Conference Call

October 13-14, 2021 Slides

Meeting Summary

The October 13-14, 2021 SIT meeting featured the finalization of SIT discussion of the 2021 updated model results and potential implication for existing Chinook salmon restoration priorities. Additional DSM updates included overview of the late-fall-run Chinook salmon beta model and planned doctoral research to support the steelhead DSM (from Lauren Diaz) and the sturgeon DSM (from Erin Lunda). Mike Beakes provided an overview of the steelhead lifecycle modeling work occurring in the Stanislaus.

The SIT also discussed the expanding use of the DSMs beyond the SIT and the kind of disclaimer and contextual information would be helpful to provide to distinguish between SIT uses of the DSMs and non-SIT uses of the DSMs. The additional text will be incorporated into the SIT Membership Guidelines.

Cyril Michel provided an overview of the 2021 field season on predator contact point research and Mike Beakes provided an update on the status of the salmon demographics work. Updates and discussions occurred related to several SIT propels for model changes, including the habitat updates proposal (from Mark Tompkins), bioenergetics proposal (from Corey Phillis and Mike Beakes), and operations proposal (from Mark Tompkins). The SIT also heard a new pre-proposal on reservoir prey subsidies from Drs. Rob Lusardi and Francisco Bellido-Leiva from UC Davis, in collaboration with Mike Beakes.

The SIT provided input to Russ Perry (USGS) regarding potential additional analyses for the Chipps Island Trawl efficiency project and their usefulness to the SIT and DSMs. The meeting ended with an optional information session regarding the FY21 CVPIA Funding Opportunity (from Matt Dekar and Rod Wittler).

Summary of Action Items and input requested from SIT Members:

(1) The following SIT proposals are available for review:

(2) Rod Wittler is requesting information to help populate the 2D hydrodynamic model inventory. The information requested is owner and operator, status or domain, calibration, uses of the model and its availability. Please email with information.

(3) Corey Phillis and Mike Beakes are requesting prey density data to support bioenergetics proposal (details bulleted below). They also soliciting a list of complexities related to the bioenergetics model that SIT members are concerned about; these items will be incorporated into the sensitivity analysis taking place next spring to determine the importance of those complexities.

  • What? Existing Prey Density estimates (individuals per volume sampled). Can come from Published manuscripts, grey literature, project reports, unpublished data
  • Where? SIT watersheds within anadromous extent; Perennial and seasonally-inundated habitats
  • When? Between now and December 15 SIT meeting
  • Who?,

(4) Tricia Bratcher is requesting input on the following:

  • Background info: Typically the Department does not conduct spring-run Chinook salmon redd surveys on upper Deer Creek, but we did this year. Between conducting that redd survey, plus other related observations over the last few years, Matt Johnson (lead spring-run biologist in Region 1) believes that spawning gravel is limiting on upper Deer Creek for spring-run, and secondarily but also important, steelhead. It could, in part, be attributed to CALTRANS management of Hwy 32 (including a sediment trap on a large trib), as Hwy 32 parallels upper Deer Creek for a lot of its upper length.

  • Request: The Department is requesting feedback on how to inventory instream habitat (i.e., a preferred methodology), relative to (1) what data may be useful AND useable by the SIT and the DSM and (2) what may be the reasons for a spawning gravel deficit so that it can be more effectively addressed. Granted, we would want to include CALTRANS in a future conversation (esp. if it’s something they need to mitigate for), and we would also want to assess if restoration is needed. Please contact Tricia Bratcher if you have any input on this important issue (

Detailed Meeting Notes



Bernard Aguilar, Denise Barnard, Mike Beakes, Francisco Bellido-Leiva, Erica Bishop, Tricia Bratcher, Matt Brown, Elissa Buttermore, Erin Cain, Felipe Carrillo, Rebekah Casey, Megan Cook, Matthew Dekar, Lauren Diaz, Adam Duarte, Chris Hammersmark, John Hannon, Brett Harvey, Rene Henery, John Kelly, Priscilla Liang, Duane Linander, Erin Lunda, Amy Lyons, Suzanne Manugian, Keith Marine, Bryan Matthias, Erica Meyers, Cyril Michel, Kirk Nelson, James Pearson, Jim Peterson, Corey Phillis, John Plumb, Bill Poytress, Emanuel Rodriguez, Derek Rupert, Alicia Seesholtz, Erin Strange, Mark Tompkins, Mike Urkov, JD Wikert, Rod Wittler, Bill Vanderwaal

Welcome, Agenda Review

Introductions/Icebreaker (Megan Cook)

  • Name, affiliation, favorite thing to do in the CV

Review SIT Guidance for making decisions (Megan Cook)

  • SIT members provide individual perspectives
  • NOT seeking consensus input / recommendations
  • SIT discussions are to promote understanding, clarity, “get on the same page”
  • Differing views are welcome and documented
  • Ultimately, Science Coordinator is responsible for identifying priorities (via the Near-term Restoration Strategy and annual Adaptive Management Updates)
  • Reminder: SIT is not a voting body and recommendations are not binding on FWS or USBR (Polling and pulse checks to solicit input, not to seek consensus)

Conclusion of model updates and priorities discussion (Jim Peterson/Adam Duarte)

Changes to Chinook Salmon DSMs

  • Model changes
  • Habitat inputs
  • All updated habitat inputs can be viewed here

The Process

  • Use revised model
  • Recalibration
  • Simulate 13 actions + no action
  • 20 years
  • Review results
  • Discussion
    • Do the new results fundamentally change the strategy?
  • Summary: For both 2019 and 2021, there were 3 different strategies in terms of best for juveniles and natural adults. 2019- strategy 10 came out well, in 2021, strategies 9 and 11 were good.

Summary of Takeaways from September SIT Call

  • Results largely similar between 2021 and 2019 models with some exceptions that warranted more exploration
  • Results of SIT requested analyses
  • Part of digging, different active floodplain in ver. 2021: fish that use floodplain have faster growth rate in current model. In less floodplain, slower growing. Fewer very large fish leaving in March
  • In calibration, rearing survival decreased

–Differences Strategy 4 (for fall-run) (Strategy 4 performed worse than no action in 2021 model)

  • Less frequent activation of floodplain (ver. 2021)
  • Less floodplain = slower growing
  • Fewer very large fish leaving much earlier (Feb-Mar)
  • Decrease in rearing survival during calibration

–Differences Strategy 10 (spring-run) (Strategy 10 performed worse than no action in 2021 model)

  • Largely due to calibration differences, lower rearing survival
  • Rescaled habitat 2019 vs. no rescaled habitat 2021
  • New delta survival model = greater juvenile mortality 2021 vs 2019 (April May)

  • Look at prespawn mortality of spring-run in Butte and other tributaries: generally low

  • Tricia: wondering about less floodplain = slower growing, to me, if you have less floodplain, you have less habitat for juveniles to use, don’t know if they’re hanging around that much because they’re on a timeline to move out. Is it slower growing, or just out migrating juveniles that are smaller? Jim: Kind of that, in the model, activate model to grow (3x). Large individuals leaving at times of year when there shouldn’t be those large individuals. Tricia: wondering if it’s food availability vs. slower growing.

Bottom line

  • Seemingly small changes cascade
  • We need to get better data for calibrations
    • Currently calibrating adult to adult, would rather do adult to juveniles leaving tributaries, to juveniles making it to Chipps Island
  • Reinforces information needs in NTRS
  • Future improvements
    • Revisit screw trap data
    • Incorporate improved Chipps Trawl estimates
    • Find better escapement estimates, PSM, ad clips
    • Juveniles movement and habitat use rules. These likely have an effect on the model but does not come out via the sensitivity analysis because the model only has one set of rules.

NTRS Priority Restoration Actions for Chinook Salmon

  • Connectivity important criteria. Importance of spatial diversity, natural productivity, is it supported by model outputs, and what runs are benefitting?
  • SIT reviewed the summary of input previously given in Aug and September SIT calls and continued the discussion, takeaways summarized below.

Evidence for change to priorities for juvenile habitat restoration?

  • Still seems valid (top optimal strategies didn’t really change)

Evidence for change to priority for connecting ephemeral non-natal tributaries?

  • Priority still relevant
  • Also benefits spring-run for yearlings and steelhead

Evidence for change to priority for improving survival in Butte Creek in downstream areas?

  • If anything, more relevant than before
  • Question on greater specificity on what was meant by “downstream areas” of Butte Creek
    • Past SIT notes did not reveal better definition
    • Problems in upper and lower Butte are probably both important. Holding habitat and temps in upper watershed really critical.
  • Consult with Cesar about previous information related to previous actions that required periodic intervention to maintain

Evidence for change to priority for maintaining spawning habitat?

  • Concern for Butte expressed – potentially would tweak to “maintain existing holding and spawning habitat for spring-run.” Concern that if a hydropower facility goes away, will be unable to maintain coldwater pools during summertime.
  • Reminder that spawning habitat is also rearing habitat

Evidence for change to Chinook salmon information needs?

  • Question regarding whether we need to distinguish fry vs smolt in juvenile rearing habitat or salmon demographics
    • We don’t have info on wild smolts, have info on hatchery fish. We need more info on wild juvenile fish for all life history stages
  • Keith Marine suggested finding data gathered by EBMUD in the early 1990s on gill ATPase on the Mokelumne - may help to look at physiological status of those migrants and the pattern of the smolt fish size. James Pearson will follow-up.
  • Rod: could or should we use physiological measurements to distinguish smolts from fry rather than just size? Keith: Size class in 50-70mm fork length where get a lot of overlap where fish physiologically smolting or not. In terms of info needs, if we have existing data and can identify data for monitoring that can help us distinguish or further refine the use of size class, may be of use in refining the model.

Matt Brown: any discussion about winter run model and how it turned out with calibration? Jim: Found the problem with Battle Creek and the problem was we have a generic model for the basin that takes monthly average temperature and it estimates a probability of exceeding 24C. Fortunately actually have the entire time series at a much finer resolution that Mike Wright created for Battle Creek. Problem was couldn’t keep a population alive in winter run in battle creek – found it was because of the temp thresholds. Have note to self for later on, will probably revisit where we have finer resolution time series of temp; look at using those rather than the thresholds.

SIT Late-fall Chinook Proposal, May 2018

  • In summary, put together model, calibrated well, and is set up to evaluate effect of uncertainty on management decision making. Hope can be a springboard to think about movement rulesets for fall, winter, and spring run.
  • Habitat
    • Only late fall-specific habitat available: spawning habitat in upper Sacramento
    • Used fall run habitat for remaining tributaries
  • Other inputs same as fall run, based off discussions with late-fall-run experts during meetings

Timing and life history

  • Hypotheses: wanted to incorporate different hypotheses on different rulesets on how fish move through system. Same structure in model except when produce juveniles – split model into three different models. Predict ocean adults using the 3 hypotheses and then combine using a weighted mean. Those weights are currently equal weights. Idea is we can update weights based on real world data and use sensitivity analysis to identify if uncertainty in how fish moving through system is driving rates.

Sturgeon DSM Update (Erin Lunda)

CVPIA SDM-Making Process: Phase 1 (Pre-SIT)

  • Sturgeon model background
  • Dissatisfaction with the calibration issues
  • Key unknowns that would need to really build a model
  • Two components: ocean adults, eggs moving to adults
  • Based on expert opinion and not empirical data
  • Needed: better empirical basis, more input from experts

Research Focus

  • Objective 1: Synthesize information of habitat usage for anadromous sturgeons in North America
  • Objective 2: Evaluate the effects of habitat conditions on survival, growth, and movement of green sturgeon.
  • Objective 3: Characterize the effects of environmental variability and individual biological characteristics on sturgeon recruitment success and apply this to a larger domain.
  • Objective 4: Use decision analysis to evaluate management alternatives for green sturgeon under extreme uncertainty.
  • Key uncertainties are specific to green sturgeon, most of presentation focusing on green sturgeon, but aspects will also help with white sturgeon
  • Email for comments/questions/feedback


  • Mike Beakes mentioned two existing studies that may be relevant to this work: carcass recovery effort in the delta (also involving John Kelly) and a microchemistry project with Cramer and Davis collaborators that would give sense of habitat use and life history composition.
  • This work perfectly overlaps with the sturgeon info needs in the Near-term Restoration Strategy

Steelhead DSM update (Lauren Diaz)

SIT steelhead model background

  • Pre-SIT era – rapid prototyping. Tried steelhead but didn’t succeed because wasn’t agreement among folks. Decided to leave steelhead out and moved forward with Chinook and sturgeon.
  • In SIT phase, initial focus on Chinook DSM and did beta version of steelhead DSM.
  • met with project work teams in 2018-19 and worked on developing conceptual models for a beta
  • when came time for calibration and running it, a lot of unanswered questions. Didn’t know what data to use to calibrate. Question of whether we had habitat data.

Research Focus

  • Evaluating the role of life history diversity in maintaining population resilience in altered landscapes
  • Objective 1: investigate the role of O. mykiss intraspecific competition in population dynamics
  • Objective 2: Evaluate the synergistic effect of anthropogenic change and intraspecific competition on population dynamics
  • Objective 3: Investigate how different systems create different life-history portfolios
  • Objective 4a: use prior information to get more robust demographic parameters that can be used to guide management. Will be utilizing data from Stanislaus steelhead lifecycle monitoring work (led by USBR/Mike Beakes)
  • Objective 4c: analyze what changes in O. mykiss carrying capacity reach management goals
  • Email with feedback on feasibility, helpful contacts/resources/data

Stanislaus steelhead monitoring (Mike Beakes)

  • Type of info hope to generate with this program: spawning fish, age structure, annual growth rates. Will get some scales for genetics analysis. PIT tag antennas – monitoring survival between PIT antennas, outmigration rates for fish detect at both antennas.
  • Developed a conceptual model to outline key life stage and transitions. Characterized in the two monitoring plans for the project. Cramer and Fishbio has monitoring plans for the stages they are in charge of implementing. Can provide PDF of those plans to see the details.
  • Initial data – approx. 300 spawning adults. Genetic approach, as collect more data, should be more refined and precise estimates and more accurate estimates of the actual spawning population size in the system.
  • Started analyzing microstructure of scales. Able to approximate age of fish and with data can start to estimate length at age and get interannual growth rates. Super preliminary.
  • Upcoming life-cycle monitoring activities: egg-to-fry survival study
  • Current plan is to continue program through 2028. Want summary reports in 2024 and 2028 (individual panel reviews)
  • Would continue sampling and monitoring as long as funding is available
  • Trying to collect environmental variables that are suspected to affect life cycles
  • Mike can share monitoring plans, preliminary data and draft reports

SIT Guidelines Revision Proposal (Megan Cook and Rod Wittler)


  • The SIT process and decision support models have a positive reputation throughout Central Valley
  • Code refactoring and documentation have greatly improved model performance and thus accessibility to others
  • There is increasing interest by others in Central Valley to explore the DSMs for multiple purposes
  • Our Guidance should be clear on our policy related to non-SIT uses of the DSMs


  • Science Coordinator shall make it clear in writing to other entities using the SIT models that they should issue a disclaimer along with any output from the DSMs. The disclaimer should state that their results and conclusions are those of the model users and are not endorsed by the SIT, FWS, or Reclamation


  • We put effort into reducing uncertainty that is important for the decisions we make. And those decisions may not be the same decisions that are being applied.
  • Maybe not disclaimer but some sort of requirement that they just include in whatever reports they put out a paragraph that describe the actual purpose of the model and how it may not fit with other purposes, best can do
  • Don’t want to be vague in statement. Want to be specific about just how wrong some uses of this would be
  • Done a fair amount of work with sensitivity analysis that outputs are particularly sensitive to. Reference that in disclaimer with general caveat that there are aspects of model particularly sensitive to. May help mitigate use of model
  • Want to make sure SIT aware of when models were being utilized by someone for another purpose. And make those who are consumers of those types of analyses know that those analyses are coming from the SIT but the entity utilizing the model.
  • Following SIT process, would want to incorporate relevant external changes through SIT process and proposals. Can come forward through proposal process and get integrated. Becomes SIT product because follows SIT process. That’s the distinction.
  • The model is calibrated to the inputs. If somebody decides to use new inputs, then they are using the model structure but not using the model. It is a different model at that point because will have to recalibrate. Add something like – any uses of this model that don’t include using the data that the model designed to take is at own peril.

Predator Contact Points update (Cyril Michel)

Predator Contact Points Charter

  • UC Santa Cruz- PI Cyril Michel; NOAA SWFSC- Co PIs: Eric Danner, Andrew Hein;
  • Metropolitan Water District: Alison Colins, Corey Philis; Bureau of Reclamation: Ian Smith
  • Original purpose: SIT came to realize that there were major unknowns regarding predation risk across landscape and more specifically with respects to man-made habitat features (aka “contact points”)
  • Study Objectives:
    • Determine highest priority contact points for further investigation with mega-analysis
    • Conduct field-based experiments to investigate the relationship between contact points and predation risk
    • Survey and georeference contact points as needed for inclusion in SIT model
  • Focus on the Delta for this particular project
  • Goal to estimate relative predation risk in relation to distance to nearest diversion. Hopefully get idea of range of possible effect sizes.

Next steps:

  • Review ARIS footage
  • Georeference and process depth and SAV data
  • In off-season right now, doing Delta light survey and lab studies
  • Remote sensing data not high enough resolution for this, did boat-based illumination survey, North Delta survey complete, South Delta TBD
  • Spring 2022: Tentatively SAV removal study
    • High SAV
    • Landowner access
    • South Delta–avoid delta smelt
    • Lake and streambed alteration permits still pending

Before after control Impact

  • Sampling methods

    • PERs
    • Paired ARIS cameras
    • Electrofishing


      Brett: Mentioned in Georgiana, where Russ et al was showing high predation rates for fish going down Georgiana – interested to hear what have to say. Cyril: talked to Russ about this, survival in actual Georgiana Slough isn’t very bad and somewhat comparable to Sac mainstem. It’s the fish that take Georgianna are then led into SJ and potentially even further into interior delta so ultimately have lower survival.

Cyril: don’t believe lights are major component of salmon mortality in delta but it’s really easy to fix, non controversial, very cheap. So think it is potentially a low hanging fruit.

Rod: Can we forecast how this important information will be incorporated into the DSMs? Megan: predators currently represented by PAD database; this work intended to assess whether that is still a reasonable representation of predation risk or not. Cyril: Can provide info on range of effect sizes on different diversions, probably better way to represent predation across landscape but would be submodel on its own. Depends on how much complexity we want to add.

Habitat Subgroup Update: Spawning Habitat Decay (Rod Wittler/Mark Tompkins)

Proposed Approach

  • See slides


  • Tricia Bratcher: using baseline velocity at which bedline would become mobilized, as well as looking at things like slope? Also wondering if there’s accounting for high flow events where gravel will be on floodplain and deposited there. Rod: Yes, that’s what the model does; sediment transport model; calculates all of those things
  • Chris: Are you thinking about this from more of a reach scale, site scale or a cross section scale? Think would affect things. Mark: think reach scale is the scale Blair walking us through, and some sort of downstream transport cold pick up additional new spawning habitat in downstream reach coming from an upstream reach. Chris: Encouraged this is advancing. Will be starting on similar effort on American River that have funding for, want to align so have apples to apples to advance this. Mark: probably want to check in with you and others on reach sizing.
  • JD Wikert: main movers of gravel in sites where augmented gravel is salmon themselves. Thoughts or considerations on incorporating that as part of the function? Mark: hadn’t thought about that. With the rating curves we have on sediment movement related to flow, those are going to be purely flow driven and past the incipient motion threshold for spawning size gravel that flow has to get to before it starts moving. Definitely somewhere there were use of gravel by fish could lower that flow at incipient motion but probably more fine scale than could get at in this analysis.
  • Derek: put a paper in chat on salmon bioturbation. Salmon-Bioturbation-and-Stream-Process.pdf ( Mark: maybe consider in augmentation piece. Could be contributing to redeposited gravel being usable and new spawning habitat still in spawning reach.

SIT Proposal Update: New Operations / Flow Inputs to DSMs (CALSIM) (Mark Tompkins)

  • Issue of Concern: Current DSM flow inputs do not reflect the most current set of operational rules
  • Proposed Change: Use latest (2019) CALSIM model run that incorporates expected future operational rules.
  • Rationale: Flow inputs affect habitat, temperature, survival, and growth.
  • Timing: Next DSM update cycle (2022)
  • Draft proposal is available for SIT review.

2D Hydrodynamic Model Inventory (Rod Wittler)

Rod is putting together an inventory of all of the 2D hydrodynamic models in the Central Valley and is requesting information to help populate the inventory. The information requested is owner and operator, status or domain, calibration, uses of the model and its availability. Please email with information.



Bernard Aguilar, Arnold Ammann, Denise Barnard, Mike Beakes, Erica Bishop, Tricia Bratcher, Erin Cain, Felipe Carrillo, Megan Cook, Flora Cordoleani, Holly Dawley, Matthew Dekar, Lauren Diaz, Adam Duarte, Harmony Gugino, Chris Hammersmark, Rene Henery, Baker Holden, John Kelly, Francisco Jesus Bellido Leiva, Priscilla Liang, Rob Lusardi, Duane Linander, Erin Lunda, Amy Lyons, Keith Marine, Bryan Matthias, Erica Meyers, Cyril Michel, Kirk Nelson, Russell Perry, Jim Peterson, Corey Phillis, John Plumb, Michael Prowatzke, Emanuel Rodriguez, Derek Rupert, Alicia Seesholtz, Erin Strange, Mark Tompkins, Mike Urkov, JD Wikert, Rod Wittler, Mike Wright

Salmon Demographics Update (Mike Beakes)

  • SIT model is still very sensitive to juvenile wild salmon survival, rearing, and growth. Haven’t secured funding to support salmon demographics work yet, but confident will get funding in FY22.
  • Work would be to implement large scale field study based on mark recapture methodology to get estimates of wild salmon growth and survival. Right now, Reclamation Bay-Delta Office working with Russ Perry on framework for general agreement, timeline, and funding required over next 3-4 years.
  • Tentative plan in year 1 would be developing project team and getting permitting in place, developing study plan. Next year would be smaller scale pilot level efforts. Then move toward larger scale full implementation.
  • Hope over summer or fall would provide study plan for SIT to review and provide input. Probably know more in winter/spring this year and come back with more confidence in terms of where we are with timeline Chris Hammersmark: talked about monitoring at Southport project. Still planning to include? Mike: open minded to that possibility. Difficult to think about how to work logistically with more traditional mark recapture design; something we should hash out with project team once get together. Info need as defined in NTRS is really specific to tributaries and that’s a really important knowledge gap that we need to fill. Preference would to get good estimates in tribs before spread out and so exploratory field work or spread out and get less precise estimates in largest geographic range. Chris: makes sense, will make plug that have mixed input on these mainstem restoration opportunities and the models are telling us holding the fish longer is causing a negative effect and yet we’re also saying we should be doing these as a priority. Think it’s also a pretty important question. Rene Henery: will fish timing be a component of the project? Mike: good question, still trying to flesh out design. Envision this working is multiple capture events that straddle rearing period like all spring and then combo of active sampling and recapture during those events and then passive monitoring through multiple PIT tag antenna rays so can track movement and survival through time through multiple mechanisms. Russ: would get at timing info through what we call fixed site monitoring where have PIT tag antennas detecting the fish that we tagged that emigrating out of a trib then get primarily growth info would come through physical recaptures. Russ: really need to leverage existing programs and work with other agencies already out there. Going to be the best way we can collect as much info as possible.

Bioenergetics Full Proposal (Corey Phillis and Mike Beakes)

Juvenile growth sub-model

  • 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. Requires prey density, temperature, and initial fish mass.

Bioenergetics model

  • Based on published bioenergetics models for salmonids
  • Parameters derived from lab studies
  • See SIT “Growth Transition Proposal” for details

SIT Temperature-Independent Growth

  • Assumed prey density (1 Daphnia pulex per liter) for in-channel prey density
  • Assumed prey density (>60 Daphnia pulex per liter) for floodplain prey density
  • Most growth rates are lower than what is used in current SIT model

Field testing the bioenergetics model

  • Measured growth rates, did a great job predicting growth

Next Steps

To implement, need help sourcing any pretty density estimates. Get sense of what data we have on hand to see how much work we need to do to populate the model with estimates of prey density and what prey densities that we have in hand.

  • Dec SIT meeting: come back with plans for how to proceed with existing prey density data
  • Jan: Mike and Corey proceed with modeling
  • Spring 2022: Mike and Corey decide if need to further dig for existing data to improve prey density estimates
  • Complete modeling work by October 2022 so changes to SIT can be prototyped and then reviewed by SIT


Rene: great to see data results. Will get prey density data from fish food team’s work so that’s coming, working on getting a meeting set up to talk about that. Another comment - Shasta work has shown that especially at low temps what is driving the differences in fish growth is activity level (volitional foraging). Cage studies wouldn’t capture that. Corey: Point about activity is really interesting and comes up when using caged data as reference points. Here, none of that caged data is used in the fitting of the model. it’s completely independent. So model doing a good job of fitting observations from caged fish and that might just be dumb luck on our part or it could be that at least at the temps those fish experience on the floodplain aren’t at the point where fish making tradeoff between

  • Several points made about the 1.06 rate and questions about where that number comes from. Corey tried to down down that number but wasn’t in the referenced papers. Russ said 1mm a day agrees with some max growth rates. Flora shared that the Sutter Bypass study is complete and for the temps covered, probably warm enough that fish wouldn’t need to forage for food. Would be curious for data earlier in the season (before Feb/March).
  • Mike: excited that if SIT does adopt this new bioenergetics framework in model will give us flexibility to address a lot of this where habitat-specific prey densities of foraging behaviors. And right now we can’t. At back end is growth transition matrices, so can complicate bioenergetics model all we want and still be producing growth transition matrices. Process relatively easy to integrate a lot of this complexity into the model.

Pre-proposal: Reservoir prey subsidies (Miek Beakes, Rob Lusardi, Francesco Bellido)

  • Issue of concern: SIT model limited ability to estimate habitat-specific food density, despite recently recognized as a predominant factor influencing juvenile growth
  • Issue of concern: This limits SIT model ability to analyze tradeoffs between water temperature and prey density at rearing habitats
  • Issue of concern: Recent research shows the important role of upstream reservoirs with respect to the advection of nutrients and food webs subsidies
  • Proposed change to the SIT model: allow SIT to evaluate scenarios that the current model cannot


  • Tricia Bratcher: Wondering if there is a good bibliography on prey and food items that fish select. Rob: interested in that question as part of project. See how different food web constituents wrapped into larger food web. So going to be conducting stable isotype analysis as well. Primary reason is to see how zooplankton reservoir experts would be taken up in to river food webs. Think zooplankton being picked off by smaller fish particularly early in life history. Think zooplankton feeding larger consumer. We will have some good answers over the next 12 months with isotope sampling.
  • Mike Beakes: Rene mentioned there is some kind of periodicity in prey production in Shasta. At some times lower prey densities and leading to shift in foraging behavior. Any thoughts or data that would indicate there is same kind of cyclical production in reservoirs? Fran: trying to see factors mostly making these spikes in prey density that we have seen in Sac River. Looking into that and comparing with what see in monitoring in natural systems to see exactly that. Rob: trying to look at that. This is different because we see the production, previous data collection in reach below Keswick suggest that it is not terribly food limited. Not talking zooplankton, talking about benthic inverts. That production is more similar to a spring fed system rather than a runoff system than the Shasta which is more of a snowmelt. Will be able to kind of look at those
  • Megan Cook: how would the prey densities from this work relate to the bioenergetics work? Mike: model premised on having tributary-specific prey densities. Recognizing that there is in-river production that’s guiding those densities. There is significant exports from reservoirs. So project trying to evaluate what that is on average and what kind of reservoir dynamics change that production so get a handle on that.
  • John Plumb: An important aspect to the bioenergetics model is the energy density of the prey. Has efforts been underway to estimate prey energy density as well as prey density? Rob: seems well documented in the literature. Corey: there are estimates for prey energy density. Gets back to, does that complexity matter. That where need to run sensitivity analyses to see the value of that additional information. Can get more complex but if not changing decisions we make then don’t know if it’s worth it. Adopting bioenergetics model will change some of the decisions because does predict growth as opposed to what we are using. Not sure if marginal increase in complexity worth the cost of that information. That’s TBD.
  • JD Wikert suggested reaching out to EBMUD for more info on reservoir produced inverts on Mokelumne. Denise Barnard to reach out to MIchelle Workman.
  • Corey: would be really helpful if people can catalog what the complexity that they are concerned with so that when we take on sensitivity analysis, we can see how important that complexity is for the bioenergetics model. Jim: keep in mind it is a coarse resolution model, hso we have to get those averages over an entire month or tributary.

Monitoring Subgroup (Megan Cook)

  • Monitoring Guidance developed prior to NTRS
    • 4 types of restoration actions
    • 3 levels of monitoring
  • Potential New Tasks
    • Request for input on Migratory Corridor Project, BACI design monitoring options (JD Wikert)
    • Additional revisions to monitoring guidelines: (1) Discuss adding guidance on how to monitor cover for large wood and rockwad installations. (2) How to integrate additional techniques related to effectiveness monitoring into guidelines (USBR sponsored meta-analysis)

JD: Buffington project associated with SJ NWR. Looking to do some small scale floodplain side channel alcove sort of projects in sand bedded reach of the river. Not aware of anybody doing restoration for habitat in those sorts of areas and so we think good candidate for more in-depth monitoring largely because it’s a relatively new thing that we’re addressing and want to determine whether or not there is value working these sort of lower reach areas on smaller scale projects. Focused on two elements: what’s good for juveniles and also what’s going to be not so good for predator species.

Rod: currently monitoring guidelines premised on shallow water in suitable habitat. Some of these going into deeper water so that’s where cover and rockwad issues come up. As part of LTO, proposed to take certain number of actions; talking about effectiveness of constructed habitats both locally and in immediate time frame. And then additionally systemically and in long-term timeframe. Right now conducting a literature survey to find out what others have done with regards to that subject.

New climate change subgroup (Megan Cook)

  • Context/Purpose: Address how to incorporate climate change scenarios into DSMs (develop model change proposal)
  • If interested in joining, please let know

Chipps Island Trawl efficiency project and additional analyses (Russ Perry, Bryan Matthias)

  • Estimate abundance at Chipps Island and Sacramento trawl site
  • Looking for SIT inputs on potential ideas on what can be done with existing funds- what’s beneficial to SIT team that leverages already done field work?
  • Additional analysis 1: analyze historical CWT survival patterns
  • Additional analysis 2: estimate efficiency of Knights Landing screw traps


  • Mike Beakes: both sound like great projects. Curious to speak to how ties back in to the SIT modeling efforts. Would this provide a revised or expanded dataset for model calibration? Russ: the abundance estimates esp at Chipps tie back in to calibration so those provide abundance estimates to be able to fit the models and particularly knights landing is an important location that is usually used when winter run are entering the delta. If can get abundance there even in calibration can partition sections of the model better in terms of the lifecycle and where the dynamics are varying essentially. Survival analysis could provide some new insights into some of the knobs that are turned in the SIT model to help understand the dynamics.
  • Jim Peterson: really cool, when would the data be ready? Russ: probably wont’ start these particular analyses until end of 2022 and through 2023. Have provisional estimates of winter run abundance. This year working on wrapping up 5-year Chipps island work. Will have new estimates for winter run by end of this year.
  • Duane Linander: capacity to do both or one or the other? Russ: can do both of these with remaining funds

2022 SIT Calendar

  • Propose 2nd Wednesdays, 10am-12pm for monthly SIT call
  • Adaptive management learning loop (monitoring, data)
  • Model change proposals: October 2022 deadline to be ready for prototyping in model
  • Improve SIT communication tools
  • Other ideas?

New Business

Tricia Bratcher is requesting input on the following:

  • Background info: Typically the Department does not conduct spring-run Chinook salmon redd surveys on upper Deer Creek, but we did this year. Between conducting that redd survey, plus other related observations over the last few years, Matt Johnson (lead spring-run biologist in Region 1) believes that spawning gravel is limiting on upper Deer Creek for spring-run, and secondarily but also important, steelhead. It could, in part, be attributed to CALTRANS management of Hwy 32 (including a sediment trap on a large trib), as Hwy 32 parallels upper Deer Creek for a lot of its upper length.
  • Request: The Department is requesting feedback on how to inventory instream habitat (i.e., a preferred methodology), relative to (1) what data may be useful AND useable by the SIT and the DSM and (2) what may be the reasons for a spawning gravel deficit so that it can be more effectively addressed. Granted, we would want to include CALTRANS in a future conversation (esp. if it’s something they need to mitigate for), and we would also want to assess if restoration is needed. Please contact Tricia Bratcher if you have any input on this important issue (

Jim Peterson offered a 1-hour SIT background call for new SIT members. Please email if you want to join.

NOFO: Central Valley Project Habitat and Facility Improvements

  • See slides
  • Contact Matt Dekar/Rod Wittler with any questions