NCEAS Project 12192

Ecosystem analysis of pelagic organism declines in the Upper San Francisco Estuary

  • Erica Fleishman

ActivityDatesFurther Information
Working Group15th—19th October 2007Participant List  
Working Group7th—11th April 2008Participant List  
Working Group6th—10th October 2008Participant List  
Working Group30th March—3rd April 2009Participant List  
Working Group6th—8th April 2010Participant List  

Abstract
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.

TypeProducts of NCEAS Research
Data Set Adib-Samii, Julio. 2008. POD! Fish- DFG 20mm Delta Smelt Survey March-July 1995-2006. (Online version)
Data Set Adib-Samii, Julio. 2008. POD! Fish- DFG Delta Smelt Larval Survey 2005-2006. (Online version)
Data Set Adib-Samii, Julio. 2008. POD! Fish- DFG North Bay Aqueduct Larval/juvenile fish sampling March-July (1992-2004). (Online version)
Data Set Adib-Samii, Julio. 2008. POD! Fish- DFG Spring Kodiak trawl sampling Jan.-April 2002-2006. (Online version)
Data Set Bauer, Marissa L. 2008. POD! Zooplankton data. (Online version)
Data Set Brown, Tiffany. 2008. POD! Water-Quality Phytoplankton species composition. (Online version)
Data Set Cadrett, Paul. 2008. POD! Fish- USFWS Beach seine and trawl data 1976-2006. (Online version)
Data Set Castillo, Gonzalo. 2008. POD! Bird data for San Francisco Bay-Delta (Christmas Bird Count_ National Audubon Society). (Online version)
Data Set Contreras, Dave. 2008. POD! Fish- DFG Fall Midwater trawl sampling Sept.-Dec.1967-2006. (Online version)
Data Set Feyrer, Fred. 2008. nceas_data_one: Fish abundance measurements and related parameters used in first POD! Change Point and MAR analyses.
Data Set Feyrer, Fred. 2008. POD! Fish- Resident Fishes. (Online version)
Data Set Feyrer, Fred. 2009. POD! Fish abundance measurements and related parameters used in first POD Change Point and MAR analyses (nceas_data_one). (Online version)
Data Set Gehrts, Karen. 2008. POD! Environmental Monitoring Program (IEP) benthic macroinvertebrate data. (Online version)
Data Set Gehrts, Karen. 2008. POD! Water-quality_daily water temp (1984-06) and EMP water quality. (Online version)
Data Set Gingras, Marty. 2008. POD! Fish- DFG Striped Bass Population estimates and stocking data. (Online version)
Data Set Gingras, Marty. 2008. POD! Fish- DFG Sturgeon Population estimates and fishery information. (Online version)
Data Set Kimmerer, Wim. 2009. POD! Code and data behind MAR variables. (Online version)
Presentations Mac Nally, Ralph. 2008. Pelagic organism decline in the San Francisco Estuary. ESA Annual Conference, Sydney, Australia, December 2008.
Journal Article Mac Nally, Ralph; Thomson, Jim R.; Kimmerer, Wim; Feyrer, Fred; Newman, Ken B.; Sih, Andrew; Bennett, William; Brown, Larry R.; Fleishman, Erica; Culberson, Steven D.; Castillo, Gonzalo. 2010. Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR). Ecological Applications. Vol: 20(5). Pages 1417-1430.
Journal Article Maunder, Mark N.; Deriso, Richard B. 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). Canadian Journal of Fisheries and Aquatic Sciences. Vol: 68. Pages 1285-1306. (Online version)
Data Set Mayfield, Ryan. 2008. POD! Fish- DFG Salvage data- Daily count and length information (1979-2006). (Online version)
Journal Article Newman, Ken B. 2008. Sample design-based methodology for estimating delta smelt abundance. San Francisco Estuary and Watershed Science. Vol: 6(3). Pages Article 3.
Data Set Norbiga, Matt. 2008. POD! Fish- Shallow water-beach seine/gill net sampling (2001 and 2003). (Online version)
Data Set Robertson, Jana. 2008. POD! Commercial Harvest records for Sacramento-San Joaquin Delta 1972-2007. (Online version)
Data Set Slater, Stephen. 2008. POD! Fish biomass analyses for DFG Bay Study by Steve Slater. (Online version)
Data Set Slater, Stephen. 2008. POD! Fish- DFG Bay Study_otter and midwater trawl, ringnet sampling 1980-2006. (Online version)
Data Set Stoms, David M. 2009. POD! Change in Percent Urban Land by Hydrodynamic Subregion, Upper San Francisco Estuary, California 1990-2006. (Online version)
Data Set Stoms, David M. 2009. POD! GIS Shapefile of 50km buffer of the Upper San Francisco Estuary. (Online version)
Data Set Stoms, David M. 2009. POD! GIS Shapefile of Hydrodynamic Subregions of the Upper San Francisco Estuary. (Online version)
Data Set Stoms, David M. 2009. POD! Landscape indicators of urban stressors on aquatic ecosystems in the Upper San Francisco Estuary, California, by Hydrodynamic Subregion. (Online version)
Journal Article Thomson, James; Kimmerer, Wim; Brown, Larry R.; Newman, Ken B.; Mac Nally, Ralph; Bennett, William; Feyrer, Fred; Fleishman, Erica. 2010. Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary. Ecological Applications. Vol: 20(5). Pages 1431-1448.
Data Set Thomson, Jim R. 2008. Change Point Analysis scripts created by POD! project analysts. (Online version)