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Open Access Publications from the University of California

Coastal Environmental Quality Initiative

The University of California Marine Council (UCMC) was established to provide leadership and direction to the University in the coordination of marine policy, research, education and public service and the exercise of responsible stewardship of the state's marine resources.

In 2000, the Marine Council was successful in developing an Initiative on California Coastal Environmental Quality that was funded by the state legislature at $1.5 million annually. This program is administered jointly by the Marine Council and the Office of the President, and through a close interaction with the State Resources Agency, has developed a set of priorities and a process for reviewing and funding research proposals focused on California's coastal ocean issues and problems. The objective is to address California's coastal issues in ways that will not only contribute to increasing our scientific understanding of both natural processes and human-induced changes, but that are also useful to legislators, public policy makers and managers who must make the decisions required for the long-term sustained health of California's ocean.

Cover page of Pinniped ecology in Santa Monica Bay, California

Pinniped ecology in Santa Monica Bay, California


We investigated pinniped ecology at sea in Santa Monica Bay, California. Animals were studied during 277 boat-based surveys conducted in 1997-2007 documenting that California sea lion Zalophus californianus was the most observed species (89%, n sightings = 1393), followed by harbor seal (Phoca vitulina richardsi: 8%, n sightings = 131), and northern elephant seal (Mirounga angustirostris: 1%, n sightings = 15). Sea lions, and occasionally harbor seals, were found in aggregations with bottlenose dolphins Tursiops truncatis in 29% of the sightings (n bottlenose dolphin sightings = 205), short-beaked common dolphins Delphinus delphis and long-beaked common dolphins D. capensis in 53% of the sightings (n common dolphins = 155). Sea lions and harbor seals were regularly observed in coastal waters (shore) but also in the entire bay, with both species showing a preference for submarine canyons. Northern elephant seals were only seen in offshore waters and mostly in proximity of the canyons. The three species were frequently observed traveling (50%, n = 728), thermoregulating (14%, n = 205), and feeding (3.2%, n = 47) but rarely socializing (.21%, n = 3). This is the first long-term study on at-sea distribution, occurrence, frequency and behavior of pinnipeds in Santa Monica Bay [Acta Zoologica Sinica 54 (1): 1-11, 2008].

Cover page of Dolphins and African apes: comparisons of sympatric socio-ecology

Dolphins and African apes: comparisons of sympatric socio-ecology


Dolphins and African apes are distantly related mammalian taxa that exhibit striking convergences in their socioecology. In both cetaceans and African apes, two or more closely related species sometimes occur in sympatry. However, detailed reviews of the ways in which sympatric associations of dolphins and apes are similar have not been done. As fi eld studies of dolphins and apes have accumulated, comparisons of how the two groups avoid direct food competition when in sympatry have become possible. In this paper we review sympatric ecology among dolphins and African apes, and examine convergences in species-associations in each taxa. We review evidence for hypotheses that seek to explain avoidance of food competition, and consider whether ape-dolphin similarities in this area may be related to the way in which social groups in both taxa optimally exploit their food resources.

Cover page of Contribution of Iron-Reducing Bacteria to Mercury Methylation in Marine Sediments

Contribution of Iron-Reducing Bacteria to Mercury Methylation in Marine Sediments


Mercury is a toxic that was mined in California’s Coast Range, and then used in the Sierra Nevada foothills for extraction of gold. Weathering of abandoned waste rock piles and mines, plus erosion of contaminated microorganisms, transform it into a more toxic form, methyl-mercury. This enters food chains where it bioaccumulates to concentrations that can cause impaired neurological function in a variety of higher organisms (fish, birds, humans). This toxic conversion has, in the scientific literature, been quite dogmatically attributed to activities of sulfate-reducing bacteria. Importantly, recent unpublished results from our laboratory with freshwater sediments show that iron-reducing bacteria can also convert inorganic mercury into methyl mercury, and do so at rates equivalent to those of sulfate-reducing bacteria. Due to California’s high concentration of iron in coastal sediments, we propose to test the hypothesis that iron-reducing bacteria also contribute significantly to the overall production of methyl mercury in marine sediments. We will do this by exploring the linkage between methyl mercury production and the activity of iron-reducing bacteria. In mercury-contaminated marine sediments, we will measure rates of methyl mercury production along with signature activities of different bacterial metabolic types, i.e. sulfate reduction and iron reduction. A second approach involves culturing evolutionarily diverse iron-reducing bacteria from contaminated marine sediments to compare (vs. sulfate-reducers) their relative abilities to methylate mercury. Understanding, based on potential in pure cultures and activities in contaminated sediments, which bacterial types contribute significantly to mercury methylation in coastal sediments will aid in modeling of marine methyl mercury problems, and in creating remediation strategies for impacted sites. This project also has implications for certain commercial fisheries that are impacted by bioaccumulation of methyl mercury.

Cover page of Speciation and Genetic Structure in a Marine Fish with an Extended Pelagic Larval Phase: an Analysis of Both the Juvenile and Adult Populations of Blue Rockfish (Sebastes Mystinus)

Speciation and Genetic Structure in a Marine Fish with an Extended Pelagic Larval Phase: an Analysis of Both the Juvenile and Adult Populations of Blue Rockfish (Sebastes Mystinus)


Several species of rockfish currently suffer from overfishing in California and remediation is required to replenish depleted stocks. Due to precipitous declines in several species, it is clear that both managers and research must focus on clarifying population dynamics and spatial connectivity of rockfish populations. All aspects of fisheries management, including ecosystem-based fisheries management tools, require knowledge of the spatial scale of genetic exchange or movement of individuals among populations and degree to which this renders stocks self-replenishing. Population genetics is one of few tools available that directly measures levels of connectivity among marine populations. My dissertation research examines genetic patterns and consequences of larval dispersal for two species of exploited rockfishes, blue and kelp rockfish, both of which inhabit nearshore rocky reefs and kelp forests along the California coast and are targeted by nearshore commercial live-fish and recreational fisheries. My goal is to characterize the effect of pelagic duration on the genetic structure of adults and of settling juveniles, and to analyze whether juveniles from different year-classes have similar patterns of genetic structure. I am using several microsatellite loci to analyze the population structure of young-of-the-year and adult rockfish. The high level of polymorphism inherent in microsatellite loci will provide a sensitive tool for finding subtle differences within and among adult samples and settling juveniles. By simultaneously describing the genetic structure of both juvenile year-classes and adult populations, this study will reveal much more about movement of larvae and constraints on reproductive output of adult populations than previous studies that have examined either larvae or adults alone. My dissertation research is designed to address critical questions on connectivity of rockfish in the coastal marine ecosystem, such that the results of this work can be directly applied to the management and conservation of exploited rockfish species.

Cover page of California Sea Lions Use Dolphins to Locate Food

California Sea Lions Use Dolphins to Locate Food


Aggregations by 3 species of dolphins (the bottlenose dolphin [Tursiops truncatus], the short-beaked common dolphin [Delphinus delphis], and the long-beaked common dolphin [Delphinus capensis]) and California sea lions (Zalophus californianus) were investigated in Santa Monica Bay, California. Groups were followed and observed during 201 boat-based surveys conducted in 1997–2001 documenting that sea lions were aggregated in 18.6% of the sightings with bottlenose dolphins (150 bottlenose dolphin sightings) and in 45.9% of the sightings with 1 of the 2 species of common dolphins (98 common dolphin sightings). Aggregations of bottlenose dolphins and sea lions were observed in inshore (,500 m from shore) and offshore (.500 m) waters, whereas common dolphins and sea lions were observed only in offshore waters. These aggregations were often recorded feeding near escarpments and submarine canyons, showing a striking preference for these bathymetric features. The results show that sea lions spend a significant amount of time following dolphins, sea lions initiate aggregation and departure from dolphin schools, these aggregations occur more often than is expected by chance, and no aggressive behavior between sea lions and dolphins was ever observed at or near the surface. I argue that sea lions may take advantage of the superior food-locating abilities of dolphins. This paper provides the 1st detailed description of mixed-species aggregations and habitat usage by 3 dolphin species and sea lions.

Cover page of Environmental Monitoring and Assessment of Environmental Estrogens in Marine

Environmental Monitoring and Assessment of Environmental Estrogens in Marine


Unregulated organic compounds (aka Pharmaceuticals and the active ingredients in personal care products) have recently been detected in surface and drinking waters throughout the United States. The most biologically potent compounds in this group of compounds are the estrogenic steroids and other estrogen mimicking compounds that target the endocrine systems of fish and wildlife. Little is known about the concentrations or the effects of these compounds on marine fisheries in the United States. Preliminary studies from our laboratories in flatfish collected from Southern California have indicated potential endocrine disruption, as male fish were shown to have equivalent concentrations of blood egg yolk protein as those observed in female fish. The specific aims of this proposal are to identify the concentrations of likely active compounds, as well as potential uncharacterized compounds using a combined analytical chemistry and bioassay approach. The latter method will be used to guide analytical studies toward the identification of causative compounds. The ultimate goal is to target causative compounds and initiate a monitoring program for California which will be the first of its kind in the United States for the presence of these compounds in sediments surrounding marine wastewater treatment outfalls.

Cover page of Macrozooplankton Assemblages in California Fronts

Macrozooplankton Assemblages in California Fronts


Coastal fronts are zones of intense biological activity, often defined by a narrow band of flotsam resulting from the convergence of two water masses. The accumulation of zooplankton at fronts has been reported many times in the literature, and is assumed to be the result of passive advection acting on organisms that lack the ability to swim effectively against currents. However, literature on zooplankton swimming behavior,specifically that pertaining to diel vertical migration, demonstrates that certain plankton groups are capable of swimming well over one hundred meters per hour. High rates of primary production are known to occur at fronts, and any behavior by zooplankton that would enhance the movement to and subsequent maintenance in these food sources should be conserved. However, it is unclear whether or not zooplankton aggregations at fronts are controlled exclusively by physical factors, or if behavior plays any role. The focus of this project is to quantify zooplankton abundance and behavior in the vicinity of a seasonally persistent front in Monterey Bay, California. This research is approached in two separate but related studies. The first uses a high-definition digital video camera mounted on a remotely operated vehicle to conduct transects along the Monterey front to visually sample the abundance and swimming orientation of the sea nettle, Chrysaora fuscescens. From initial observations, we hypothesize that sea nettles may be actively swimming towards the front, conceivably to take advantage of the rich feeding opportunity. The second study will address the distribution of smaller zooplankton in the vicinity of the front in an attempt to assess whether or not behavior plays any role in determining the observed distribution. This will be achieved by comparing different groups of zooplankton, for which swimming speeds are known, to that of non-swimming stages, namely fish and invertebrate eggs. Any difference between the distributions of swimming and non-swimming stages should provide a first-order estimate of behavior. These studies will offer further information on the biological dynamics at these important feeding zones.

Cover page of Availability, usage and expected contribution of potential nursery habitats for the California halibut

Availability, usage and expected contribution of potential nursery habitats for the California halibut


Over the last several decades, human alterations have greatly changed the face of the California coastal zone, including the widespread loss of estuaries. The California halibut, Paralichthys californicus, is an ecologically and economically important finfish, and is known to depend upon inshore waters for nursery grounds. However, it remains poorly understood as to which specific habitat types (open coast, enclosed bays and estuaries, small lagoons) are most important as productive nursery grounds. In light of continued coastal change, information is needed on the relative importance of nursery habitat types for the proper implementation of marine reserves designed to protect the halibut.

The contribution of nursery habitat types will be determined using trace element analysis of California halibut otoliths (ear bones). These elements can be viewed as signatures that serve as a record of the environmental conditions experienced by fish over time and which differ across habitat types. Also, statistical analysis of long term CalCOFI data will be analyzed to examine how changes of coastal habitat types over time have affected the larval abundances and distributions of the halibut. To determine the level of connectivity between halibut populations, stable isotope analysis of otolith material (which varies with temperature and indicates latitudinal position over time) will be employed as well as molecular tools. A matrix model, that includes life-history information on halibut from specific habitats, will be created. With sensitivity analysis, this model will describe how halibut standing stocks are affected by coastal habitat alteration. Additionally, a patch isolation model will be employed to examine the effects of disturbance on halibut metapopulations (why connectivity data is needed).

This study will identify key nursery habitat for juvenile California halibut and reveal the sensitivity of halibut standing stocks to perturbations of coastal habitat types. Also, this study will be one of few to incorporate microconstituent analysis, molecular tools, and modeling in order to more fully understand population structure and dynamics within a species.

Cover page of Understanding Nutrient Loading to the Coastal Zone from Urban Watersheds

Understanding Nutrient Loading to the Coastal Zone from Urban Watersheds


Nutrient loading from urban development and intensive agriculture can have a significant adverse impact on coastal environments. The focus of this research proposal is to (1) measure and characterize nutrient loading by landuse on a watershed scale to the near-shore coastal environment using representative watersheds in southern California; and (2) develop a model to predict future nutrient export from these watersheds resulting from projected changes in landuse. The model will be based on an integrated modular framework and should prove a useful tool in watershed planning and management. The selected study watersheds drained by Carpinteria and Franklin creeks are distinctive but regionally characteristic catchments. Santa Monica Creek, draining an adjacent catchment, will be used to test the portability of the model. Both Franklin and Santa Monica Creeks carry a high nutrient load from urbanization and intensive agriculture to one of southern California's few remaining wetlands, the Carpinteria Salt Marsh (Ferren et al, 2000).

With an intensive sampling program throughout the wet and dry seasons, I will characterize nutrient loading by landuse type. Existing information on landuse, soils, geology, vegetation and basin hydrology will be gathered and structured in a geographical information system (GIS) database. This will guide the sampling strategy and provide basic data for determining export coefficients for various landuses. A nutrient export coefficient model (NEC-M) will be constructed and integrated with an existing urban growth model for the Santa Barbara area of California (SLEUTH/UCIME). The combined model will be used to predict nutrient export for various growth scenarios, which can be used to evaluate zoning and "best management practice" pollution control alternatives. In addition, the project results will provide important watershed discharge data for the Santa Barbara Coastal Long Term Ecological Research (SBC-LTER) project in a collaborative effort to understand the dynamics of near-shore oceanic water quality.