Modeling the Delta Smelt Population

of the San Francisco Estuary

Wim KimmererRomberg Tiburon Center for Environmental Studies

San Francisco State University

Modeling Team

• Particle tracking model– Steve Monismith, Derek Fong, Jim Hench

• Matrix models– Bill Bennett

• Individual-based model– Kenny Rose– Wim Kimmerer– Post-doc to be named later

Topics to cover

• Some basic factoids about delta smelt• Current understanding• Recent concerns• The three models

World’s biggest delta smelt (Hypomesus transpacificus)

Delta Smelt

• Endemic, threatened species• Annual life cycle• Limited habitat

– Salinity from fresh to ~10– Close to the export pumps in the Delta

• Declining abundance

Fall MidwaterTrawl:90%

confidence limits of mean catch per trawl

Source: Kimmerer & Nobriga

IEP Newsletter

Abundance pattern of delta smelt

1970 1980 1990 2000

0.1

1

10

100

1000

Cat

ch p

er T

raw

l

YearA

bund

ance

Inde

x

Sudden public interest in estuarine foodwebs

Source:Mike Taugher, CC Times

J

F

AM

JJ

M

N

SA

O

D

Kodiak

20-mm

Midwater

Townet

Spawning;Temperature

Effects

Food limitation;Density dependence?

2-year-oldSpawners?

Life history and sampling

Delta Smelt Distribution in 1999

Data Source:20 mm surveys

Mid-May

Mid-July

A M J J A S O N D0

1

2

3

20

40

60

Wei

ghte

d M

ean

Sal

inity

MonthM

ean

Leng

th, m

m

Delta Smelt Distribution vs. Salinity

Data Source:IEP/DFG surveys

Delta smelt spawn in freshwater and after early summer are in

the Low-Salinity Zone

82

8384

8586

8788

8990

91

92

93

94

95

96

9798

9900

01

02

69

70

717273

75

7677

78

80

81

0 3 6 9 12 150

450

900

1350

Adu

lts

Juveniles

0 15 30 45 600

450

900

1350

1800

0 15 30 45 600

450

900

1350

1800

0 15 30 45 600

450

900

1350

1800

Juveniles

Adu

lts

Post-decline

Curved line suggests a limited carrying capacity

Source: Bennett 2005

Pre-decline

Potential Density Dependence

Spring Fall0

10

20

30

40

50

60

70N = 61

N = 153

Perc

ent o

f Ind

ivid

uals

Season

Toxic damage Undernourishment

Evidence of food limitation, not much

toxic damage(how much is too

much?)

Source: Bennett 2005

Food Shortages vs. Toxic Chemicals: 1999

Limnoithona spp.: Percent in plankton and in delta smelt diets

Zooplankton abundance:IEP Zooplankton Survey

(Low-Salinity Zone)

Diet data:Lott 1998

IEP Newsletter 11 (1):14-18M J J A S O N D

0

20

40

60

80

100

Diet: 1993-1996

1995

1994

19961993

Month

Per

cent

1975 1980 1985 1990 1995 200050

60

70

80

50

60

70

80

Leng

th, m

m

Year

Length distributions of delta smelt

Data Source:IEP/DFG surveys

Delta smelt have become ~10%

smaller

Fall Midwater Trawl SurveySept-Dec

San Francisco Bay StudyAug-May

Percent of population lost to export pumping during spring

1996 1998 2000 2002 20040

5

10

15

20

Ann

ual L

oss

(%)

Year

Source: DFG 20mm survey

Delta Smelt Loss Rates to Export Pumping

Environmental Water Account

EWA Expenditures: 2000 - 2004

Graph from Jerry Johns

Key questions

• Movement patterns– Entrainment (EWA)

• Probability of extinction– Management options– Uncontrolled factors

• Basic ecology (relevant to management)– Importance of density dependence– Importance of Age-1+ adults– Growth and survival

Why model?

• Figure out movement patterns– Particle tracking model

• Examine probability of extinction– Matrix models

• Investigate ecology– Individual-based model

Low High

Low

High Low

High

Interpretationand

Analysis

Indiv.-BasedModels

Particle-TrackingModels

Biological DetailSi

mpl

icity

and

Spe

ed

Spatial Detail

MatrixModels

Differences among models

Connections among models

Interactions among models

are implicit:Models are not

formally connected

External Data

Individual-basedmodels

Matrix models Particle-trackingmodels

Transition matrix

Vital Rates

Scen

arios

,

compa

rison

sVital

Rate

s,

Compa

rison

s

Entrainment losses

Scenarios to run

N

Suisun Bay

Pumping PlantsState Federal

Sacramento-San

JoaquinDelta

Napa River

NorthDelta

SouthDelta

South Suisun

North Suisun CentralDelta

Napa

Model Domains

PTM NodesIBM Regions

Particle-tracking model

• Based on DSM-2 hydrodynamic model– Calibrated for Delta– Fast– Separate PTM

• Suitable for early life stages• Large numbers of particles• Use observed spatial distributions

Particle-tracking model

• Conditions modeled:– Six water year types (examples)– Two barrier configurations– To VAMP or not– Alternative export management (EWA)

• Synthesis– Entrainment probabilities– Transition probabilities– Effect of alternative behaviors

Release point:Mossdale

Release point: Hood

Particle Tracking Results

LowProbability of entrainment

High

90-day runs: time series of particle fate

Q = 12

, X =

10

Q = 12, X = 6

Q = 21, X = 10

Q = 21, X = 6

0.00 0.25 0.50 0.75 1.000.00

0.25

0.50

0.75

1.000.00

0.25

0.50

0.75

1.00

Flow Export 12 10 12 6 12 2 38 10 120 10

Export Pumps

Rem

ain

in D

elta

Chipps Island

HoodParticle Tracking Results

Release point: Hood

Inflow, Export (cfs)

Q = 120, X = 10

Q = 120, X = 6Q = 38, X = 2

Q = 120 X = 2Q = 67, X = 2

0.00 0.25 0.50 0.75 1.000.00

0.25

0.50

0.75

1.000.00

0.25

0.50

0.75

1.00

Flow Export 12 10 12 6 12 2 38 10 120 10

Export Pumps

Rem

ain

in D

elta

Chipps Island

MossdaleParticle Tracking Results

Release point:Mossdale

Inflow, Export (cfs)

Matrix (stage-based) models

• Rapid computation• Uncertainty explicit• Examine sensitivity to parameters• Purposes:

– Extinction probability– Importance of age structure– Alternative management (as mortality)

Periodic Stage-Based with 1+ Adults

Spring Fall Winter

LateCohort

EarlyCohort

SmallLarvae

LargeLarvae

LargeJuveniles

SmallJuveniles

LargeAdults

SmallAdults

as11

as21 af21

as22

af11

af22

SmallLarvae

LargeLarvae

Following Spring

aw11

aw22

aw21aw12

Yr. 1+Adults

Yr. 1+Adults

Yr. 1+Adults

Yr. 1+Adults

af11 0 0

af21 af22 0

0 0 af33

aw11 aw12 0

aw21 aw22 aw23

aw31 0 0

as11 0 0

as21 as22 0

0 0 as33

• •

aw31aw23

as33 af331+

Adults

Age 0 Age 1+

-0.50

-0.25

0.00

0.25

0.50

Rat

e of

incr

ease

, rModel

Without Exports With Exports

Age 1+ Spawner and Export Effectson Population Growth

Parameters

Probability of 1+ adult surviving into summer

as33 = 0.95

Probability of 1+ adult surviving into winter

af33 = 0.80

Number of small adults surviving into spring

aw31 = 12 (approx. 1%)

Number of large larvae produced by 1+ adults

aw23 = fecundity/2 * 0.01 * 0.6 = 42

1+ are larger fish = higher survival

Less than ≈ 10% of population

Lab fecundity data

Individual-based model

• Tracks “representatives” through life cycle• Management interventions = mortality

– Not explicit– Burden is on investigator to supply mortality

• Alternative formulations– Density dependence– Importance of Age-1+

Individual-based modelSet up geometry

Initialize environment

Initialize population

Years

Determine hydrological year type

Spawning

Days

Individuals

Egg development, mortality

New individuals

GrowthMortality

Movement

HydrodynamicModel;

EnvironmentalConditionsLoop

Loop

Loop

Related Projects• Delta Smelt Foodweb (CALFED funded)

– Basis of the foodweb– Sources and processing of organic carbon

• Delta Smelt Monitoring (CALFED: submitted)– Histopathology (Food limitation, toxicity)– Growth rate, origin– Feeding (gut contents)

• POD (Pelagic Organism Decline)– Delta smelt abundance, distribution, entrainment– Copepod population dynamics– Clam salinity tolerance

• Ongoing studies– Delta smelt culture– X2 investigations

Schedule

Current status of delta smelt

Spring 2006 Hire post-doc

Fall 2006 Initial workshop – adjust scope

Fall 2006 CALFED Science Conference

2006 - 2007 Model development

Spring 2008 Complete model development

January 2009 Final reporting