suisun marsh: the role of food and cover in supporting a...

Suisun Marsh:The role of food and cover in

supporting a fish nurseryDenise Colombano, Amber Manfree, John Durand, Teejay O’Rear, Brian Williamson, Peter Moyle

Bay Delta Science ConferenceSacramento, CA

November 15, 2016

UC Davis Suisun Marsh Fish & Invertebrate Study (1980-present)

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Suisun Buy

Grizzly Bay

Sample Sites

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Long-term trends

O’Rear and Moyle 2014

60

Shimofuri goby first collected

Drought

Major flood

density I Overb ile c lam reaches high

Suisun Marsh Salinity Control Gates

Shokihaze goby first collected

Siberian prawn reaches high density

Patterns of space use

Manfree 2014

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on carp Whtt cat1tsh

SUirry flounder

0

Jun 1992

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X X

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Catch fish/hr X No sample

• Snmpte site

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Changes in community composition

Rank 1980-1989 2002-20121 Striped Bass Striped Bass

2 Threespine Stickleback Sacramento Splittail

3 Tule Perch Tule Perch

4 Sacramento Splittail White Catfish

5 Longfin Smelt Yellowfin Goby

6 Prickly Sculpin Shimofuri Goby

7 Yellowfin Goby Prickly Sculpin

8 Common Carp Threespine Stickleback

9 Sacramento Sucker Common Carp

10 Shimofuri Goby Black Crappie

Food web utilization

Schroeteret al. 2015

midge

Co rbic

ove rbite

b. shrmp

or . shrmp

S. prawn

SB

SCP

YFG

% of Diet

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Conceptual model: Marsh food web transferKneib 2000, Beck et al. 2001

Conceptual model: Marsh food web transferKneib 2000, Beck et al. 2001

Nursery= Greater than average density,

biomass, growth, survival per unit area compared to other areas

Conceptual model: Marsh food web transfer

• Recruitment• Migration• Predation

• Senescence

Kneib 2000, Beck et al. 2001

Conceptual model: Marsh food web transfer

= Trophic transfer to open estuary

Kneib 2000, Beck et al. 2001

1984 1986

Dependence of Fishery Species on Salt

Marshes: The Role of Food and Refuge

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The Modification of an Estuary

fllEDSJUC H . NICHOLS, }AMES E. CLOilaN, SAMU'IlL N . LUOMA, DAVID H. PBTBilSON

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0 Leveed or filled marsh

• Exist ing marsh

0 20km

Manfree 2014

Water infrastructure

0 Operating

® Repurposed or non-operational

• Non-operational

0 2.5 5 10 km

Conceptual model: Marsh food web transfer

Focal Species

Photos: Matt Young & Amber Manfree

Sacramento Splittail (Pogonichthys macrolepidotus)

Tule Perch (Hysterocarpus traskii)

Striped Bass (Morone saxitilis)

0.00.20.40.60.81.01.21.4

1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

2008

2009

2010

2011

2012

2013

2014

2015

CATC

H PE

R M

INU

TE

Sacramento Splittail

0.00.51.01.52.02.53.03.5

1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

2008

2009

2010

2011

2012

2013

2014

2015

Striped Bass

Age-2+

Age-1

Age-0

0.000.100.200.300.400.500.600.700.80

1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

2008

2009

2010

2011

2012

2013

2014

2015

CATC

H PE

R M

INU

TE

Tule Perch

Age-1+

Age-0

n=21,409 n=52,855

n=9,738

Testing the nursery-role hypothesisBeck et al. 2001

1. Identify areas with “disproportionately greater than average” juvenile fish abundance on an annual basis = hotspots

2. Examine site-specific attributes to better understand what explains juvenile fish abundance

0

50

100

Splittail Striped Bass Tule Perch

% Annual Hotspot0

50

100

Splittail Striped Bass Tule Perch

% Annual Hotspot0

50

100

Splittail Striped Bass Tule Perch

% Annual Hotspot

0

50

100

Splittail Striped Bass Tule Perch

% Annual Hotspot

By Region…

0.0

0.5

1.0

% Annual Hotspot

Splittail Striped bass Tule Perch

0.0

0.5

1.0

Denverton Nurse

% Annual HotspotSplittail Striped Bass Tule Perch

0.0

0.5

1.0

Montezuma

% Annual Hotspot

Splittail Striped Bass Tule Perch

0.0

0.5

1.0

SuisunLower Goodyear

% Annual HotspotSplittail Striped Bass Tule Perch

By Slough…

Testing the nursery-role hypothesisBeck et al. 2001

1. Identify areas with “disproportionately greater than average” juvenile fish abundance on an annual basis = hotspots

2. Examine site-specific attributes and their influence on juvenile fish abundance

Biotic Abiotic Landscape

Larval supply Water depth Spatial pattern

Structural complexity Physico-chemical environment (Patch size, shape, connectivity)

Predation (Dissolved oxygen, salinity) Relative location

Competition Disturbance regime (To larval supply, other juvenile

Food availability Tidal regime habitats, adult habitats)

Table. Factors influencing site-specific variability in nursery value

Testing the nursery-role hypothesisBeck et al. 2001

Biotic Abiotic Landscape

Larval supply Water depth Spatial pattern

Structural complexity Physico-chemical environment (Patch size, shape, connectivity)

Predation (Dissolved oxygen, salinity) Relative location

Competition Disturbance regime (To larval supply, other juvenile

Food availability Tidal regime habitats, adult habitats)

Table. Factors influencing site-specific variability in nursery value

Testing the nursery-role hypothesisBeck et al. 2001

Quantifying Emergent VegetationVegetation area to channel area ratio – 100m

increment

Wetland

Corridor

Hypotheses

1. The number of juvenile fish increases with vegetation complexity

2. The number of juvenile fish increases in the presence of mysids

3. The impact of mysid presence on juvenile fish is increased by vegetation complexity

= That is to say that the association between juvenile fish abundance and food availability depends on cover

Hypotheses

1. The number of juvenile fish increases with vegetation complexity

2. The number of juvenile fish increases in the presence of mysids

3. The impact of mysid presence on juvenile fish is increased by vegetation complexity

= That is to say that the association between juvenile fish abundance and food availability depends on cover

Hypotheses

1. The number of juvenile fish increases with vegetation complexity

2. The number of juvenile fish increases in the presence of mysids

3. The impact of mysid presence on juvenile fish is increased by vegetation complexity

= That is to say that the association between juvenile fish abundance and food availability depends on cover

Generalized linear mixed models (GLMMs)

• Multivariate regression• Using more than one predictor to model an outcome• Statistical control to avoid spurious correlations• Multiple causation• Interactions

• Multilevel models• Improved estimates for repeat sampling• Improved estimates for imbalance in sampling• Estimates of variation• Avoid averaging, retain variation• Impute missing values

McElreath et al. 2015

Generalized linear mixed models (GLMMs)

• Multivariate regression• Using more than one predictor to model an outcome• Statistical control to avoid spurious correlations• Multiple causation• Interactions

• Multilevel models• Improved estimates for repeat sampling• Improved estimates for imbalance in sampling• Estimates of variation• Avoid averaging, retain variation• Impute missing values

McElreath et al. 2015

Generalized linear mixed models (GLMMs)

Model exercise:Assess the relative influences of food and cover on juvenile fish abundance and test for interactions

Model structure:

𝐽𝐽𝐽𝐽𝐽𝐽𝐽𝐽𝐽𝐽𝐽𝐽𝐽𝐽𝐽𝐽 𝐹𝐹𝐽𝐽𝐹𝐹𝐹 𝐴𝐴𝐴𝐴𝐽𝐽𝐽𝐽𝐴𝐴𝐴𝐴𝐽𝐽𝐴𝐴𝐽𝐽 ~ 𝑃𝑃𝑃𝑃𝐽𝐽𝐹𝐹𝐹𝐹𝑃𝑃𝐽𝐽 𝜆𝜆𝑖𝑖log 𝜆𝜆𝑖𝑖 = log 𝐸𝐸𝐸𝐸𝐸𝐸𝑃𝑃𝐸𝐸𝐸𝐸 𝑚𝑚𝐽𝐽𝐽𝐽 + 𝛼𝛼 + 𝛼𝛼𝑌𝑌𝑌𝑌𝑌𝑌𝑌𝑌 𝑖𝑖 + 𝛼𝛼𝑆𝑆𝑖𝑖𝑆𝑆𝑌𝑌 𝑖𝑖 + 𝛽𝛽1𝑇𝑇𝐽𝐽𝑚𝑚𝑇𝑇𝑖𝑖 + 𝛽𝛽𝑣𝑣𝑉𝑉𝐽𝐽𝑉𝑉𝐽𝐽𝐸𝐸𝐴𝐴𝐸𝐸𝐽𝐽𝑃𝑃𝐽𝐽𝑖𝑖 + 𝛽𝛽𝑚𝑚𝑀𝑀𝑀𝑀𝐹𝐹𝐽𝐽𝐴𝐴𝐹𝐹𝑖𝑖 + 𝛽𝛽𝑣𝑣𝑉𝑉𝐽𝐽𝑉𝑉𝐽𝐽𝐸𝐸𝐴𝐴𝐸𝐸𝐽𝐽𝑃𝑃𝐽𝐽𝑖𝑖 ∗ 𝛽𝛽𝑚𝑚𝑀𝑀𝑀𝑀𝐹𝐹𝐽𝐽𝐴𝐴𝐹𝐹𝑖𝑖

Trawl time

Inter-annualvariability

Repeated sampling

Intercept

Seasonality

Vegetation complexity

Mysid presence/ absence Interaction

McElreath 2015, Carpenter et al. 2015, Little & Rubin 2002

GLMM results

Model # Predictor variables Varying Intercepts

SplittaildWAIC Wt Striped Bass

dWAIC Wt Tule perch dWAIC Wt

8 Temp + Vegetation*Mysids Year + Site 0 1 0 1 30.5 0

7 Temp + Vegetation + Mysids Year + Site 58.7 0 1284.1 0 13.3 0.04

6 Temp + Mysids Year + Site 43.1 0 1330.6 0 0 0.96

5 Temp + Vegetation Year + Site 38.3 0 2177.1 0 49.2 0

4 Temp Year + Site 37.3 0 2142.7 0 47.4 0

3 - Year + Site 232.5 0 3523.8 0 13.3 0

2 - Year 2833.8 0 42095.2 0 1196.1 0

1 - - 10898.6 0 67123.7 0 5313.4 0

GLMM results

Model # Predictor variables Varying Intercepts

SplittaildWAIC Wt Striped Bass

dWAIC Wt Tule perch dWAIC Wt

8 Temp + Vegetation*Mysids Year + Site 0 1 0 1 30.5 0

7 Temp + Vegetation + Mysids Year + Site 58.7 0 1284.1 0 13.3 0.04

6 Temp + Mysids Year + Site 43.1 0 1330.6 0 0 0.96

5 Temp + Vegetation Year + Site 38.3 0 2177.1 0 49.2 0

4 Temp Year + Site 37.3 0 2142.7 0 47.4 0

3 - Year + Site 232.5 0 3523.8 0 13.3 0

2 - Year 2833.8 0 42095.2 0 1196.1 0

1 - - 10898.6 0 67123.7 0 5313.4 0

Interaction modelsEstimating variation among parameters by evaluating marginal posterior distributions

McElreath 2015

Parting thoughts and next steps…

1. Suisun Marsh provides rearing habitat for splittail, striped bass and tule perch, the top 3 most abundant species in the marsh

2. Annual hotspots• Splittail: Denverton (38%) and Spring Branch (48%)• Striped bass: Denverton (24%), Spring Branch (24%), Upper Suisun (24%) • Tule perch: Cutoff Slough (38%)

3. Model support for hypothesis #3 that the association between juvenile fish abundance and mysid availability depends on vegetation complexity (positive interaction)

4. Continue to work on modeling approach and predictions

Parting thoughts and next steps…

1. Suisun Marsh provides rearing habitat for splittail, striped bass and tule perch, the top 3 most abundant species in the marsh

2. Annual hotspots• Splittail: Denverton (38%) and Spring Branch (48%)• Striped bass: Denverton (24%), Spring Branch (24%), Upper Suisun (24%) • Tule perch: Cutoff Slough (38%)

3. Model support for hypothesis #3 that the association between juvenile fish abundance and mysid availability depends on vegetation complexity (positive interaction)

4. Continue to work on modeling approach and predictions

Parting thoughts and next steps…

1. Suisun Marsh provides rearing habitat for splittail, striped bass and tule perch, the top 3 most abundant species in the marsh

2. Annual hotspots• Splittail: Denverton (38%) and Spring Branch (48%)• Striped bass: Denverton (24%), Spring Branch (24%), Upper Suisun (24%) • Tule perch: Cutoff Slough (38%)

3. Model support for hypothesis #3 that the association between juvenile fish abundance and mysid availability depends on vegetation complexity (positive interaction)

4. Continue to work on modeling approach and predictions

Parting thoughts and next steps…

1. Suisun Marsh provides rearing habitat for splittail, striped bass and tule perch, the top 3 most abundant species in the marsh

2. Annual hotspots• Splittail: Denverton (38%) and Spring Branch (48%)• Striped bass: Denverton (24%), Spring Branch (24%), Upper Suisun (24%) • Tule perch: Cutoff Slough (38%)

3. Model support for hypothesis #3 that the association between juvenile fish abundance and mysid availability depends on vegetation complexity (positive interaction)

4. Continue to work on modeling approach and predictions

…and supporters

Thanks to research sponsors …

Questions?