2024-03-28T14:11:39Zhttps://escholarship.org/oaioai:escholarship.org:ark:/13030/qt71p140482017-12-15T18:05:32Zqt71p14048Adaptive Management of Marine Protected Areas: Predicting Responses to MPA Implementation for Comparison to Monitoring Data Botsford, Louis W2017-12-15application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/71p14048publicationoai:escholarship.org:ark:/13030/qt8mx6c9q42014-09-02T22:59:19Zqt8mx6c9q4Noroviruses in coastal waters: Implications for seafood cultivation and human healthWuertz, StefanShapiro, KarenHanley, KaitlynSchriewer, AlexanderSmith, Woutrina A2014-09-02Norovirusfood safetymarine snowaggregationQMRAapplication/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/8mx6c9q4publicationoai:escholarship.org:ark:/13030/qt63k6d3jd2014-05-21T15:14:21Zqt63k6d3jdControlling Marine Invasive Species: The case of the Indo-Pacific Lionfish Invasion in the Southeast U.S. and CaribbeanKling, David MJames, Sanchirico N2014-05-16Our hypothesis is that modeling features common to marine biological invasions, like the ability of the invader to disperse over long distances, will call for invasive Indo-Pacific lionfish (Pterois volitans and P. miles) control policies that diverge from those that are efficient based on models geared towards terrestrial and freshwater species, and that these differences will be economically significant.Marine Invasive SpeciesLionfishapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/63k6d3jdpublicationoai:escholarship.org:ark:/13030/qt0kz462cn2014-05-16T18:16:44Zqt0kz462cnExploting marine actinomycete diversity for natural product discoveryJensen, Paul RMoore, Bradley2014-05-16The project hypotheses have not changed. We continue to address questions related to the diversity and distributions of MAR4 actinomycetes in marine sediments, the relationships between who these bacteria are (phylogeny), the types of secondary metabolites they produce, and the mechanistic biochemistry responsible for their biosynthesis.Naturaldiversitybacteriamarine sedimentsmetabolitesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0kz462cnpublicationoai:escholarship.org:ark:/13030/qt7zz429tm2014-05-16T18:15:56Zqt7zz429tmControlling Marine Invasive Species: The case of the Indo-Pacific Lionfish Invasion in the Southeast U.S. and CaribbeanKling, David MSanchirico, James N2014-05-16Our hypothesis is that modeling features common to marine biological invasions, like the ability of the invader to disperse over long distances, will call for invasive Indo-Pacific lionfish (Pterois volitans and P. miles) control policies that diverge from those that are efficient based on models geared towards terrestrial and freshwater species, and that these differences will be economically significant.Marine invasive speciesLionfishbioeconomicapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7zz429tmpublicationoai:escholarship.org:ark:/13030/qt9kr018qq2014-05-01T18:11:05Zqt9kr018qqAssessing selected Pacific Oyster stocks for disease resistance in Tomalas Bay, CaliforniaFriedman, Carolyn2014-05-01Pacific OysterDiseaseTomalas Bayapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9kr018qqpublicationoai:escholarship.org:ark:/13030/qt5348z9572014-05-01T17:23:35Zqt5348z957MPA-Based Collaborative Techniques to Improve Management of Nearshore FisheriesLenihan, Hunter2014-05-01application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5348z957publicationoai:escholarship.org:ark:/13030/qt0bm9k25c2014-04-30T21:31:20Zqt0bm9k25cEffects of Freshwater Flow and Population Connectivity on Benthic Community Dynamics in the San Francisco EstuaryChang, Andrew2014-04-30Climate 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.San Francisco EstuaryBenthic Community DynamicsFreshwaterapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0bm9k25cpublicationoai:escholarship.org:ark:/13030/qt1700k91t2013-04-08T20:16:55Zqt1700k91tPatch Dynamics of Nutrients, Fecal Indicator Bacteria and Chlorophyll near the Tijuana RiverFeddersen, FalkFranks, Peter2013-04-07The overall project goal is improved understanding of the physical and biological controls on nearshore (0-15 m water depth) patchiness of nutrients, fecal indicator bacteria (FIB) and chlorophyll (chl) near the Tijuana River.pollutantsfecal indicator bacteriaTijuana Rivernutrient deliveryapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1700k91tpublicationoai:escholarship.org:ark:/13030/qt7gs9938x2013-04-04T23:16:01Zqt7gs9938xInvestigating Sources, Transformations and Fates of Brominated Compounds in the Coastal EnvironmentAluwihare, Lihini2012-05-30Methoxylated and hydroxylated polybrominated diphenyl ethers (MeO- and OH-PBDEs) and polybrominated dibenzo-p-dioxins (PBDDs) found in marine biota in the coastal environment are not derived from the anthropogenic, PBDE flame retardant compounds.coastal environmentmussel tissuePBDDsmarine biotaapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7gs9938xpublicationoai:escholarship.org:ark:/13030/qt1b93k5zs2013-03-15T17:07:38Zqt1b93k5zsSea Urchin Gonad Index a Key to Understanding Secondary Production in the Restoration of Giant Kelp Forests off Palos VerdesFord, TomPondella, Dan2011-10-31Red and purple sea urchins (Strongylocentrotus franciscanus and S. purpuratus) that live in persistent barrens are perennially starved and will have lower gonad indices (the proportion of the weight of the whole urchin that is comprised of the weight of its gonad) than their counterparts living in persistent kelp forests. Establishing sea urchin gonad indices can be use as a measure of fishery-related secondary production in nearshore rocky reef ecosystems because gonad condition is linked to the quality of the urchin's diet and correlated with environmental conditions on a fine spatial scale.sea urchinkelp foresturchin barrengonad indexgonad indicestop down controlsecondary productionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1b93k5zspublicationoai:escholarship.org:ark:/13030/qt6x28w5kf2013-03-06T17:51:20Zqt6x28w5kfHigh-Throughput Molecular Identification of Fish Eggs and LarvaeBurton, Ronald2013-02-01Ichthyoplankton surveys can reveal the location, timing and intensity of spawning activity for many fish species and are widely used to assess fisheries resources. However, the utility of these surveys is limited by the fact that many eggs and larvae cannot be identified to the species level using morphology alone. This project was motivated by the hypothesis that fish eggs and larvae can be more accurately identified by species specific DNA sequences than by morphology alone.fishegg identificationLuminexbead arrayapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6x28w5kfpublicationoai:escholarship.org:ark:/13030/qt77r8c8kn2013-01-16T23:26:49Zqt77r8c8knCross-shelf Larval Migrations Regulating Larval Supply and Connectivity in a Network of Marine ReservesMorgan, StevenLargier, John2013-01-161. Does larval transport and recruitment vary markedly across an upwelling cell? 2. Do interspecific differences in larval behavior affect transport and recruitment? 3. How far from natal populations do larvae with different dispersal “strategies” travel at and away from a major upwelling center? 4. How should spatial variation in larval transport affect the placement, size, spacing and evaluation of MPAs across upwelling cells?larval recruitmentdispersaltransportpopulation connectivitymarine protected areasapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/77r8c8knpublicationoai:escholarship.org:ark:/13030/qt4p45x2p72013-01-04T19:19:13Zqt4p45x2p7Connectivity of West Coast Marine Sanctuaries: Tracking Sooty Shearwaters Throughout Dynamic Upwelling Ecosystems in the California Current SystemHarvey, JamesAdams, Josh2013-01-03We propose that as a super-abundant, top-level-predator, Sooty Shearwaters are an ideal California Current Ecosystem (CCE) bioindicator species. Sooty Shearwaters dominate the CCE avifauna during the spring-summer 'upwelling season' and depend on massive amounts of energy-dense forage fishes (anchovy, sardine, krill). We hypothesize that Sooty Shearwater distribution (and abundance), and residency patterns, are related to upwelling dynamics (i.e., offshore transport, upwelling retention, wind-stress curl) that structure and control bottom-up productivity and energy transfer through the CCE foodweb.seabirdhabitatmarine protected areassanctuaryupwellingapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4p45x2p7publicationoai:escholarship.org:ark:/13030/qt0w29f2932012-11-27T18:32:31Zqt0w29f293Making Restoration More Efficient: Testing the Contributions of Planting Diversity and Introduced Plant Legacy Effects to Recovering Coastal EcosystemsDayton, PaulTalley, Theresa2012-11-26Hypothesis: Plant invaders with an architecture that is novel to the invaded system, will dramatically alter the abiotic and biotic environment through changes to physical properties, primary production food sources and/or living space.Hypothesis: The addition of organic litter and higher planting diversity, characteristics of a mature system, would lead to faster ecosystem development of soils, plant communities and invertebrate communities after the removal of plant invaders than no litter addition and a monoculture.coastal wetlandcoastal sage scrubcommunity ecologydiversity functioneducationecosystem restorationapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0w29f293publicationoai:escholarship.org:ark:/13030/qt0n52f3s62012-08-13T18:30:46Zqt0n52f3s6Exposure of Santa Cruz Wharf Anglers to Domoic Acid ToxinsPomeroy, CarolineSilver, Mary W2009-04-09The goals of this pilot project were to determine the extent of the public health threat posed by pier anglers’ consumption of self-caught seafood containing domoic acid (DA), and to lay the foundation for further research, education and outreach to address the threat. Year 1 project objectives were to: 1) design, test and initiate an intercept survey of SCW anglers to identify and characterize their seafood consumption patterns; and 2) determine the concentrations of HAB toxins in the species targeted by SCW anglers, while monitoring ambient DA toxins and toxic Pseudo-nitzschia species in the SCW area and at a more open-water site. Year 2 project objectives were to: 1) determine whether a quantitative link exists between toxic phytoplankton in the water and DA contamination of commonly caught fish at the SCW; 2) determine the relationship between SCW anglers’ seafood consumption patterns and their socio-cultural and economic characteristics; 3) identify subpopulations of SCW anglers whose seafood consumption patterns put them at risk for exposure to DA; and 4) work with state agencies and other interested parties to determine how best to export these results to support their efforts to protect public health.seafood consumptionsurvey researchsubsistence fisheriesrecreational fisheriesdomoic acidharmful algal bloomsanchovyjacksmeltwhite croakersculpinperchsanddabsPacific sardinehuman dimensionsSanta Cruz WharfPseudo-nitzschia australisP. multiseriesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0n52f3s6publicationoai:escholarship.org:ark:/13030/qt7vp3872b2012-08-03T16:42:24Zqt7vp3872bReefs that Rock and Roll: Critical Assessment of Rhodolith Bed HabitatSteller, Diane L.Aiello, Ivano2012-04-04The main hypotheses of this proposal are that 1) a novel benthic marine habitat exists, rhodoliths, exists that has been unrecognized in prior surveys and 2) that human induced disturbance is degrading this common coastal California benthic habitat - rhodolith beds. These beds are diverse and threatened marine habitats that are common in Southern California should be included in coastal protection, monitoring and management decisions. By determining the distribution, measuring habitat metrics and determining the common sources of disturbance in beds around Catalina Island, the information can be used to inform the Southern California MPA process.rhodolithCatalina Islandmooring disturbancehigh biodiversityapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7vp3872bpublicationoai:escholarship.org:ark:/13030/qt4xb239jq2012-07-11T17:58:55Zqt4xb239jqParadigm or Paradox: Can we Attribute Species Changes to Global Climate Change in Light of Decreasing Water Temperatures in Central California?Breaker, LaurenceCailliet, GregorLauner, AndreaWadsworth, Tom2012-07-11The main goal of this study was to gather information about historical changes in water temperature and species composition, in order to identify variables that will enable us to predict changes in water temperatures and species abundances in California caused by global climate change. Our primary objectives were to (1) review the existing published and unpublished data sets to refine our understanding of trends in sea surface temperature in central California; (2) review fish and climate data sets to determine if we could identify how species abundances changed relative to changes in water temperatures and basin-scale environmental indices; and (3) identify recent changes in species abundances in central California that are related to water temperatures.El NiñoLa NiñaPacific Decadal OscillationPDOCalifornia currentpole-ward shiftsMonterey Baywater temperaturespecies compositionclimate changeapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4xb239jqpublicationoai:escholarship.org:ark:/13030/qt0gn2r3xx2012-04-25T16:12:45Zqt0gn2r3xxLong-term Faunal Changes in California Nudibranchs: Climate Change and Local Ocean HealthGoddard, JeffreyPearse, John2011-02-22(1) The abundance, species richness, and community composition of nudibranchs in central California has changed significantly in the past 30 to 70 years.(2) The observed changes are consistent with those predicted by climate variability on interannual and decadal time scales. Specifically, during warm phases: (a) the proportional abundance and speciesrichness of southern species should increase, as northern species decline, and (b) geographic ranges should shift poleward. The reverse of these should occur during periods of cooling. Further, these changes should be apparent at multiple, widespread sites (otherwise, more localized environmentalfactors, and not broad scale climate factors, would be implicated as the cause).(3) Long-term, anthropogenic climate warming is superimposed on natural climate variation, and its biological signal (similar to that described above for natural periods of warming) should be apparent bycomparing the abundance, species richness, and community composition across (1) full cycles of natural decadal variation, preferably at multiple sites, and (2) across entire single phases of decadal variation.(4) While climate change may be the ultimate factor behind community changes we document, especially those related to shifts in geographic ranges, climatic impacts on ecologically important species could result in a cascade of indirect effects on other species. In 1977, the large aeolidnudibranch, Phidiana hiltoni, began spreading northward from Monterey, California. By 1992 it had reached Duxbury Reef, 100 km to the north, where other nudibranchs subsequently appeared todecline. We will also test the hypothesis that P. hiltoni attacks and consumes other species of nudibranchs and has caused these apparent declines.climate changenudibranch gastropodshistorical ecologyrocky intertidalEl NiñoLa NiñaCentral CaliforniaMonterey BaySouthern OscillationPacific Decadal OscillationNorth Pacific Gyre Oscillationcoastal upwellinggeographic range shiftsCalifornia Currentlarval recruitmentocean circuclationpoleward transportapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0gn2r3xxpublicationoai:escholarship.org:ark:/13030/qt2f05550r2012-04-17T22:15:12Zqt2f05550rEstimating the Impact of Invasive Spartina densiflora on Primary Productivity in Humboldt BayPurcell O'Dowd, Alison2012-04-15Invasive dense-flowered cordgrass (Spartina densiflora) is impacting the primary productivity of Humboldt Bay salt marshes.Spartina densiflorainvasive speciesHumboldt Baynet primary productivitynet ecosystem exchangeapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2f05550rpublicationoai:escholarship.org:ark:/13030/qt3kp0f5702012-04-06T20:12:12Zqt3kp0f570Parasites as Indicators of Coastal Wetland HealthHechinger, Ryan F.Lafferty, Kevin2012-04-04Trematodes can provide a powerful and cost-effective ecological indicator tool to assess and monitor biodiversity in estuarine habitats.trematodeswetlandsestuariesparasitesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3kp0f570publicationoai:escholarship.org:ark:/13030/qt4270m3f32012-04-06T16:32:41Zqt4270m3f3A Comprehensive Oyster Disease Survey in CaliforniaMoore, James D.2010-04-19The goal of this project was to investigate and document the presence of disease agents in cultured and wild oyster populations throughout California. This is the first comprehensive survey to be conducted since that of Katkansky and Warner in the late 1960s to early 1970s (Katkansky and Warner, 1974). Particular emphasis was placed on detection of the agent of Denman Island Disease (Mikrocytos mackini, Farley et al., 1988). This pathogen of the Pacific oyster (Crassostrea gigas) was detected in the State of Washington in 2002, and many California oyster growers receive seed from Washington State. All major populations of farmed and feral commercial oysters and wild native oysters Ostrea lurida were targeted for sampling. Sufficient numbers from each population were collected so that relatively rare pathogens should have been detected when they are present.oysterdiseasepathogenCaliforniasurveyapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4270m3f3publicationoai:escholarship.org:ark:/13030/qt9nq245jw2012-04-05T18:53:08Zqt9nq245jwSolid Phase Absorption Toxin Tracking (SPATT) and Nutrient Loads: Testing a New Tool for Algal Toxin Monitoring in Fresh, Brackish and Coastal EcosystemsKudela, Raphael2009-03-10 We are interested in testing a new methodology called Solid Phase AbsorptionToxin Tracking (SPATT), which is a man-made resin that passively captures algal toxins in water; it can be thought of as a man-made, passive, sentinel “mussel”.This technology was developed in New Zealand (MacKenzie et al. 2004), and is inlimited use in the UK (Turrell et al., 2007) and Australia (Takahashi et al.,2007), but has not yet been tested in the US. Our hypothesis was that this resin, deployed using the same methodology as described by others (outside the US), would passively capture domoic acid, providing an integrated time-series of toxin levels in the coastal ocean.harmful algaedomoic acidyessotoxinsaxitoxinmicrocystinpassive toxin absorptionamnesiac shellfish poisoningcoastal monitoringPseudo-nitzschiaMicrocystisapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9nq245jwpublicationoai:escholarship.org:ark:/13030/qt7bt1725b2012-04-04T17:52:39Zqt7bt1725bA Novel Approach to Evaluating Patterns of Vertical Distribution in Cryptic Larvae: Application of Fluorescence in situ Hybridization (FISH) and a Large-Particle Cell SorterLevin, Lisa A.2011-01-15We hypothesized that differences in the distribution of adult mussels are the result of differences in the selection pressures ontheir larvae, such that the vertical distribution of larvae from the inner bay species (M. senhousia) facilitates bay retention, while that of the open-coast species (M. californianus) enhancesalongshore dispersal.mussel larvaelarval dispersallarval vertical distributionMytilus californianusMytilus galloprovincialisMusculista senhousiapopulation connectivityapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7bt1725bpublicationoai:escholarship.org:ark:/13030/qt3n32574v2012-04-03T21:50:39Zqt3n32574vEvaluating the Functional Recovery of Restored Coastal Wetland in Southern CaliforniaWhitcraft, Christine R.Bengt, Allen J.2010-05-26Within the Huntington Beach Wetlands (HBW), we hypothesized that Brookhurst and Magnolia Marshes (marsh areas isolated from tidal influence for approximately 100 years) would have significantly different physical characteristics (salinity, temperature, moisture, sediment parameters), more terrestrial plant, algal, invertebrate and microbial communities and altered food web structure from neighboring Talbert Marsh (a marsh area whose tidal connect was restored 20 years ago). In addition, we hypothesized that once Brookhurst Marsh was restored (Summer 2009), these differences would decrease and with time, resemble those of Talbert Marsh. This restoration of structure and function will occur on differing time scales; we predicted that physical parameters would quickly become similar while algal, invertebrate and microbial communities would begin to change on a month-year time scale. Changes to the plant community and the food web structure are anticipated to occur on a year-decadal time scale (beyond the funding cycle for this project).Huntington Beach Wetlandsphysical parametersplant communityfood web structureapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3n32574vpublicationoai:escholarship.org:ark:/13030/qt2g35r3152012-04-03T21:32:53Zqt2g35r315Shelter Use, Movement, and Home Range of Spiny Lobsters in San Diego CountyHovel, KevinLowe, Chris2007-05-04The California spiny lobster is an ecologically and economically important species in southern California coastal waters. In San Diego County, commercial lobster landings average approximately 500,000 pounds per year with a subsequent value of ca. $5 million, and recreational fishing for lobsters is a valued part of life in San Diego for many people. Lobsters are a major predator of benthic invertebrates along the southern California coastline, and they act as a keystone species by preying upon competitively dominant mussels on rocky shorelines and sea urchins that consume kelp, thereby promoting the existence of diverse shoreline communities. Despite the fact that P. interruptus has supported a fishery in California for over 100 years and may presently be overfished, we have relatively little fishery-independent information on lobster population dynamics and behavior that could be used to implement conservation efforts. Our goal in this research was to fill some of these gaps in our knowledge by determining linkages between spiny lobster habitat and lobster population structure and movement. Specifically, we tested (1) how characteristics of lobster shelter and of benthic landscapes influence lobster shelter selection and their nocturnal foraging behavior; and (2) how risk of predation influences lobster shelter use behavior. By addressing these objectives we evaluated the utility of various habitats as essential fish habitat for lobsters, and we addressed two priorities set out in the California Marine Life Protection Act (MLPA): (1) to assess the home range of exploited mobile invertebrate species, and (2) to provide baseline information on the abundance, size frequency, population structure and location of nearshore invertebrates.spiny lobsternearshore invertebratesPoint Loma kelp forestMarine Life Protection Actapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2g35r315publicationoai:escholarship.org:ark:/13030/qt6337t5f12012-04-03T20:44:11Zqt6337t5f1Collaborative Fisheries Research in Support of Ecosystem-‐Based Salmon Management in Northern CaliforniaThayer, Julie A.Sydeman, WilliamField, John2010-07-31The state of the Chinook salmon (Oncorhynchus tshawytscha) fishery in California is imperiled. One of the proposed mechanisms for recent population declines and fisheries closures is environmental variation having deleterious effects on prey availability and the ocean survival of Sacramento River fall Chinook (Lindley et al. 2009). To address this hypothesis, we analyzed collaborative fisheries research data (stomach samples obtained from commercial and recreational fisherman) on Chinook salmon diet in central California during the early-mid 1980s and mid 2000s. We compared this information with historic diet records for this population from 1955. Salmon diet composition changed significantly through time, with a decline in diet diversity. Specifically, previously important prey groups including juvenile rockfish (Sebastes spp.), krill (Euphausiidae), Pacific herring (Clupea pallesi) and market squid (Loligo opalsecens) were either greatly reduced or disappeared from the diet altogether. Conversely, Pacific sardine (Sardinops sagax), conspicuously absent from the diet (and environment) since the 1950s, became the second most important prey item in the 2000s. Northern anchovy (Engraulis mordax) remains an important prey item. The strongest correlation between salmon diet and environmental conditions was for local SST for all years in the study between 1955-2007. In the early 1980s, SST best explained salmon diet composition. While relationships were not significant in the mid 2000s, likely due to the short time period sampled, upwelling or the NPGO were the best descriptors of salmon diet variation. These physical pressure-state indicators have exhibited increasing trends and increasing variability through time and are indicative of the changing climate. Finally, we decomposed multiple prey variables into a univariate annual index and thus compared diet variation with the Sacramento Index (SI) of Chinook ocean abundance. We found a relationship between diet and the SI lagged by 2 years, potentially an indication of prey availability experienced by smolts after ocean entry (Figure 5). Collaborative fisheries research offers a means to track variation in salmonid diet with implications for understanding the connections between environmental variation, salmon survival, and declining fisheries in California.chinook salmonOncorhynchus tshawytschamanagementprey groupsdietSacramento Indexapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6337t5f1publicationoai:escholarship.org:ark:/13030/qt6934b5zw2012-04-03T19:08:16Zqt6934b5zwTransferrable Antibiotic Resistance Plasmids in Urban Coastal WetlandsCummings, David E.Top, Eva2011-09-26The overarching hypothesis driving this research is that antibiotic resistance genes released into the natural environment through urban storm water may persist, creating a reservoir of resistance genes that have the potential to return to the human community through various vectors such as birds, insects, and fish. The specific aim of this Program Development grant is to assess the diversity of multidrug-resistance plasmids in sediments of two urban wetlands.urban wetlandsantibiotic resistanceplasmid isolationapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6934b5zwpublicationoai:escholarship.org:ark:/13030/qt1h76c6j22012-04-03T18:23:05Zqt1h76c6j2Economic Evaluation of Tradable Property RightsBrandt, SylviaHanemann, Michael2004-09-27Economists have for decades advocated transferable property rights, in which the total annual allowable catch is divided into shares, which are then tradable, as a market mechanism to decrease overcapacity. Tradable property rights, or individual transferable quotas (ITQs), are a significant departure from command-and-control regulations that impose combinations of gear restrictions, season limitations, license limitations and trip limits. While in theory tradable property rights have clear economic advantages over command and control, Federal fisheries managers face the challenge of evaluating and ranking regulatory options in a world of complexity and uncertainty.The goal of this project is to describe the changes in the composition of the Mid-Atlantic surf clam fishery, which has been regulated with first command and control and then tradable property rights. The data analysis indicates that while there were changes in the structure of the clam industry, the introduction of tradable property rights did not lead to a redistribution of welfare across different types of participants in the industry.annual allowable catchclam industryITQstradable property rightsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1h76c6j2publicationoai:escholarship.org:ark:/13030/qt54z8h2842012-03-16T18:21:29Zqt54z8h284Ecology and Trophic Interactions of Jumbo Squid (Dosidicus gigas) in the California Current EcosystemGilly, WilliamField, John2012-03-15Humboldt squid have recently demonstrated a range expansion into the waters off California from the previous northern extent of their range in Mexico. In this new environment, we expected the vertical and horizontal migratory behavior and the diet to be generally similar those previously documented in Mexico. However, we also expected significant differences in diet and reproductive activity, with potentially great impacts on ecosystems in the California Current System. In particular, consumption of numerous ecologically and economically important species could greatly affect both nearshore and offshore environments and fisheries in the California Current System. We hypothesize that mechanisms driving the range expansion include tolerance of environmental variability and flexibility in diet.squidecologyfisheriesdiettaggingmigrationslife historyapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/54z8h284publicationoai:escholarship.org:ark:/13030/qt5b1489ww2012-02-08T19:34:51Zqt5b1489wwValidation of a New Method for Population Assessment of Pacific Salmonids Using Genetic MarkersClemento, Anthony2011-08-16The goal of the proposed research project is to evaluate a novel method of efficient genetic tagging through an experiment with Chinook salmon (Oncorhynchus
tshawytscha) from California’s Central Valley. The proposed parentage-based tagging (PBT) experiment has four components: marker discovery, development of analysis tools, implementation of the parent database, and assignment of known offspring and mixed fishery samples. Utilizing new methods for large scale parentage assignment, the collection of genetic information from a parental breeding generation can be used to “tag” the offspring cohort. When this is done at a hatchery or at a weir, the entire breeding population of a stock or population can be sampled, and the entire next generation tagged. Offspring can be non-lethally sampled during their seaward migration, in fisheries, and upon return to spawn (at hatcheries or instream). Genotyping is followed by high confidence parentage assignment wherein the inherited genetic tags are used to locate the parents of sampled individuals in the parent database, thereby identifying the stock and cohort of origin. Additionally, we will evaluate whether the same set of genetic markers for PBT are also effective for genetic stock identification (GSI). While PBT can identify the specific parents of an unknown individual (as long as their genetic data is in the parent database), GSI employs baseline samples from each population to which an unknown individual can be assigned.Chinook salmonCentral Valleyspring-runSNPgeneticshatheryparentage-based taggingPBTgenetic stock identificationGSIapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5b1489wwpublicationoai:escholarship.org:ark:/13030/qt5sg3c6qz2012-02-06T23:18:54Zqt5sg3c6qzKrill and Krill Predators: Ecosystem-Based Management in the Gulf of the Farallones-Cordell Bank Krill Production DomainSydeman, William J.Jahncke, Jaime D.Largier, John L.2009-04-01We will test the primary hypothesis that coastward advection of bottom cold-salty water during intense wind-driven upwelling provides conditions conducive forE. pacifica(the more oceanic species) to move onto the continental shelf where they become abundant and available to predators “early” in the season each year. As a corollary, we will test the hypothesis that as upwelling relaxes “later” in the season each year,E. pacificamoves offshore where it is less available to predators, andT. spinifera(the more coastal species) develops, becoming the dominant euphausiid in shelf waters and predator diets. California CurrentupwellingCassin's aukletsPtychoramphus aleuticuscommon murresUria algaeeuphausiidskrillEuphausia pacificaThysanoessa spiniferaapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5sg3c6qzpublicationoai:escholarship.org:ark:/13030/qt4535t0pg2012-02-06T21:23:18Zqt4535t0pgNovel, Post-Translationally Modified Peptide Antibiotics from Solitary TunicatesVacquier, VictorTaylor, Steven2004-04-16Although the pharmaceutical industry has “mined” the world of soil bacteria,streptomycetes and fungi to find novel antimicrobial molecules, the emergence of resistant superbugs necessitates identifying new antibiotic sources. Recent research into the innate immune system has focused attention on antimicrobial peptides – molecules that equip animals to resist infection without assistance from antibodies and other accoutrements of adaptive immunity. In recent years, potent antimicrobial peptides have been identified in the blood cells (hemocytes) of horseshoe crabs, shrimp, mussels and tunicates ("sea squirts"). Our studies centered on three tunicates (Styela clava, Styela plicata and Ciona intestinalis) that are abundant in Southern California's shallow waters.antimicrobial peptidestunicatesStyela plicataStyela clavaCiona intestinalissea squirtsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4535t0pgpublicationoai:escholarship.org:ark:/13030/qt9p94899h2012-02-03T21:31:51Zqt9p94899hThe Role of Symbiotic Metabolites in the Development of Toxic Phytoplankton BloomsCarrano, CarlKuepper, Frithjof2012-02-01Most phytoplankton, including the toxic species of interest, cannot be grown axenically and require cohabitabing,associated, or symbiotic bacterial partners. However we have been able to prepare stable binary cultures of phytoplankton of interest with just a single species of bacteria (most of which are species of Marinobacter). While we recognize the culturable bacteria that we have isolated and are now studying are not necessarily qualitatively orquantitatively representative of the bacterial population associated with the phytoplankton in the wild, the ability to produce viable binary phytoplankton/bacterial cultures represents a critically important experimental tool. While other non-culturable bacteria could be quantitatively more important inhabitants of the "phycosphere" in the wild, our ability to ascertain the specific chemical determinants supplied by these bacteria and necessary tophytoplankton survival would be severely limited or impossible with such a heterogeneous and constantly changing assemblage. The ability to form stable, viable binary cultures indicates that the bacteria in question, irrespective of their numerical importance in a natural state, must provide some important factor for phytoplankton growth and greatly enhances our ability to define the nature of that substance and to test hypotheses based on it. Our hypothesis is that the critical element provided by the bacteria that control algal growth and survival involves siderophores, either directly through some form of iron trafficking between the species or indirectly possibly as boron-mediated interspecies cell-cell signaling molecules.ironalgaebacteriasiderophoresphotochemistrysymbiosisapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9p94899hpublicationoai:escholarship.org:ark:/13030/qt8d31f19d2012-02-01T22:18:45Zqt8d31f19dParentage in White SturgeonMay, Bernie2012-01-31We hypothesize that the addition of six microsatellite loci to an existing panel of eight microsatellite loci will increase the accuracy rate of parentage assignment of farmed white sturgeon to 95%.farmed white sturgeonparentagemicrosatellite lociaquacultureapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8d31f19dpublicationoai:escholarship.org:ark:/13030/qt33x9f3vc2012-01-19T21:35:30Zqt33x9f3vcDevelopment of Novel Stable Isotope Approaches to Evaluate Carbon Flow in a Restored Coastal Wetland in Southern CaliforniaDillon, JesseWhitcraft, Christine2012-01-18We hypothesized there would be differences in the microbial and infaunal communitiesprimarily responsible for degrading macrophyte vs. microalgal carbon. Specifically we predicted that:
The invertebrate community degrading macrophyte-derived carbon will be
significantly different from those degrading algal-derived carbon.
The microbial communities (bacteria and fungi) degrading macrophyte-derived
carbon will be significantly different from those not using this carbon source.
restored wetlandinvertebratesSouthern Californiastable isotope analysesSpartina foliosamacrophyte-derived carbonapplication/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/33x9f3vcpublicationoai:escholarship.org:ark:/13030/qt6bg9w0cz2011-12-19T20:48:47Zqt6bg9w0czClimate change and restoration factors affecting fecal pathogen dynamics in wetland systemsMiller, Woutrina A.Watson, Fred2011-12-16This project has three main hypotheses: 1) Increased water temperatures, decreased salinity, and increased flow rate will enhance transport of protozoal oocysts through wetland systems. 2) Larger vegetation, increased vegetation density, and increased wetland length will enhance retention of protozoal oocysts in wetland systems. 3) Factors found to maximize protozoal retention in the laboratory-based models will also significantly affect protozoal transport in a natural and constructed wetland.application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6bg9w0czpublicationoai:escholarship.org:ark:/13030/qt6hw0v4rq2011-10-12T17:18:35Zqt6hw0v4rqExploring the Impact of Avian Predators on Central California SalmonidsShaffer, ScottMoore, Jonathan W.2011-10-01Avian predators, Western Gulls in particular, are having significant impacts on juvenile salmonid populations along the central California coast. Exclusion efforts can reduce predator impact and increase juvenile salmonid survival.Environmental Monitoringavian predationendangered salmonidssteelheadcohoradiotelemetrystable isotopesseabirdsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6hw0v4rqpublicationoai:escholarship.org:ark:/13030/qt6tf9637q2011-10-03T16:40:27Zqt6tf9637qExtending the Use of Solid Phase Adsorption Toxin Tracking to the Land-Sea InterfaceKudela, RaphaelMiller, Melissa2011-09-30Harmful algal blooms (HABs) are an escalating problem in coastal ecosystems, inflicting massive economic losses on commercial fisheries and causing death and illness to both humans and marine fauna. Paralleling the rise of marine HAB problems, cyanobacteria (previously identified as "blue-green algae") have a worldwide distribution and can form extensive blooms in freshwater and estuarine habitat. Microcystins are fast becoming a global health concern, with severe and recurrent blooms with toxin elaboration reported globally, including central California. Until recently, microcystin intoxication was considered a public health issue mainly of freshwater habitat, reflected by the vast body of published literature on potential human health risks due to microcystin exposure in rivers, lakes, reservoirs and freshwater aquaculture. In contrast, monitoring of marine water and seafood for similar risks has been limited, despite confirmation of outflows of microcystin-contaminated freshwater to the ocean. A passive sampling method for determination of dissolved toxins in seawater, Solid Phase Adsorption Toxin Tracking (SPATT), allows for field-deployment of adsorbent resin sealed within a polyester mesh bag and have been used for a suite of lipophilic toxins, but until recently have never been evaluated for use with hydrophilic (water-soluble) toxins such as domoic acid (amnesic shellfish poisoning) and saxitoxin (the primary toxin associated with paralytic shellfish poisoning).Environmental Monitoringharmful algal bloomsHABscyanobacteriaSolid Phase Adsorption Toxin TrackingSPATTtoxin loadPajaro River systemElkhorn Sloughshellfish poisoningapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6tf9637qpublicationoai:escholarship.org:ark:/13030/qt3cm379612011-09-22T22:37:49Zqt3cm37961Developing the capability to monitor and predict upwelling along the California coast using an ocean circulation modelWang, XiaochunChao, Yi2011-09-22Coastal ocean forecasting models can be used to monitor and predict coastal upwelling.Environmental Monitoringforecast modelsupwellingCalifornia coastMonterey Bay Bloom Experimentapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3cm37961publicationoai:escholarship.org:ark:/13030/qt8hb970832011-08-30T18:58:53Zqt8hb97083Trophic ecology of the Gopher Rockfish (Sebastes carnatus): providing baseline information for monitoring marine protected areasEbert, David2011-08-29Gopher Rockfish diets will differ inside vs. outside of marine protected areas (MPAs) due to higher Gopher Rockfish densities inside MPAs.gopher rockfishSebastes carnatusmarine protected areasMPAsdietsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8hb97083publicationoai:escholarship.org:ark:/13030/qt9296c41b2011-08-09T18:05:15Zqt9296c41bDetecting, Characterizing and Determining the Biological Response to Regime Shifts off the California CoastBreaker, Laurence C.Welschmeyer, Nicholas A.2010-02-28First, using one method of change detection analysis called the cumulative sum, it is possible to detect and characterize regime shifts along the California coast using sea surface temperatures (SSTs) and other variables. Second, physically-determined regime shifts and changes in ocean climatology, determined largely through detailed temperature time-series, can be linked to corresponding changes in biological communities, particularly phytoplankton, which exhibit rapid generation times.Environmental Monitoringregime shiftssea surface temperaturedetecting regime shiftscumulative sumsMonterey BayHopkins Marine StationSouthern CaliforniaScripps PierVancouver Island1976-77 regime shiftchange pointssustained changespattern recognitionmethod of expanding meansapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9296c41bpublicationoai:escholarship.org:ark:/13030/qt38f8t5q22011-07-11T19:51:18Zqt38f8t5q2Harnessing the Pharmaceutical Potential of Marine CyanobacteriaGerwick, WilliamGerwick, Lena2011-07-11We hypothesize that the secondary metabolite pathways in cyanobacteria can be manipulated by applying transcriptional promoters, either of a genetic or chemical nature (elicitors), to produce more secondary metabolites with potential pharmaceutical utility.cyanobacteriaelicitorsLyngbya majusculaapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/38f8t5q2publicationoai:escholarship.org:ark:/13030/qt0jh9f7642011-07-08T17:46:01Zqt0jh9f764A Field Experimental Investigation of the Effects of Black Brant Geese Grazing on Eelgrass Growth and the Animals in an Eelgrass BedShaughnessy, Frank J.Black, Jeffrey M.2009-08-20Eelgrass (Zostera marina) beds and other seagrass ecosystems around the world are recognized for their trophic support, nursery, refuge, water quality and recreational functions (Williams and Heck 2001).Environmental MonitoringPoultry or Avian ScienceeelgrassZostera marinablack brantgrazingHumboldt Bayapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0jh9f764publicationoai:escholarship.org:ark:/13030/qt3zg6m44v2011-07-08T17:45:56Zqt3zg6m44vEcological Impacts of Beach Grooming on Exposed Sandy BeachesDugan, Jenifer E.Hubbard, David M.Page, Henry M.Schimel, Joshua P.2008-12-03Kelp and phytoplankton washed ashore by tides and waves support a rich diversity of shore life. On many of the most popular sandy beaches in California, however, local municipalities regularly rake up litter and kelp in a process called beach grooming. The ecological consequences of this process on plants and animals that live and forage in regularly raked areas are evaluated. The information gathered may help guide and improve the state's beach maintenance practices.Environmental Monitoringexposed sandy beachesshorebirdstrophic interactionsmacrophyte wrack subsidiesintertidal invertebratesdunesdune plantssediment characteristics and transportapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3zg6m44vpublicationoai:escholarship.org:ark:/13030/qt4f85c5d52011-07-08T17:42:20Zqt4f85c5d5California spiny lobsters and benthic community structure in Southern California: top-down and bottom-up interactionsHovel, KevinLowe, Christopher2010-09-30We hypothesize that: spiny lobster movement behavior is governed by a combination of forces acting from the bottom-up (i.e. food availability) and from the top-down (i.e. risk of predation); and that spiny lobsters significantly influence the structure of benthic communities in kelp forest and seagrass habitat.spiny lobstermarine reservestop-downpredationmovementurchinhabitatapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4f85c5d5publicationoai:escholarship.org:ark:/13030/qt94q158zd2011-07-08T17:41:51Zqt94q158zdUnderstanding submarine groundwater discharge and its influence on coastal water quality along the California CoastBoehm, Alexandria BPaytan, Adina2010-01-26We proposed directed field and modeling research to address the following hypotheses: (H1) Submarine groundwater discharge (SGD), its quality, and the percentage that is fresh versus saline, is modulated by season, tides, and wave conditions; (H2) the chemical (nutrient, carbon, trace metal) and biological (human health indicators) composition of SGD is affected by land use and geology; (H3) human health indicators and nutrients can be freely transported through the beach aquifer and are not removed via interactions with the sediments, and (H4) SGD impacts the water quality of the nearshore environment at a level comparable to surficial runoff.submarinegroundwaterdischargeradiumfecal indicator bacterianitrogenphosphateapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/94q158zdpublicationoai:escholarship.org:ark:/13030/qt1jt8z9bb2011-07-08T17:40:46Zqt1jt8z9bbBinational Studies Leading to an Ecosystems-based Management Strategy for Common Thresher Shark in the Southern California Bight (SCB).Graham, Jeffrey B.Cartamil, Daniel P.2010-02-26Survey of the Mexican SCB Sector Artisanal and Commercial Shark Fisheries Hypotheses: a) Common thresher sharks represent a substantial portion of the catch of artisanal and commercial shark fisheries in the Mexican SCB sector. b) Exploitation of common threshers and other elasmobranchs is important to the economy of northern Baja California and, by extension, is directly linked to U.S. fishery management. Mexican SCB Longlining Survey Hypotheses: a) Thresher shark nursery grounds extend south throughout the Mexican sector of the SCB. b) Juvenile threshers in Mexican SCB waters will exhibit seasonal patterns of abundance similar to those observed in the California SCB (i.e. higher abundance in early Spring and Summer when pupping is thought to occur). Tracking and Archival Tagging Hypotheses: a) Juvenile thresher sharks utilize distinct inshore areas as nursery grounds and have a strong preference for continental shelf waters. b) Within these nursery grounds, juveniles have specific habitat preferences (e.g., substrate composition, algal coverage, topography, etc.). c) Juvenile threshers display the same diel movement patterns noted for adults, remaining in the warmer mixed layer by night, and making vertical forays by day. However, we expect that juveniles will inhabit shallower depths and higher temperatures than adults, and also swim at slower speeds. d) Juveniles undergo relatively large-scale movements that take them throughout the SCB and further south.SustainabilityThresher sharkelasmobranchartisanal fisheryecosystem managementacoustic telemetryarchival satellite taggingnursery groundsmovement patternsobserver programapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1jt8z9bbpublicationoai:escholarship.org:ark:/13030/qt6n43g6ch2011-07-08T17:30:57Zqt6n43g6chEvaluating Ocean Management Systems to Facilitate the Development of Ecosystem-Based ManagementYoung, Oran R2009-02-16The hypothesis of this project is that information about how the oceans are governed can be gleaned from text analysis of laws and regulations.The objective of this project is to improve the understanding of existing ocean governance to assist ecosystem-based management initiatives and ocean stakeholders. The project goals include: (1) to compile a database of laws and regulations relevant to the California Current; (2) to develop techniques that quantitatively and objectively provide information about gaps and overlaps in management (using laws and regulations as proxy to represent management); (3) to ground-truth the utility of the techniques and format of results with feedback from government agencies and other ocean stakeholders; (4) disseminate synthesized results in useful format for ocean managers; (5) to make compilation of laws and regulations freely accessible and searchable by the public.GovernanceCalifornia Currentmarine policymarine affairslawlegislationregulationstatuteLarge Marine EcosystemCaliforniaOregonWashingtoninstitutionsecosytem-based managementEBMhuman dimensionsocial scienceapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6n43g6chpublicationoai:escholarship.org:ark:/13030/qt5fn0543h2011-07-08T17:30:51Zqt5fn0543hTemporal Variation in Fish Communities off Santa Cruz Island, CaliforniaGraves, Michelle R.Larson, Ralph J.Alevizon, William S.2006-12-31The assemblage of fishes inhabiting subtidal rocky reefs off Santa Cruz Island, California has changed noticeably since the 1970s. Subtidal surveys were conducted annually in 1971-74, in 1996, 2004 and 2005, using the “cinetransect” method. The period 1971-74 fell during the last cool “regime” of the Pacific Decadal Oscillation, while 1996 was near the end of the recent warm phase. Some of the changes observed between the 1970s and 1996 were consistent with ocean warming, while others seemed associated with a large-scale decline in kelp. Several southern species increased in abundance, while a number of northern species either declined in abundance or disappeared altogether. Current oceanographic data indicate cooler ocean conditions from 1999 through early 2005. Although kelp has returned to the south side of Santa Cruz Island, there appears to be little recovery of kelp at the original survey sites on the north side of Santa Cruz Island. However, analysis of data collected in 2004-05 suggests some interesting changes since 1996, including a slight increase in more northerly-distributed species.fish communitiesSanta Cruz IslandPacific Decadal Oscillationapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5fn0543hpublicationoai:escholarship.org:ark:/13030/qt6sc937102011-07-08T17:30:45Zqt6sc93710Developing New Management Techniques for Sharks in the Drift Gillnet Fishery of the Southern California BightGraham, Jeffrey B.Cartamil, Daniel P.2009-08-25The Southern California Bight (SCB) is a contiguous geographical region that extends from Point Conception, California to northern Baja California and west into the California Current. This region’s productive ecosystem supports various recreational and commercial fisheries, some of which target pelagic sharks. For example, the common thresher shark (Alopias vulpinus) comprises the largest commercial shark fishery in California waters (the California drift gillnet fishery, or CA-DGF. Mako sharks (Isurus oxyrinchus) are also taken in large numbers.The biology and status of pelagic sharks within the SCB have implications for California’s marine resource sustainability. In addition, the SCB is known to be an important nursery area for these and other pelagic shark species. It is thus important to learn what defines mako and thresher shark essential habitat (i.e., the specific areas important for the growth and survival of these species). The objectives for this grant were to learn more about the fine-scale movement patterns and depth distributions of SCB mako and threshers in order to understand ways to reduce their potential vulnerability to the CA-DGF. We accomplished this goal using acoustic telemetry (juvenile makos and threshers) and archival tagging (threshers) technology. This work supported three Scripps Institution of Oceanography (SIO) graduate students as Sea Grant trainees (C. Sepulveda, N. Wegner, D. Cartamil), and provided material for three SIO doctoral thesis chapters (one for trainee Sepulveda, two for trainee Cartamil).For further information on this study, please contact Jeffrey B. Graham (jgraham@ucsd.edu) or Daniel P. Cartamil (dcartamil@ucsd.edu)shark conservationfishery managementIsurus oxyrinchusMako sharkAlopias vulpinuscommon thresher sharkSouthern California Bightapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6sc93710publicationoai:escholarship.org:ark:/13030/qt4r73h01x2011-07-08T17:30:39Zqt4r73h01xAnnual prey consumption of a dominant seabird, Common Murre, in the California CurrentRoth, Jennifer E.Nur, NadavWarzbok, PeteSydeman, William J.2008-06-27We collated information on population size, diet composition, energy requirements, energy densities of prey species, and assimilation efficiency from the literature to estimate annual prey consumption by Common Murres (Uria aalge) between Cape Blanco, Oregon and Point Conception, California in 2004. We estimated that the population consumed approximately 242,250 metric tons of prey, including 70,500 metric tons consumed by breeding adults, 51,920 metric tons consumed by nonbreeding adults and subadults during the breeding season (March-August), 119,620 metric tons consumed by all birds during the wintering period (September –February), and 214 metric tons consumed by dependent chicks prior to leaving breeding colonies. Pacific hake (Merluccius productus) and market squid (Loligo opalescens) each made up over 20% of annual prey consumption. Other species making up at least 10% of annual consumption included shiner surfperch (Cymatogaster aggregata), northern anchovy (Engraulis mordax), and rockfish (Sebastes spp.). Chick diet was dominated by anchovy/sardine (Sardinops sagax; 63%), rockfish (21%), and smelt (Osmeridae spp.; 7%). Understanding these prey requirements is important for understanding the dynamics of predator and prey populations and for effective management of ocean resources.preyconsumption modelmarket squidrockfishanchovysardinebio-energeticsdietfisheries management plancompetitionmarine birdscommon murreapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4r73h01xpublicationoai:escholarship.org:ark:/13030/qt9kq8h0mw2011-07-08T17:28:02Zqt9kq8h0mwSizing fish with an acoustic systemJaffe, Jules S.2009-06-11Observation of acoustic scatter from fish at multiple views can be used to estimate their size and orientation in situ.ocean engineeringbioacousticsfisheries acousticsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9kq8h0mwpublicationoai:escholarship.org:ark:/13030/qt7qv660dp2011-07-04T03:12:55Zqt7qv660dpUnderstanding connectivity to sustain and manage coastal resourcesLevin, Lisa A.Rasmussen, Linda L.2011-03-03We seek to test hypotheses about rates of self seeding, the role of passive circulation and behavior in larval transport, and to identify regional source and sink populations in mytilid mussels. We assessed temporal variability in connectivity patterns for Mytilus spp, using experiments conducted previously (in 03, 04, 05, 06, and 07) and during this grant (08–10), compared results to passive transport predictions corrected for larval supply, and synthesize the information to generate generalized conceptual models of open coast, inner and outer bay connectivity patterns in Southern California.Environmental Health and ProtectionEnvironmental Monitoringmusseldispersallarvaeconnectivityinvertebratetransportinvasive speciesMytilusMusculistaaquaculturemarine reserveself seedingapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7qv660dppublicationoai:escholarship.org:ark:/13030/qt3qd3c1tx2011-07-04T02:54:23Zqt3qd3c1txTransport of Ghost Shrimp as Live Bait: Potential Effects on Impacted Southern California PopulationsPernet, BrunoArchie, James2011-03-02The bait industry in Southern California imports live ghost shrimp, Neotrypaea californiensis, from Oregon and Washington. Though ghost shrimp occur naturally in Southern California, southern populations may be genetically different from northern ones.introduced specieslive baitghost shrimpNeotrypaeabopyrid isopodIoneparasiteapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3qd3c1txpublicationoai:escholarship.org:ark:/13030/qt3s52n48s2011-07-03T23:29:47Zqt3s52n48sDispersion in the Surfzone: Tracer Studies for Water Quality and EcologyFeddersen, FalkGuza, Robert T.2010-10-13Measurement of the spatial and temporal scales of nearshore chlorophyll-a (chl) is critical to our ability to understand or predict dense, and potentially harmful blooms of phytoplankton along the California Coast. Patchiness in chl may result from patchiness in nutrient availability, swimming or sinking, predation, or transport and mixing by breaking waves, currents, internal waves and tides. We performed a study during the Fall 2006 Huntington Beach (HB06) experiment to investigate the biological and physical factors that affect phytoplankton patchiness. Autotrophic phytoplankton require light and nutrients to survive. However, the nearshore euphotic zone (the critical depth for photosynthesis) is often nutrient-depleted due to uptake and planktonic growth. In order to sustain populations, phytoplankton rely on delivery of new nutrients from below the euphotic zone through upwellling or vertical mixing. or 2) terrestrial sources (from rain, ground water, tidal flushing or river outflow) that feed directly into the nearshore.Environmental MonitoringOther Pharmacology, Toxicology and Environmental Healthred tideinternal wavebloomnutrient fluxesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3s52n48spublicationoai:escholarship.org:ark:/13030/qt8zr5h69f2011-07-03T22:40:09Zqt8zr5h69fInvestigating the Limits of Native Oyster Recovery and RestorationGrosholz, Edwin DZabin, Chela2010-02-23The project hypotheses were as follows: A. Oyster recruitment will be higher at inner bay sites than the outer bay sites and density of recruits will be positively associated with adult oyster density. B. Mortality due to predators will be greater in the inner bay than the outer bay sites. C. Introduced predators have a greater per capita impact on oysters than native predators. D. Growth rates of oysters will be higher in the inner bay than the outer bay. E. Mortality due to overgrowth by space competitors will be higher in the inner bay than the outer bay. F. Oyster growth and survival will be higher at inner bay sites and will show a positive linear increase with increasing temperature and phytoplankton abundance.Environmental MonitoringEuropean green crabseastern oyster drillcompetitionpredationrecruitmentphytoplanktonapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8zr5h69fpublicationoai:escholarship.org:ark:/13030/qt56n967pp2011-07-03T22:18:59Zqt56n967ppNematode Community Analysis for Monitoring Meiofaunal Response to the Bolsa Chica Wetlands Restoration ProjectDe Ley, Paul2010-02-25The Bolsa Chica Wetlands have undergone extensive engineering works in 2004-2007 to restore different levels of tidal action in different sectors of the wetlands. Different properties of nematode communities can be used to make management decisions and evaluate restoration success. Published studies have shown among others that nematode abundance increases, while their diversity and evenness decrease, in conditions of nutrient enrichment. From past observations we hypothesize that the following spatial and temporal patterns will occur in Bolsa Chica:- From the beginning of our sampling efforts, we expect to find that Outer Bolsa Bay harbors fewer nematodes, but more species and more equitable numbers per species, compared to Inner Bolsa Bay.- As the effects of tidal restoration kick in, we expect to find progressively more species and evenness but lower abundance in the full tidal restoration area.- As the effects of tidal restoration kick in, we expect to find a more moderate increase in species and evenness versus a moderate drop in abundance in the muted tidal restoration area.- Additionally, we expect a significant change in the taxonomic composition of nematodes in the two restoration sectors.Environmental Monitoringecologyecosystem functioningcoastal managementmeiofaunasedimentswetlandsestuariesnematodesinventorybiodiversity indicesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/56n967pppublicationoai:escholarship.org:ark:/13030/qt34g4z2342011-07-03T22:06:43Zqt34g4z234Tackling Ecological Complexity and Climate Change: Matches and Mismatches in the Seasonal Cycle of California's Marine Flora and FaunaSydeman, William J.Bograd, Steven J.2010-02-26Matches and mismatches in predator needs and prey availability account for changing reproductive success of top predators (fish and seabirds) in the California Current Large Marine Ecosystem (CCLME).climate changephenologymatch-mismatchseabirdssalmonrockfishkrillspatial variabilitytemporal variabilityapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/34g4z234publicationoai:escholarship.org:ark:/13030/qt6q37k2jq2011-07-03T22:06:34Zqt6q37k2jqUnderstanding the Pathogenesis of Streptococcus iniae Infection in Fish and Development of an Effective Vaccine for Use in AquacultureNizet, Victor2010-03-22S. iniae infection has emerged as a serious fish health and economic problem in intensive U.S. aquaculture operations. Current antibiotic options are few and possess severe practical limitations and potential adverse environmental impacts. We believe the major factor contributing to the large burden of S. iniae disease in aquaculture is the lack of fundamental knowledge of S. iniae virulence factors and the fundamental pathogenesis of infection.Fish healthbacterial infectionsStreptococcus iniaevirulence factorvaccineaquaculturestriped bassapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6q37k2jqpublicationoai:escholarship.org:ark:/13030/qt6hp9v9rp2011-07-03T20:55:35Zqt6hp9v9rpEnhancement of fertilization success in abalone: Increasing effectiveness of transplanting and out-planting recovery strategiesZimmer, Richard K.Zimmer, Cheryl Ann2009-03-06This study tests the very general hypothesis that field fertilization success in red abalone is a predictable function of the hydrodynamic regime, and the density, sex ratio and spacing of animals within aggregations.Project Goals and Objectives (1) To determine the hydrodynamic mechanisms that facilitate fertilization of abalone inhabiting coastal waters; (2) To establish the optimal adult density, spacing and sex ratio to maximize fertilization success within a given flow regime; (3) To identify optimal field environments for transplanting or out-planting abalone aggregations, as well as natural abalone distributions that likely experience little or no reproductive success.abalonefertilization successsperm-egg interactionsgametesbroadcast spawnersmating aggregationstransplantingout-plantinghydrodynamicsthreatenedpopulation enhancementapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6hp9v9rppublicationoai:escholarship.org:ark:/13030/qt24n3h68v2011-07-03T20:46:55Zqt24n3h68vAssessing Withering Syndrome Resistance in California Black Abalone: Implications for Conservation and Restoration: Part IIFriedman, CarolynVanBlaricom, Glenn2008-07-25Hypothesis: Quantitative real-time PCR can be used to quantify loads of the WS rickettsial bacterium (infection intensity) in abalone.Hypothesis: Juvenile black abalone recruiting on the California Channel Islands are more resistant to WS than are black abalone in northern Central California that have not experienced high disease (WS) selection pressure.NOTE: only abstract of study available at this time pending publication of papers. For further information, please contact Carolyn S. Friedman (carolynf@u.washington.edu) or Glenn VanBlaricom (glennvb@u.washington.edu ).withering syndromeabalonediseasereal-time PCRpolymerase chain reactiondisease resistanceapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/24n3h68vpublicationoai:escholarship.org:ark:/13030/qt2sv8v6nz2011-07-03T20:46:18Zqt2sv8v6nzEnhancement of Growth Rates and Swimming Performance in Juvenile Marine Finfish in AquacultureLowery, Mary S.Kelley, Kevin2009-04-11We hypothesize that exercise enhances growth of hatchery-reared white seabass by reducing stress and modulating key growth-regulatory factors, and that this will be associated with positive effects on swimming performance. It is secondarily hypothesized that positive effects of exercise on growth and swimming performance will be applicable to other marine finfish, including California yellowtail and California sheephead.AquacultureExerciseEndocrineCortisolMuscle PhysiologyWhite SeabassCalifornia YellowtailCalifornia Sheepheadapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2sv8v6nzpublicationoai:escholarship.org:ark:/13030/qt41g0k84v2011-07-03T20:38:13Zqt41g0k84vBiomedical Development of New Marine Microbial ResourcesJensen, Paul R.Moore, Bradley S.2010-01-13Unique marine actinomycetes reside in ocean sediments and represent a resource for drug discovery. Genome sequences can be mined for new biosynthetic genes and their products.marine actinomycetesmarine natural productsdrug discoverygenomicsbiosynthesisapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/41g0k84vpublicationoai:escholarship.org:ark:/13030/qt7c39q78n2011-07-03T18:57:18Zqt7c39q78nAssessing withering syndrome resistance in California black abalone: Implications for conservation and restorationLenihan, Hunter S.2009-01-29Our overall research objectives were to (1) assess population trends along San Nicolas Island and in Monterey County; (2) optimize black abalone spawning methods; (3) develop and validate a real-time PCR assay for quantification of RLP loads (infection intensity); and (4) examine if progeny of surviving black abalone along the California islands are more resistant to WS than are animals without this disease pressure. At UCSB we were focused primarily on objective (2). We tested the following hypotheses to fulfill our objectives.Hypothesis 1: Black abalone spawning requires environmental conditions similar to their intertidal and shallow subtidal habitat, and not standard methods that were developed for subtidal species. Hypothesis 2: Quantitative real-time PCR can be used to quantify loads of the WS rickettsial bacterium (infection intensity) in abalone. Hypothesis 3: Juvenile black abalone recruiting along the California Channel Islands are more resistant to WS than are black abalone in northern Central California that have not experienced high disease (WS) selection pressure.black abaloneHaliotis cracherodiicaptive breedingdisease resistanceapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7c39q78npublicationoai:escholarship.org:ark:/13030/qt7416r6382011-07-03T18:57:13Zqt7416r638Using Matrix Models to Evaluate Abalone Conservation and FisheryRogers-Bennett, Laura, Dr.2008-09-05The objectives of the project were to create practical quantitative tools to address applied fishery management and marine conservation problems for California's abalone populations. We accomplished both goals during this project.abalonefishery managementquantitative modelingendangered specieselasticity analysissustainabilityapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7416r638publicationoai:escholarship.org:ark:/13030/qt40x397242011-07-03T18:57:08Zqt40x39724California Central Valley Chinook Salmon: A Comparison of Statistical Forecasts for 2007 and 2008Mills, Kyra L.Sydeman, William J.2008-08-07Adult Chinook Salmon returns (ocean catch plus escapement) to the Sacramento River watershed in 2007 were the second lowest on record. This prompted severe management actions, as well as a great deal of speculation into possible causes. In response to the unpredicted and precipitous decline, the Pacific Fisheries Management Council (PFMC) closed the fishery for the 2008 season, the most drastic management measure in the history of West Coast salmon fisheries. The socioeconomic impacts of this measure will be extreme for fishers and coastal communities.central valleychinook salmonecosystem-based managementsocio-economicsSacramento Riverapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/40x39724publicationoai:escholarship.org:ark:/13030/qt4s26f09j2011-07-03T18:57:03Zqt4s26f09jRadiometric age validation and demographic analysis of commercially important, long-lived rockfishesAndrews, Allen H.Cailliet, Gregor M.Coale, Kenneth H.2005-07-01As nearshore fish populations decline, many commercial fishers have shifted effort to deeper continental slope habitats to target fishes for which biological information is limited. One such fishery that developed in the northeastern Pacific Ocean in the early 1980s was for the blackgill rockfish, Sebastes melanostomus, a deepdwelling (300-800 m) species that congregates over rocky pinnacles, mainly from southern California to southern Oregon. Growth zone-derived age estimates from otolith thin sections were compared to ages obtained from the radioactive disequilibria of 210Pb, relative to its parent, 226Ra, in otolith cores of blackgill rockfish. Age estimates were validated up to 41 years, with a strong pattern of agreement supporting a longevity exceeding 90 years. Age and length data fitted to the von Bertalanffy growth function indicate blackgill rockfish are slow-growing (k = 0.040 females, 0.068 males) and that females grow slower than males, but reach a greater length. Age at 50% maturity, derived from previously published length-at-maturity estimates, was 17 years for males and 21 years for females. The results of this study agree with general life history traits already recognized for many Sebastes species, such as long life, slow growth, and late age at maturation. These traits may undermine the sustainability of blackgill rockfish populations when heavy fishing pressure, such as that which occurred in the 1980s, is applied.The canary rockfish (Sebastes pinniger) has been an important part of the recreational and commercial rockfish fisheries from southeast Alaska to southern California for a long time, but stocks have declined considerably over the past few decades. Based on age estimates from otoliths and other structures, longevity estimates vary from just over 20 years to more than 80 years. For the purpose of monitoring stocks, age composition is routinely estimated by counting growth zones in otoliths using the break-and-burn technique; however, age estimation procedures and high longevities for this species remain largely unvalidated. Typical age validation techniques have limited application for the canary rockfish because they are deep dwelling and appear be long-lived fish. In this study we have taken the unaged otolith of the pair from aged fish and have measured the disequilibria of lead-210 (210Pb) and radium-226 (226Ra) as an indicator of age estimate accuracy. The technique proved successful in determining a minimum longevity of about 51 years and provided strong support for the estimation procedures used to determine longevity at over 80 years.California Sea Grant funded publications that pre-date and resulted from this study are listed below. Please contact Allen H. Andrews allen.andrews@noaa.gov for further information.Andrews, A.H., K.H. Coale, J.L. Nowicki, C. Lundstrom, Z. Palacz, E.J. Burton and G.M. Cailliet. 1999. Application of an ion-exchange separation technique and thermal ionization mass spectrometry to 226Ra determination in otoliths for radiometric age determination of long-lived fishes. Can. J. Fish. Aquat. Sci. 56:1329–1338 (R/F-148)Andrews, A.H., G.M. Cailliet and K.H Coale. 1999. Age and growth of the Pacific grenadier (Coryphaenoides acrolepis) with age estimate validation using an improved radiometric ageing technique. Can. J. Fish. Aquat. Sci. 56:1339–1350 (R/F-148)Andrews, A.H., G.M. Cailliet, K.H. Coale, K.M. Munk, M.M. Mahoney and V.M. O’Connell. 2002. Radiometric age validation of the yelloweye rockfish (Sebastes ruberrimus) from southeastern Alaska. Mar. Freshwater Res. 53:139–146 (R/F-148)Kerr, L.A., A.H. Andrews, B.R. Frantz, K.H. Coale, T.A. Brown and G.M. Cailliet. 2004. Radiocarbon in otoliths of yelloweye rockfish (Sebastes ruberrimus): a reference time series for the coastal waters of southeast Alaska. Can. J. Fish. Aquat. Sci. 61:443-451.Stevens, M.M., A.H. Andrews, G.M. Cailliet, K.H. Coale, C.C. Lundstrom. 2004. Radiometric validation of age, growth, and longevity for the blackgill rockfish, Sebastes melanostomus. Fish. Bull. 102:711–722Andrews, A.H., E.J. Burton, L.A. Kerr, G.M. Cailliet, K.H. Coale, C.C. Lundstrom and T.A. Brown. 2005. Bomb radiocarbon and lead-radium disequilibria in otoliths of bocaccio rockfish (Sebastes paucispinis): a determination of age and longevity for a difficult-to-age fish. Proceedings of the 3rd International Symposium on Otolith Research and Application. Mar. Freshwater Res. 56:517–528Kerr, L.A., A.H. Andrews, B.R. Frantz, K.H. Coale, T.A. Brown, K. Munk and G.M. Cailliet. 2005. Age validation of quillback rockfish (Sebastes maliger) using bomb radiocarbon. Fish. Bull. 103(1):97–107Kerr, L.A., A.H. Andrews, G.M. Cailliet, T.A. Brown and K.H. Coale. 2006. Investigations of Δ14C, δ15N, and δ13C in vertebrae of white shark (Carcharodon carcharias) from the eastern Pacific Ocean. Environ. Biol. Fish. 77:337–353.Ardizzone, D.A., G.M. Cailliet, L.J. Natanson, A.H. Andrews, L.A. Kerr and T.A. Brown. 2006. Application of bomb radiocarbon chronologies to shortfin mako (Isurus oxyrinchus) age validation. Environ. Biol. Fish. 77:355–366.Andrews, A.H., L.A. Kerr, G.M. Cailliet, T.A. Brown, C.C. Lundstrom and R.D. Stanley. 2007. Age validation of canary rockfish (Sebastes pinniger) using two independent otolith techniques: lead-radium and bomb radiocarbon dating. Mar. Freshwater Res. 58:531–541rockfishesSebastes melanostomusSebastes pinnigerradiometrylead-210radium-226agegrowthage validationlongevityapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4s26f09jpublicationoai:escholarship.org:ark:/13030/qt79k1b2b82011-07-03T18:54:44Zqt79k1b2b8Relationship Between Bluff Erosion and Beach Sand Supply for the Oceanside Littoral CellAshford, Scott A.Driscoll, Neal W.2008-12-03Ongoing research by Ashford and Driscoll suggests that erosion of the sea cliffs is an important source of sand to the beaches (50%) in the Oceanside Littoral Cell. This hypothesis is in marked contrast to the established paradigm that rivers supply the majority of sand (up to 85%) to the beaches in the Oceanside Littoral Cell and the cliffs are an unimportant source of sand.bluff erosionsource of beach sandLIDARapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/79k1b2b8publicationoai:escholarship.org:ark:/13030/qt79k0542s2011-07-03T17:33:54Zqt79k0542sRecovery of Trophic Function in Restored Pacific WetlandsLevin, Lisa A.Currin, Carolyn A.2005-01-12Given the increasingly widespread wetland restoration activities in California(Zedler 1996), it is imperative that reasonable measures of success be adopted. In thepast, monitoring of restored wetlands has focused on superficial indicators of structure, such as density or species number. Functional measurements have been more elusive(Zedler 2000). In this study we compared the trophic structure and function of a 6-7 yearold created salt marsh and adjacent natural marsh in Mission Bay, San Diego, Californiain an effort to develop means to assess recovery of trophic function. The majorobjectives of the study were to (1) evaluate of benthic community structure (density,composition and diversity), (2) track seasonal and interannual changes in trophicstructure based on natural abundance stable isotopic analyses, (3) conduct isotopicenrichment experiments to identify consumers of specific food sources (microalgae,cyanobacteria, Spartina and other bacteria), (4) perform of plant cover manipulations toevaluate the mechanisms by which Spartina influences benthic processes, and (5)improve conceptual understanding of trophic successional processes associated withrestoration. In combination these research results allow us to assess the extent to whichthe Crown Point Mitigation Site (CPMS) in Mission Bay California has come to resemblethe natural wetland (Northern Wildlife Preserve [NWP] and Kendall Frost Marsh) and themechanisms underlying this recovery.macrofaunafood websuccessionmicroalgaeSpartina foliosanatural abundanceisotopic analysisisotopic enrichmentsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/79k0542spublicationoai:escholarship.org:ark:/13030/qt3d67w27z2011-07-03T16:42:09Zqt3d67w27zAssessing the Impact of Climate Change on the California Squid Fishery: An Integrated ApproachMarinovic, Baldo B.Croll, Donald A.Mangel, Marc S.2003-07-30The overall objectives of this project were to: 1. Establish the nature and magnitude of the link among the physical dynamics of coastal upwelling, primary production, krill production, and productivity of the most important commercial fish species in California (market squid, Loligo opalescens); 2. Using the information from the first objective, construct models to explore various scenarios of the impacts of global climate change on nearshore krill and squid productivity.ClimateEcosystemFisheryKrillSquidapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3d67w27zpublicationoai:escholarship.org:ark:/13030/qt5rd5v0kd2011-07-03T16:42:05Zqt5rd5v0kdBacterial and Protozoal Contamination of Nearshore Marine Environments in California, with Ecologically Sustainable ManagementAtwill, Edward R.Conrad, Patricia A.2008-06-04This project was developed to apply novel study designs and microbiology techniques to better understand and control fecal pollution flowing from terrestrial to aquatic ecosystems in California. The first objective was to evaluate the distribution of the fecal pathogen Cryptosporidium in nearshore waters, using mussels as bioconcentrators of the parasites from fecal contaminated waters. The second objective was to evaluate the distribution of fecal protozoa and bacteria on and around coastal farms, as well as evaluating the efficacy of a variety of Benefical Management Practices (BMPs) in reducing the load of fecal pathogens in storm runoff on these farms. The third objective was to extend our study findings to the local and regional stakeholders, the regulatory community, and the scientific community.bacteriacoliformprotozoacryptosporidiumgiardiawater qualityapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5rd5v0kdpublicationoai:escholarship.org:ark:/13030/qt7t14p22h2011-07-03T16:41:59Zqt7t14p22hDetermination of Chinese mitten crab, Eriocheir sinensis, year-class strength through investigation of their reproductive life historyTsukimura, Brian2008-04-08We have attempted to determine the environmental factors that may regulate the year-class strength of the invasive mitten crab, Eriocheir sinensis. Specifically, we are attempting to correlate the environmental factors that are involved in crab larvae (zoeae) survivorship, thus determining the numbers of mitten crab adults that occur in successive years. This type III life history suggests that under optimal conditions, the more zoeae survive, more adults will occur in 3-4 years.mitten crabinvasive speciespopulation ecologyapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7t14p22hpublicationoai:escholarship.org:ark:/13030/qt1d59v84t2011-07-03T16:41:53Zqt1d59v84tEradicating Arundo Donax from California Ecosystems: Establishing the Most Effective Timing of Mechanical and Chemical ProceduresWijte, Antonia2001-07-31Arundo donax (giant reed) is a tall grass that is native from the lower Himalayas and invaded the Mediterranean region, prior to its introduction in the America's (Rieger and Kreager, 1989; Granval, et al., 1993; Abissy and Mandi, 1999). It is suspected to first have been introduced to the United States in the 1700s, and in the Los Angeles area in the 1820s by Spanish settlers (Bell, 1993, Iverson, 1993 #1573). Its primary use was for erosion control in drainage canals. A number of other uses for Arundo have been identified. It is the source of reeds for single-reed wind instruments such as clarinet and the saxophone (McFadden and others 1992, Popov and others 1990; Perdue 1958, Van Der Wegen and others 1991). In Europe and Morocco Arundo is used for waste-water treatment (Abissy and Mandi, 1999), such as nutrient and heavy metal removal, and water volume evapotrans-piration. The high rate of evapotranspiration by stands of this species, used as a benefit in these countries, is one of the characteristics that is detrimental in the California ecosystems invaded by Arundo.Arundo donaxinvasive grassasexual reproductionrootingcritical nitrogen contentseasonal patternsoptimizing timingcuttingherbicide application.application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1d59v84tpublicationoai:escholarship.org:ark:/13030/qt0jj5c19h2011-07-03T16:41:27Zqt0jj5c19hThe San Diego–La Jolla Ecological Reserve: Implications for the Design and Management of Marine ReservesParnell, P. EdDayton, Paul K.Lennert-Cody, Cleridy2004-04-05The kelp forests of California are an important habitat for many species of economically important fish and invertebrates. There has been an alarming downward trend for many of these species over the last two decades to the extent that the kelp forests resemble ghost towns. It is becoming increasingly apparent that these so-called “ghost-forests” are in need of protection. In response to this downward trend in marine populations off California, the state legislature passed the Marine Life Protection Act in 1999. This Act mandates the establishment of a network of marine reserves to reverse these declines. Unfortunately, political pressure based on the dearth of focused science has impeded implementation of the law.AbaloneFishKelpUrchinapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0jj5c19hpublicationoai:escholarship.org:ark:/13030/qt6bs8t20x2011-07-03T16:41:13Zqt6bs8t20xPreservation of Genetic Variation within Aquaculture Stocks of White SturgeonMay, Bernard P.Rodzen, Jeff A.2001-05-01The overall intent of this project was to develop a breeding plan for white sturgeon, using Stolt Sea Farm California LLC as a model system for broodstock management and selection using molecular markers. While the title of this project implies the function of the breeding plan to be of maintaining existing genetic variation as inferred from nuclear DNA markers, it is in the best interest of those parties involved in commercial production of this species to evaluate the feasibility of directed selection for economic traits such as growth rate. Thus, this project involves the estimation of quantitative genetic variation in addition to developing specific applications of molecular markers to broodstock management. Recommendations for their integration into a breeding plan and an overview of our research will be summarized in a manuscript being prepared (Rodzen et al. in prep4).white sturgeonbroodstock managementDNA markersaquaculturegenetic variationapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6bs8t20xpublicationoai:escholarship.org:ark:/13030/qt5qt9p1r92011-07-03T15:15:57Zqt5qt9p1r9Investigation of Anti-cancer Compounds in the Marine Bryozoan Bugula pacificaHaygood, Margo G.2003-04-08The original overall project objective was to discover anti-cancer compounds in Bugula pacifica. B. pacifica is related to B. neritina, whose bacterial symbionts produce anti-cancer polyketides called bryostatins. Preliminary results showed biological activity in B. pacifica extracts. B. pacifica also harbors a bacterial symbiont which also may produce bioactive polyketides.Evolutionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5qt9p1r9publicationoai:escholarship.org:ark:/13030/qt8fk2b5q82011-07-03T15:15:47Zqt8fk2b5q8Studies on the rapid self assembly of elastic tensile fibers from a natural protein polymer found in marine snailsWaite, J. HerbertShadwick, Robert E.2009-03-311. Whelk egg case precursor proteins are stockpiled in the nidamental gland of a gravid female whelk and assembled post-fertilization into an impervious protective coating for the egg. 2. Egg case maturation is rapid and involves extensive chemical crosslinking. 3. Egg case material is quasi-elastic and completely reversible in tension, but relies primarily on nonentropic forces. 4. Fibers with the mechanical properties of whelk egg case can be electrospun from protein precursors.whelk egg capsuleBusycon canaliculusnidamental glandprecursor proteinalpha to beta transitionnonentropic elasticityself-healingelectrospinningapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8fk2b5q8publicationoai:escholarship.org:ark:/13030/qt4x3467362011-07-03T15:15:25Zqt4x346736A Historical Analysis of the Collapse of Pacific Groundfish: U.S. Fisheries Science, Development, and Management, 1945–1995Oreskes, NaomiFinley, Carmel2007-06-05The objective of this study had been to understand the historical development of U.S. fisheries science. We hoped to gain a better understanding of why fisheries management has failed to achieve the goal of sustainable fisheries that would protect fish stocks, as well as the livelihoods of fishermen and the coastal communities in which they live. This has been a historical project, based on archival research in the history of fisheries management, science, and policy.fisherieshistory of sciencegroundfishmodelspolicyMSYfisheries historyapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4x346736publicationoai:escholarship.org:ark:/13030/qt3c02z6td2011-07-03T15:14:43Zqt3c02z6tdConservation Genetics of California Abalone: Developing Tools for ManagementBurton, Ronald S.2005-05-04Over the past three decades, we have witnessed dramatic declines of abalone stocks along the southern California coast. What was once an important fisheries resource (commercial and recreational) has completely disappeared and there is now a moratorium on all abalone harvesting in the region (California Department of Fish and Game 2002). Populations of white, red, black, pink and green abalone have all been impacted; the former species, Haliotis sorenseni, has become the first marine invertebrate to be listed as an endangered species. Both anthropogenic (overexploitation and habitat destruction) and natural (disease and predation) processes have contributed to the decline in abalone abundance. Attempts to develop effective conservation and recovery strategies for abalone require understanding many aspects of the biology of these species. The primary question is: can reproduction in remnant populations provide the recruits necessary for recovery of abalone populations that have gone locally extinct? Two factors are important in answering this question. First, there is the question of fertilization success in low abundance populations of broadcast spawning invertebrates; can males and females locate one another and successfully produce fertilized eggs? The second issue regards the level of "connectivity" of abalone populations; can success in one part of the species range provide a natural reseeding in other parts of the range? This project used population genetic methods to address the latter question.abalonegeneticsconservationapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3c02z6tdpublicationoai:escholarship.org:ark:/13030/qt9vv2r9t42011-07-03T15:08:55Zqt9vv2r9t4Aquatic Nuisance Species: A multi-stage approach to understanding the invasion ecology of exotic crayfish in Northern and Southern CaliforniaKats, LeePintor, LaurenSih, AndrewKerby, Jake2006-07-03Biological invasions are widely thought to have major negative impacts on native communities and ecosystems (Vitousek et al. 1996; Parker et al. 1999; Mack et al. 2000). Exotic species are the second most important cause of species extinctions (after habitat destruction) in the United States (Enserink 1999) and an important cause of losses in biodiversity worldwide (Sala et al. 2000). From an economic, resource management view, exotic species can have major direct and indirect impacts on commercially-important natural resources – e.g., fisheries, crops (Pimentel et al. 2000). Although exotic species can impact native species via various mechanisms (e.g., competition, spread of disease, hybridization), for aquatic animals, a key mechanism is clearly predation (Moyle and Light 1996; Gamradt and Kats 1996; Knapp et al. 2001). Thus an important goal on the interface between basic and applied ecology is to understand the ecology of potentially damaging invasive predators (including omnivores), in order to minimize their negative impacts.invasive speciesexotic speciesinvasion biologyimpactsrecoverycrayfishPacifastacus leniusculusProcambarus clarkiisignal crayfishred swamp crayfishstream communitiesamphibiansapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9vv2r9t4publicationoai:escholarship.org:ark:/13030/qt1rj6h8br2011-07-03T15:08:23Zqt1rj6h8brAssessing Environmental Control of Domoic Acid Production by the Planktonic Diatom Pseudo-nitzschia australis in California WatersSilver, MaryGarrison, DavidTjeerdema, Ron2001-06-15This Sea Grant project focused on domoic acid production by the toxin-producing diatoms (Pseudo-nitzschia australis and P. multisieries) in coastal California waters. There were two major aspects of our work: 1) the development of a laboratory HPLC assay for measuring domoic acid and the tracking of DA in a field mortality event using the HPLC assay, and 2) developing continuous culture facilities and examining the nutrient physiology of Pseudo-nitzschia species.domoic aciddiatomsPseudo-nitzchia australisP. multisieriescoastal Californiaapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1rj6h8brpublicationoai:escholarship.org:ark:/13030/qt7p89d60f2011-07-03T15:07:59Zqt7p89d60fMEIOSIS IN TETRAPLOID PACIFIC OYSTERS, THEIR TRIPLOID MOTHERS, AND DIPLOID GRANDMOTHERSHedgecock, Dennis2004-09-30The Pacific oyster occurs on all continents but Antarctica (Mann 1979) and for the past several years has had the highest annual production of any freshwater or marine organism (4.2 million metric tons in 2002, worth $3.5 billion; FAO 2004). About 92 million pounds of Pacific oyster meat were produced on the West Coast in 2000, with a farm-gate value of nearly $70 million (Toba and Chew 1999). West Coast production exceeds the harvest of Eastern oysters on either the Gulf or Atlantic Coasts, primarily because diseases have wiped out those natural stocks. As the Pacific oyster does not naturally reproduce along much of the West Coast, seed was imported from Japan for decades (Chew 1984). In the early 1980s, however, the industry adopted hatchery techniques and now relies mainly on hatchery seed. This sets the stage not only for commercial breeding programs, which industry identifies as a top priority (Pacific Shellfish Institute 1999), but also for development in the future of a mature seed industry servicing global markets.Pacific oystertetraploidstriploidsmeiosisrecombinationlinkageapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7p89d60fpublicationoai:escholarship.org:ark:/13030/qt6c1161292011-07-03T09:53:40Zqt6c116129California's Dungeness Crab: Conserving the Resource and Increasing the Net Economic Value of the FisheryHankin, David G.Hackett, Steven C.Dewees, Christopher M.2005-01-19Along the Pacific coast (CA/OR/WA), the historical mainstays of the fishing industry have been thePacific salmon, groundfish, and Dungeness crab fisheries. However, recent cuts in allowablelandings of salmon and groundfish have shifted fishing effort toward crab. Diminishingopportunities in salmon and groundfish in California will further increase fishing effort onDungeness crabs, resulting in the intensifying derby that now characterizes the fishery andimposing increased pressure on stocks at deeper depths. Projected increased fishing effort will alsolikely create new biological conservation concerns for Dungeness crab populations and diminish itsnet economic value of the fishery.fishery economicsDungeness crabsmortality ratesnet economic yieldapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6c116129publicationoai:escholarship.org:ark:/13030/qt5rf6x1qw2011-07-03T09:50:05Zqt5rf6x1qwModeling Water and Sediment Quality in the Coastal OceanStolzenbach, Keith D.McWilliams, James C.2008-07-30The overall goal of the research project is to develop a model of water and sediment quality capable of forecasting environmental events occurring over small space and time scales in the coastal zone, including embayments, harbors, and shoreline regions.circulationCalifornia coastalcurrentdiffusionecosystemoceanographypollutionsedimentstratificationapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5rf6x1qwpublicationoai:escholarship.org:ark:/13030/qt842822bq2011-07-03T09:49:56Zqt842822bqCalifornia Beach Health: Evaluation of Grunion as an Indicator SpeciesMartin, Karen2008-11-06On sandy beaches throughout California, we evaluated three stages of the life cycle of the grunion Leuresthes tenuis for their potential as possible indicators of local ecological health and condition. We examined spawning runs of the adults, embryonic development of the terrestrially incubating eggs, and the viability of hatchlings from multiple spawning runs and beaches over three years. We looked for characteristics that lead to strong runs and high embryo survival on grunion beaches and at changes over time through the season. Using this unique long-term dataset we may be able to assess the strength of the population of this species for the first time over its entire range. We predicted that assessment of differential success of grunion reproduction can provide new indicators for ecological health of sandy beaches. In addition we intend to provide increased scientific justification for establishing best management practices for sandy beaches, to restore and protect the sandy beach habitat for the benefit of wildlife and human visitors.beachCaliforniacoastecosystemeggfishgrunionreproductionsandspawningmanagementcitizen scientistsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/842822bqpublicationoai:escholarship.org:ark:/13030/qt98n9v6sx2011-07-03T07:26:27Zqt98n9v6sxNovel Post-Translationally Modified Peptide Antibiotics from Solitary TunicatesLehrer, RobertVacquier, Victor D.Taylor, Steve2004-04-16Although the pharmaceutical industry has “mined” the world of soil bacteria, streptomycetes and fungi to find novel antimicrobial molecules, the emergence of resistant superbugs necessitates identifying new antibiotic sources. Recent research into the innate immune system has focused attention on antimicrobial peptides – molecules that equip animals to resist infection without assistance from antibodies and other accoutrements of adaptive immunity. In recent years, potent antimicrobial peptides have been identified in the blood cells (hemocytes) of horseshoe crabs, shrimp, mussels and tunicates ("sea squirts"). Our studies centered on three tunicates (Styela clava, Styela plicata and Ciona intestinalis) that are abundant in Southern California's shallow waters.Antibioticapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/98n9v6sxpublicationoai:escholarship.org:ark:/13030/qt0qz1k6j42011-07-03T07:26:18Zqt0qz1k6j4Fisheries Habitat: Recruitment, Growth, and Survival of Coastal Fishes on an Experimental Artificial ReefAnderson, Todd W.Reed, Daniel C.Schroeter, Steven C.2004-04-15Currently, many fisheries are under severe pressure from anthropogenic impacts, including over-fishing and habitat degradation. Several approaches have been developed to ameliorate such impacts, including the reduction of catch quotas, implementation of marine reserves, and habitat enhancement. Artificial reefs, as supplemental habitat to coastal systems, often has been used under the premise that additional habitat will increase production of coastal fishes, thereby increasing fish stocks. Several criticisms have been leveled at artificial reefs as a tool in habitat enhancement for a failure to (1) decouple attraction and production in assessing the contributions of artificial reefs, (2) evaluate regional production on artificial and natural reefs, (3) construct artificial reefs to be similar in habitat to natural reefs, (4) replicate artificial reefs for rigorous experimentation and statistical analysis, and (5) consider process-oriented studies at more appropriate spatial scales.AccidentFishHabitatProductionRecruitmentapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0qz1k6j4publicationoai:escholarship.org:ark:/13030/qt1k8479q72011-07-03T07:25:57Zqt1k8479q7Full-scale Lateral Load Testing of Pier 3 at the Port of Long BeachWalsh, Sean M.Ashford, Scott A.2004-01-30Before the release of the Seismic Design Criteria for California Marine Oil Terminals (Ferrito et. al, 1999), the seismic design of piers and wharves was a nonuniform procedure. Design practices of the past typically underestimated earthquake intensities, a fact that has become clear after seismic events such as the Loma Prieta (1989) and Northridge (1994) earthquakes. Based on the damage to port facilities observed in such events, the Marine Facilities Division (MFD) of the California State Lands Commission, with funding through FEMA and the California Office of Emergency Services, is developing specific regulations for the seismic performance of marine oil terminals in California. The goals of the criteria established by Ferrito et al., (1999) are to (i) ensure safe and pollution-free transfer of petroleum products between ship and land-based facilities, (ii) ensure the best achievable protection of public health, safety, and the environment, and (iii) maximize utilization of limited resources. A major component in the effort to realize these goals is the development and implementation of standardized design criteria, hence, the Seismic Design Criteria for California Marine Oil Terminals.EarthquakePortSoilapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1k8479q7publicationoai:escholarship.org:ark:/13030/qt2d97c5wk2011-07-03T07:25:49Zqt2d97c5wkAssessing Sanctuary Shorelines: A Role for Volunteers, Particularly High
School Students, in Resource ManagementPearse, John S.Osborn, Dawn A.Roe, Christy A.2003-06-01During 2001-2003, we developed a rocky intertidal monitoring program to be used by NOAA’s National Marine Sanctuary program on the west coast of the US. The goals were to 1) inform the public about the rocky intertidal habitat and the species that live there, 2) directly involve students (7th - 12th grade) and other volunteers in the field, and 3) collect and archive data that can be analyzed to detect changes in intertidal life over time.EducationShorelineStudentapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2d97c5wkpublicationoai:escholarship.org:ark:/13030/qt1gp9c2c62011-07-03T07:25:38Zqt1gp9c2c6Nearshore Temperature VariabilityLargier, John2004-04-01Near-surface ocean temperatures off California vary from cold upwelling values as low as 8oC to warm El Nino summer values greater than 23oC (and even higher values in enclosed bays, over 26oC). Temperature varies from place to place, with colder waters typical along upwelling shores north of Pt Conception, and temperature varies in time, with the seasons and in response to upwelling events. This project set out to explore the patterns of temperature variability across different time and space scales, to explain the causes of these patterns, and to identify the relationships with key ecological or environmental concerns. Primarily based on several existing data sets, new data were collected to describe notable temperature pattern at small alongshore scales associated with coastal headlands and embayments.CaliforniaCoastalEcologyEnvironmentapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1gp9c2c6publicationoai:escholarship.org:ark:/13030/qt1pv5f4cw2011-07-03T07:25:07Zqt1pv5f4cwAnthropogenic Impacts on Rocky Intertidal Mollusks in Southern California: Compiling Historical Baseline and Quantifying the Extent of the ProblemRoy, Kaustuv2007-08-08Anthropogenic activities such as illegal harvesting and trampling is generally considered to be responsible for a decline in the biological diversity of rocky intertidal habitats along the southern California coast (Littler, 1980; Littler et al. 1991; Murray and Bray 1994; Lindberg et al. 1998; Murray et al. 1999; Roy et al. 2003). Yet relatively little information exists about the nature and extent of such declines, largely due to the lack of baseline data against which one can compare the exploited or disturbed populations. This is a difficult problem because at present very few rocky intertidal assemblages in southern California are undisturbed enough to serve as an ecological baseline(s) against which other sites can be compared. Similarly, reliable ecological census data from the past are very rare and we will never be able to quantify temporal changes in abundances of species except at a few localities (such as that by Barry et al. 1995). However, data on past species occurrences (i.e. presence/absence data) can be compiled much more easily and across much larger spatial and temporal scales. Museum collections and the literature are a rich source of such data and once compiled they have the potential to provide us with a picture of how species occurrence patterns have changed over the last century or so. The primary goal of this project was to use historical data collected over the last century to construct a long-term perspective that can be used to quantify the ecological consequences of anthropogenic impacts on rocky intertidal molluscan species and populations. In particular, we refined and expanded a database of historical occurrences and body sizes of rocky intertidal molluscan species at multiple localities in southern California. These data, for the first time, provide a comprehensive picture of our knowledge of past occurrences of rocky intertidal molluscan species in southern California. We then used analyses of site occupancy patterns over time to identify sites with the best historical data on species occurrences and undertook ecological surveys at a selected subset of these localities. We are using comparative analyses of the historical information and the survey data to quantify how patterns of site occupancy as well as body sizes of individual species have changed over time.intertidalconservationhuman impactsmollusksbody sizeapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1pv5f4cwpublicationoai:escholarship.org:ark:/13030/qt9v05t4xw2011-07-03T07:24:51Zqt9v05t4xwMitigation of Coastal Bluff Instability in San Diego County, California/Evaluating Seacliff Morphology and Erosion Control in San Diego County Using LIDAR and GISAshford, Scott2005-10-28In order to evaluate seacliff erosion, morphology, and erosion control, this project applied new LIDAR (LIght Detection And Ranging) technologies and advanced geographic information systems (GIS) analysis. LIDAR is the newest and most accurate technology being used to map the coastline. Both aerial and ground-based LIDAR data were analyzed during this study. This project focused on the Oceanside Littoral Cell which extends from Dana Point at the northern end, to La Jolla at the south.coastal bluffsstabilizationerosionLIDARGISapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9v05t4xwpublicationoai:escholarship.org:ark:/13030/qt70j9t8zj2011-07-03T07:24:21Zqt70j9t8zjINTEGRATED MODELING OF THE SOUTHERN CALIFORNIA COASTAL OCEAN: BIOGEOCHEMISTRY AND PARTICULATE DYNAMICSStolzenbach, Keith D.McWilliams, James C.2002-07-24The Southern California Coastal Ocean (SCCO), defined as the region inclusive of the Southern California Bight and the Santa Barbara Channel, from the shoreline to beyond the continental shelf, has significant anthropogenic injections of many materials through the air, rivers, runoff, outfalls, sediments, and marine spills. These inputs are superposed on a dynamic system of internal processes including water motions, biological production in the surface layers, particle sinking, dissolution, and scavenging. In spite of lengthy and continuing sequences of SCCO measurements at various scales, a synthetical understanding and an ability to make skillful predictions and comprehensive assessments of the fate and transport of these materials in the SCCO remains illusive. In many cases the interpretation of localized measurements lacks a regional context. Conversely, there is little information on the regional impacts of localized sources. It is clear that an integrated computational model of the most relevant processes is needed before these goals can be achieved. An integrated model will be of great value to environmental managers responsible for sewage discharges, storm water discharges, and coastal fisheries. The overall project objective is to develop, test, and use for practical purposes an integrated computational model of the physical, chemical, and biological processes relevant to the distributions of natural and anthropogenically injected materials in the Southern California.water-quality modelscirculation modelsecosystem modelsregional ocean modelsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/70j9t8zjpublicationoai:escholarship.org:ark:/13030/qt1pc7h0942011-07-03T07:24:14Zqt1pc7h094Characterizing Vegetation-Hydrology Relationships for Tidal Marsh RestorationFoin, Theodore C.2002-04-15Sea Grant sponsorship to this program was used to establish the role of some of the many factors affecting vegetation distribution and zonation in San Francisco Bay-Delta marshes. Although much of the more recent research has emphasized species interactions, we emphasized physical factors in the belief that these were the principal factors that could be manipulated in early restoration. In particular, we found in our comparative studies of tidal marshes that seasonal changes in soil salinity were likely controlling distribution and biomass production in the vegetation. However, soil salinity itself is partly a function of tidal hydrology, since tidal input is capable of both increasing and decreasing salinity. As one of the principal accomplishments of this past year, we were able to develop a conceptual model of vegetation response to physical gradients in the marsh environment, for the major dominant vegetation species.San Francisco Bay-Deltatidal marshrestorationsoil salinityapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1pc7h094publicationoai:escholarship.org:ark:/13030/qt2rc455m12011-07-03T07:24:06Zqt2rc455m1Bioeconomic Modeling of the Spatial/Strategic Interactions of Fishermen and Regulators in Alaskan Seasonal FisheriesAbbott, Joshua K.Wilen, James E.2006-10-09Prohibited species catch (PSC) by the groundfish fleet in the Bering Sea has been a persistent and mounting policy concern since the early 1990s. Prohibited species are those species that are prohibited for retention by the groundfish fleet, often in an effort to sustain lucrative targeted fisheries for these species. The allowable catch of these species is controlled by the allocation of fleet-wide quotas to particular gear and fishery target combinations. For instance, those fleets using bottom-trawl gear to catch yellowfin sole in the Eastern Bering Sea are limited in the quantities of Pacific halibut, C. bairdi tanner crab, and red king crab that they can catch in a given fishing year or season.bioeconomicsseasonal fisheriesBering SeaPSCquotasflatfish fisheriesH&Gprohibited species bycatchapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2rc455m1publicationoai:escholarship.org:ark:/13030/qt1n07g5sn2011-07-03T07:24:01Zqt1n07g5snMolecular and Bioassay-Based Investigation of Bivalves as Transmission Vectors of
Protozoal Encephalitis in Southern Sea OttersConrad, Patricia A.2003-08-01An epidemiological study was conducted to determine whether Toxoplasma gondii protozoal brain infection and seropositivity in southern sea otters are associated with specific risk factors, including age, sex, geographic distribution and month of sampling.EffluentOtterPollutionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1n07g5snpublicationoai:escholarship.org:ark:/13030/qt24g728g12011-07-03T07:23:49Zqt24g728g1Vertical Flow Dynamics in Kelp Forests: Implications for Nutrient Uptake, Condition and SurvivalEdwards, Matthew S.2008-08-08(1) The influence of ocean waves on giant kelp fronds results in the vertical transport of water along the thallus(2) Morphological traits of giant kelp result in vertical transport being greater than in the absence of giant kelp(3) Vertical flow along giant kelp thalli is persistent, but flow rate is correlated with vertical orbital displacements of the incident ocean waveskelpthermoclinenutrientstemperatureMacrocystisvertical flowapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/24g728g1publicationoai:escholarship.org:ark:/13030/qt4443m5v82011-07-03T07:19:23Zqt4443m5v8Modeling of Water and Sediment Quality in Impacted Coastal EmbaymentsStolzenbach, Keith D.McWilliams, James C.2003-03-01The purpose of this document is to present in a compact form the capabilities of the UCLA version of the Regional Ocean Modeling System (ROMS), incorporating sediment transport algorithms developed in collaboration with the U.S. Geological Survey, to address water and sediment quality issues in the coastal ocean with particular reference to the Southern California Bight and the coastal region near Los Angeles and Orange County. In the following sections the components of the ROMS model are discussed, including examples of applications. The document concludes with a summary of needs for future model development and potential new applications.CoastalPollutantSedimentWaterapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4443m5v8publicationoai:escholarship.org:ark:/13030/qt9205j0bg2011-07-03T07:18:21Zqt9205j0bgControl of Rickettsial Infections in White Sea Bass (Atractoscion nobilis)Hedrick, Ronald P.Arkush, Kristen D.2002-04-17This project was designed to address an emerging disease problem encountered in restoration efforts for the white seabass (Atractoscion nobilis) in California. Once an abundant species, declines have encouraged hatchery-based enhancement of this popular sport fish. Infections with a rickettsial-like intracellular pathogen caused serious losses in the hatchery in 1998. Losses in the hatchery exposed serious knowledge gaps with respect to the type of intracellular parasite causing the disease, the potential sources of the parasite, what diagnostic methods could be developed to detect it, what impacts could the parasite have on other marine or anadromous species (e.g., Pacific salmon) and lastly what means might be developed to control the disease caused by the parasite.Piscirickettsiosiswhite seabassPiscirickettsia salmonisapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9205j0bgpublicationoai:escholarship.org:ark:/13030/qt8b8438pc2011-07-02T23:27:23Zqt8b8438pcMarine Bio-Nanotechnology: High-Performance Materials from Sponge SilicateinMorse, Daniel E.2007-05-29We recently discovered the molecular mechanism by which a common California marine sponge synthesizes the fiberglass-like structures that form the internal skeleton of this simple marine animal. Our goals are: (1) to harness the proteins and molecular mechanisms that control this synthesis to make valuable semiconductors inexpensively under environmentally friendly conditions; and (2) to use this new approach to develop, low-cost, high-efficiency solar energy converters and other practical electronic applications. Training of students in the unique interdisciplinary approach of this project, combining new developments in biotechnology, advanced instrumentation, and materials engineering to produce advanced high-performance materials, also is a major objective of our project.marine biotechnologynanotechnologyspongesilicasilacateingeneticDNAproteintitaniumsolar energyphotovoltaicsemiconductorelectronicsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8b8438pcpublicationoai:escholarship.org:ark:/13030/qt0hn0d2332011-07-02T23:27:14Zqt0hn0d233Environmental Effects on Anti-Microbial Activity of Bacterial Symbionts in the Reproductive System of SquidEpel, David2004-04-29The goals of this grant were: 1). To identify and characterize the symbiotic bacteria associated with the accessory nidamental gland and egg sheath of squid and cuttlefish. 2). To describe the changes in quantity and distribution of these bacteria in the egg sheath during development of the squid embryo. 3). To grow these bacteria in culture. 4). To determine culture conditions that permit production of secondary products that are anti-bacterial and anti-fungal. 5). To determine if synthesis of secondary products is related to quorum sensing, to microaerophily, to surface effects and/or to interspecies interactions referred to as synthropy. 6). To develop methods to determine which bacteria are responsible for secondary products should it prove impossible to grow the candidate bacteria in culture. 7). Once the conditions are worked out for identification of the bacteria and their growth, then to identify and characterize these bacterial secondary products through collaborative research with natural products chemists. We have made exceptional progress on most of these goals as will be described in this final report.bacteriasymbiosisanti-microbialanti-fungalsquidbacterial consortiaquorum sensingapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0hn0d233publicationoai:escholarship.org:ark:/13030/qt3vk7g6j82011-07-02T23:27:10Zqt3vk7g6j8New High-performance Nanocomposite Materials from Marine Biomineralization: Biotechnological and Interdisciplinary ApproachMorse, Daniel E.2004-03-31To help meet the needs for a new generation of advanced, high-performance composites required for new construction materials, new micro-electronic, optoelectronic and catalytic devices, chemical and biological sensors (Bright, 1994), energy transducers, "smart" medical implants (Newnham, 1997) and faster and higher capacity “biochips” (Kozal et al., 1996; Travis, 1997), materials scientists have turned to the biomimetic production of mineralized nanocomposites modeled on those produced by marine organisms (Eisner, 1991; Mann et al., 1992, 1993; Heuer et al., 1992; Pennisi, 1992; Mann, 1993; Walsh et al, 1994; Hoch et al., 1996; Mann and Ozin, 1996; Yang et al., 1997). These ceramic-like composites of mineral and biopolymers offer unique combinations of strength, anisotropy, biocompatibility, precise structural control at the nanoscale level, and coupling between mineral and organic polymeric phases that make them especially attractive models for commercially valuable new materials (e.g., Bouchon et al., 1995; Hoch et al., 1996).BiotechnologyCatalystPolymerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3vk7g6j8publicationoai:escholarship.org:ark:/13030/qt68s6s1f52011-07-02T23:26:25Zqt68s6s1f5Model Selection in the Stock AssessmentLucero, Yasmin2007-07-12For my Sea Grant/NMFS population dynamics graduate fellowship I spent three summers as an intern with Dr. Alec MacCall at the Southwest Fisheries Science Center Santa Cruz Lab. During that time we investigated the problem of model uncertainty in the stock assessment. I was particularly concerned the population biology of the slow growing genus Sebastes.To understand the influence of model uncertainty, I developed a population simulation model. I fit population models to the simulation model and compare parameter estimates to the "true" simulation values [3]. I also compare goodness of fit measures. The simulation model was parameterized to mimic the biology of widow rockfi�sh (Sebastes entomelas).There are three sources of stochasticity in the simulation model. The model has stochastic recruitment, stochastic natural mortality and stochastic individual growth. Stock assessments routinely estimate stochasticity in the recruitment function [5]. However, it is very rare to estimate uncertainty in the natural mortality rate. And, to the best of my knowledge, no stock assessment has assumed stochasticity in individual growth.widow rockfi�sh (Sebastes entomelas)stock assessmentsimulation modelrecruitmentpredationapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/68s6s1f5publicationoai:escholarship.org:ark:/13030/qt1pz5r5rj2011-07-02T23:26:07Zqt1pz5r5rjPopulation Genetics of the Commercially Important CabezonVillablanca, FrancisNakamura, Royden2008-01-16The Marine Life Management Act, closure of several near-shore demersal fisheries and the establishment of no-take marine reserves are recent embodiments of long standing disagreements between California’s fishing industries and California regulatory agencies (CDFG 2002). Fundamental arguments are over data on population trends and local versus regional population recruitment patterns. Species of concern in the latest closure included the “rockfish-cabezon-greenling” complex (Musick et al. 2000). This project deals with one of the target species of the closures. We propose to estimate population genetic structure in a species central to the commercial and recreational over-fishing debate: the cabezon (Scorpaenichthys marmoratus).cabezongenetic subdivisionpopulation geneticsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1pz5r5rjpublicationoai:escholarship.org:ark:/13030/qt7500h4r12011-07-02T23:24:54Zqt7500h4r1Empirical evaluation of regional scale marine reserves and the groundfish trawl fisheryDalton, MichaelRalston, Stephen2006-08-01This Sea Grant project responded to a call from the California Sea Grant Strategic Plan 2001- 2005, which stated a need to model the performance of area closures from a resource management standpoint (including assessment of reserve size and the response of commercial and recreational fisherman to creation of reserves and the economic and conservation implications of reserves). Analyzing responses to spatial management, for example marine reserves, has been a topic recently in the literature on marine resource economics. This project made an important contribution to that literature (Dalton and Ralston, 2004), which extended previous work on dynamic models of fishing effort. Previous work treated abundance, ex-vessel prices, and climate as uncertain factors with a testable hypothesis, known as rational expectations, of how fishermen forecast future values of these variables.GISbioeconomic modelsrational expectationsspatial fisheries managementtime series analysisapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7500h4r1publicationoai:escholarship.org:ark:/13030/qt1ck9b3qs2011-07-02T23:24:36Zqt1ck9b3qsEstablishing a DNA Sequence Database for the Marine Fish Fauna of CaliforniaHastings, Philip A.Burton, Ron S.2008-11-01The overall goal of this project was to develop the necessary infrastructure to permit species identification of California marine fishes using molecular sequence data. This involved the following efforts. 1) Compilation of an up-to- date list of marine fish species occurring in and around California. 2) Collecting and archiving in the Marine Vertebrate Collection, Scripps Institution of Oceanography, tissues and voucher specimens of California marine fish species. 3) Development of a standardized protocol for molecular identification of fishes, including sample preparation/DNA extraction, DNA amplification via polymerase chain reaction (PCR) and DNA sequencing, using three mitochondrial gene sequences (cytochrome b, 16S ribosomal DNA, cytochrome oxidase 1). 4) Making sequence data available on-line permitting remote comparison of sequence data with reference sequences from known species.barcodeCaliforniacytochrome b16scytochrome oxidase IdatabaseDNAeggsfinfishfisheslarvaemolecular identificationGenBankFishBOLgeneticsichthyofaunaspecies identificationapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1ck9b3qspublicationoai:escholarship.org:ark:/13030/qt7jt5s90w2011-07-02T23:22:38Zqt7jt5s90wPelagic Fish Egg Abundance and Mortality Estimation by CUFES and Real-Time Machine VisionCheckley, David M.Cosman, Pam2004-04-24Assessment of the distribution and abundance of fish eggs in the sea is necessary to estimate fish spawning stock size and habitat. Knowledge of stock size is needed by fisheries managers to control catch. Knowledge of spawning habitat is needed to better manage fished stocks in an ecosystem context, and for policy formation. Our primary objective was to improve the methods used to assess the distribution and abundance of fish eggs. We did so by using machine vision, involving video and computers, to image, identify, and count eggs of target fish species collected with CUFES, the Continuous Underway Fish Egg Sampler, in real time. The result is REFLICS, the Real-time FLow Imaging and Classification System. Our secondary objective was to use this technology to investigate the spawning and mortality of eggs of pelagic fish, including the Pacific sardine (Sardinops sagax) and northern anchovy (Engraulis mordax) off Southern California.fish-egg samplinganchovysardinepelagicfishery managementpopulationmortalityvideooceanographyapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7jt5s90wpublicationoai:escholarship.org:ark:/13030/qt0565c0b22011-07-02T23:10:16Zqt0565c0b2Heterogeneous Preferences for Water Quality: A Finite Mixture Model of Beach Recreation in Southern CaliforniaHilger, JamesHanemann, Michael2006-02-01This 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.non-market valuationbeach recreationwater qualitydiscrete choicemixed logitlatent class/segmentationheterogeneitytime-consistent preferencesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0565c0b2publicationoai:escholarship.org:ark:/13030/qt9gr5784d2011-07-02T23:10:04Zqt9gr5784dForaging Ecology of the California Sea Lion: Diet, Diving Behavior, Foraging Locations, and Predation Impacts on Fisheries ResourcesCosta, Daniel P.Kuhn, CareyWeise, Michael2007-06-05Recent revisions of the federal Magnuson-Stevens Fishery Conservation and Management Act, vigorous implementation of the Endangered Species Act, and the enactment of the California Marine Life Management Act of 1998 have placed a new emphasis on restoring the health of coastal ecosystems and fisheries resources. Increases in many formerly depleted pinniped populations, coupled with declining fish resources, have intensified competition between humans and pinnipeds (Harvey 1987, Mate and Harvey 1987, Weise and Harvey 2005, MMC 2002). California sea lions (Zalophus californianus) compete with almost all commercial and recreational fisheries along the California coast by directly interacting with fisheries causing entanglement and damage to fishing gear and loss of catch (Beeson and Hanan 1996, NMFS 1997, Weise and Harvey 2005), and indirectly by competing for fisheries resources (Harvey 1987, Mate and Harvey 1987, Olesiuk 1993, Weise 2000).California sea lionforagingdiving behaviorpredationfishery resourcesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9gr5784dpublicationoai:escholarship.org:ark:/13030/qt4cn982x92011-07-02T23:09:48Zqt4cn982x9Diablo Canyon Archaeology: Trans-Holocene Faunal Exploitation Along the Central California CoastJones, Terry2007-02-28The objectives of the Diablo Canyon Archaeology project were to (1) refine the dating of archaeological sites CA-SLO-2 and CA-SLO-585; (2) identify the mammal, bird, and fish bones from these sites; (3) employ the resulting temporally controlled faunal matrix to improve understanding of California’s earliest coastal inhabitants and (4) address issues of nearshore ecology related to prehistoric human predation on sea otters and abalone as represented in the faunal record. The project was supposed to result in a published peer-reviewed paper and possible participation in a symposium on restoration ecology.prehistorysea ottersabaloneextinct flightless ducksoverexploitationapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4cn982x9publicationoai:escholarship.org:ark:/13030/qt0mj0s8qz2011-07-02T23:08:45Zqt0mj0s8qzSurfzone drifters: A new tool for observing nearshore circulationGuza, Robert T.2003-04-01Surfzone circulation, driven primarily by breaking waves, transports sediments, pollutants, and swimmers. Changes in patterns of wave breaking owing to variations in wave height and direction along curving coastlines, over irregular bathymetry, and near man-made structures can cause complex surfzone circulation, including rip currents.CaliforniaCoastalapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0mj0s8qzpublicationoai:escholarship.org:ark:/13030/qt13g399m72011-07-02T23:08:35Zqt13g399m7Biological Control of Invasive Green Crabs: a New Rapid and Reliable Safety Test of a Proposed Control AgentKuris, ArmandGoddard, Jeffrey2002-01-22Introduced marine species are a major environmental and economic problem. The rate of these biological invasions has substantially increased in recent years due to the globalization of the world’s economies. The damage caused by invasive species is often a result of the higher densities and larger sizes they attain compared to where they are native. A prominent hypothesis explaining the success of introduced species is that they are relatively free of the effects of natural enemies. Most notably, they may encounter fewer parasites in their introduced range compared to their native range. Parasites are ubiquitous and pervasive in marine systems, yet their role in marine invasions is relatively unexplored. Although data on parasites of marine organisms exist, the extent to which parasites can mediate marine invasions, or the extent to which invasive parasites and pathogens are responsible for infecting or potentially decimating native marine species have not been examined.invasive speciesparasitesmarine invasionsgreen crabsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/13g399m7publicationoai:escholarship.org:ark:/13030/qt7cg1z5hc2011-07-02T23:08:27Zqt7cg1z5hcTesting Ballast Water Treatment at a Municipal Wastewater Treatment PlantCohen, Andrew N.2001-09-08The main goal of the project was to investigate the feasibility of treating ships' ballast water in existing municipal wastewater treatment plants (= publicly-owned treatment works or POTWs). The main objectives included identifying and characterizing the limiting factors that could restrict the volume of ballast water that can be treated at POTWs; and test, in a series of laboratory experiments, the effectiveness of standard municipal wastewater treatment in removing or killing ballast water organisms. We worked with staff of the City and County of San Francisco to analyse the effects of treating ballast water at San Francisco's Southeast Treatment Plant (SETP) as a model. We report here on the experimental tests and analyses of the effectiveness of treating ballast water organisms in POTWs.ballast waterwastewater treatmentpublicly-owned treatment worksapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7cg1z5hcpublicationoai:escholarship.org:ark:/13030/qt7m8291kw2011-07-02T23:08:08Zqt7m8291kwIntegrated Culture of Seaweeds and Red Abalone in Monterey HarborGraham, Michael H.2008-07-14(1) Red algae and kelp can be effectively cultivated in Monterey Harbor and harvested as abalone feed. (2) Mixed diets are superior to all kelp diets in enhancing farmed abalone marketability (growth and shell color) (3) Seaweed culture can sustain a small to moderately-sized California abalone farm.redabalonekelpfarmingseaweedalgaeMacrocystisGracilariopsisChondracanthusdietapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7m8291kwpublicationoai:escholarship.org:ark:/13030/qt3f80822s2011-07-02T22:02:46Zqt3f80822sEffects of the San Diego-La Jolla Ecological Reserve on the Abundance, Diversity and Population Structure of Reef FishesHastings, Philip A.Dayton, Paul K.2006-07-24This project compiled current and historical records of fishes occurring in the vicinity of the San Diego-La Jolla Ecological Reserve (SDLJER), and assessed the effects of the Reserve on the abundance, diversity and population structure of resident fishes. This was accomplished by collection of quantitative data within the Reserve, immediately adjacent to the Reserve, and at site relatively distant from the Reserve that is not part of any marine reserve and subject to more intense fishing pressure. These assessments included transect surveys of densities and size distributions of conspicuous fishes. This study provides critical, but heretofore absent, baseline data for population monitoring of fishes in the Reserve and adjacent rocky-reef and kelp-forest communities in the San Diego region. In addition, records of fishes recorded within the vicinity of the SDLJER were compiled from the Scripps Institution of Oceanography Marine Vertebrate Collection in order to provide a detailed list of the ichthyofauna recorded in and around the Reserve.Marine ReservesMarine Protected Areasfish assemblageSan Diego-La Jolla Ecological ReserveSouthern Californiaapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3f80822spublicationoai:escholarship.org:ark:/13030/qt5h4816dx2011-07-02T14:55:47Zqt5h4816dxSpatial Management of FisheriesWILEN, JAMES EBotsford, Louis W.2005-02-22The overall project objective was to develop, calibrate, and refine an integrated spatially explicit bioeconomic model of the California sea urchin fishery. The model was designed to gain some insights into how spatial management measures, primarily reserves, might impact both the biological and economic health of a fishery in general, as well as how spatial policies might impact the California sea urchin fishery, in particular. We were successful in meeting our primary objectives for this project, and we have a variety of new and interesting results that we are in the process of publishing and presenting in workshops. This project involved fieldwork, econometric and statistical estimation, and programming, calibration, and simulation with a newly developed integrated bioeconomic model.fisheries managementspatial managementbioeconomicmarine reservesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5h4816dxpublicationoai:escholarship.org:ark:/13030/qt4b71x8d72011-07-02T13:13:46Zqt4b71x8d7MIGRATORY MOVEMENTS OF PACIFIC BLUEFIN TUNA OFF CALIFORNIABlock, Barbara A.Farwell, Charles J.2005-02-04The genus Thunnus of the family Scombridae includes three species of bluefin tunas (Atlantic bluefin tuna – T. thynnus, Pacific bluefin tuna - T. orientalis and southern bluefin tuna - T. maccoyii). The bluefin tunas were first recognized as two independent species (Northern and Southern bluefin) based on subtle differences in morphological characters. Northern bluefin tunas are now recognized as morphologically, geographically and genetically separate species located in the Atlantic and Pacific oceans.The Pacific bluefin (T. orientalis) is the only species which remains unmanaged; this lack of management persists despite intensive fisheries on both sides of the Pacific. The current life history model indicates that these fish spawn in the western Pacific (Sea of Japan, Philippine Sea and East China Sea). Either late in the first year or early in the second year, a portion of the population migrates to the western coast of the United States and Mexico, a journey of over 8700 km (Bayliff et al., 1991). The young fish that have migrated into the eastern Pacific are thought to remain there for several years, feeding on sardines and anchovies in regions of intense upwelling (Bayliff et al., 1991, Bayliff, 1993). While these tuna are fished only seasonally off California and Mexico, they may be a year-round resident (Bayliff, 1991). The migrants then travel back to the western Pacific to spawn. Why some bluefin remain in the western Pacific while others migrate across the ocean basin is unresolved. How long they stay in the eastern Pacific, what habitats are most important, what triggers their return to the west is unclear.bluefin tunamigrationfisheries managementelectronic taggingwestern Pacificapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4b71x8d7publicationoai:escholarship.org:ark:/13030/qt4nf6z8gb2011-07-02T11:05:34Zqt4nf6z8gbMolecular Approaches in Marine PharmacologyButler, Alison2005-10-11Many marine natural products and enzymes have important medical applications in the pharmaceutical, diagnostic and biotechnological industries. These compounds and enzymes are at various stages of development, ranging from evaluation of their biological activities, to testing in clinical trials, and to their incorporation into commercial products. Notwithstanding this success, the rise in drug-resistant infections demands new drugs and strategies for eradication or control of invading pathogenic organisms. In addition, early disease detection requires new or more sensitive biochemical diagnostic tools. Solutions to these problems can be provided through discovery of new bioactive compounds, studies of their biogenesis, including endogenous biosynthetic enzyme investigations, and elucidation of their molecular mechanisms of action. Such strategies will allow chemists and pharmacologists, working in a collaborative effort, to pursue the development of novel drugs and diagnostics.haloperoxidasehalogenated marine natural productsterpenesRhodophytamarine algaeapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4nf6z8gbpublicationoai:escholarship.org:ark:/13030/qt7bg754pc2011-07-02T10:48:15Zqt7bg754pcDispersion of Passive Tracers in the SurfzoneFedderson, FalkGuza, Robert T.2007-05-31In Southern California, terrestrial runoff pollution often drains directly onto the beach, degrading water quality and leading to increased beach closures each year. Beaches are a significant piston in California’s economic engine and beach closures can have significant economic impact on local communities. Runoff pollution can be localized, as from a storm drain, or can be more diffuse with many smaller, distributed sources. In either case, upon entering ocean waters, the pollution is first mixed, dispersed, and advected within the surfzone (the region of breaking waves). However, behavior of polluted waters upon entering the surfzone is not understood, and advancing this understanding is crucial to improved beach water quality.The dispersion of passive tracers, such as pollutants, in the surfzone was be examined using both drifter observations and nearshore wave/circulation models with the goal of understanding the mechanisms of dispersion and to develop formulations for predicting dispersion.surfzonedispersion driftersapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7bg754pcpublicationoai:escholarship.org:ark:/13030/qt8kq3s1xw2011-07-01T07:58:50Zqt8kq3s1xwSec.I: Age, growth, and radiometric age validation of the blackgill rockfish, Sebastes melanostomus; Sec.II: Age validation of the canary rockfish (Sebastes pinniger) using the disequilibria of lead-210 and radium-226Andrews, Allen H.Cailliet, Gregor M.Coale, Kenneth H.2005-07-01Abstract Section I: As nearshore fish populations decline, many commercial fishers have shifted effort to deeper continental slope habitats to target fishes for which biological information is limited. One such fishery that developed in the northeastern Pacific Ocean in the early 1980s was for the blackgill rockfish, Sebastes melanostomus, a deep- dwelling (300-800 m) species that congregates over rocky pinnacles, mainly from Southern California to southern Oregon. Growth zone-derived age estimates from otolith thin sections were compared to ages obtained from the radioactive disequilibria of 210Pb, relative to its parent, 226Ra, in otolith cores of blackgill rockfish. Age estimates were validated up to 41 years, with a strong pattern of agreement supporting a longevity exceeding 90 years. Age and length data fitted to the von Bertalanffy growth function indicate blackgill rockfish are slow-growing (k = 0.040 females, 0.068 males) and that females grow slower than males, but reach a greater length. Age at 50% maturity, derived from previously published length-at-maturity estimates, was 17 years for males and 21 years for females. The results of this study agree with general life history traits already recognized for many Sebastes species, such as long life, slow growth, and late age at maturation. These traits may undermine the sustainability of blackgill rockfish populations when heavy fishing pressure, such as that which occurred in the 1980s, is applied.Abstract Section II: The canary rockfish (Sebastes pinniger) has been an important part of the recreational and commercial rockfish fisheries from southeast Alaska to Southern California for a long time, but stocks have declined considerably over the past few decades. Based on age estimates from otoliths and other structures, longevity estimates vary from just over 20 years to more than 80 years. For the purpose of monitoring stocks, age composition is routinely estimated by counting growth zones in otoliths using the break-and-burn technique; however, age estimation procedures and high longevities for this species remain largely unvalidated. Typical age validation techniques have limited application for the canary rockfish because they are deep dwelling and appear be long-lived fish. In this study we have taken the unaged otolith of the pair from aged fish and have measured the disequilibria of lead-210 (210Pb) and radium-226 (226Ra) as an indicator of age estimate accuracy. The technique proved successful in determining a minimum longevity of about 51 years and provided strong support for the estimation procedures used to determine longevity at over 80 years.Blackgill rockfishSebastes melanostomuscanary rockfishSebastes pinnigerage validationlead-210radium-226application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8kq3s1xwpublicationoai:escholarship.org:ark:/13030/qt5kj0k3q32011-07-01T07:58:25Zqt5kj0k3q3Assessing changes in life history traits and reproductive function of CA sheephead across its range: historical comparisons and the effects of fishingCaselle, Jennifer E.Lowe, Christopher2010-02-18Project Hypotheses The specific predictions can be summarized as: P1: Life history parameters will vary across the range of this species and spatial differences in life histories will be determined by population density, sex ratios, environmental factors, and fishing pressure. P2: Fish collected in this study will be smaller and younger than fish collected from previous times (historical collections from 1970-1980) and the effects will be greatest at sites where fishing is intense (i.e. southern California vs. Baja California). P3: Fish collected in this study will change sex from female to male at a younger age and smaller size than previous times, especially at sites where fishing is intense (as predicted by size advantage model). P4: As a result of P3 (females mature younger and smaller), operational sex ratios will increase (also predicted by size advantage model). P5: Stricter harvest limits may have initiated recovery in heavily exploited populations and may result in increases in lengths, the timing of maturation, and the timing of sex change. P6: Individual growth rates will differ both spatially (sites across the species range) and temporally (historical vs. 1998 vs. this study) and variance will be more related to site location (e.g. water temperature and food availability) than type or amount of fishing. P7: Ultrasound techniques will provide a cost effective, non-destructive, and reliable tool to assess sex, fecundity, and reproductive state in these important fish. P8: Radioimmunoassays of estradiol and testosterone will verify the utility of visual assessments of sexual state and provide a non-destructive means to survey reproductive function during the breeding season. P9: Potential reproductive output will be less in this study than that of past studies at sites where fishing pressure is intense.California sheepheadsex changefisherypopulation dynamicsbiogeographyreproductive functionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5kj0k3q3publicationoai:escholarship.org:ark:/13030/qt8vk3q4dj2011-07-01T07:57:15Zqt8vk3q4djOyster Disease Research Program: Building Gene Expression-Based Predictors of Oyster Summer Mortality SyndromeGracey, Andrew Y.2010-01-04Pacific oyster (Crassostrea gigas) fisheries on the U.S. West Coast, Mexico, France and Japan, are significantly impacted by high rates of oyster mortality in the summer months, in California ranging from 52-63%. This summer mortality syndrome (SMS) occurs predominantly in near-market ready oysters and seems to impact reproductive females the most. There is an urgent need for studies to investigate the metabolic and molecular basis of the syndrome, with the goal of identifying, and then producing summer mortality-resistant stocks. The specific hypotheses that we are testing is that changes in hemocyte gene expression could be used as a predictor of the onset of summer mortality, and that these changes in gene expression could be used as a predictor of the onset of the syndrome as well as providing insights into the pathophysiological basis of the disease.Other Physical Sciences and Mathematicsgene expressionoystersummer mortalityheatapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8vk3q4djpublicationoai:escholarship.org:ark:/13030/qt9mh4f40k2011-07-01T07:52:42Zqt9mh4f40kMapping and Monitoring Large-Scale Ocean Fronts Off the California Coast Using Imagery from the GOES-10 Geostationary SatelliteBreaker, Laurence C.Mavor, Timothy P.Broenkow, William W.2005-04-18There is little readily available information on when and where oceanic fronts occur off the coast of California despite their important to fisheries management, environmental monitoring, search-and-rescue operations, and underwater sound. To help fill this gap, scientists at Moss Landing Marine Laboratories, together with NOAA's National Environmental Satellite Data and Information Service, with support from California Sea Grant, have produced a series of monthly maps showing the locations of fronts off the California coast. They were created using remote sensing data from the GOES-10 geostationary satellite. A total of 48 frontal maps were produced on a monthly basis over the four-year period from July 2000 to June 2004.ocean frontsGOES-10 geostationary satelliteCalifornia coastsatellite imageryfrontal mapsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9mh4f40kpublicationoai:escholarship.org:ark:/13030/qt284260xx2011-07-01T07:50:32Zqt284260xxPhysiological Adaptation and Invasion Success: A Comparison of Native and Invasive Species of Bay Mussels in the Central California Hybrid ZoneSomero, George N.Braby, Caren E.2004-10-19Marine species invasions pose serious ecological and economic threats to coastal areas throughout the world. The mechanisms by which invasive species are introduced to a new habitat are generally well understood, and frequently involve release of invasive larvae or adults in ballast water. However, we currently have little knowledge concerning the physiological characteristics of an invasive species that allow it to succeed, following its introduction. What characteristics of an invader enable it to succeed and, in some cases, to out-compete and replace a closely related native species? We examined the physiological basis of invasive success by comparing two congeneric bay mussels found along the coast of Central California. Mytilus trossulus is a native bay mussel that formerly occurred along the Pacific Coast of the United States from Mexico to Canada. At some point in the early to middle decades of the past century, a second species of bay mussel, M. galloprovincialis, was introduced into Southern California waters. Since its introduction, this invasive species has replaced the native species from the Mexican border to the approximate latitude of Monterey Bay. Between Monterey Bay and areas just to the north of San Francisco Bay, the two species coexist in what is termed a “mosaic hybrid zone.” In this zone, one can find the native and the invasive species and their hybrids.bay musselinvasive speciesMytilussalinitytemperatureapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/284260xxpublicationoai:escholarship.org:ark:/13030/qt1ds609822011-07-01T07:49:41Zqt1ds60982Market Channels and Value Added to Fish Landed at Monterey Bay Area PortsPomeroy, CarolineDalton, Michael2005-07-11Recent and pending federal marine management actions on the U.S. West Coast, from groundfish regulations to marine reserves and National Marine Sanctuary management plan revisions, have highlighted the critical need for socioeconomic information on marine resource uses and associated communities. The need for this information is both practical and legal. In practical terms, because resource users affect and are affected by management, socioeconomic information can be used to inform and enhance the effectiveness of management design, implementation and evaluation. In legal terms, the Magnuson-Stevens Fishery Conservation and Management Act (MSFCMA, and amendments), the National Environmental Policy Act (NEPA), and the Regulatory Flexibility Act (RFA) require consideration of the "human dimensions" in the design and implementation of federal actions that affect the human and biophysical environments.In central California, the site of three National Marine Sanctuaries (NMSs) and diverse federally- and state-managed fisheries, socioeconomic information to assess the impacts of management actions has been critically lacking. Among the types of information needed are qualitative and quantitative analyses of market channels through which value is added to the catch. These market channels are defined by the social and economic linkages among fishermen, receivers, processors and others, and are manifest in the spatial distribution of the quantity and value of fish products within and beyond the region.1To address these information needs, we conducted a study of the production and distribution of fish products landed at the three main Monterey Bay area (MBA) ports: Moss Landing, Monterey and Santa Cruz. The overarching goal of the research was to help inform the assessment of potential social and economic impacts of fishery management and other measures and events. Specific objectives were: 1) todescribe the spatial organization of processing activities for fish landed at Monterey Bay ports (i.e., Moss Landing, Monterey and Santa Cruz); and 2) to estimate value added in Monterey and Santa Cruz Counties to fish landed at Monterey Bay ports. This report provides a technical summary of the study background, followed by the methods, results and conclusions drawn.seafood productionMonterey Bay fisheriesvalue-addedmarket channelssocio-economics of fish productionfish processingSanta CruzMoss Landingsocial and economic networksapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1ds60982publicationoai:escholarship.org:ark:/13030/qt8v42t9372011-07-01T07:49:37Zqt8v42t937Molecular Genetic Analysis of Recruitment Patterns in the Dungeness Crab, Cancer magisterToonen, Robert J.Grosberg, Richard K.2003-08-25If there is any generalization to be made about populations of commercially harvested marine species, it is that they all show dramatic numerical fluctuations in both space and time. Traditional approaches to fisheries management, based on standard stock-recruitment models, have repeatedly led to overexploitation of commercially valuable stocks throughout management history. Notable examples in California fisheries include the halibut, sardine, anchovy, salmon, and urchin fisheries. A recent survey of Dungeness crab fisheries practices and catch history suggests that this fishery is also in imminent danger of collapse (Orensanz et al. 1998). It is becoming clear that sustainable management of commercially harvested finfish and shellfish with complex life cycles must include an understanding of how patterns of larval distribution, abundance and dispersal regulate adult population dynamics. This, in turn, depends on explicit knowledge of population structure as well as patterns and amount of larval dispersal between localities. However, to date inferences of the patterns and magnitude of gene flow among populations of marine invertebrates have been “deduced only through weak inference” (Hairston 1989).CrabCurrentGeneticLarvaeRecruitmentapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8v42t937publicationoai:escholarship.org:ark:/13030/qt6rf2w0vj2011-07-01T07:49:32Zqt6rf2w0vjExploring the 1990s: Investigation into Factors Controlling Siliceous Microplankton Distribution in Santa Barbara ChannelVenrick, Elizabeth L.2004-04-13The project objectives were: To characterize intra- and interannual variations in the production of siliceous flora and fauna, and hydrography in the Santa Barbara Channel from 1993-present, a period that is marked by several abrupt oceanographic/climatic changes. To investigate relationships of microplankton distribution and species composition with water column properties of temperature, salinity and nutrients. To merge trap data with buoy and drifter data into qualitative synoptic circulation models. To test the hypothesis that siliceous microplankton in the Santa Barbara Channel are a result of both advection (horizontal and vertical) and in situ production. To characterize relationships between zooplankton biomass fluctuations and phytoplankton variability over the past decade.siliceous flora and faunaSanta Barbara Channelclimate changemicroplanktonbiomass fluctuationsphytoplanktonapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6rf2w0vjpublicationoai:escholarship.org:ark:/13030/qt5p16k0cp2011-07-01T07:49:24Zqt5p16k0cpUse of cDNA microarray to isolate differentially expressed genes in White Spot Virus infected shrimp (penaeus stylirostris)Dhar, Arun K.Klimpel, Kurt R.Bullis, Robert A.McClenaghan, Leroy R.2006-05-01White spot syndrome virus (WSSV), the etiologic agent of white spot disease, is currently the most important viral pathogen infecting penaeid shrimp worldwide. Since the initial report, white spot disease has caused losses of catastrophic proportion to shrimp aquaculture globally. Although considerable progress has been made in characterizing the WSSV and developing detection methods, information on the host genes involved in the immune response in shrimp due to WSSV infection is not available. During this research, the mRNA expression profiles in healthy and WSSV-infected shrimp were determined by analyzing the expressed sequence tags (ESTs) and by microarray analysis. Our data show that WSSV infection alters the expression of a wide array of genes including those that are involved in immune function, signal transduction, structural genes, as well as mitochondrial genes among others. Using EST analysis and real-time RT-PCR, we also identified a candidate receptor gene for another viral pathogen of shrimp, the Taura syndrome virus (TSV). These data show that the potential for using the mRNA expression level of candidate genes as biomarkers for identifying virus-resistant or virus-susceptible lines in shrimp.white spot syndrome virusWSSVwhite spot diseaseshrimp aquacultureapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5p16k0cppublicationoai:escholarship.org:ark:/13030/qt7mw5z4b82011-07-01T07:27:36Zqt7mw5z4b8The Biomedical Potential of California Marine OrganismsFenical, William H.2005-03-11The search for new pharmaceuticals continues to demand our greatest efforts. Despite tremendous advances in medical science, there are no comprehensive cures for HIV or AIDS, certain forms of cancer, arthritis and other inflammatory conditions, and a large assortment of viral and fungal diseases. In fact, the incidence of some previously curable illnesses, such as tuberculosis, is on the rise due to the spread of drug-resistant infections. Currently, about half of the medicines prescribed are derived from natural sources such as terrestrial plants and micro-organisms. In addition, many drugs that are now produced by total synthesis were originally derived by modification of natural products. Although few marine natural products are currently used medicinally or are in clinical trials, marine organisms comprise the greatest unexploited source of potential pharmaceuticals. Because of the unusual diversity of chemical structures isolated from marine organisms, there is great interest in screening marine natural products in new mechanism-based bioassays.biomedicalmarine compoundsspongesascidiansopisthobranch molluscsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7mw5z4b8publicationoai:escholarship.org:ark:/13030/qt2fc8h4682011-07-01T07:27:32Zqt2fc8h468ASSESSMENT OF THE REPRODUCTIVE POTENTIAL OF NEARSHORE ROCKFISH AND THE IMPACT OF ENVIRONMENTAL CONDITIONSCollins, Peter M.2004-08-18The overall objective of the project was to improve our understanding of the unique reproductive processes in a representative nearshore rockfish, Sebastes rastrelliger (grass rockfish). The research contributes to the available scientific information on the reproductive biology of an important component of the Californian nearshore fishery which may be incorporated into the development of a comprehensive management plan as envisaged in the California State legislation, Senate Bill AB 1241.rockfishSebastesatresiafecunditylarvaeoocytesparturitionpregnancyembryogenesisspawningenvironmenttemperaturesalinitynutritionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2fc8h468publicationoai:escholarship.org:ark:/13030/qt7p77r74x2011-07-01T07:27:25Zqt7p77r74xQUANTIFYING AND MINIMIZING RISK THAT HATCHERY-ENHANCEMENT
WILL REDUCE GENETIC DIVERSITY OF WHITE SEABASSHedgecock, Dennis2004-09-14Demand for seafood on a global scale is projected to increase by 70 percent in the next 30 years, though most fisheries are at or beyond their sustainable yields and many are in decline (Botsford et al. 1997). Fisheries management must be augmented by new strategies for protecting and enhancing marine resources, such as “no-take” marine reserves (Allison et al. 1998; Hastings and Botsford 1999) or enhancing natural stocks through artificial hatchery propagation. Despite criticisms from conservationists and fisheries biologists alike (e.g. Meffe 1992; MacCall 1989), large-scale hatchery supplementation programs are already in place for many anadromous and marine fisheries (Travis et al. 1998), and in Japan, a substantial fraction of marine production is attributable to enhancement programs (Masuda and Tsukamoto 1998). The global extent of enhancement of wild fisheries is poorly documented, however, especially for marine species (A.F. Born, A.J. Immink, and D.M. Bartley, FAO Fisheries, pers. com.). In Japan, to take just one example, nearly 70 marine species are supplemented, some at very high levels. To date there have been very few analyses of the potential genetic impact of these marine supplementation programs.conservationgeneticshatcheryenhancementrisk assessmentapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7p77r74xpublicationoai:escholarship.org:ark:/13030/qt29n8c5n82011-07-01T07:27:18Zqt29n8c5n8The Role of Symbiotic Bacterial Siderophores in the Development of Toxic Phytoplankton BloomsCarrano, Carl J.Kuepper, Frithjof2009-06-24Research Hypothesis. The working hypothesis of this proposal is that a) phytoplankton growth can be controlled by the availability of the essential micronutrient iron b) symbiotic bacteria produce iron-binding compounds (siderophores) that can be utilized by the plankton to provide the iron needed for prolific growth, c) bacterially produced boron containing molecules may also contribute to control of phytoplankton growth d) a more complete understanding of this process could provide a means to predict where, when and under what conditions heavy growth of these organisms would occur.ironbacteriaphytoplanktonsiderophoresapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/29n8c5n8publicationoai:escholarship.org:ark:/13030/qt8tx3g4m22011-07-01T07:27:12Zqt8tx3g4m2Controlling Undaria and invasive kelps through management of the gametophyte.Chapman, David J.2005-10-01Undaria pinnatifida is an invasive species of Asian kelp that was first discovered in California harbors in 2001 (Silva et al. 2002). It has established itself as a successful invasive species in other countries and the California coast is also speculated to be a beneficial habitat for it. To better understand where this new kelp might spread, how successful it might be, and how to manage it in terms of containment more information needs to be gained on its biology and ecology. Along the coast of California there are a variety of native kelps that play key roles in their habitats. An invasive kelp like Undaria has the potential to compete with, or out compete, some of these native kelps. Since Undaria is a species of kelp it has a heteromorphic life history that includes a microscopic gametophyte stage that has the potential to act as a perennial seed stock. The presence of a seed bank for an invasive species is a very useful reproductive strategy since it could provide an invasive species with multiple opportunities to establish a population in a new habitat. The studies conducted examined this gametophyte life history stage to better understand how it might affect the success of Undaria as an invader in California waters.Undariakelpinvasive speciesmacrocystisEgregiaallelochemistryalgal competitiongametophyteshybridizationpartheogenesisapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8tx3g4m2publicationoai:escholarship.org:ark:/13030/qt48h0g7ws2011-07-01T07:27:08Zqt48h0g7wsPatterns of Recruitment in Red Sea Urchins: A Population Genetics ApproachBurton, Ronald S.2003-06-01Management of sea urchin fisheries is hampered by a lack of understanding of recruitment processes.Geneticapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/48h0g7wspublicationoai:escholarship.org:ark:/13030/qt7v2676922011-07-01T07:26:56Zqt7v267692Tools for Management of Withering Syndrome in Abalone, Haliotis spp: PCR Detection and Feed-Based Therapeutic TreatmentFriedman, CarolynHedrick, R PMoore, James D.2003-11-25Withering syndrome is a chronic, often fatal disease of multiple species of California abalone. It was first observed in the mid-1980s at the Channel Islands off Southern California and has since spread along the main coastline as far north as the San Francisco bay area. Recent research has demonstrated that the causative agent is a Rickettsiales-like prokaryote (WS-RLP, Friedman et al. 2000), and that WS expression is much more rapid and severe at elevated water temperatures (Moore et al. 2000). Aside from impacts on wild populations, WS has resulted in substantial losses in red abalone farms. As a result of these losses and our observation that the WS-RLP is sensitive to tetracyclines, we developed and oral administration of oxytetracycline in conjunction with researchers at The Abalone Farm, Inc.abaloneaquaculturePCRwithering syndromeRickettsiaoxytetracyclinetherapeutantapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7v267692publicationoai:escholarship.org:ark:/13030/qt7k79z6jb2011-07-01T07:26:52Zqt7k79z6jbAcoustic Method for Fish Counting and Fish Sizing in TanksRoux, PhilippeConti, StéphaneDemer, DavidMaurer, Benjamin D.2005-08-18The project goal successfully accomplished its intended goals of (a) Designing a prototype to demonstrate the use of acoustic reverberation in a tank to count/size fish in an aquaculture environment. (b) Building an interactive exhibit based on the proposed science at the Birch Aquarium of the Scripps Institute of Oceanography.fish densitybehaviorgrowth rateacoustic reverberationaquacultureapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7k79z6jbpublicationoai:escholarship.org:ark:/13030/qt0qp8835h2011-07-01T07:26:43Zqt0qp8835hDevelopment of Molecular and Cellular Tools for the Detection of Environmental Endocrine Disruption in Aquatic InvertebratesSnyder, Mark J.Cherr, Gary N.Peeke, Harman V.S.2003-11-03Environmental endocrine disruptors (EDC’s) are environmental contaminants that act by alteration of one or more aspects of the endocrine system of affected individuals. Though well characterized for vertebrates, the extrapolation of EDC effects information to aquatic invertebrates has been inhibited by the large differences in physiological regulatory pathways. There is a significant need for test methodology development and the identification of ‘biomarkers’ of EDC effects for aquatic invertebrates (Hutchinson and Pickford 2002).BehaviorCrustaceanEchinodermInvertebrateLarvaeResistanceUrchinapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0qp8835hpublicationoai:escholarship.org:ark:/13030/qt6pc6b7sd2011-07-01T07:24:09Zqt6pc6b7sdAntibiotic Drug Discovery from the New Marine Actinomycete Genus MarinomycesFenical, William H.2007-07-19Actinomycetes are high G+C content Gram-positive bacteria with an unparalleled ability to produce diverse secondary metabolites. These bacteria, which are best known from soils, have been studied extensively by the pharmaceutical industry and account for a disproportionately large amount of the $25.3 billion annual global sales of microbially derived pharmaceuticals. In recent years however, the yield of new lead compounds from common soil-derived actinomycetes has diminished significantly, thus providing incentive to broaden the search for new metabolites to include actinomycetes that occur in the sea. The goals of this proposal were to gain a better understanding of actinomycete diversity in the ocean and their ability to produce unique secondary metabolites. The approach taken was to develop cultivation techniques specific for marine actinomycetes and to assess the diversity of cultured strains using molecular systematics. Representatives of various taxonomic groups were then cultured, extracted, and the extracts assessed for biological activity and the presence of novel secondary metabolites. Special efforts were made to focus on a unigue group of chemically prolific marine actinomycetes that we discovered and called MAR2 or "Marinospora".actinomycetesmarine compoundsmarine natural productsgram-positive bacterianovel secondaryapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6pc6b7sdpublicationoai:escholarship.org:ark:/13030/qt18n674n82011-07-01T07:24:03Zqt18n674n8Molecular and Biochemical Characterization of Microbial Symbiont Bioactivities in Sepioid and Loliginid SquidsEpel, David2001-05-01Previous research on characterization of the microbial community associated with the accessory nidamental gland (ANG) and egg sheath (ES) of the squid relied mostly on molecular techniques (i.e. analysis of 16S ribosomal DNA sequence) with the majority of the symbionts being uncultured. Although these studies and previous work in our lab provided valuable initial descriptions of the ANG microbial community, it was evident that a more extensive attempt at cultivation and molecular characterization of the ANG and ES bacteria was warranted and also necessary for describing any potent bioactivies against fungi or other bacteria.cephalopodegg sheathnidamental glandmolecular characterizationANG/ES bacteriaapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/18n674n8publicationoai:escholarship.org:ark:/13030/qt52v5x0442011-07-01T07:23:57Zqt52v5x044Using life history characteristics to determine optimum placement of marine reservesBerkeley (deceased), Steven A.Parker, Steven J.2007-06-01The purpose of this study is to use rockfish life history and reproductive dynamics to determine marine reserve locations to protect the species that demonstrate age-related differences in parturition timing or quality of larvae produced. These long-lived species are extremely vulnerable to overfishing because of their slow population growth rates and late ages at reproduction. Several species of California rockfish are currently in overfished status. Previous research by the principal investigator has demonstrated that in a number of nearshore rockfish species, older females spawn earlier in the season and produce larvae with characteristics that are more likely to survive (Berkeley et al. 2004). Evidence of similar age-related patterns in spawning seasonality and progeny quality has been observed in a diverse range of teleost species. Because even moderate rates of fishing rapidly eliminate older fish from the population, the burden of reproduction is shifted to younger and younger fish. Elimination of older age classes would effectively shorten the parturition season and eliminate reproductive output from the early part of the spawning season. As a consequence, the likelihood of larval production matching peak plankton production will be reduced (the match-mismatch hypothesis; Cushing 1969, 1990). Fish species that display these “maternal age effects” are most likely to benefit from the protection offered by marine reserves, where no fishing is allowed and the population ages naturally, creating a higher percentage of older individuals.rockfishmaternal effectslarval qualityparturitionmarine reservesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/52v5x044publicationoai:escholarship.org:ark:/13030/qt69g9946q2011-07-01T07:23:47Zqt69g9946qRestoration of Endangered White Abalone, Haliotis sorenseni: Resource Assessment, Genetics, Disease and Culture of Captive AbaloneBurton, Ronald S.McCormick, Thomas B.Moore, James D.Friedman, Carolyn S.2008-06-05The white abalone , Haliotis sorenseni, supported valuable commercial fisheries only 30 years ago. In 2002, this species became the first marine invertebrate in the United States to achieve federal endangered species status. The overall goal of this project was to collect life history, genetic and disease susceptibility data that to support recovery.white abaloneHaliotis sorenseniendangered growthfecunditylarvaetemperaturedietmacroalgaebenthiccryptic speciesmarineraftingdrift macroalgaedispersalwound treatmentbenthic monitoringbehaviorapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/69g9946qpublicationoai:escholarship.org:ark:/13030/qt3142f5nz2011-07-01T07:23:41Zqt3142f5nzLife History Studies of California Chondrichthyans: Determining Essential Biological Information for Effective Management of Bycatch and Emerging FisheriesEbert, David A.Cailliet, Gregor M.2007-05-29In cooperation with NMFS Northwest Fisheries Science Center and Southwest Fisheries Science Center, Santa Cruz Lab, researchers from the Pacific Shark Research Center/Moss Landing Marine Laboratories have been participating and assisting in groundfish surveys since 2002. Vertebrae for age and growth estimation, reproductive tracts, and/or stomachs for feeding analyses were collected from over 5,000 specimens. Studies on the age and growth of the roughtail (Bathyraja trachura) and sandpaper (Bathyraja kincaidii) skates were completed, with one paper having been published and another having been accepted for publication. Age and growth studies for several other commonly encountered chondrichthyans are continuing. Studies on the reproductive biology of the big (Raja binoculata), California (Raja inornata), longnose (Raja rhina), roughtail, and sandpaper skates, and the white-spotted chimaera (Hydrolagus colliei) were completed and manuscripts are currently being prepared for publication. A study on the reproductive biology of three deepsea catsharks (Scyliorhinidae) was completed, with two publications currently in press. Dietary studies were completed for four species, the big, California (Raja inornata), longnose, and sandpaper skates, with analyses continuing for several other species. Research results for this project have resulted in two Masters Theses, ten publications, and 18 presentations at seven conferences. This project funded two California Sea Grant trainees both of whom worked on projects that served as their Masters Theses.chondrichthyansskatescatsharkschimaeraslife historyage and growthreproductiondietfeeding ecologybycatchapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3142f5nzpublicationoai:escholarship.org:ark:/13030/qt5j17k79b2011-07-01T07:23:37Zqt5j17k79bBomb carbon in the yelloweye rockfish, Sebastes ruberrimus, as a chronological benchmark for age validation of commercially important fishesKerr, Lisa A.Andrews, Allen H.Frantz, Brian R.Coale, Kenneth H.Brown, Thomas A.Cailliet, Gregor M.2004-11-19The overall goals of this study were to (1) establish a chronological benchmark for bomb radiocarbon in the waters of southeast Alaska by determining radiocarbon levels in otoliths of the yelloweye rockfish (Sebastes ruberrimus), for which age was validated, (2) validate the age of quillback rockfish (S. maliger), bocaccio rockfish (S. paucispinis), cowcod (S. levis), and canary rockfish (S. pinniger) using the yelloweye rockfish radiocarbon chronology, (3) provide a basis for future age and growth studies of marine fishes in the northwest Pacific using the radiocarbon record, and (4) apply the technology to sharks (e.g. validate the age and ageing methodology of the shortfin mako, Isurus oxyrinchus, and investigate its application to the white shark, Carcharodon carcharias).California Sea Grant funded publications that pre-date and resulted from this study are listed below. Please contact Allen H. Andrews at allen.andrews@noaa.gov.Andrews, A.H., K.H. Coale, J.L. Nowicki, C. Lundstrom, Z. Palacz, E.J. Burton and G.M. Cailliet. 1999. Application of an ion-exchange separation technique and thermal ionization mass spectrometry to 226Ra determination in otoliths for radiometric age determination of long-lived fishes. Can. J. Fish. Aquat. Sci. 56:1329–1338 (R/F-148)Andrews, A.H., G.M. Cailliet and K.H Coale. 1999. Age and growth of the Pacific grenadier (Coryphaenoides acrolepis) with age estimate validation using an improved radiometric ageing technique. Can. J. Fish. Aquat. Sci. 56:1339–1350 (R/F-148)Andrews, A.H., G.M. Cailliet, K.H. Coale, K.M. Munk, M.M. Mahoney and V.M. O’Connell. 2002. Radiometric age validation of the yelloweye rockfish (Sebastes ruberrimus) from southeastern Alaska. Mar. Freshwater Res. 53:139–146 (R/F-148)Kerr, L.A., A.H. Andrews, B.R. Frantz, K.H. Coale, T.A. Brown and G.M. Cailliet. 2004. Radiocarbon in otoliths of yelloweye rockfish (Sebastes ruberrimus): a reference time series for the coastal waters of southeast Alaska. Can. J. Fish. Aquat. Sci. 61:443-451.Stevens, M.M., A.H. Andrews, G.M. Cailliet, K.H. Coale, C.C. Lundstrom. 2004. Radiometric validation of age, growth, and longevity for the blackgill rockfish, Sebastes melanostomus. Fish. Bull. 102:711–722Andrews, A.H., E.J. Burton, L.A. Kerr, G.M. Cailliet, K.H. Coale, C.C. Lundstrom and T.A. Brown. 2005. Bomb radiocarbon and lead-radium disequilibria in otoliths of bocaccio rockfish (Sebastes paucispinis): a determination of age and longevity for a difficult-to-age fish. Proceedings of the 3rd International Symposium on Otolith Research and Application. Mar. Freshwater Res. 56:517–528Kerr, L.A., A.H. Andrews, B.R. Frantz, K.H. Coale, T.A. Brown, K. Munk and G.M. Cailliet. 2005. Age validation of quillback rockfish (Sebastes maliger) using bomb radiocarbon. Fish. Bull. 103(1):97–107Kerr, L.A., A.H. Andrews, G.M. Cailliet, T.A. Brown and K.H. Coale. 2006. Investigations of Δ14C, δ15N, and δ13C in vertebrae of white shark (Carcharodon carcharias) from the eastern Pacific Ocean. Environ. Biol. Fish. 77:337–353.Ardizzone, D.A., G.M. Cailliet, L.J. Natanson, A.H. Andrews, L.A. Kerr and T.A. Brown. 2006. Application of bomb radiocarbon chronologies to shortfin mako (Isurus oxyrinchus) age validation. Environ. Biol. Fish. 77:355–366.Andrews, A.H., L.A. Kerr, G.M. Cailliet, T.A. Brown, C.C. Lundstrom and R.D. Stanley. 2007. Age validation of canary rockfish (Sebastes pinniger) using two independent otolith techniques: lead-radium and bomb radiocarbon dating. Mar. Freshwater Res. 58:531–541rockfishSebastes ruberrimusS. maligerS. paucispinisS. levisS. pinnigerScorpaenidaeradiocarbonage validationlongevityotolithsharkIsurus oxyrinchusCarchardon carchariasvertebraeapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5j17k79bpublicationoai:escholarship.org:ark:/13030/qt4mt7b6tv2011-07-01T07:23:31Zqt4mt7b6tvCollecting Sea Palms: Planning for Sustainable Use in a Variable EnvironmentNielsen, Karina JBlanchette, Carol A.2008-03-12Sea palm harvesting is a largely unregulated cottage industry centered along the rugged rocky coast of Sonoma County, California. The project's scientists tested different harvesting practices to identify those that were most sustainable, given the plant’s growth and reproductive cycles.Postelsia palmaeformissea palmconservationharvestsustainable managementkelpintertidalLaminarialesapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4mt7b6tvpublicationoai:escholarship.org:ark:/13030/qt5jp4s8mj2011-07-01T07:23:26Zqt5jp4s8mjObservation of Physical Fluxes Between an Estuary and the OceanStacey, MarkPowell, Thomas2005-01-10The work has been focused on observations of ocean-estuary exchange at the mouth of San Francisco Bay. The observational program consisted of 6 transect experiments, each capturing a complete 24-hour tidal day (with 2 exceptions due to instrument failures), spanning various seasons and tidal conditions. Using repeated transects of water velocity, conductivity, temperature, optical backscatter, and chlorophyll fluorescence, we have made great strides in developing a clear, quantitative understanding of ocean-estuary exchange in San Francisco Bay.ocean-estuary exchangesbiological fluxestidal asymmetriesdensity-driven flowsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5jp4s8mjpublicationoai:escholarship.org:ark:/13030/qt6fm563nn2011-07-01T07:23:21Zqt6fm563nnQUANTATITIVE PCR ASSAY FOR MARINE BACTERIABrunk, Clifford F.2003-04-04Monitoring the bacterial flora in coastal marine waters by conventional techniques has been difficult as most of the bacteria do not readily grow on culture plates and their morphologies are virtually identical in the microscope. Molecular techniques, particularly characterizing bacteria using polymerase chain reaction (PCR) amplification of their small subunit ribosomal RNA (SSU rRNA) genes, has dramatically improved the ability to identify bacteria from environmental samples. Identification of bacteria by PCR amplification is specific and very sensitive. However, it is exactly these properties of PCR amplification which make it difficult to determine the amount of each individual bacterial species in the population.marine bacteriamonitoringpolymenrase chain reactionpollutionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6fm563nnpublicationoai:escholarship.org:ark:/13030/qt0r9964vd2011-07-01T07:21:08Zqt0r9964vdExpression of Recombinant Proteins in MicroalgaeMayfield, Stephen P.Franklin, Scott E.2003-02-21Our initial objectives in this project were three-fold. I. Express functional antibodies in the chloroplast of Chlamydomonas reinhardtii II. Express functional antibodies in the nucleocytoplasmic compartment of C. reinhardtii and III. Define optimal parameters for the large scale culture of antibody producing strains of C. reinhardtii.microalgaerecombinant proteinsChlamydomonas reinhardtiiapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0r9964vdpublicationoai:escholarship.org:ark:/13030/qt0h3704p12011-07-01T07:18:55Zqt0h3704p1The effects of habitat composition, quality, and breaks on home ranges of exploited nearshore reef fishesLowe, Christopher G.Caselle, Jennifer2008-02-13No-take marine reserves have become a popular tool in fisheries management worldwide; ever, many aspects of their design, including optimal size and location, are still debated. This is due, in part to a lack of critical knowledge on behavior of many exploited marine organisms. Because a primary application of no-take marine reserves is to protect adult reproductive stock, which may serve to supply larvae and juveniles to adjacent unprotected areas, reserves must be large enough at minimum to encompass the daily movement patterns of adult fishes. Previous studies on home range sizes and site fidelity of kelp bass and sheephead in California marine reserves have suggested that habitat composition may influence the size and shape of home ranges, and that breaks in habitat may serve as natural barriers, restricting the home ranges of some fishes. Surprisingly, little is known about how habitat composition, quality and gradients may influence home range sizes and site fidelity of nearshore kelp bed fishes. Knowing fish-habitat relationships and how habitat edges affect fish movement will allow managers to site reserves knowledgeably with goals of optimizing “leaky” boundaries that allow for spillover into the fishery or “tight” boundaries that minimize movements of fish across the boundary.fishfisheriesmarine protected areasmovementshabitatGISkelp basssheepheadocean whitefishbarred sand bassapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0h3704p1publicationoai:escholarship.org:ark:/13030/qt6wc6v44s2011-07-01T07:09:29Zqt6wc6v44sDynamics and Ecosystem threats of Bidirectional Cordgrass Hybridization in San Francisco BayStrong, Donald R.Ayres, D R2005-04-01Hybrids between alien cordgrass, Spartina alterniflora, introduced in the 1970s, and native California cordgrass, S. foliosa are a menace to the ecology of San Francisco Bay, spreading to aggressively invade open mud, displacing native species, hindering flood control, navigation, and other uses of this habitat. We proposed to determine the key elements of the ecology of the hybrid cordgrass invasion: ecological amplitude of parental species and hybrids, dynamics of seedling movement and recruitment, and broad spread of hybrids around the Bay and up the Sacramento Delta. Our previous field and molecular work suggested that vigorous hybrids grow taller and more densely than either parental species; they should have greatest competitive abilities and tidal range. To experimentally compare ecological amplitudes among cordgrass plants, we measured vegetative vigor and sexual reproduction of cordgrass genotypes planted in common gardens on the intertidal plane. To identify essential components of seedling recruitment, we planned to characterized seed movement on the tides, persistence in the soil seed bank, and germination and establishment of cordgrass genotypes in experimental field plots. To document the rate and extent of the spread of hybrids around the Bay, we annually surveyed and genetically characterized cordgrass seedlings and plants in marshes where hybrids were established as well as previously un-invaded marshes.invasive speciesSpartinacordgrassapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6wc6v44spublicationoai:escholarship.org:ark:/13030/qt248568292011-07-01T07:09:24Zqt24856829Initial Steps Towards Evaluating the Potential Disease Impacts of Propagated Marine Fish on Wild Stock: Examination of a New Herpes-like VirusHedrick, Ronald P.Arkush, Kristen D.2009-08-07The project hypothesis is that with the development and application of the appropriate tools for pathogen detection, we can gain major initial insights into the potential impacts of diseases among propagated fish upon wild fish populations.white seabassherpes virusfish sporozoanapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/24856829publicationoai:escholarship.org:ark:/13030/qt4vt1x4qp2011-07-01T07:09:18Zqt4vt1x4qpToward the genetic engineering of disease resistance in oystersFriedman, CarolynBurns, Jane C.2003-08-15The focus is on research conducted and the progress made toward the achievement of all specific aims outlined in the original proposal. Three abstracts describing aspects of our work in oysters were presented at national and international meetings. Specific Aim: Test methods of introducing pantropic vectors into C. virginica embryos to create transgenic oystersResistanceapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4vt1x4qppublicationoai:escholarship.org:ark:/13030/qt4h71t5rk2011-07-01T07:09:08Zqt4h71t5rkCombating Arundo donax and Other Rhizomatous Aquatic and Estuarine Nuisance Grasses By Exploiting Their Ecophysiological CharacteristicsWijte, Antonia2005-02-02During the past three to four decades, parallel expansions of populations of non-indigenousrhizomatous grasses have occurred in aquatic and estuarine habitats around the nation.Among these expansions are Spartina alterniflora invasions in the salt marshes of thePacific Northwest (Callaway and Josselyn, 1992), take-over of large sections of theriparian ecosystems in Southern California by Arundo donax (Bell, 1997) and Phragmitesaustralis invasions in the upper regions of salt marshes in the mid-Atlantic states(Hellings and Gallagher, 1992).nuisance grassesrhizomatousN:C ratiocritical nitrogen contentleavesrhizome fillingsystemic herbicideglyphosateArundo donaxSpartina alternifloraPhragmites australisapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4h71t5rkpublicationoai:escholarship.org:ark:/13030/qt11b051kk2011-07-01T07:08:59Zqt11b051kkFate and transport of planar and mono-ortho polychlorinated biphenyls and polychlorinated naphthalenes in Southern California sedimentsVenkatesan, M. Indira2003-09-01Polychlorinated biphenyls (PCBs) are an important class of industrial pollutants that areubiquitous in the marine and freshwater environments (NAS, 1979). Although the “planar” or“non-ortho” PCB congeners are present in much lower concentrations than other PCBcongeners, they can be responsible for much of the dioxin-like (TCDD) toxicity in the marineecosystem. Further, their environmental fate may be different from other PCBs. Theirdetermination is, therefore, crucial for assessment of contaminant status of environmentalcompartments. Mono-ortho PCBs and polychlorinated naphthalenes (PCN) although less potent,also exhibit TCDD-like toxicity. Yet, only total PCBs are usually reported and the levels of non-and mono-ortho PCBs relative to total PCBs have rarely been studied and data on PCN areuncommon in oceanic samples (Jarnberg et al., 1993). Among the known sources, municipalwaste dischargers could be a significant contributor of these synthetic compounds to the ocean(i.e., Venkatesan, 1998; Zeng and Venkatesan, 1999).marine pollutioncntaminantssedmentspolychlorinated biphenylspolychlorinated naphthalenesSouthern California coastal regionapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/11b051kkpublicationoai:escholarship.org:ark:/13030/qt4xm6w8422011-07-01T07:08:53Zqt4xm6w842Linking Early Fish Growth and Transport to Circulation Using Otolith Microstructure and MicrochemistryLove, Milton S.Warner, Robert R.Washburn, Libe2003-06-01An estimate of the degree of connectivity among local populations through larval dispersal can help to define the appropriate geographic scale of resource management (e.g., spatial extent of fishery closures, placement of marine reserves).CoastalFishOceanographyapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4xm6w842publicationoai:escholarship.org:ark:/13030/qt00p6b2wk2011-07-01T07:08:47Zqt00p6b2wkPost-invasion Genetic Structure of European Green Crab Populations on the US West Coast and Its Implications for Their ControlGeller, JonathanGrosholz, EdwinBagley, Mark2002-06-14One of the most ecologically significant invaders in the coastal waters of the U.S.is 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.marine biological invasionsmicrosatellite DNACarcinuscrabspopulation geneticsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/00p6b2wkpublicationoai:escholarship.org:ark:/13030/qt2p00q86j2011-07-01T07:08:42Zqt2p00q86jIdentification of Natural and Synthetic Peptides for Controlling Marine Larval SetZimmer, Richard K.Krug, Patrick J.2001-12-09Colonization of the benthic environment requires planktonic larvae to settle from the water column and metamorphose to a juvenile stage. For many species, planktonic larvae can discriminate between settlement sites; the larvae not only choose consistently between substrates in the laboratory, but cluster on preferred substrates in the field. Chemical properties of benthic environments are known to provide essential cues for larvae actively colonizing habitat sites. The requirements for chemical inducers to trigger settlement and metamorphosis can be exploited for ecological management and commercial benefits.biotechnologyoysterbarnacleabalonepeptidebiofoulingfertilizationsettlementmetamorphosishabitat colonizationfisherymaricultureapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2p00q86jpublicationoai:escholarship.org:ark:/13030/qt7pg7b24d2011-07-01T07:08:36Zqt7pg7b24dManagement and Risk Assessment of Sabellid Polychaete Infestations in Abalone Mariculture FacilitiesKuris, Armand M.1996-12-16In October 1993, growers at some commercial abalone mariculture facilities (AMFs) in Southern California brought an interesting sabellid polychaete to our attention.The worm infested shells of cultured red abalone, Haliotis rufescens. Heavily infested abalone ceased growth. Their shells exhibited domed teratology often lacking respiratory holes. The worms appeared to bore into the shell.We discovered that all AMFs in California were infested; several were so heavily infested that domed specimens were abundant. The objectives of our study were to describe the worm (Associate principal investigator, K. Fitzhugh, Los Angeles County Museum of Natural History), investigate transmission to abalone, its mechanism of attachment and the cause of shell damage. We also examined the host specificity among common intertidal molluscs. In the course of our research we discovered that a natural rocky intertidal site at Cayucos, California had become infested. Here we sought to investigate how the worms had escaped into the adjacent facility, determine whether the worms had become established there, quantify transmission at that site and devise and supervise an eradication plan.abaloneaquaculturesabellidgrowthshellintroduced speciesmarine pesthost specificityapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7pg7b24dpublicationoai:escholarship.org:ark:/13030/qt5ft5878r2011-07-01T07:08:30Zqt5ft5878rPharmacokinetics and Efficacy of Oxytetracycline in RLP-infected AbaloneTjeerdema, Ronald S.Friedman, Carolyn S.Moore, James D.Viant, Mark R.2007-05-30Withering syndrome (WS) is a catastrophic disease of both wild and cultured abalone caused by “Candidatus Xenohaliotis californiensis”, a Rickettsia-like procaryote (WS-RLP). Losses from this disease have severely hampered the abalone aquaculture industry and abalone restoration efforts in California. Oxytetracycline (OTC) was recently demonstrated to be an effective therapeutant for WS-RLP infections and associated losses due to WS. In addition, a long duration of protection (approximately one year) was noted anecdotally. Part one of this study examined the efficacy and pharmacokinetics of OTC treatment in red abalone, Haliotis rufescens, held at 13.4oC. Medication was administered orally in an artificial diet containing 1.85% active OTC at a rate of 103.4 mg/kg abalone for 10, 20 and 30 days. Control abalone were fed the same diet lacking OTC. Significant differences in prevalence and intensity of infection in both the post-esophagus and digestive gland were observed. Although the digestive gland from abalone medicated for 10 days and foot muscle from those medicated for 30 days was best described with a two-compartment model, pharmacokinetic trends were adequately described by a one-compartment model. Significant differences in OTC accumulation and depletion were observed among treatments. Animals medicated for 10 days accumulated significantly less than those medicated for 20 or 30 days. Despite this, terminal elimination rate constants were similar. Significantly less OTC was present in foot muscle samples relative to corresponding digestive gland samples. Estimated half-life values were similar among treatments for both foot muscle (10.7-13.4 d) and digestive gland (23.8-27.5 d) samples.red abaloneHaliotis rufescenswithering syndromeWSNMR metabolomicsRLPoxytetracyclineEl Niñoapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5ft5878rpublicationoai:escholarship.org:ark:/13030/qt57h3x7002011-07-01T07:08:25Zqt57h3x700Characterizing the Role of Environmental Stressors in the Development of Withering Syndrome in Red AbaloneTjeerdema, Ronald S.Friedman, CarolynViant, Mark R.2004-03-31Withering syndrome (WS) is a disease of wild and cultured abalone, caused by aRickettsiales-like prokaryote (WS-RLP). While WS has decimated black abalone populationsthroughout most of California, both wild and cultured red abalone have shown resilience incertain environmental conditions. The changes in seawater temperature and food availabilityassociated with El Niño events may, however, stimulate the pathogenesis of WS in WS-RLP-infected red abalone. This study sought to examine the relative contributions and synergisticeffects of multiple stressors on development of WS, and establish sensitive and robust markersfor characterizing the sequential pathological changes associated with disease progression. This information is critical for the proper management of WS by both private aquaculturists and stateresource managers.red abaloneHaliotis rufescenswithering syndromeWSenvironmental stressRLPenergetic statusEl Niñoheat shockproteinNMRmetabonomicsmetabolomicsbiomarkerapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/57h3x700publicationoai:escholarship.org:ark:/13030/qt5mk942k62011-07-01T07:08:20Zqt5mk942k6Development of a Recirculation System and Diet for the Culture of California Halibut (Paralichthys californicus)Piedrahita, Raul H.Conklin, Douglas E.2004-04-01The major goal of the project was the development of recirculation systems and diets for the California halibut (Paralichthys californicus). Specific objectives included the determination of bioengineering design parameters (rates of oxygen consumption and ammonia and urea production in tank culture), the characterization of major nutrient requirements and the development of a suitable practical diet; and the design and testing of a prototype recirculation system for the commercial culture of California halibut.California halibutflatfishnutritionaquacultural engineeringrecirculation systemsapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5mk942k6publication