NCEAS Working Groups
Ecosystem analysis of pelagic organism declines in the Upper San Francisco Estuary
Project Description
In late 2004, scientists noted that abundance indices of several pelagic fishes in the upper San Francisco Estuary (delta smelt, age-0 striped bass, longfin smelt, and threadfin shad) had remained unusually low since 2001. Delta smelt is an endemic species listed as threatened under both the California and U.S. Endangered Species Acts. Protection of delta smelt often determines water management actions in the estuary, which supplies drinking water to more than 22 million people and supports a multi-billion dollar agricultural industry. The abundance of longfin smelt, another native species, has a strong positive relationship to freshwater outflow. Striped bass and threadfin shad are both introduced species that contribute substantially to the total biomass of pelagic fishes in the ecosystem and support valuable recreational fisheries. NCEAS and the Interagency Ecological Program are collaborating to convene several working groups on issues related to decline of pelagic organisms. We hope not only to gain a better understanding of the specific causes and mechanisms behind the organism declines in the San Francisco Estuary, but to place these declines in the broader context of estuarine degradation, organism declines, and approaches to solving these problems in other geographic regions. Among other goals, we seek to examine simultaneously the effects of multiple potential drivers on one or more fishes. Further, we aim to investigate whether fishes differ in their response to given drivers. We also wish to explore the ability of Bayesian analysis, path analysis, or other modeling approaches to draw inference regarding ecological relationships among pelagic fishes, human actions, and inherent variability in the estuarine system.
Principal Investigator(s)
Erica Fleishman
Project Dates
Start: June 7, 2007
End: May 14, 2010
completed
Participants
- Marissa L. Bauer
- US Geological Survey (USGS)
- William Bennett
- University of California, Davis
- Marjorie L. Brooks
- University of California, Santa Barbara
- Larry R. Brown
- US Geological Survey (USGS)
- Jon Burau
- US Geological Survey (USGS)
- Gonzalo Castillo
- US Fish and Wildlife Service (FWS)
- Steven D. Culberson
- CALFED Science Program
- Fred Feyrer
- California Department of Water Resources
- Erica Fleishman
- University of California, Santa Barbara
- Michael Healey
- CALFED Bay Delta Program
- Michael L. Johnson
- University of California, Davis
- Wim Kimmerer
- San Francisco State University
- Ralph Mac Nally
- Monash University
- Mark N. Maunder
- InterAmerican Tropical Tuna Commission
- John M. Melack
- University of California, Santa Barbara
- Sue Meyer
- Nossaman Gunther Knox & Elliott LLP
- Dennis Murphy
- University of Nevada, Reno
- Ken B. Newman
- US Fish and Wildlife Service (FWS)
- Thomas L. O'Halloran
- University of California, Santa Barbara
- Catherine Ruhl
- US Geological Survey (USGS)
- Andrew Sih
- University of California, Davis Extension
- David M. Stoms
- University of California, Santa Barbara
- Jim R. Thomson
- Monash University
- Howard Townsend
- National Oceanic and Atmospheric Administration (NOAA)
Products
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Data Set / 2008
POD! Fish- DFG 20mm Delta Smelt Survey March-July 1995-2006
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Data Set / 2008
POD! Fish- DFG Delta Smelt Larval Survey 2005-2006
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Data Set / 2008
POD! Fish- DFG North Bay Aqueduct Larval/juvenile fish sampling March-July (1992-2004)
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Data Set / 2008
POD! Fish- DFG Spring Kodiak trawl sampling Jan.-April 2002-2006
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Data Set / 2008
POD! Zooplankton data
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Data Set / 2008
POD! Water-Quality Phytoplankton species composition
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Data Set / 2008
POD! Fish- USFWS Beach seine and trawl data 1976-2006
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Data Set / 2008
POD! Bird data for San Francisco Bay-Delta (Christmas Bird Count_ National Audubon Society)
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Data Set / 2008
POD! Fish- DFG Fall Midwater trawl sampling Sept.-Dec.1967-2006
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Data Set / 2008
nceas_data_one: Fish abundance measurements and related parameters used in first POD! Change Point and MAR analyses
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Data Set / 2008
POD! Fish- Resident Fishes
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Data Set / 2009
POD! Fish abundance measurements and related parameters used in first POD Change Point and MAR analyses (nceas_data_one)
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Journal Article / 2015
Estuarine fish communities respond to climate variability over both river and ocean basins
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Data Set / 2008
POD! Environmental Monitoring Program (IEP) benthic macroinvertebrate data
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Data Set / 2008
POD! Water-quality_daily water temp (1984-06) and EMP water quality
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Data Set / 2008
POD! Fish- DFG Striped Bass Population estimates and stocking data
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Data Set / 2008
POD! Fish- DFG Sturgeon Population estimates and fishery information
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Data Set / 2009
POD! Code and data behind MAR variables
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Presentations / 2008
Pelagic organism decline in the San Francisco Estuary
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Journal Article / 2010
Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR)
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Journal Article / 2011
A state-space multistage life cycle model to evaluate population impacts in the presence of density dependence: Illustrated with application to delta smelt (Hyposmesus transpacificus)
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Data Set / 2008
POD! Fish- DFG Salvage data- Daily count and length information (1979-2006)
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Journal Article / 2008
Sample design-based methodology for estimating delta smelt abundance
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Data Set / 2008
POD! Fish- Shallow water-beach seine/gill net sampling (2001 and 2003)
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Data Set / 2008
POD! Commercial Harvest records for Sacramento-San Joaquin Delta 1972-2007
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Data Set / 2008
POD! Fish biomass analyses for DFG Bay Study by Steve Slater
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Data Set / 2008
POD! Fish- DFG Bay Study_otter and midwater trawl, ringnet sampling 1980-2006
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Data Set / 2009
POD! Change in Percent Urban Land by Hydrodynamic Subregion, Upper San Francisco Estuary, California 1990-2006
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Data Set / 2009
POD! GIS Shapefile of 50km buffer of the Upper San Francisco Estuary
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Data Set / 2009
POD! GIS Shapefile of Hydrodynamic Subregions of the Upper San Francisco Estuary
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Data Set / 2009
POD! Landscape indicators of urban stressors on aquatic ecosystems in the Upper San Francisco Estuary, California, by Hydrodynamic Subregion
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Journal Article / 2010
Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary
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Data Set / 2008
Change Point Analysis scripts created by POD! project analysts