Advanced Ecosystem Research

Farallon Institute Projects

Scientific Projects of FI include work in three main thematic areas: Climate and Marine Ecosystems, Marine Spatial Ecology and Planning, and Ecosystem Approaches to Fisheries. We also conduct research in Seabird Conservation and Ocean Energy Development (wind and wave). These five themes are interrelated.

Climate and Marine Ecosystems

Farallon Institute places emphasis on building a deeper and more comprehensive understanding of the relationships between global climate and marine ecosystems. Until recently, marine ecosystem impacts were poorly represented in Intergovernmental Panel for Climate Change (IPCC) Assessment Reports. Therefore, a primary goal of the Farallon Institute is to obtain and provide up-to-date information on marine ecosystem responses to climate variability and change for inclusion in state, federal and international policy forums concerning global warming and society.

Are Pacific Rim Marine Ecosystems Becoming More Variable (and Less Predictable)?


Changes in variance are infrequently examined in climate change ecology. In this project, we are documenting changes in ecosystem variance of the North Pacific to provide insight into varying relationships between climate variables and ecosystem dynamics. Specifically, physical (SST) and biological data from ecosystems of the Pacific Rim are being synthesized and investigated for changes in variance statistics (e.g., coefficient of variation, skewness) over the past 60 years.

Seabird Sentinels of Marine Climate Change


Due to their existence at the boundary layers of the atmosphere and the ocean, seabirds are the most conspicuous of all marine organisms which rely on surface and near-surface ocean habitats. Seabirds also are less exploited than other upper level predators such as fish and mammals. Owing to these and other characteristics, seabirds have been put forth as reliable ecological indicators of coupled physical-ecological change. In this project we are investigating changes in the abundance, distribution, and spatial organization of seabirds in the California Current. In this study FI biologists make counts of seabirds from fisheries research vessels. The seabird data is valuable for several reasons: 1) information on seabird/mammal distribution and abundance provides an upper trophic level perspective which complements the hydrographic and lower trophic-level (plankton) data collected by others, 2) estimates of seabird/mammal distribution and abundance contributes to understanding the spatial ecology of these regions, and 3) by extending our existing records (May 1987-present off southern CA; May 1996-present off central-northern CA), these data contribute to understanding the effects of natural and anthropogenic climate variability on the southern and central sectors of the California Current ecosystem. Survey data reports are available upon request. The project is supported by Southern California Coastal Ocean Observing System and the California Current Ecosystem Long-Term Ecological Research project.

History and Future of Coastal Upwelling Modes and Biological Responses in the California Current


Climate variability on multiple temporal scales is increasingly recognized as a major factor influencing the structure, functioning, and productivity of the California Current Ecosystem (CCE). Despite many long-term and integrative studies, a detailed understanding of climatic impacts on upwelling and biological processes is still lacking, compromising our ability to assess important concepts such as ecosystem "health" and "resilience". In this project sponsored by the National Science Foundation Biological Oceanography program, we are testing the hypothesis that seasonal upwelling modes are forced by contrasting atmospheric-oceanographic processes, exhibit different patterns of low- and high-frequency variability, and will be differentially impacted by global climate change, with corresponding impacts on biology. To address this hypothesis we are taking a three-tiered approach focusing on the past, present and future of upwelling in the CCE. First, for the past, tree-ring data co-varies with fish growth and seabird reproductive success and all are similarly sensitive to a driver of winter upwelling, the Northern Oscillation Index (NOI). Therefore, we have used tree rings to reconstruct winter climate variability. Our reconstruction indicates that variability in upwelling has increased over the instrumental record, but nonetheless remains within the range of natural variability (Black et al. submitted to Nature Geosciences; Bryan Black, University of Texas).

Second, for the present, we examined the responses of a suite of species to seasonal modes of upwelling, including Pacific sardine (recruitment), black rockfish (growth), rhinoceros auklet and Brandt's cormorant (survival), and coho salmon (survival). To conduct this work, we integrated winds and temperatures from local buoy data to better capture climate variability on finer timescales than we had in the past (Garcia-Reyes et al. 2013). Third, for the future, we are investigating seasonal upwelling modes in relation to various climate-change scenarios using IPCC-class global climate models (GCM; Ryan Rykaczewski, University of South Carolina, Program for Climate Model Diagnosis and Intercomparison).

Overall, this study is of significance as it will reveal the past variability, current causal forces, and potential future changes in upwelling as well as its biological consequences in the California Current. In addition to the basic intellectual merits of our study, we have contributed results to state, national, and international policy-makers, including the IPCC's Assessment Report 5 (AR5), Chapter 30.

Importance of Wintertime Upwelling to Ecosystem Dynamics in the California Current


Krill Habitat Climate change is expected to alter the amplitude and timing of upwelling. This project, related to the Match-Mismatch Project, focused on investigating how upwelling during the winter months "pre-conditions" the ecosystem which then can lead to either productive or unproductive years for fish (rockfish, salmon) and seabirds. In this interdisciplinary project, we coupled research on wintertime upwelling and physical oceanography with biological indicators of productivity to provide a holistic ecosystem perspective. Supported by NOAA's Fisheries and the Environment Program and the National Science Foundation Biological Oceanography Program, this was a collaborative effort of Farallon Institute, Oregon State University (Dr. Bryan Black, previous position), NOAA's Northwest Fisheries Science Center, and the Environmental Research Division of NOAA. Scientists will integrate this information with rockfish stock assessments and developing Integrated Ecosystem Assessments (see below).

Seabirds and Climate Change


In a new project with collaborators from Pacific Rim Conservation and Oregon State University, supported by Region 1 of the U.S. Fish and Wildlife Service, scientists from Farallon Institute will prepare an update of the Pacific Region Seabird Conservation Plan to address the effects of climate change on Pacific seabird species. This update will provide a synthesis of available information on existing and potential effects of climate change on seabirds and seabird habitats, such as impacts of sea level rise, changes in air and sea temperature, changes in circulation and currents and upwelling, and seabird food webs for the California Current System (Washington, Oregon, and California) and Hawaii and the U.S. Pacific Islands. Sections will include: (1) a review Global and Regional Climate Models (GCM and RCM) for possible application to the USFWS regions of interest, (2) an overview of observed trends in relevant climatic (atmospheric and oceanographic) parameters, (3) a chapter on observed or probable responses of California Current System seabirds, (4) a chapter on observed or probable responses of Hawaii/U.S. Pacific Islands seabirds, and (5) recommended management actions to mitigate climate change impacts for 58 species listed in the original conservation plan. The draft report will be completed by 31 March 2011.

Tackling Ecological Complexity and Climate Change: Matches and Mismatches in the Seasonal Cycle of California’s Marine Flora and Fauna


Climate change may change the timing of annual events in species' life cycles, such as the egg-laying dates of seabirds or spawning dates of fish, but there is no reason to assume that species of different trophic levels will change at the same rate. Different responses in timing could lead to uncoupling of predator-prey trophic relationships. Farallon Institute scientists hypothesized that this could explain recent reproductive failures of seabirds and poor recruitment of fish (salmon) in central-northern California during 2005-2007. This collaborative, interdisciplinary project funded by the California Ocean Protection Council and California Sea Grant includes researchers from NOAA's Environmental Research Division (Drs. Steven Bograd and Isaac Schroeder), Southwest Fisheries Science Center (Drs. Steven Ralston, Brian Wells, and John Field), Oregon State University Hatfield Marine Science Center (Dr. Robert Suryan), UC Berkeley (Drs. Zack Powell and Jeff Dorman), and Old Dominion University (Dr. Chester Grosch). As part of this project, Dorman and Powell developed a novel model on the oceanographic factors affecting the abundance and availability of the euphausiid Euphausia pacifica. With NOAA-NMFS fisheries scientists, Dr. Jarrod Santora led studies of krill-krill predator spatial organization and spatial "match or mismatch". Peer-reviewed publications resulting from this effort include Bograd et al. 2009 (phenology of upwelling along the U.S. west coast), Schroeder et al. 2009 (relationships between winds, ocean temperatures, and seabird timing of breeding and productivity), and Sydeman et al. 2009 (synthesis of seabird responses to climate change in the California Current).

An Integrated Ecosystem Assessment (IEA) for the California Current


With support from the U.S. Integrated Ocean Observing System (IOOS), and in collaboration with NOAA-ERD and a plethora of other marine scientists along the west coast of the U.S., Canada, and Mexico, we developed Integrated Ecosystem Assessments (IEA) for the California Current Ecosystem (CCE). Products to date include Module 1: Select Time Series of Ecosystem State, Module 2: Climate, Trends and Variability in System State, and The Integrated Marine Ecological Database (IMED).

What is an IEA?

An Integrated Ecosystem Assessment (IEA) is a dynamic, decision-support tool for management of living marine resources. Our specific objectives include: (1) to compile data sets representative of key ecosystem processes and outcomes from climate (e.g., physical oceanography, atmospheric, and weather) to patterns and statistics of human use, (2) to evaluate data time series and provide suites of key indicators of ecosystem state (status), and propose reference levels for safe and for desired states of the ecosystem, (3) to integrate and synthesize time series data to link important ecological outcomes to changes from climate and human use drivers (i.e., forecasting), (4) to report on current conditions and trends in key indicators of physical, biological and human uses, (5) to forecast relationships between state indicators and pressure indicators to inform management.

Module 1: Select Time Series of Ecosystem State

In Module 1, we present records (time-series) of key biological organisms, describe these data in the context of recent and long-term changes in the ecosystem, identify apparent gaps in knowledge, and outline possible future directions for CCLME IEA development. We emphasize that this initial [biological indicator] approach to development of a CCLME IEA should be complemented by other approaches (e.g., ecosystem modeling) and that the indicators shown herein are not comprehensive. Nonetheless, we suggest that the species and parameters selected are useful for understanding the population biology of species of management concern, and are therefore of great value to state and federal authorities in the CCE.

Module 2: Climate, Trends and Variability in System State

In Module 2, we present a trend analysis on select physical and biological indicators of ecosystem state, including indicators of atmospheric, oceanographic and biological conditions. We evaluate the importance of these trends relative to the 2007 salmon stock collapses and fisheries closures throughout the CCLME. In this report, we will test the hypothesis that trends in physical and biological attributes of the California Current vary by latitude. This hypothesis has been examined by others, but not in a comprehensive "ecosystem-wide" manner. To test this hypothesis we have compiled 123 time series on atmospheric, oceanographic and biological conditions at various latitudes in the California Current, and have evaluated each series for trends in a measure of central tendency (mean) and variability (variance).

The Integrated Marine Ecological Database (IMED)

Data sets gathered and used in the IEA are stored in the IMED. This comprehensive database was originally called the California Current Integrated Ecological Database (CCIED). Click here for a poster describing the IMED and some of its uses.

Spatial Ecology And Planning

"Hotspots" of Productivity and Trophic Transfer in the Open Ocean


Understanding spatial variation in biological activities is critical to the ecosystem approach to management, especially for marine spatial planning. In this project we are using satellite remotely-sensed data on phytoplankton (proxied by chlorophyll-a concentrations) and shipboard acoustic surveys of zooplankton (krill) and visual observations on marine birds and mammals to test the hypothesis that "hotspots" of phytoplankton, krill, and consumers co-vary spatially in the California Current. We define "hotspots" based on the persistence of elevated values of chl-a, krill, and marine bird density in space and time. We are modeling chl-a and krill "hotspots" in relation to seafloor and coastal topographies and water mass characteristics, and contours of seabird densities in relation to krill and chl-a concentrations. Satellite imagery provides a holistic perspective on productivity in this large marine ecosystem which is not available by other means, yet provides key information on spatial variability in ecosystem properties of significance to upper trophic level species of management and conservation concern. Our ecosystem-wide analyses have revealed open ocean "hotspots" within the California Current that appear to be of special biological significance and warrant future research, monitoring, and possibly protection to maintain and/or enhance ecosystem functions, such as feeding interactions of top predators. This project has been supported by the Resources Legacy Fund Foundation, the Marisla Foundation, and NOAA's California Current IEA Program.

Modeling Krill Distribution and Abundance


Krill Habitat With respect to ecosystem-based management and protection (e.g., design of marine protected areas), it is important to understand, and if possible predict, the abundance and spatial distribution of key mid trophic level prey species. Krill are an integral component of the California Current Ecosystem (CCE) that support commercially valuable as well as protected species. It has been postulated that krill have affinities for particular bathymetric and hydrographic habitats (i.e. canyons, isobaths, fronts), but it is unclear how these factors collectively influence krill aggregations. We surveyed the spatial distribution of krill using hydroacoustics in central-northern California and modeled their distribution in relation to bathymetric slope, distance from shelf break/canyon heads and fronts, phytoplankton/chl-a concentrations, and sea-surface height anomalies (eddy structures) using a Regional Ocean Modeling System (ROMS) coupled to an ecosystem model (CoSINE; Ocean Modeling Group, Santora et al. 2013), as well as an Individual-Based Model (IBM) parameterized for Euphausia pacifica (Dorman et al. 2005). The model also outputs spatially-explicit distributions and can be used to understand "hotspot" formation. This project has been supported by the NASA ROSES program and California Sea Grant.

Ecosystem Approach To Fisheries

The North Coast Program


The North Coast Program is designed to measure and assess physical, chemical, and biological oceanographic properties as well as ecosystem and food web conditions known to affect salmonid survival at sea. To cover the extensive marine habitats of northern California salmonids, bi-monthly small vessel sampling of plankton on four transects, from Bodega Bay in the south to Newport, Oregon in the north, will be used to quantify food web variability and change. Sampling will include:

Surveys of prey patches of euphausiid crustaceans and forage fish will be coordinated (at great cost savings) with ongoing surveys in the region, particularly the NOAA-NMFS-SWFSC Juvenile Rockfish Ecosystem Survey and California Current Ecosystem/Pacific Coast Ocean Observing System (PaCOOS) surveys (NOAA-NMFS-NWFSC). These surveys are planned in perpetuity and provide platforms for obtaining information that would be difficult and prohibitively expensive to obtain directly as part of the line-based sampling.

To measure ocean climate and place ecosystem (food web) observations and considerations in an oceanographic context, a variety of sampling techniques will be used including remote sensing (from satellites and the State’s HF radar coastal currents mapping system), mooring data, and new technology.

A cost-effective and scientific enhancement to hydrographic sampling on the survey lines will be the use of Spray Gliders. This new technology will allow for measurements of the water column (temperature, salinity, and a proxy for primary productivity) in all weather conditions and to sample salmon habitat between survey lines. This will facilitate rigorous computations to be made of environment changes (e.g., ocean warming, upwelling, stratification, mixed layer depth) that are known to affect the ecosystem and salmonid food webs.

Comprehensive California Current Forage Fish Management Program


Recently, studies have indicated that reductions in forage fish fisheries worldwide are required to recover and sustain marine predator (e.g., seabird, marine mammal) populations. Moreover, delineation of ecologically important areas to protect predator trophic (feeding) interactions is needed for effective management of forage fish on appropriate scales. To conserve the forage fish community in the California Current Ecosystem (CCE), key scientific challenges include the need to quantify and implement spatially-explicit regional thresholds for forage fish fisheries. In this project we are tackling this important, yet heretofore unstudied aspect of forage fish conservation in this ecosystem. Given the diversity of predator species in the CCS, this is a substantial undertaking. Fortunately, much of the data needed to produce these models exists, yet just needs to be collated, processed, and analyzed. Once these models are developed, we will conduct targeted outreach to fisheries managers to both demonstrate the quality of the information as well as suggest how to apply model results in a practical fashion. In this manner we will integrate results into fisheries management strategies and tactical decisions such as harvest-control rules designed to protect ecosystem functions.

In this 24-month project we will undertake multiple interrelated tasks, including: (1) develop prey resource thresholds that significantly affect predator performance from numerical response modeling, (2) derive predator consumption estimates of prey from bio-energetic, 3) delineate ecologically important areas (EIA) for principal forage species and dependent predators , (4) quantify predator forage needs via model synthesis, and (5) disseminate predator needs products to fisheries scientists and managers. Our quantitative syntheses of predator needs will be able to fit directly into existing harvest control rules (e.g., sardine) as well as shape management of emerging fisheries. Spatially-explicit products will serve to further the implementation of marine spatial management. Outreach to federal governing agencies will include the National Marine Fisheries Service and Pacific Fisheries Management Council; state agencies include California, Oregon and Washington Departments of Fish and Wildlife, and the California Fish and Game Commission. This project is supported by the National Fish and Wildlife Foundation, Pew Charitable Trusts, and Marisla Foundation.

Utilizing Ecosystem Information to Improve the Decision Support System for Central California Salmon


Conventional wisdom once suggested that ecological conditions in the riverine environments that support salmon spawning determine variability in population abundance at return. More recently, however, it has been recognized and widely accepted that the ocean plays a critical role in determining salmon returns and fisheries catch (Mantua et al. 1997). In particular, the abundance of food (e.g., zooplankton) during the initial months of ocean life, when the salmon are small and most susceptible to predation, affects the at-sea survival of salmon as they first migrate to the sea and ultimately changes in populations years later when cohorts return to spawn. In this new project, supported by NASA-ROSES, we will integrate numerical and empirical-statistical modeling approaches (Wells et al. 2008) to enhance our knowledge of salmon survival at sea and improve abilities to forecast salmon population dynamics. The poor returns of Sacramento River fall run chinook salmon in 2007 and 2008, and resulting fisheries closures in 2008-present can be related to a period of anomalous ocean conditions in the California Current which began in 2004 and continued at least through 2006 (Wells et al. 2012).

Seabird Conservation

Alcatraz Island Seabird Monitoring


La Isla de los Alcatraces, "Island of Pelicans", dubbed by Juan Manuel de Ayala in 1775 for the abundance of pelicaniforms and other seabirds, is a regionally important breeding site for seabirds on the West Coast of North America. In conjunction with the National Park Service Golden Gate National Recreation Area, we have studied the populations and productivity of seabirds on Alcatraz Island since the early 1990s (Saenz et al. 2006). Potential disturbance to breeding birds is of concern because Alcatraz is the most heavily-visited tourist destination in northern California, with well over one million visitors annually. Moreover, given its proximity to San Francisco, various activities including firework displays and the America's Cup sailboat racing may cause disturbance to the birds. Field studies focus on the breeding ecology of Brandt's cormorant and western gull. Data reports are available upon request.

Ocean Energy Development

Sonoma County Hydrokinetic Energy Project


The Sonoma County Water Agency received permits from the Federal Energy Regulatory Commission (FERC) to further explore wave energy develop in coastal waters off Sonoma County. Farallon Institute scientists are serving on an advisory panel to help ensure ecological integrity of coastal habitats potentially affected by these activities.

Potential Socio-economic and Environmental Effects of Developing Wave Energy in Coastal California


Along the west coast of the United States, wave energy technology development is proceeding. In California, with support from the California Energy Commission, California Ocean Protection Council, and California Coastal Conservancy, scientists from H.T. Harvey and Associates (lead organization), Farallon Institute, UC Santa Cruz, Bodega Marine Lab, and Humboldt State University evaluated potential ecological and socio-economic impacts of wave energy development on the environment and coastal communities. The final report suggests important ecological considerations to the development and implementation of wave energy "parks".