Conference Call

November 20-21, 2019 Slides

Model Summary Notes

Meek et al. 2019

Grade Model Sheet

Day 1

By phone:

Mark Tompkins, Flora Cordoleani, Ed, Brian Elrott, Sadie Gill, Mike Prowatzke Mike Memeo

In person:

Jim Peterson, Adam Duarte, Bernard Aguilar, Steve Tsao, John Kelly, Mike Urkov, Cesar Blanco, Chris Hammersmark, Mike Wright, Emanuel Rodriguez, Mike Berry, Susan Strahn, Robyn Bilski, Erica Meyers, Carl Deally, Pam Taber, Bruce McGlaughlin, Mike Beakes, Priscilla Liang, Rod Wittler, Matt Brown, JD Wikert, Corey Phillis, Brett Harvey, Tricia Bratcher, James Scott, Kate Spear

Status of Science Coordinator (Cesar)

  • No update

Timeline for Near Term Restoration Strategy (All)

  • See Slides
  • Set Strategy
  • Two week review for final

Review of Chinook Strategy

  • See Slides
  • Various strategies developed at last in-person meeting
  • See
  • And
  • And
  • How to allow time for review?
  • How constraineed are we by the model
  • Intend to include in strategy
  • SIT Metrics = Model Results
  • Yuba have identified Spring-run - not currently in model
  • Scenario 8 (winter run optimization) is worse than the do nothing scenario
  • Results rescaled to Utility
  • Some results indicate that juveniles are sometimes leaving too late to result in subsequent adults.
  • Satterthwaite model determines juvenile success - too early is bad, too late also bad
  • Count should be the same number of actions across Scenarios
  • Stochasticity run went to zero because 137 parameters
  • Floodplain activation can happen in dry years
  • Sometimes not realistic in managed watersheds
  • Some bypasses could be realistic
  • Will need to follow up with design criteria for floodplain projects - JD, Robyn, Chris, and Mark T. would like to update how we treat floodplain actions across the Central Valley.
  • Mike Berry suggested building a yearling life history for winter run. If they stick around they may just stick around for a year.
  • On Sacramento - side channels stay wet even during dry years
  • Opportunities to revisit key elements in the model in the Near-term Restoration Strategy
  • Always making progress for Spring Chinook
  • Some negative results may be occuring because actions are holding fish in wrong area too long


Sensitivity Analysis

  • See slides
  • Vary inputs / parameters by +/-50%
  • Changing inputs keeps rule sets the same
  • Top ten spawning habitat / floodplain / delta inflow / in-channel / proportion flow into bypass / initial abundance
  • Stochastic dominance - opportunity to simplify model
  • Top DSM parameters Juv delta rearing / delta rearing survival / delta outmigrant survival /
  • More often than not, most parameters parallel lines
  • Key uncertainties Juvenile growth / juvenile survival / adult survival / reproduction / fish routing (georgiana slough) / territory size
  • Winter-run sensitivity to SJ temperatures is questionable - needs to be reviewed in terms of routing. Question for Russ Perry
  • Reducible uncertainty - survival / growth
  • General SIT consensus that quality of habitat inputs, juvenile survival and growth, and reproduction is the biggest driver of model sensitivity.
  • Sensitivity related to habitat inputs also related to ruleset about how organisms use habitat
  • Juvenile survival, habitat, and some adult survival drives model results.
  • Winter-run optimized negatively affects spring-run populations
  • Should the model be revised to allow rearing fish to move when temperatures rise versus increasing mortality?
  • How to focus on improving survival? PIT tags
  • Columbia estimates are less than 3 percent range in variation
  • Need to increase the number of measurements to drive survival estimates
  • Think about strategies over lunch


Review of actions undertaken in scenarios

  • Places that keep popping up: Upper Sac, Upper mid-Sac, Lower Sac
  • Newish projects at Bullocks Bens and Southport - neither has been included in the habitat estimates
  • Would be possible to monitor Southport?
  • Other projects also coming on-line
  • Floodplain assumed to have fixed survival rate - should survival vary by region? Survival already varies by region, but the relative increase in survival from in channel rearing habitat to floodplain habitats is constant
  • Confluence with Feather seems to be a good location
  • Potential downside in lower sac for spring / fall run where they would be better off in the Delta
  • Possible that drought year higher temperatures
  • Is it possible to change logic to move fish when temperature starts to rise? Yes
  • Also possible for temperature to become an issue if we are constructing floodplain that inundates at lower flows, because could be lower flows in drier year
  • Is connectivity of habitat important? How much migration travel between habitat?
  • Question: is current habitat suitable or is more needed?
  • Conceptual model: speed of migration could be better for avoiding predators
  • Below Feather is channelized - is it possible to put in Southport type projects?
  • Proposed change to Yolo bypass would also increase access to floodplain.
  • Model currently can include notched weir operations
  • Fish moving 8-12 hours of movement
  • Willing landowners are an important part of the equation
  • Connectivity is important
  • Decision-makers will ask for proposals to develop specific actions
  • Only a certain amount of work that can get done in next five years
  • What are the safe areas for investment.
  • Rearing habitat additions
  • Also opportunities for monitoring of floodplain
  • Need to find a projects to monitor
  • FY20 Tech memo identified “Increase perennially inundated juvenile habitat and floodplain, Sacramento River above the American River confluence”
  • Would be some value in monitoring Southport
  • Could the SIT recommend concept of connectivity in projects - looking to link projects together?
  • Prioritizing research to reduce uncertainty in lower reaches
  • Add notion of lack of habitat below Feather
  • Provide guidance on how important it is to learn from projects
  • Will calculate cost of adults per dollars - incorporate concept of value of information generated
  • Will that be useful?
  • Will be helpful to develop metrics and ways to evaluate efficiency.
  • Some of the measures are unitless
  • CVPIA four classes of performance Admin / Restoration / Research / Monitoring


Review of actions undertaken in scenarios (continued)

  • Upper Sac strategy
  • Battle Creek / winter-run approach? In near-term Sacramento strategy would benefit the winter-run
  • Meeting tomorrow at C-1003 near the cafeteria
  • Would we evaluate non-natal tributaries? Yes
  • Commonly addressed in the past
  • Some non-native streams are ephemeral and support O Mykiss
  • What actions would be taken?
  • Removing fish passage diversions, eliminating ag returns, mostly passage and screens
  • Look to NFPP to fund projects? Not currently in their priority list
  • Current charters to evaluate non-natal rearing being evaluated
  • Some otolith and tagging studies indicating that rearing is occuring in American, Bear Creek, and others?
  • Strategy: increasing connectivity in the Sacramento, including ephemeral streams that provide opportunities for O Mykiss and Winter-run
  • How do you achieve that re-connectivity?
  • If opportunities exist then build upon them. Support robust science to build upon these opportunities
  • What’s the population level benefit of doing this work?
  • No decisions have been made for 2020 funding. Draft under review at Commissioner level
  • As it stands right now - no funding likely for non-natal investigation because of lack of adaptive management / BACI plan for review by SIT.
  • Retain notion from previous FY20 Tech Memo - recognize potential of these areas to benefit winter-run and O Mykiss
  • Could be part of model improvement effort, possibly from Landsat imagery
  • How to develop text for Near-term Restoration Strategy including editing
  • Non-natal as a proposal for a change to the model
  • Could be tied to a specific monitoring or research effort
  • Winter-run sized fish were found high up in the American
  • Diversity Group Optimized scenario looks to be switching back and forth between Feather and the American
  • Looking at focusing efforts described in the Fall Run Diversity group Optimized scenario
  • Moving from the most productive scenarios will require justification - which is fine - it will just need to be explained
  • New selected scenario could be run for comparison
  • Keeping American and Stanislaus on the list can keep some diversity goals in place
  • Run-specific strategies or all together?
  • All the runs
  • Spring run was excluded from Yuba
  • Recent genetic analysis showed some spring run genetics
  • Would not lump Deer and Mill in with Antelope - also remember Clear has ability to segregate spring from fall
  • Not proposing to swap Yuba looking to cull list to fewer watersheds
  • How to take advantage of opportunities that are not included in the prioritization
  • Yuba could be good point of focus for research - understand better why not raising in priority
  • Current mainstem sacramento above american confluence + non-natal rearing + stanislaus and downstream to SJ + clear creek + butte creek + battle creek (to pick up Thursday)
  • Model inputs

Identify Chinook strategy (All)

  • Lower Sac huge floodplain project just implemented that would give us an ability to learn. There is also a backwater project at Bullets bend near the confluence of the Feather River.
  • Matt said that if we do that as a project we need to set it up so that we are monitoring things in a way to learn from them.
  • Chris said that they just created 152 acres of floodplain, so it may be what the models are telling us what we need (because the model does not include those new floodplain habitats – note that only ~25% of the 152 acres is suitable).
  • Mike Berry suggested making a new rule set that fish move when the temps get too high.
  • JD suggested we make options on where to stop along the migratory corridor. Brian and Mike Berry agreed.
  • Chris mentioned that the proposed changes to the weir that adds more access to the bypass is also not in the model. So we may be doing the actions that the model is suggesting we do.
  • Matt Brown listed a few other projects that CVPIA is funding in the mainstem that are not in the model yet. He thinks we learn from these ongoing projects and focus habitat actions where we know we will see the benefits. He also mentioned we have CWT data that suggest fish move really fast through this area, sure they are hatchery fish but this is the information we have.
  • For upper and upper mid, Chris pointed out that they are often combined actions with floodplain and in-channel rearing habitat…so we might just say juvenile rearing habitat is important. Matt said that we could learn a lot more by doing both. Mike Berry said it will give us more resources to monitor floodplains as well so we need to identify that as an important component.
  • JD agrees that focusing on upper sac and upper mid sac where the model says to is a good idea as long as we include something about taking advantage of opportunities to piggy back with partners to create habitat lower in the system to work toward a “string of pearls” in habitat along the mainstem. Mike Beakes and others agreed. Brian does not agree and would like to dive in and learn in lower Sac sections. Tricia agrees we need to know more but we need to pull in someone who knows about this sections involved in the SIT. Susan suggested doing a lower Sac section project only if we have the opportunity to learn. Brian suggests 2 or 3 projects in upper and 1 in lower Sac with opportunity to learn. Mike U suggested a priority above the American River confluence without specifying. Brian liked that.
  • “Narrative of spatial connectivity as long-term goal. Near-term SIT wants to see restoration actions above American river and recognized high uncertainty with restoration actions below the Feather and would give a high priority for that if there is an opportunity to learn through a tier 3 monitoring effort”. Brian would add something about “due to the lack of habitat below the Feather” as a reason for this too.
  • We have a Sacramento strategy. Now what? Battle Creek for fall and winter? Matt thinks we should think about non natal tribs, like low elevation with warm water in fall and winter, dry in summer. They do a lot of growth here and support steelhead spawning. Thomes, Dye creek, sulfur and many more Cow cottonwood and bear creek, American). He would remove fish passage areas, eliminating/screening diversions, eliminating ag returns. Mostly passage due to road crossings and screens. “part of larger increasing connectivity. Reconnect mainstem Sac with ephemeral tribs that provide juvenile rearing and steelhead spawning opportunities. – goal is to maintain the same notion as what was in the last tech memo with BACI design monitoring to learn of the benefits” Mike Beakes suggested wording on jumping on opportunities to learn. Matt said he thinks it is more than jumping on opportunities, but what is the population level benefits. Matt said that the charter is submitted but no decisions have been made for FY2020. Mike Beakes would like to see a SIT proposal to include this in the DSMs.
  • JD noted that we need a way to prioritize actions within the strategy so the CORE team can prioritize.
  • Steve noted that there are a lot of diversions in the Merced. JD noted that there is a big restoration happening at Tuolumne and Merced confluence. JD noted that if we are going to maintain diversity group the prop of SJ from Stan on down is where a bulk of fish are coming through. If there was water available we could do more actions in some of the smaller tribs down there. JD would advocate for connectivity by adding habitat throughout the migratory corridor. “Do rearing habitat north of Stan proper and mainstem to provide migratory corridor benefits”.
  • Chris would say we need to include Stan and American in order to maintain spatial diversity and do actions where there is more fish.
  • Mill Deer Butte Yuba is what Brian would suggest to work on for spring run. He thinks the yuba river is much more important than antelope creek for spring run. Brian said recent genetic analysis shows feather river hatchery and nat. produced springers can be differentiated from fall run. Jim suggested a proposal be submitted to the SIT to add them back into the mix. He said Antelope is small, very few fish so he would swap Yuba for Antelope. Tricia noted that we have not talked about clear creek where we can spatially segregate them. Brian would put in channel rearing and floodplain habitat in the Yuba.
  • JD would like to include something in the strategy to say something about taking advantage of opportunities where there is cost share. Rod said that is a step beyond the SIT. But we can say something about opportunity for progress/utility in certain streams.
  • Matt would put Clear creek because of multiple runs and capacity to grow. He would recommend American for learning, fish numbers, and non-natal rearing. He would recommend Butte (first – included in model output) and Battle Creek (second) for winter and spring run.
  • Mike Urkov would put Feather on for an updating habitat estimates based on current events before spending resources there.
  • Flora said survival correlated with 2 reaches in the bypass for butte creek fish. Probably related to predation. There is a paper out on this. They are not looking at fish going through the west borough. They are looking at tagging fish higher in the channel. She will send a link for the study. Tricia said Butte Creek diversions have challenges because of old structures. Brett said that there seems to be justification for keeping it on the list. Tracey McReynolds can help fill in in

Day 2

In Person:

Jim Peterson, Adam Duarte, Matt Brown, Page Vick, Caesar Blanco, Susan Strachan, Mike Berry, Robyn Bilsky, Erica Meyers, JD Wilkert, Emmanuel Rodriguez, Mike Urkov, Priscilla Liang, Rod Wittler, Kate Spear

By Phone:

Corey Phylis, Tricia Brachter, Brian Ellrot, John Kelley, Chris Hammerskmark, Mark Tompkins, Mike Beakes, MIchael Prowatzke, Flora Cordoleani

Review draft strategies

  • See slides
  • Habitat estimates is a large uncertainty in model in general, not just Feather
  • Convene sub group to make recommendations for habitat updates
  • Consideration of Battle Creek - was identified as a Spring-run benefit
  • How will winter - spring-runs be spatially segregated?
  • Opportunity on lower Deer Creek, too? Would be fall- and spring-run.
  • Focused efforts: anything else than Battle? Maybe Deer Creek (would be survival actions ie flow)
  • Cow Creek consideration?
  • How to use model output and structured decision-making to direct investment
  • Structured decision making means interpretation of model results
  • Feather / Yuba spring run are not counted towards the metrics
  • How to consider projects that aren’t specifically considered in the model? Research requests
  • Need to get to recommendations based on model results and interpret for implementation
  • Developing better understanding while still implementing “no regrets” actions
  • Developed model to see how rule sets result in optimized results
  • Model results are banging up against preconceived notions of what is happening
  • Trying to stick to themes of connectivity and biodiversity
  • Review of current proposal - Slide 3 / 4 + Battle Creek
  • Updating NTRS every year, every 2 years reevaluation with results from some monitoring back, and update to model
  • Tech memo supplements NTRS
  • How to address Delta / bypasses?
  • Also coordination with other ongoing projects
  • Whiteboard: Evaluated in model? (results) Connectivity? Spatial Diversity? Numbers produced / biomass.
  • Tribs to consider: Deer / Feather / Cow
  • Adding lower Feather to recommended strategy
  • Overview of the model next
  • Mike Berry noted they rebuilt the habitat below the weir on Feather River so he does not think it is a higher priority. Chris Hammersmark disagrees and said there was a tremendous amount of sediment that came downstream and changed habitat. Mark T. seconds what Chris is saying and thinks we need to identify other areas to update these estimates. Mike Berry agrees that the estimates we have are outdated given the amount of work that has been done in Feather River. Rod thinks a subgroup should get together to identify tribs for habitat estimates updates based on benefits to the SIT’s modeling efforts.
  • Matt said that Battle is not great for fall run, but it does make sense for winter run even though it is not in the model yet. It is also important for steelhead and spring run. Mike Berry mentioned that the south fork area in particular is good for spring run and steelhead.
  • Tricia thinks there is opportunity on lower Deer Creek for fall and spring run.
  • Mike Berry said Cow would be good for fall, winter, spring, and steelhead by opening up habitat. Tricia agreed. There was lots of discussion on why Cow did not come up.
  • Jim suggested: was it evaluated in the model? If so, is there support based on the model? Does it contribute to connectivity, spatial diversity, and/or numbers of fish?
  • Lower Feather seems to meet this criteria and it would still help Yuba fish.


Pulse Flow Monitoring RST results

  • Data associated with pulse flow
  • See Slides

Review Chinook model inputs and parameters

  • Slides
  • New Data inputs
  • Hatchery operations
  • Reproduction / Growth / Survival
  • Movement
  • Review of submodels
  • Grading of model: low / medium / high confidence
  • Push Habitat review to sub-group to create priority list for updates
  • Possible subgroup to consider proposal for side channel versus in-channel
  • Working with winter-run modelers to improve estimates
  • Ephemeral habitat versus perennial habitat definitions?
  • Grading spreadsheet to be sent to group for review / input


Grade Chinook models (All)

  • See slides