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Open Access Publications from the University of California


NOAA’s California Sea Grant College Program is a statewide, multi-university program of marine research, extension services, and education activities administered by Scripps Institution of Oceanography at the University of California, San Diego. It is one of 32 Sea Grant programs and is part of the National Oceanic and Atmospheric Administration (NOAA), U.S. Department of Commerce. Visit our website ( to sign up for email announcements or follow us on Facebook or Twitter.

California Sea Grant College Program

There are 689 publications in this collection, published between 1974 and 2018.
Research Summaries (162)

A Mechanistic Model to Evaluate and Improve Riparian Restoration Success

In California’s Central Valley, freshwater diversions and land development have greatly reduced the extent and sustainability of native cottonwood and willow riparian forests, which provide critical habitats for many species of wildlife and offer other environmental benefits such as slowing erosion, maintaining soil quality and filtering pollutants.

The cumulative result of human activity in the region over the last century and a half has been the loss of about 90 percent of all riparian forests. Efforts are underway to protect and restore remaining forested areas, which are often fragmented and vulnerable to replacement by less ecologically beneficial vegetation.

  • 2 supplemental PDFs

Calcium Requirements and the Spread of Zebra Mussels

Zebra mussels (Dreissena polymorpha) are pistachio-sized freshwater bivalves native to the regions around the Black and Caspian seas. Since their discovery in Lake St. Clair, Michigan, in the late 1980s, they have spread distressingly fast through the Great Lakes and Mississippi River basin, as well as to other lakes and rivers in the eastern United States and Canada.

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Research Final Reports (161)

Post-invasion Genetic Structure of European Green Crab Populations on the US West Coast and Its Implications for Their Control

One of the most ecologically significant invaders in the coastal waters of the the European green crab, Carcinus maenas. It is a voracious, generalist predator in its native range in Europe as well as invaded regions which include including South Africa, Australia, Japan, and both coasts of North America (reviewed in Grosholz and Ruiz 1995, Cohen et al. 1995, Geller et al. 1997). Previous work in its native range and in the eastern U.S. has provided much evidence for its strong control over the abundance of benthic organisms in soft sediment communities (e.g. Ropes 1968, Reise 1977, 1985, Morgan et al. 1980, Jensen and Jensen 1985, Tettlebach 1986). Furthermore, work in Bodega Bay Harbor, CA has documented significant changes in the local food web as the direct result of green crab predation: Grosholz et al (2000) found 5- to 10-fold declines in the abundances of previously abundant invertebrate taxa. Lafferty & Kuris (1996) estimated that the annual net value of crab, mussel, oyster, and bait harvests threatened by green crabs in Western North America (WNA) is $43.7 million.

Heterogeneous Preferences for Water Quality: A Finite Mixture Model of Beach Recreation in Southern California

This paper uses a finite mixture logit (FML) model to investigate the heterogeneity of preferences of beach users for water quality at beaches in Southern California. The results are compared with conventional approaches based conditional logit (CL) and random parameters logit (RPL). The FML approach captures variation in preferences by modeling individual recreator preferences as a mixture of several distinct preference groups, where group membership is a function of individual characteristic and seasonal variables. The FML parameter estimates are used to calculate welfare measures for improvements in beach quality through a reduction of water pollution. These bound the traditional CL and RPL mean welfare estimates, and have the advantage of highlighting the distribution of the population sample's preferences. The data indicate the existence of four representative preference groups. As a result, willingness to pay measures for improvements in water quality can be weighted across individuals to calculate the distribution of individual welfare measures.

One of the groups is people who go to the beach with small children. An interesting finding is that these people have a lower mean WTP for improving water quality than people who go without a small child. This may well be an example of cognitive dissonance: parents find they go to the beach more often than others who don't have small children, since that keeps the children occupied and happy, and they adapt their perception of the water quality to be consistent with their behavior.

Previous environmental and resource economic applications of the FML have been limited to applications with small choice sets (6) and group membership variables (4). This paper extends the FML model through the estimation of a large (51) choice set with 9 membership variables. This application is the first to incorporate seasonal variables into the group membership function to capture seasonal heterogeneity.

Effects of Freshwater Flow and Population Connectivity on Benthic Community Dynamics in the San Francisco Estuary

Climate change and water diversions have greatly modified freshwater outflow into the San Francisco Estuary, changing the Estuary’s salinity regime. These climate- and water diversion-driven changes in salinities may have a wide range of impacts on important components of the San Francisco Estuary including the distribution of threatened/endangered species, the success of habitat restoration and the management of invasive species.  Previous work has shown significant variation in the recruitment and survival of numerous species throughout the Estuary linked to freshwater outflow levels.

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Research Theses and Dissertations (321)

Biomolecular Interactions Using Machine Learning

This thesis explores the automatic prediction of biomolecular interactions using machine learning. The overriding philosophy motivating these investigations is to model the interactions between biomolecules (proteins and small-molecule ligands) using simple features to represent characteristics that are hypothesized to contribute to binding.

For these investigations, I use "support vector" learning to build discrimination functions that separate input features into classes, resulting in a hypothesis as to whether or not (or how strongly) the biomolecules will interact. These discrimination functions are based on training data sets of known interactions.

Individual chapters of the thesis center on different investigations which predict protein-protein interactions in a multi-species database, within a single organism and across species. A final study focuses on the prediction of binding free energy between a receptor and ligand.

An important contribution made by this research is the demonstration that no explicit information about three-dimensional protein structure is necessary to make pre­dictions of protein interactions. This implies that researchers may proceed directly from sequence to inference of protein function, as represented by the context of its interaction with other biomolecules.

Assessing Trophic Ecology and Nutritional Status of Marine Mammals with Bulk and Compound-Specific Amino Acid Isotope Analysis

Compound-specific isotope (CSI) analysis is rapidly growing tool in the field of ecology to assess the trophic position and foraging behavior of an animal. Only a handful of studies have examined the values and patterns of carbon and nitrogen amino acid isotopes ( δ 13C-AA and δ 15N-AA), and have primarily been done on plankton and other low trophic position organisms. Since AA data separate into unique biochemical groupings, much more detailed information is revealed than the widely used bulk isotope technique - such as source of diet (offshore vs. coastal), base of the food web, trophic positions, and an animals physiology. To examine the usefulness and power of the CSI method, we tested how  δ 13C-AA and  δ 15N-AA patterns and values appear in several populations of harbor seals (Phoca vitulina) off the California coast, primarily comparing seals from San Francisco Bay (SFB) and the Channel Islands (CI).

In Chapter 1, we compared bulk isotopes in captive seals from The Marine Mammal Center to wild seal populations. Our results indicated similar trophic transfer δ 15N values between predator and prey compared to other organisms. It concluded that weaner seals (< 1 year) from SFB and CI had recently weaned from their mother's milk, and were transitioning to a diet offish and invertebrates. Chapter 2 was the very first CSI study δ 15N-AA on marine mammals, where we examined the 'trophic' and 'source' AA grouping differences in captive seals. A smaller trophic enrichment factor (TEF) was shown compared to past studies on plankton. We hypothesize this is attributed to an animal's main form of nitrogen excretion (ammonia vs. urea), where urea-excreting animals exhibit this lower TEF value. Thus, we propose using a new multi-TEF trophic position equation to estimate the foraging ecology of wild harbor seals (Chapter 3). This equation provides more accurate predictions, suggesting they consume prey around 2.5 to 3 trophic positions. The coupled δ 13C-AA and δ15N-AA data suggest SFB yearlings (1–2 years) are nutritionally stressed, as they show higher than expected trophic position estimations. While seals in CI are consuming different types of prey (offshore vs. nearshore), but at expected trophic positions.

The population dynamics of mitten crab larvae in the San Francisco Bay

The Chinese mitten crab, Eriocheir sinensis, has a history of invasions in numerous countries. In 1992, the Chinese mitten crab was introduced to the San Francisco Bay/Delta system. Since its invasion in the San Francisco Bay, it has become an aquatic nuisance species. Little is known about the population dynamics of the megalopa stage of the Chinese mitten crab in the San Francisco Bay estuary, particularly the megalopa stage. Light traps are often used to sample marine larvae and can provide measures for relative abundance of larvae between sampling locations. As part of an ongoing study to monitor mitten crab larvae in the San Francisco Bay, light trap and plankton tow samples were analyzed formitten crab megalopae and zoeae. In order to implement low cost sampling devices for mitten crab megalopae such as light traps, it is necessary to be able to identify their larvae in collected samples. Thus, the main objective of this work was to develop a means to distinguish mitten crab megalopae from other native and invasive brachyuran megalopae inhabiting the San Francisco Bay Estuary. The minimal amount of mitten crab megalopae found in light trap samples may be linked to the recent decline of mitten crab zoeae in San Pablo Bay.

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Extension Publications (39)

California’s North Coast Fishing Communities Historical Perspective and Recent Trends: Crescent City Fishing Community Profile

This profile of the Crescent City fishing community describes the history of the area and its fisheries, present-day fishery operations, activities and associated infrastructure. It identifies key regulatory and economic factors highlighted by study participants that interact with and affect the local fishing community. It is intended for use in a range of processes, from local planning and education to state and regional management.

Human dimensions perspectives on the impacts of coastal zone marine renewable energy

Climate change and soaring energy costs have fueled attention to renewable energy. In coastal areas, the potential to harness the clean power of offshore wind, wave, and tide is irresistible. Our extensive coasts and oceans offer what appears at first glance to be virgin territory for development of energy producing facilities. A closer look,however, reveals that these areas are teeming with productive activity, activity that cannot be ignored in planning and implementing marine renewable energy (MRE) development and production.

Movements of subadult prickly sharks Echinorhinus cookei in the Monterey Canyon

The prickly shark Echinorhinus cookei is a poorly known predatory shark that occurs in the Monterey Canyon, USA. Between March 2005 and September 2006, 15 subadult prickly sharks (170 to 270 cm total length) were tagged with acoustic transmitters and tracked to determine their site fidelity, home range, habitat use, rates of movement, and diel activity. An array of moored receivers extending 3.5 km offshore from the apex of the Monterey Canyon recorded the occurrence of 8 sharks tagged with coded transmitters for 400 to 561 d. Four sharks were tagged with continuous transmitters and monitored by a moored receiver that recorded date, time, and depth for 123 to 212 d. Three sharks were tagged with archival transmitters that were monitored by a 2-way communicating moored receiver. One female and 2 males tagged with continuous transmitters were also tracked manually from a surface vessel for 61.0, 51.8 and 62.8 h, respectively, over a period of 64 to 71 d. Home ranges for these sharks were 0.20, 2.20, and 1.46 km2. All tagged sharks showed a high degree of site fidelity to the study area and demonstrated pronounced diel movements, moving along the axis of the canyon offshore to discrete areas during the day and inshore at night. Sharks were sedentary during the day and actively swam in the water column at night and were most active during crepuscular and nighttime periods.

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Conference Proceedings (5)

International Caulerpa taxifolia Conference Proceedings

Among the many invasions that have stressed coastal marine systems in recent years, none have had such broad-reaching biological and political impacts as the Caulerpa taxifolia invasions of the Mediterranean Sea, Australia, and the United States. From its initial invasion of the northwest Mediterranean in 1984, to its discovery in Agua Hedionda Lagoon and Huntington Harbour in the summer of 2000 in California, this invasive alga has produced dramatic changes both in the biological landscape of coastal bays and estuaries and the political landscape of invasive species management.

Ocean Acidification Impacts on Shellfish Workshop: Findings and Recommendations

For at least the past six years, the West Coast Shellfish industry has observed larval mortality in hatcheries and poor larval recruitment success for some species in the wild, especially during periods of high upwelling. One hypothesis is that these dramatic declines in productivity may be related to increasing ocean acidity and the corresponding decrease in the saturation state of carbonate minerals which shellfish use to create their shells. The West Coast shellfish industry sought help from scientists to explore the causes of the shellfish losses, what role ocean acidification and other factors might be playing, and how to adapt to sustain West Coast shellfish resources. Addressing questions about ocean acidification requires integration of ocean observing measurements, laboratory exposure studies, shellfish recruitment and production data, and field studies of organism performance in relation to ocean conditions. However, these data are collected by different sectors that, to date, have had limited interaction. To stimulate collaborations among these sectors, and at the request of the shellfish farming and wild harvest communities, the Integrated Ocean Observing Systems, California Sea Grant, USC Sea Grant, Oregon Sea Grant, Washington Sea Grant, and California Ocean Science Trust convened a workshop. Fifty‐one participants were invited, including state and federal managers, industry representatives, and leading academic researchers and oceanographers with expertise in larval recruitment, laboratory studies, and ocean chemistry.

Current Perspectives on the Physical and Biological Processes of Humboldt Bay

The Humboldt Bay Stewards hosted a one-day public symposium titled, “Current Perspectives on the Physical and Biological Processes of Humboldt Bay,” on March 15, 2004. The purpose of the symposium was to ex- amine biological and physical processes to gain a better understanding of Humboldt Bay. The need for the symposium was clear, as there were many plans, projects and studies ongoing at the time.

The symposium included 19 presentations and a panel discussion. Ten of the presentations are included as papers or in the appendices as a report or plan. A major topic addressed in several papers was sediment sources and transport. Sediment was addressed historically (Tuttle), oceanographically (Crawford and Claasen), in the watershed (Barrett), relative to eelgrass (Shaughnessy et al.), fouling communities (Boyle et al.), and management (Davenport). Though Davenport did not submit a paper on the California Sediment Management Plan, Appendix A includes a copy of this important and innovative plan that was completed in 2006.

Other management topics included an overview of the Humboldt Bay Management Plan. From the biological perspective, papers are included on marine invasive species, eelgrass, fish and fouling communities. Worldwide, increasing attention is directed towards aquatic invasive species and their impacts on biodiver- sity and ecosystems.

The presentation on invasive species at this symposium showed their occurrence around Humboldt Bay. The purpose of the study was to provide reliable baseline information for further studies and monitoring. The “Non-indigenous Marine Species of Humboldt Bay, California” is included in Appendix II. This study was part of a program funded by the California Department of Fish and Game that included most of the bays and estuaries in California. The innovative fish habitat paper, (Gleason et al.) uses a novel GIS approach to the study of Humboldt Bay fishes. Eelgrass provides a major habitat in Humboldt Bay. Summarizing what we know, don’t know and need to know about Humboldt Bay eelgrass provides a fruitful source of many possible studies. Fouling com- munities have not been previously studied in Humboldt Bay. The study presented here is the beginning of a long-term project that we can expect to hear more about at future symposia.

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Other Recent Work (1)

Living Shorelines & Resilience in Southern California: A Summary of a Series of Workshops held as part of The Resilient Coastlines Project of Greater San Diego

In 2016, a series of workshops were held to discuss living shorelines in Southern

California. The workshops specifically focused on the unique benefits, challenges and

opportunities for implementing living shorelines in the region, and the nexus between

nature-based solutions and ongoing local adaptation planning. Approximately 140

participants partook in these dialogues, and some of the key themes that emerged


 Letting nature do the work for you

 Designing for the future

 Integrating nature into shoreline management projects

 Project goals distinguishing living shorelines

 Engineering and urban living shorelines

 Space constraints along urban coastlines

 Permitting pathways to support demonstration projects

 Living shorelines and phased sea level rise planning

 Designing with watersheds and sediment management in mind

 Exploring emerging commercial opportunities

 Public access and project success

 Planning for living shorelines alongside the community

 Sharing monitoring and best practices to ensure future success

 Citizen science and socio-ecological monitoring

The workshops provided the first ever opportunity for Southern California stakeholders

to outline what is unique about designing living shorelines in the context of Southern

California shorelines for state and federal entities.