SacPAS: A real-time decision support system to predict and assess

operational benefits and risks to Central Valley Salmon

J.J. Anderson1 and J. Israel2

1. Columbia Basin Research, School of Aquatic and Fishery Sciences, University of Washington

2. Bay-Delta Office, Reclamation Mid Pacific Region, 801 I Street, Suite 140, Sacramento, CA 95814-2536,

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SacPAS in the context of Sacramento fish models

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Spawning

Rearing

River passage

Delta passage

Ocean residence

Adult migration

Water Export management

Harvestmanagement

Current forms of Winter Chinook management

Flow Temperaturemanagement

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Spawning

Rearing

River passage

Delta passage

Ocean residence

Adult migration

Water Export management

Harvestmanagement

SacPAS targets real-time effects of flow on fish

Flow Temperaturemanagement

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Spawning

Rearing

River passage

Delta passage

Ocean residence

Adult migration

Water Export management

Harvestmanagement

By linking real-time environmental conditions

Flow Temperaturemanagement

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Database

Spawning

Rearing

River passage

Delta passage

Ocean residence

Adult migration

Water Export management

Harvestmanagement

To models of spawning to river passage

Flow Temperaturemanagement

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DatabaseModel

Let’s go to the SacPass web page

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~ SacPASSacramento Predic ... )( \ +

~www.c:br.washlngton.edu/sacramento I o. search I ... ~ * lEI C7 4 fl f!. ~ ---SacPAS: Sacramento Prediction & Assessment of Salmon UW Columbia Basin

BETA- Web Site Under Development Research

Home Data Queries & AlertsUFish Modell I Maps I Contact

SacPAS: Sacramento Prediction and Assessment of Salmon through Ecological Data and Modeling for In-Season Management

Mission: Provide web-based services to link data and science to in-season management.

This website will provide monitoring, evaluat ion, and weba-t~~~ data products and services for primary and associated activit ies funded by the U.S. Bureau of Reclamation (USBR) and mandated by the Endangered Species Act (ESA). It will serve as a means by which information integration serv ices can be provided to the Central Valley Proj ect Improvement Act (CVPIA) and ESA part icipants. Web-based services wi ll re late f ish passage to environmental condit ions and provide resources for evaluat ing the effects of river management and environmental condit ions on salmon passage and survival.

= Data Queries & Alerts

Provide a publicly accessible, web-based query and report ing system of historical and current f ish, environmental, and hydrologic information, vit al t o year-round planning and adaptive management of t he Cent ral Valley Project and State Water Proj ect. Data uploads will provide the most up-to-date data as it is made available, whether it be daily, biweekly, monthly or annually. Basic condit ions, performance measures, and threshold-based alerts are available through data aggregat ion and analysis of environmental condit ions.

Fish Model

Adapt a smolt passage model based on NOAA's Comprehensive Passage (COMPASS) Model @ to characterize movement of water and j uvenile fish through the Sacramento River system to t he head of the San Francisco Bay Delta. The model uses available data from long-term monitoring sites. Physical data may include water velocit y, t emperat ure, and f low.

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The database links to the fish model

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Database tools provide analysis relevant to fish and water management

Examples of database tools

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Fish Monitoring

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Home Data Quer ies

Alerts Juvenile Sampling &

Estimates

Delta Juvenile Monitoring for Unmarked Older Juvenile Chinook, 8/1/2016 to 7/31/2017

<< return to querv page

Sacramento River

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Red Bluff Diversion Dam Rotary Screw Trap w ith CDEC Daily Average River Data Unmarked Older Juvenile Chinook (Frank Fisher length-at-date DWR river model)

Total 518 309 for Sam lin Dates: 2016-08-01 to 2016-11-03 100

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Preliminary data from USFWS Red Bluff and CDEC; subject t o revision. Older juvenile Chinook def inEd as matching winter run length -at .Oate criteria (Frank Fisher WOdel) up to max length-at-date si ze.

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Weir Overtopping Monitoring

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Hum~ uata Queries

Alt!rls Juvenile sampling &

E!!jlimdles

Alert: sacramento River Weirs overtopping

Below Crest OanQer !reak Value in rcr io(J !w ithin 1 ft of Flood! !r eak Value & Within 1 ft of Flood!

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Minimum : /6.::! ~1i nimum: ol.::! M'nimum: 4~ .0 Minimum: N.C.

Ri ver Stage _eve!s Crest : 76.8 Crest: 61.8 Crest: -15. 5 Crest: 33.5 FluucJ: 84.4 FluucJ : 7 1.0 Fluutl : 53.0 Fluut.l : 40.8 Danger: 8:>.4 Danger: 72.0 Danger: ~4.0 Danger: 41 .8

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Temperature Monitoring

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2 016 Sacramento Ri ver Temperature Target Analysis based on RPA 1.2.4 Temperature Locations from Keswick Dam to Bend Bridge

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The Fish Model

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Fish Model Physical geography Data Sub-models for

Temperature Sacramento River Keswick Dam {RM 302) • Egg development

Flow Inputs and Emergence

Geography Redd and Carcass

Movement - 0 bse rvatio ns and survival Data Hwy 44 Bridge (RM 297) e

Sub-models

Juvenile Passage Passage Red Bluff Dam (RM 243) e -Observations distr ibutions

;;... Data 1/0 at nodes Movement ;;... Flexible use of and survival

movement & survival models

Knights Landing (RM 90) • Limited

+--Juvenile Passage )- Web interface 0 bse rvatio ns

Mouth (RM O) e

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Model Input PageEmergence model

- - - - -Home DatJI_~;tuerleo • Alerts Fish Model Maos Contact

Fish Model Geogrephy -Reference• end Notes Model OVerview

Fi$h Model : Spawning to Migration

The SacPAS fish modeling process begins with egg dcposltlon at the tlmc of spawning. Development rate and survival can be modeled by various methods to d~tennlne fry emeroenr~ fr()m the gr11vP.I. On thl~ ~!JP you ~n control t f"mpPr.,ture Inputs, redc'I/CJ.IrcA$.$/~dult cnunt.s 3nd ~urvlval detAIIt; for egg development modeling. The outputs of this process become the Input for the migration model, COMPASS.

Specify Temperature Data

~~~~~~: Of!OOHfllt ,Mh1:1!06tn

Use column : ~ Units: • Centigrade farenhelt

Specify Spawning Data

• Winter Chinook redds: 20•• Br1dge" ror Wirllel Run Chinook.

Wifll t:!r ChinOOk t:t~rt:(I$S~S ~Gii •

_j.)Jlload fi le: <::tiOOM FIIt ·No- .. d\t:iffn

use column: ~ Urtlts: • Red<Js Adults or carcasses.

Adult and Carcass Handling

• n lest • Lines

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Header I

Adults/carcasses • This divides the count to ge per redd: 9 counts to get the correct m

use 2. More Importantly. re the Sacramento River wlnte

Timing offset: -t2 days.

• Integer days only. for carC-iJ p~.ak redd day to peak care SJ)dWiling gfOUI)d S. FOI Uciu/

$J>e<ify Egg Development model

Chinook Mechanistic (B~r and Ander<;on 1997) Chinook Emplrlcal (Jensen et al. 1999) Chinook I'Owe1 low (BeUChalll/Murroy 1990) Do

• Chinook Linear (Zeug et al. 2012): lllrget ATUs

• Default linear value 958 is centigrade equlval

• Enter a value In either box to convert betwee • Farenhelt ATUs are accumulated above 32. Tt

Eggs per Re<ld ,.,. Oppenheim (2014) (AIIowe<l

S pecify Survival model

Consldnl survival {Oppenheim, 2014 ): Spuwn!r1

• survival from ~pawning to fry passing HBDD. s

l cmpcraturc dependent mortality parameters Tcm: = GJ7l cF or u.or °C. Temperatur l}f • OOIJ) °F·l or 0.0~9 "C"l. Rh l e ~

• To remove the temperature related para11

Non·tempe rature related mortality parameter IJo - o .. v- oenslty .. lndepende-nt b~se su IJJ - ~·'* Density-dependent survrval

• To remove the density relat ed parameter

Specify Anal ysis ahd Results Display

• use Jedd or CcJrCtJss value di!ta set as 1s. srnc

Dt~te Range: ~«Filfll>•:..

Specify Temperature Data

• Query database: 20 16 • 1 Caily Average iKWKJKeswici< (WO) • Data provided as a cowtesy by COEC.

l Jnlond fi iP.: __ Choose Fie I No flle t~o~>

• Fl e should be a comma or tab delimited text file with at least 2 columns. • I i n<>~ r~r<> n ,. rprl v ;:,h '"'~ 1 ~t r"OI11mn i~ flilv-of-vp;:,r- ? n rl nr nth<>r l"n l 11mn I~ t<>mn<>rilh ""' H <>MI<>r lin<' I~

Specify Spawning Data

• Winter Chinook redds: 201s • 1 Combined counts from "Keswick Dam to A.C.I.D. Dam" and "A.C.I.D. Dam to Highway 44 Bridge" for Winter Run Chinook.

WintP.r Chinook r.ilrr.ilSSP.S f~o,.; , RP.dd and r:arr.as,c; datnhn.'>P. {lmv idP.d i'lS a r.o•Jrtp,c;y hy ('.f)FW nnd /JSAR. Or~tr~ Oisdil imP.r ili'

Upload file: Choose File, I No me th>sen • File should be a comma or t ab delimited text f ile with at least 2 columns.

Use c::>lumn: U Units: • Redds Carcasses.

• Lines are paired values. 1st column Is Day-of-year. 2nd or other column Is redd, adult or carcass count.

Adults or Header line Is Ignored.

Adult and Carcass Handling Adults/carcasses • This divides the count to aet redds. Positive inteaer onlv. If vou are uoloadlna adult or carcass counts. th is will ad1ust those

Specify Egg Development model VIew egg growth models comoarlson ii'

Chinook Mechanistic (Beer and Anderson 1997): Egg mass :oo mg. (Allowed Range: 100 ~ x 5 400) Chinook Empirical (Jensen et al. 1999) Chinook Power law (Beacham/Murray 1990) Days= el0.404 - 2.043'1og:T•c + 7.575)

• Chinook Linear (Zeug et al. 2012) : Target ATUs J9ss 1 degree C days. (Allowed Range: 700 ~ x ~ 1200)

• Default linear value 958 is centigrade equivalent of ATUs accumulated at the published daily rate: 0.00058 * T Farenheit - 0.018 • Enter a value In either box to convert between ATU-Centlgrade I£__J and ATU-Farenhelt ~· • Farenhelt ATUs are accumulated above 32. This cal:u latio1 is NOT a temperature conversion tool.

Eggs per Reod 4925 Oppenheim (2014) (Allowed Rang:: 1000 5 x ~ 6000)

• survival from spawning to fry passing KtsOD. !::iacramento Klver temperature 1as1< Group model (!::iK I I G)

Temperature-dependent mortality parameters. Tc,it - '•;;.rl I " F or IZUf oc. Temperature below w11ch there Is n::> temperature dependent mortality.

Specify Analysis and Results Display

• Use redd or c:~ rcass value data set as is. Smooth redd or carcass values. See Notes &'

Date Range: RMge o<FishData

l Run Emergence ;to an outp<t tab} I I Run Emergence (new~ eao1 ellck) Reset

Model

Data

Results

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Emergence model results

Home Fish Model

l§idownload CSV ~view PDF .... run migration model

Spawning to Emergence Results

Emergence Specifications Species: Chinook Development model: Zeug Target ATUs : 958 Egg survival model: TaskGroup Fry survival model : TaskGroup

Eggs per redd: 4925 Adults/ carcasses per redd: NA Offset used for redd t iming:

Temperature Source:

Spawning Data Source:

Emergence Results Total Redds: Mean Emergence Day: Timing from Emergence to RBDD: Variance: STD: Expansion: Eggs: Fry: Passage: Survival, Egg to Fry : Survival, Fry to RBDD pass: Survival, Egg to RBDD pass:

NA

SacPAS database 2016 KWK: DailyAvg SacPAS database 2016 Redds

12 267

NA

612.1 24.7 o Days 59100 NA 20472 NA

NA

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Fish Model

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12

References and Not es

Temps: 2016KWK Redds:2016

-- Spawning - Emergence (Fry) -- Temperature -- Distribution

Contact Model Overview

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Passage model input

Passage model results

Run Migration passage model with Emergence Results

Specify Flow

@Fixed Flow: flow observations at a single site with 10 year averages for missing/future values: July 2015- June 2017 • Obs. and/or 10 year avg. flow at: KWK •

e:l User Provided Flow: I Browse... I No file selected. Use column: -2- Needs 18 months of values from Jan.1 of spawning year . First column is day and other columns are values. Comma or space delimited. Units: @ CFS e:l KCFS/TCFS.

Specify Opt ional configuration

CiAdjust the mrgrat ion rate equat ions: Above Red Bluff, Miles/Day =~ + o.os x River_Velocity Below Red Bluff, Miles/Day =~+ 0.07 x River_ Velocity

Run Passage I I Run Passage (new tab)

Note: At this time, migrat ion can ONLY be modeled for Winter Chinook from the upper Sacrament o.

Fish Model References and Notes

Passage Model Results - - for DEMONSTRATION purposes only

Stock:

contact Model Overview

Temps: Winter _Chinook 2016 ~ - r---- Observed flow at KWK 2016

~ 10 year averages KWK Distributions of fish Flows: Mean emefl}ence:

simple

2016-09-23

Travel to RBD_Dam Mean arrival: 2016- 10- 10 Mean Travel Time: 16.8 Days

Survival: 34.6% (previously compu ted)

Travel to Knights_ Landing Mean arrival : 2016- 11-20 Mean Travel Time: Survival:

41.5 Days from RBD_ Dam to Knights_ Landing 68.2%

Emergence to Knights_landing Travel Time: 58.3 Days Survival: 23.5%

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This open-access web-based system provides historical and real-time environmental data and predictions of movement and survival of winter Chinook salmon from adult spawning to passage of juveniles into the San Francisco Bay Delta.

The system provides:• Easy access to historical and real-time environmental and fish data• Retrospective analysis of fish movement and survival under different

historical conditions and model assumptions• Sensitivity analysis of fish passage to differing assumptions of conditions

and mechanisms• Quantitative estimates of benefits and risks of management decisions on

salmon populations• A web-based modeling framework that can be readily modified to

incorporate new models, data and user-specified analysis tools.

• Models• Rich Zabel (NOAA Seattle) for providing the COMPASS passage model• Sacramento River Temperature Task Group

• Data Providers• California Data Exchange Center (CDEC)• California Department of Fish and Wildlife (CDFW)• California Department of Water Resources (CDWR)• NOAA• US Fish and Wildlife Service, Lodi and Red Bluff (USFWS)• US Geological Survey (USGS)• 34 North / Bay Delta Live

• Columbia Basin Research Staff, University of Washington• W. Nicholas Beer• Susannah Iltis• Chris Van Holmes

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This project is funded by US Bureau of ReclamationBay-Delta Office, Mid-Pacific Region

We wish to especially thank

SacPAS: www.cbr.washington.edu/sacramento/