In-person Meeting

May 23–24, 2018 Slides

Day 1


Corey Phillis, Brian Wells, John Hutchings, Mark Gard, Doug Killam, Mike Hendrick, Mike Urkov, Dick Pool, Jason Hassrick, Cesar Blanco, Dan Kratville, Russ Perry, Chris Hammersmark, JD Wikert, Whitney Friedman, Lisa Hunt, Rod Wittler, Mike Berry, Matt Brown, Brett Harvey, Shane Abeare, Flora Cordoleani, Jim Peterson, Adam Duarte

Update on watershed expert meetings and possible pause on regular SIT meetings

Jim talked about funding delays through the DOI review process. Jim and Adam will have to pause their efforts at the end of the month if we do not get approval of money transfer. Shane said things will still proceed, but it does mean adjustments to the schedule.

Discuss proposals for changes to DSMs

  • Late fall run Chinook salmon DSM

This proposal was sent out to the SIT earlier. Dick talked about the current concerns for late fall run Chinook. Jim reviewed the proposal and where late fall run "populations" would be. Rod was concerned about data availability and current workload. Rod asked about what we would gain that the winter and fall run models don't get us. Dick talked about the migration differences and how that is related to environmental factors. Corey said he thinks NMFS has late fall and fall in the same ESU but that they are very different in timing. Dan said it may be useful to have the yearling life history for late fall run. Russ mentioned that they may be influenced more by the delta cross channel gates. Jim asked if there is any data to calibrate this model to. Russ said the length at date in Chipps Trawl. Matt said they have a different life history and different stressors. Corey said that if it is a workload issue, we can use more of a qualitative approach at first until we can invest in a quantitative model. Corey said that he thinks they have different thermal tolerances. Dick would like to see the quantitative model fleshed out. Jim asked about if this would be a priority over a sturgeon DSM. SIT agreed to have the Sturgeon model as a priority and do a qualitative assessment for late fall run for the near term restoration strategy.

  • Spawning habitat decay function

There is a draft proposal for this and we are in the process of trying to refine the relationship between flow and habitat decay. Chris thinks we should send it to the subgroup to work on the decay rate before sending it out to the SIT. He is thinking if we need a decay rate for an unregulated tributary. Chris would like to relate the proposed curves with real data and he invites others to contribute to this if they have data on this. Rod said this all sounds real good to him. Matt said that is matters in how you put gravel in. For example, some methods need the higher flows to create that habitat, so in these cases it would be a habitat addition with flow. He said it also depends on where the material is placed in the tributary. Chris thinks the next step is to have another subgroup meeting and see what data are available to build out these relationships. If you want to be in this group, please email Shane and Adam. (subgroup so far: Rod, Chris, JD, Matt)

  • Ocean survival

Corey said they have otolith data for winter and spring run. The challenge is that we do not have matching screw-trap data to figure out what life history they were exhibiting. Rachel and Anna have a paper from the Stan that has the paired screw-trap data. Brian talked about the selection criteria they used to include fish when estimating in-ocean survival, so there are caveats with those estimates. Brian can talk to Will about talking with the group more about that. We will continue to pursue that as a subgroup. Russ and Dick would like to be on the ocean survival group.

  • Temperature models

Rod discussed how Mike Wright is working on the ability to predict temperatures under different flow regimes on gaged or ungagged tributaries. Right now temperatures are estimated from flow based on historical data. Mike is allowing us the ability to manipulate/forecast temperatures with changes in flow. Mike can do a demo of this at an upcoming SIT meeting. Mike Berry has contacts of folks with data for this. Doug will help Mike B. find these data.

  • Food for fish

There might be a project in place to actually do this. Rod said there is an 18 charter on this and he wanted to know if this is related to Rene's proposal. Russ said you would want the measurement to be proportion of maximum consumption to feed it into a bioenergetics model. Jason said Rod should contact Irwin as he is very involved in these efforts. Brett is putting together a draft proposal for this.

Update on large diversion screening unit of effort

Shane is trying to gather this information. In the past, some were around 900 cfs. Right now, 350 cfs is the biggest project currently being screened, but it is not being funded by CVPIA. There is 1 of these on Stan. There are 2 on the upper middle Sac. They are ~175 cfs – Cesar can get us those numbers. However, the timing of the middle Sac is thought to be not matched when juvenile fish are running through. We will take this information and propose a unit of effort to the SIT.

Update on fall run Chinook integrated analysis

Adam reviewed the integrated analysis of screw-trap and escapement data. He also showed preliminary results which can be found in the slides for the meeting.



  • Standardize low for each tributary before fitting the model instead


  • Use a conditional binomial to help with convergence


  • Is bigger total diversions related to bigger tributaries?
  • Stan <- look to state water resources and contact Jesse Anderson about diversion information


  • Might have 2 traps
  • Check where trap is related to habitat inputs
  • Check with Jason Kindopp and Brad Cavallo about trap locations

Hatchery fish

  • Only 25% marked
  • Might remove hatchery juveniles using an expansion factor
  • Ask Robyn and John Hannon to figure out the best way to deal with this


  • Check with Robyn to see when they ran the traps multiple times in a day. Might have to sum catch data in a single day

Prespawn mortality

  • JD will send reports
  • Matt has information from Clear
  • Mokelumne information is in EBMUD reports
  • Contact John Hannon for American River

Egg-to-fry survival

  • Joe Maerz and Chris Hammersmark might have information on this
  • Ben Martin (Ecology Letters) is what is used for the RBDD egg-to-fry (outmigrant) survival

What is a restoration strategy? An example using the American River

Jim reviewed some work Kevin McDonnell and he have done for developing a restoration strategy for the American River.

Is there a fish metric that can tell us something about habitat without having to do massive habitat surveys

  • Brett said that maybe an abundance vs. size distribution metric for juvenile fish.
  • Matt said you might look at more than the metrics last year, but a series of years as the states when creating the policy plots.

Discuss SIT Chinook metrics

The group discussed the complications with trying to interpret the juvenile metrics across different tributaries. Some tributaries are for rearing. Some shoot out small fish to rear in other areas. Matt thinks both metrics help him evaluate tradeoffs. The group agreed to pick a common check point like biomass at Chipps while keep track of where those juveniles come from for the watershed metric.

Next steps for Chinook

Adam reviewed what the next steps are for Chinook salmon efforts

Day 2


Corey Phillis, Brett Harvey, Doug Killam, Mike Berry, Michelle Workman, Shane Abeare, JD Wikert, Mike Hendrick, Mark Tompkins, Josh Israel, Sarah Gallagher, Mark Gard, Alicia Seesholtz, Matt Brown, Cesar Blanco, Rod Wittler, Jim Peterson, Adam Duarte

Review quantitative O. mykiss DSM, DSM inputs, and calibration data

Jim reviewed the O. mykiss DSM.

Feedback on DSM inputs:

Adult habitat

  • Mark G. said he gave Mike U. what he has for adult O. mykiss habitat.

Angler effort

  • Mike B. said there is hardly any tributary angler effort.
  • James Lyons has been doing creel surveys for last 20 years. Rob Titus is the overall supervisor for the different streams. Doug can share that contact information.

Angler disturbance on redds

  • Mike B. said that no one has done those surveys, but areas they indicated high angler effort in a previous email can be assumed to be disturbed by anglers. Mike B. can draw these areas on a map so we have that information.

% tributary well lit

  • Might look at using road crossings or something about urbanization as a proxy
  • Mike U. has the inventory of lighting from Mike B. Mike B. and crew went from Stockton to Keswick, so they have a decent inventory on the mainstem. Mike B. said to have Mike U. contact him on this because he has some other information on this.
  • Sadie is looking at pulling information from satellite imagery

Food availability

  • Mark G. said Larry Brown at USGS would be a good source for this information.
  • Sarah said Clear Creek has reports on this as well, so we should contact Matt about this.
  • Jim Herrington, CDFW does a rapid assessment across the state, so he might have information on this.
  • Some monitoring is going on in side channels near a restoration project and Mike B. can be the point of contact on that.
  • Robert Lusardi is doing work in Upper Sacramento and might have that information.

Hyporheic condition of substrate

  • Mark G. said a lot of restoration projects have done that so we should have that information.
  • Rod said there are contacts in John Hutchings database of projects.
  • Mike B. said Tim Horner has information on this for the American.
  • Carl Mesic has information on this in the Stan. JD can dig up some information on this.
  • Mark Tompkins did some studies on at least Deer Creek in early 2000's
  • Rod said if we have gradation information we can say something about interstitial flow

Jim reviewed what parameters are included in the model

  • Mark G. said only apply juvenile chinook diversion information for lower size classes makes sense. The bigger fish stay in the thalweg.
  • Mike B. said it might be important to have the influence of hatchery fish on juvenile survival due to eating food, occupying space, and preying on wild fish. Mike B. said he is not sure any studies have been done on this, but there is anecdotal evidence of this. Michelle said that on the Mokelumne they see hatchery age 1+ O. mykiss full of juvenile Chinook: wild O. mykiss are usually still in redds at this release time. In Sacramento they are released in December at catchable size, so they are competing for space and eating other fish. Mike B. will talk to Jason on the Feather to see if it is an issue.
  • Lisa Tompson did a study on temperature and movement. At 1000 ft elevation they move up. Below that they move down to the mainstem. They are moving to cold water. Michelle said in American River down, they fish move up to the water released by the dam to get cold water. Mike B. said Clear Creek, Feather River, and Battle Creek predominately stay suitable (cold) for the whole tributary year round.

Jim reviewed the decision windows in the DSM

  • 1998 is the first year they marked all hatchery fish
  • Michelle is wondering if fall outmigrants are due to cross channel gate operations.
  • Decision was to leave fall outmigrants as a possibility.
  • Decision was to not have a 125 minimum size threshold for anadromy. All fish sizes can be anadromous.
  • What makes half pounders? Corey said it is the timing. If they leave too late they can't follow the colder water, but that is from data in Klamath and Puget Sound area. Decision was "half pounders" are fish that leave late (say June) stay in the estuary and come back to freshwater when conditions were more favorable.
  • JD has information of fish lengths at Mossdale, which are all considered to be anadromous.
  • Corey thinks that if you are fastest growing smolts, intermediate growth rate residualizing, and slow growth doesn't do anything. Maturation decision happens first and then energy is put into either growth or reproduction.
  • JD thinks going through SJ in 14 days is probably too long for a smolting steelhead. It is ~7 river miles.
  • Michelle said in Mokelumne the returns are different (earlier to January – February). She thinks the monitoring data is less robust following January because of the increase in water going through the system.
  • Sarah said spawning starts in mid September in Clear and Battle. Mike said they ask for a pulse flow in Jan 15 of Mill and Deer Creeks. But, October is the majority.
  • September to December was thought on Stan, but they are finding fish in (adult returns) every month
  • Decision was the spawning window to be tributary specific. Contact folks this information (include John Hannon).

Jim reviewed calibration data

  • Check EBMUD Escapement Reports for redd counts
  • Clear Creek should have redd counts 2003+
  • Should be more recent video reports from Doug or Matt Johnson in Deer and Mill Creek.
  • Mossdale should give decent information on timing, size, and adclipped or not (but it's a small number of fish). Export facility has more catch data.
  • Mokelunne has used Chinook efficiency trials to estimate O. mykiss abundance. This year they have started steelhead calibration. Matt said they have tried efficiency trials from Clear but use Chinook information.
  • Paul Caudret and Mary Kate are trying to do Yuba stuff
  • Mill, Deer, South Cotton, and Bear Redd counts in reports (contact Doug)
  • Email Felipe for O. mykiss RST data

Refine O. mykiss objective attributes and management scenarios that could be used to evaluate big questions/hypotheses


  • Weir counts have to subtract what goes into the hatchery
  • smolt passage might base this on Chinook


  • CDEC has unimpaired flow calculations for Shasta
  • Handling effects at hatchery was done 15 or so years ago by CDFW. Matt said it hasn't been documented at the population level but you do recapture them. Might look at Coleman Adaptive Management Plan. That information might be in there. There was discussion on the value of this scenario. This scenario is unique to Battle Creek where there is habitat upstream of the hatchery (Coleman). Mike B. said above Coleman you have virtually 100% wild fish because all hatchery are taken in for spawning.
  • Put and take Mike B. said CDFW maintains a map of where they plant fish. The effect would be any fish that washes downstream would be a predation or competition effect because they are triploid (so no spawning competition). This is a particular problem on Deer Creek, and minimized everywhere else.
  • Carlos Garza and Devon Pearce papers on genetics above and below rim dams
  • Passage barriers Stan, but only during warmer months (May-September). The solution would be groundwater recharge.
  • redd dewatering not really an issue for upper Sac (Doug)
  • Predator contact points – Matt said not very many on Clear

Next steps for O. mykiss

Thinking August to have a calibrated O. mykiss model

Time permitting: We ran out of time and did not cover these topics

  • Refine Sturgeon objective attributes and management scenarios that could be used to evaluate big questions/hypotheses
  • Next steps for Sturgeon

Marching Orders…

Jim and Adam

  • Create a list of questions for watershed expert meetings to make sure we get the information we need.


  • Update integrated model
  • Contact folks for O. mykiss DSM inputs


  • Email habitat decay subgroup to set up meeting to discuss the decay rate for spawning habitat
  • Try to schedule the regional watershed expert meeting in Late July – August (Cesar is our first couple weeks of August)
  • Invite Mike Wright to do a demo for his water temperature modeling efforts
  • Invite John Hutchings to give update on his efforts
  • Invite folks from the upper Sac efforts (Water user folks - GCID, Todd handly… the managers of the northern water districts). Matt knows them and can provide a point of contact.
  • Work with Cesar to gather large diversions information

Mike B. and Doug

  • Contacts folks with data for modeling temperature (i.e., Mike Wright's effort) and relay information to Mike W. and Rod.


  • Develop food for fish proposal


  • Contact Irwin concerning food for fish