Conference Call

June 23, 2021 Slides

By phone:

Bernard Aguilar, Denise Barnard, Tricia Bratcher, Erin Cain, Felipe Carrillo, Charlie Chamberlain, Megan Cook, Flora Cordoleani, Ammon Danielson, Holly Dawley, Carl Dealy, Lauren Diaz, Adam Duarte, Jim Earley, Laurie Earley, Chris Hammersmark, John Hannon, Jason Hassrick, Priscilla Liang, Duane Linander, Erin Lunda, Todd Manley, Erica Meyers, Bryan Matthias, Cyril Michel, Kirk Nelson, Kevin Niemala, Russ Perry, Jim Peterson, Corey Phillis, Michael Prowatzke, Derek Rupert, Ian Smith, Erin Strange, Mark Tompkins, Annalisa Tuel, Mike Urkov, JD Wikert, Heidi Williams, Rod Wittler, Michael Wright

Meeting Summary

Near-term Restoration Strategy Available
The Science Coordinator reminded the SIT that the final formatted version of the Near-term Restoration Strategy is complete and posted to the SIT website.

SIT 2021 Calendar
The Science Coordinator provided an overview of the remaining SIT tasks and calendar for 2021, highlighting the Near-term Restoration Strategy communications plan, completion and release of the new version of the Chinook salmon DSMs, SIT reviewing updated model output and determining whether priorities need revision, and announced that the FY20 and FY21 Adaptive Management Updates would be combined and available for review in early November.

NEW: SIT Background Workshop
The Science Coordinator announced that an optional workshop would be held August 18, 1-3pm Pacific time, to provide a refresher on SIT process, decision support models, and the development of the Near-term Restoration Strategy. This will be an interactive forum to ask questions and understand the necessary background information to be prepared for the August 25 SIT call that will cover updated model calibration, sensitivity analysis, and model output. SIT members are encouraged to email with any questions or topics you hope to see covered during this session.

Additional Time to Review Updated SIT Guidance
The Science Coordinator offered additional time for SIT members to provide feedback on the draft updated SIT Guidance and requests feedback by July 15 to
1. Revised SIT Guidelines for review (clean version)
2. Revised SIT Guidelines for review (tracked changes version)

Late-fall-run Chinook Salmon DSM
Jim Peterson presented the results of the input received during late-fall-run Chinook salmon expert meeting to support the development of the late-fall-run DSM. This included late-fall-run habitat inputs, geographic extent, timing, supporting data, and calibration data sources. Also presented were several hypotheses related to timing and life history and approaches to modeling those hypotheses and assessing via sensitivity analysis. We hope to show results no later than the October SIT meeting.

New SIT Proposal
Mark Tompkins (FlowWest) presented an overview of a new SIT proposal to 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 GrandTab escapement data used in calibration). The proposal will be posted with the meeting notes for the SIT to review and SIT approval will be sought at either the Sept or Oct SIT meeting (the change would be incorporated in the next cycle of DSM updates in 2022).
1. SIT Proposal on Updating CalSim Inputs

CVPIA Data Guidance
Erin Cain (FlowWest) provided an update on the CVPIA Data Guidance and accomplishments thus far. We now have multiple CVPIA datasets available on the Environmental Data Initiative (EDI) with more in the queue. FlowWest has developed EMLaide, a tool to assist in creating metadata for uploading to EDI.

CVPIA Funding Update
Rod Wittler (USBR) provided an update regarding CVPIA supplemental funds and announced partial funding of the habitat assessment charter and salmon demographics charter, which address key Near-term Restoration Strategy information needs.

Winter-run Trawl Efficiency Study
Russ Perry (USGS) provided the SIT with an overview of a project to estimate the abundance of winter-run Chinook salmon leaving the delta (largely funded by CVPIA), using data from Chipps Island and developing a trawl efficiency model. Russ outlined options for future analyses for the SIT to consider and the SIT will revisit the topic at a fall meeting to provide input.

Spring-run Chinook Salmon Updates
Patricia Bratcher (CDFW) provided an update on spring-run Chinook salmon, including recent counts in various tributaries (with notably high returns), observations of Columnaris bacterial infection, and genetics sampling and analysis needs.

Predator Contact Points Update
Cyril Michel (NMFS) briefly reported that the conclusion of the latest predator contact points field season was completed and went well. A longer update will be incorporated into a future SIT meeting.

Summary of Action Items
1. Please provide any final comments on the revised SIT Guidelines by July 15 to
2. If attending the SIT Background Workshop, please send questions and topics to
3. Please review the new SIT proposal on the CalSim updates and identify any questions. The SIT will consider the proposal and approval in the fall.
4. Consider about the potential future analyses that Russ Perry (USGS) presented. The SIT will revisit this topic in the fall.

Detailed Meeting Notes


Welcome, Agenda Review – Megan Cook (FWS)


Upcoming in SIT for 2021 – Megan Cook (FWS)

  • Completing and releasing a new version of SIT Chinook DSMs
  • Reviewing calibration and sensitivity analysis results, review updated results based on 13 strategies used to create NTRS
  • Threshold for changing priorities is high. Don’t want to keep tinkering with priorities. If something has really shifted and is really different than before, that triggers that we have to look at prioritization and what it means.
  • SIT 2021 Overview: please refer to chart in meeting slides
  • New: SIT background workshop (Aug 18, 1-3pm)
  • August 25 SIT Call (9am-1:30pm)
  • September 15 SIT Call (10am-12pm)
  • October 13-14 SIT Meeting (9am-4pm)
  • December 15 SIT Call (10am-12pm)
  • The FY20 and FY21 Adaptive Management Updates will be combined and will be available for review in early November.

Revised SIT Guidelines


Model Updates: Late-fall-run Chinook Salmon DSM – Jim Peterson (OSU/USGS), Adam Duarte (USFS)

  • 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
  • Modeling juvenile dynamics: fry leave natural tributaries and rear in the Sac and delta using habitat filing rules identical to fall run, fry leave natal tributaries and rear in the Sac with 25% migrating below RBBD rear in Sac and delta, fry leave natal tributaries and rear in the Sac and delta but they do not pass a downstream segment is temp > 18 C
  • Give each equal weight and average, sensitivity analysis
  • Calibration data: GrandTab, spawning ground surveys
  • Hope to show results no later than the October SIT meeting


SIT Proposal: CalSim Update – Mark Tompkins (FlowWest)

  • Issue of concern: Current DSM monthly flow inputs are from an older version of the CALSIM model run of CV 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: Would replace the flow inputs from the older CALSIM model with 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 GrandTab escapement 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)
  • SIT Proposal on Updating CalSim Inputs


CVPIA Data Guidance Update – Erin Cain (FlowWest)

  • Presentation to finding packages on EDI portal
  • Data package summary
  • FlowWest has developed EMLaide, a tool to assist in creating metadata for uploading to EDI
  • EDI does provide metrics on the number of downloads of datasets and views of full metadata


CVPIA Funding Update – Rod Wittler (USBR)

  • Via supplemental funding obtained by Reclamation, charters for two SIT subgroups were partially funded: habitat assessment (Wittler & Tompkins) and salmon demographics (Beakes & Matthias)
  • Chris Hammersmark: Is Blair’s group doing this work? Yes
  • Summary of 2D Hydrodynamic Modeling Activities on the Sacramento River and Clear Creek


Trawl Efficiency Project Updates and Discussion – Russ Perry (USGS): “Counting the needles in the haystack: Estimating abundance of endangered winter run Chinook salmon leaving the Delta”

  • 6 system-wide recommendations to bolster winter run monitoring network. Today’s presentation addressing genetic run ID and estimates of abundance
  • Long-term trawl monitoring in the Delta: > 40 years of juvenile salmon catch data, coded wire tag recoveries, index of survival and abundance, genetic and otolith sampling
  • What can we infer from catch data? 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, critical nexus between freshwater and ocean, inform life cycle models
  • 5-year study: acoustic telemetry, CWT catch and trawl efficiency
  • Part 2: Trawl Data and CWT catch: ten 20-min tows per day, operate 3-7 days per week
  • Factors affecting trawl efficiency: release-group level, daily level, tow level
  • 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 *Jason Hassrick: Do you have any plans to evaluate the assumption that fish carrying acoustic tags have similar survival as CWT fish? Russ: Yes, difficult to evaluate, but one way to ensure it is to make sure that the population we select has no tag bias. Focused on some hatcheries that have larger sized individuals that can carry the tag. Also evaluating the timing of arrival at Chipps Island. Trying to estimate size-dependent survival. Not completely through analysis yet, is the current assumption.
  • Part 3: Genetics Data and Abundance Model- trawl genetic sampling: unmarked fish classified by length-at-date (LAD)
  • Genetic tissue samples
  • Assumes fish uniformly distributed throughout the day (take sampling fraction as fraction of the day). Can be assessed with the acoustic tags. Acoustic tag data provides a lot of data on the timing of passage at chipps island. Really strongly driven by the tides.
  • Jim: How does this compare to other trawl efficiency studies? Russ: Pretty good
  • Corey: Clarify what number actually using in your comparison to JPE? JPE is production estimate for # of juveniles entering the delta. Are you actually using JPI (production of individuals at RBFF)? Russ: yes using JPI. Will correct slides
  • Russ interested in SIT input on future analyses. Potential uses of a trawl efficiency model include: abundance and composition (natural vs hatchery origin, by race (using genetics), by population), survival (hatchery groups, natural groups), retrospective analyses (40 years of trawling data with CWT captures, long-term patterns of freshwater and ocean survival)
  • SIT will revisit this topic and provide input at a fall SIT meeting.

New Business

2021 Spring-run update (compiled and submitted by Tricia Bratcher, CDFW):

Spring-run Chinook Count Data thus far in 2021:

  • From Charlie Chamberlain (USFWS) Clear Creek: As of June 18, USFWS counted 1,459 spring run on the pre-emergency-pulse flow snorkel survey last week! Data from video weir is forthcoming.
  • From Tricia Bratcher (CDFW): Cow Creek observations—possibly as many as 5 SRCS entered Cow Creek (one dead female collected upon being alerted by a landowner).
  • From Matt Johnson (CDFW) Mill and Deer Creeks: Deer and Mill counts on video this spring (approx. 510 and 650 fish respectively) but the creeks are crazy low (Deer has been setting new min flow records for the past 105 years of data).
  • From Tracy McReynolds (CDFW): Butte Creek has an initial estimate of 15,000+ SRCS in holding reaches (likely 18k.This spring a large portion of SRCS tried to enter Butte Creek at the Butte Slough Outfall gates with unknown success. We know some made it through the flap gates when water was flowing but due to being a drought year, flow conditions were less than ideal. I imagine many SRCS ended up in the upper Sacramento tributaries, probably with a lot of head injuries trying to make it into the flap gates.

Columnaris Observation (bacteria infection):

  • USFWS has encountered only 1 mort so far on Clear Creek, but MANY of the fish had head wounds that looked symptomatic of failed snagging attempts. Columnaris appears to be colonizing some of those wounds, and Charlie expects to encounter more mortalities as summer progresses.

The Need for Genetic Sampling and Analysis:

  • There is a lot of interest in adult spring-run genetics analysis for 2021 returns from the State; This is a unique opportunity to gather a large sample set from the Upper Sacramento tributaries.
  • Having genetic analysis of these tributary populations would be insightful and provide important information. The very large Butte population is going to have a difficult time surviving summer to successfully spawn. Water from Philbrook and Round Valley Reservoirs is below capacity and the hot start to summer has not been kind. Butte SRCS have similar wounds and some of the pre-spawn mortalities we have had to date, show columnaris infection.
  • Initial coordination is already initiated between Charlie, Matt, and Tracy as to collecting tissue samples (email so far mostly).

Why share this info / Things to think about:

  • To better inform the SIT and NTRS and in real time
  • Somewhat unprecedented SRCS returns, relative to last 10+ years of escapement data, and a unique monitoring opportunity, with newer(ish) technologies
  • Possible funding need:
    • USFWS has a backlog of tissue samples from previous years to run too and are interested in getting them processed with the new SNPs markers tied to entry timing.
    • DWR has a contract in place with the Department’s Central Valley Tissue Archive (CVTA) to process and run genetics on spring-run tissue samples. Matt Johnson is planning to contact DWR on exactly how much funding they have for spring-run genetics in 2021, their timeline for getting samples into their lab before their contract expires, and DWR’s management goals or scientific questions behind this funding. That may or may not suffice in terms of analyzing samples.
  • Drought-related impacts, as they relate to water management, structure management (e.g. Butte Creek), restoration “influence” (to offset impacts?)

Update on predator contact point field season (Cyril Michel)

  • Just wrapped up the latest predator contact point field season and things went very well. Can provide more detailed update at future meeting.