re referring to NTRS
  • Comments and edits requested by April 2 to let Megan know if April 2 is not doable
  • Guiding documents moving forward

Summary of Model Change Proposal Process

  1. Describe change to conceptual model
  2. Present initial idea to SIT
  3. Develop full model change proposal
  4. Prototype model change
  5. Discuss results of model change with SIT
  6. Based on SIT input, finalize model change

SIT Proposal Templates

  • New Pre-proposal template
  • UPDATED: Full proposal template
  • Comments and edits requested by April 2 to if deadline not doable, let Megan know
  • Documents located on SIT website

SIT 2021 Overview (see slide with chart)

  • Rod Wittler: Priorities should be based off of: Output of models, models, expertise, modeling showing state, implementing in policy plots important
  • Jim Peterson: Some policy plots involved, used in strategies for individuals in specific runs
  • Preview of SIT 2021 Schedule




Model Updates: Results of Prototyping Changes

Updating survival in Sacramento River and Delta

  • New flow vs. survival relationship for the Sacramento River
  • Thoughts of incorporating size?
  • Russ Perry thinks correlating relationship between size and out migrating fish, has done some analysis on his work
  • Richard Pool: would argue that include new survival model will help understand new survival dynamics due to flow standard at Wilkins Slough
  • Rene: what do we see as future in these models in terms of incorporating/not the operational constraints? Current models give us potential to see conditions fish are experiencing to see where fish population dynamics are concerned
  • Rod: Is there a way to upgrade how we do temperature?
  • Mark Tompkins: Talked about in habitat subgroup, can be challenging to do temporal downscaling, topic worth thinking about if there’s a proposal to update CalSim runs
  • Rod: philosophical discussion in 2015 when SIT was started, talked about scale and resolution of all the ways to represent system
  • Adam: Need temp, flow gages, water year types
  • Mark: The reason I feel we use CalSim is because it allows us to create a period of record in hydrology that reflects a current set of operating rules that might not be in effect in period we’re covering. We’re doing 20-year simulation for life cycle model, don’t know if rules of system operation have changed that much from 2000-2020, might be model where we can use measured flows- los ability operational rules, but would have measured daily flows for a 20-year period, wonder if that’s worth thinking about as an exercise
  • Kept original EMM gage
  • Adam: was idea to incorporate size to use existing offsets between small, medium large?
  • Jim: Yes, what was suggested
  • Poll: Should we finalize model change for survival updates? Majority yes
  • Poll: Should we incorporate size classes? Majority yes

Updating habitat inputs

  • Prototyping report topics: SIT proposal process/status, objective of the SIT habitat input improvement proposal, refresher on difference between old and proposed new habitat inputs, habitat input prototyping on Deer Creek, next steps
  • SIT Proposal status:
    • January 2020 - August 2020: pre-proposal and proposal development
    • September 2020: presented full proposal to SIT and authorized prototyping
    • September 2020 - February 2021: prototyping
    • March 2021: prototyping presentation to SIT and SIT feedback
  • SIT Proposal for Improved Habitat Inputs
    • Hydraulic model outputs (2D) from entire river and floodplain
    • Spawning and instream rearing
    • Floodplain rearing
  • Habitat Input Prototype on Deer Creek
    • Old input= regional (instream) and scaled 1D (floodplain)
    • Fall Run DSM scaled old input by 2x for calibration***
    • Recent lidar, bathy, and high res photos (2017-2019)
    • Highly resolved 2Dd hydraulic model for CDFW Prop 1 project
    • Extensive ground-based habitat observations
  • Next Steps
    • Solicit SIT feedback (today)
    • Finalize perennial (instream) delineation rule
    • Test DSM calibration and sensitivity for Deer Creek and report back to SIT
    • Assuming SIT approval of DSM testing, replace old habitat inputs with updates as available
    • Recommend DSM improvements around inundation duration, food availability, and conduct field verification
  • Poll: Should we proceed with model change for updating habitat inputs? Majority yes.




Adding winter-run Chinook salmon Battle Creek habitat

  • Got info from Matt Brown to map extent of winter-run, applying habitat estimate
  • Poll: Should we finalize model change for winter-run Chinook salmon Battle Creek habitat? Majority yes.


Feedback on late-fall-run Chinook salmon habitat inputs

  • List developed of late-fall-run experts to invite to a meeting to go over this in detail
  • Same model structure as fall/winter/spring run Chinook salmon DSMs
    • not a lot of late-fall run information; in most cases will have to borrow from other runs (fall/winter most appropriate?)
  • Same DSM inputs as fall run Chinook salmon?
  • Adult estimates (GrandTab)
  • For calibration, seeding the model, and specifying where populations are/can go

Feedback on integrating Chinook salmon DSMs

  • Are we at a point that we want to take this on? (Formal integration of Chinook salmon DSMs). If so, who needs to be in the conversation (subgroup)?
  • Note: Has always been on the list of things to do
  • Note: We currently evaluate strategies across runs, but as separate steps
  • Pros: Reduce the number of model runs needed (4 model runs becomes 1)
  • Pros: Different runs will compete for space with each other (more realism)
  • Cons: Increase model run time (uncertain by how much)
  • Cons: Substantial increase in model complexity (number of parameters, calibration, and sensitivity analyses)
  • Decisions to be made: how do we avoid double counting habitat? What is the ruleset for habitat competition? Should we share more parameters across runs for the calibration/sensitivity analyses?
  • More to come


Proposal Update: Growth/Bioenergetics–Mike Beakes (USBR), Corey Phillis (MWD), Jim Peterson (USGS/OSU)

  • Issue of concern: current SIT life-cycle model does not account for temperature or prey in the growth transition matrices. Model lacks capability to evaluate: change in growth rate through the rearing period as river temperatures warm, tributary-specific growth rates, trophic subsidies from managed floodplains
  • Proposed change to model: update growth transition matrices with mass-specific growth rates
  • Slide on SIT temperature-independent growth and temperature-dependent growth, growth transition matrices
  • Next steps: share update proposal with SIT by June 2021, work with Jim and Sadie to integrate bioenergetics code into SIT model (spring/summer), work with Megan to develop data ask for prey densities (spring/summer), bioenergetics sensitivity analysis (summer/fall)


Summary of SJ Steelhead Monitoring Workshop–Mike Beakes (USBR)

  • NMFS supportive of BOR: Proposed Action
  • Broad interest and workshop attendance: 254 people from 72 different institutions (mostly from state and federal agencies)
  • Material produced during the workshop will inform development of the San Joaquin Basin monitoring plan
  • Next steps: Reconvene agency members that assisted with the Long-Term operations non-flow action steelhead charter spring 2021; host meetings to discuss workshop scope/content and how workshop can inform steelhead life-cycle monitoring on Sacramento tributary CVP/SWP watershed and the San Joaquin Basin Monitoring Plan.
  • Additional agency members and stakeholders may be invited to participate in drafting sections of the monitoring plan. Aiming to have a complete draft of monitoring plan by fall 2021.




CVPIA Funding Process Update–Matt Dekar (FWS), Rod Wittler (USBR)

  • Stay tuned for more info


New Business (All)

O. mykiss habitat size classes (Jim Peterson)

  • Defer to another meeting
  • Don’t have adult habitat for O. mykiss, need ruleset.

Project completion updates (Rod Wittler)

  • Incorporate into future meetings


  • Closing