http://www.rssboard.org/rss-specification 720 https://escholarship.org/uc/csgc_rtd/rss Recent eScholarship items from Research Theses and Dissertations Fri, 15 May 2026 08:54:22 +0000 https://escholarship.org/uc/item/6ks2b401 <p>For nearly 90 years the shellfish mariculture industry in Humboldt Bay has coexisted with various stakeholder groups and the Bay’s delicate ecology. Presently, the shellfish mariculture industry in Humboldt Bay is composed of six shellfish producing businesses ranging in operational size from small-scale to large-scale. Commercial shellfish production from Humboldt Bay yields over 70 percent of California’s mature, market-sized, Pacific oysters (Crassostrea gigas) and Kumamoto oysters (C. sikamea). Shellfish growers in the Bay also produce seed from Pacific oysters, Kumamoto oysters, and Manila clams (Tapes semidecussata).</p><p>As the mariculture industry in Humboldt Bay is poised to expand its footprint, very limited data about the industry have been made available for planners and decision makers. The purposes of this thesis were to: (1) Gather reliable socioeconomic data about</p><p>the state of the mariculture industry in Humboldt Bay. (2) Evaluate the industry’s</p><p>strengths... https://escholarship.org/uc/item/6ks2b401 Mon, 9 Dec 2024 00:00:00 +0000 Smith, Wyatt G https://escholarship.org/uc/item/4c12v43m <p>This study provides the first assessment of demographic and habitat information</p><p>for pinto abalone (Haliotis kamtschatkana) in San Diego, California, two decades after</p><p>the closure of all abalone fisheries in southern California. SCUBA surveys conducted</p><p>from June 2014 to December 2016 indicate that current low densities (0-0.03</p><p>individuals/m2) were far below critical thresholds identified for other abalone species</p><p>(0.15-0.30 abalone/m2) for successful spawning and recruitment. A broad range of sizes</p><p>were represented (13-146 mm), however, only 95 individuals were found. Some sites</p><p>showed significant aggregation of adult (&gt; 50 mm) pinto abalone, 30% of adults had a</p><p>nearest-neighbor within a critical spawning distance of 2 m, and 65% had a neighbor</p><p>within 5 m, indicating that at least a small proportion of individuals may be capable of</p><p>reproducing successfully. Pinto abalone showed a significant preference for boulder</p><p>habitat... https://escholarship.org/uc/item/4c12v43m Mon, 9 Dec 2024 00:00:00 +0000 Bird, Amanda C https://escholarship.org/uc/item/0764s0mr <p>Studies of fish diets can improve the understanding of trophic distributions</p><p>and the predatory role of a species in an ecosystem. Identifying the spatial and</p><p>temporal variability in the diets of fishes can provide useful information for stock</p><p>assessments and management. Yellowtail Rockfish (Sebastes flavidus) are a</p><p>commercially and recreationally important fishery species, and abundant along</p><p>the central California coast, yet the most recent studies of diets occurred over 20</p><p>years ago in Oregon and Washington. To provide current information from</p><p>California, I examined the food habits of Yellowtail Rockfish collected near</p><p>Cordell Bank, the Farallon Islands, and Half Moon Bay in 2013 and 2014 using</p><p>gut content and stable isotope analyses. Yellowtail Rockfish analyzed in this</p><p>study were semi-pelagic predators, feeding primarily on tunicates, crustaceans,</p><p>and teleosts. Based on δ15N values, fish caught in 2013, on... https://escholarship.org/uc/item/0764s0mr Fri, 20 Sep 2019 00:00:00 +0000 Chiu, Jennifer A https://escholarship.org/uc/item/0630k85f Riverine landscapes are shaped by dynamic and complex interactions between streamflow and floodplain landforms, and these physical processes drive productive and diverse freshwater ecosystems. However, human activities have fundamentally altered river-floodplain processes and degraded ecosystems. Flow regime variability has been homogenized and floodplains disconnected from rivers due to dams, diversions, levee building, and land use change. Reconciling competing demands to support ecosystems and resilience to future change is a core scientific and management challenge. This dissertation describes spatiotemporal dynamics of floodplain environments, introducing a method for flood regime classification and establishing a methodological approach for hydrospatial analysis to quantify and evaluate the response of floodplain inundation patterns and related physical habitat to restoration and flow regime change under climate change. It is motivated by the need to develop process-based... https://escholarship.org/uc/item/0630k85f Fri, 6 Jul 2018 00:00:00 +0000 Whipple, Alison A https://escholarship.org/uc/item/6t96k2rn The majority of Northern California estuaries are small, flooded, river valleys that are largely unstudied due to their small sizes and remote locations. Yet these estuaries serve as important nursery areas for many marine fish species including rockfish, flatfish, smelt, and herring, and they are vital to anadromous species such as Chinook Salmon (Oncorhynchus tshawytscha) and Steelhead (O. mykiss). I sampled the summer and winter fish and invertebrate communities of the Big, Mad, and Ten Mile river estuaries. Fish were sampled via beach seine or fyke net and invertebrates were sampled via benthic cores, June 2014-June 2016. This research is part of a larger suite of studies establishing baseline conditions in Northern California Marine Protected Areas (MPAs). Big and Ten Mile river estuaries in Mendocino County were designated as MPAs in 2012. The Mad River Estuary in Humboldt County was selected as a non-MPA site to investigate its potential as a reference estuary. In the Mad... https://escholarship.org/uc/item/6t96k2rn Tue, 23 Jan 2018 00:00:00 +0000 Osborn, Katherine https://escholarship.org/uc/item/6qw3k2rb <p>The Scott and Shasta rivers, Klamath River tributaries, experience spatial disparity in habitat quality in spring and summer as a result of historical and current landuse.</p><p>Juvenile Coho Salmon (Oncorhynchus kisutch) born in the upper tributary reaches often rear in natal streams before migrating to sea. However, those born in the lower reaches often encounter unsuitable habitat and emigrate during their first spring to seek non-natal rearing habitats. It is assumed that these early outmigrants are population losses. This study evaluated first-summer survival, and contribution to the adult population, of non-natal rearing juveniles in the Klamath River Basin. In the spring of 2014 and 2015 juveniles were tagged using Passive Integrated Transponder (PIT) tags as they were leaving the lower Scott and Shasta Rivers. Movement and survival was subsequently tracked using recapture and detection efforts in potential mainstem summer rearing locations. Strontium microchemistry... https://escholarship.org/uc/item/6qw3k2rb Tue, 23 Jan 2018 00:00:00 +0000 Gorman, Molly https://escholarship.org/uc/item/3rr806vn Marine Protected Areas (MPAs) are a management tool used to protect and sustain many ecologically and economically important fish species from overexploitation by recreational and commercial fishing. Lingcod (Ophiodon elongatus) and some of its prey species, such as rockfish (Sebastes spp.), are species that are protected from fishing in some California MPAs. Lingcod is an apex predator that consumes a variety of fish and invertebrate species. In this study, I sought to assess the effect of an MPA on the abundance, size and diet of Lingcod. I hypothesized that Lingcod in a no-take MPA would be more abundant and larger than Lingcod in an adjacent reference site (REF) that was open to fishing. Furthermore, I hypothesized that diet would differ between Lingcod in caught the MPA and Lingcod in the REF. I collected Lingcod from the Point Buchon State Marine Reserve (MPA) and an adjacent REF site that was open to fishing. I measured, weighed, sexed, and collected stomach contents from... https://escholarship.org/uc/item/3rr806vn Tue, 23 Jan 2018 00:00:00 +0000 Anderson, Eric https://escholarship.org/uc/item/2171q02z Traditionally, the recreational fishery for Pacific halibut has been open in California from 1 May through 31 October. In 2014, however, the Pacific halibut fishery was closed in California during the month of August for the first time in history in an effort to reduce harvest and bring total catch closer to what is allocated to our region by the Pacific Fisheries Management Council (PFMC) Catch Sharing Plan. To determine the effects that the closure had on businesses along the North Coast, I conducted an economic impact survey in 2014. The results of the survey showed that fishing-related businesses lost between zero percent and eight percent of their revenue in 2014, as a result of the closure; lodging and traveler service companies lost between 0.3 percent and one percent of their revenue in the same year. None of the businesses changed the number of employees as a result of the closure. We estimated a decrease in revenue for businesses on the North Coast to be between $189,750... https://escholarship.org/uc/item/2171q02z Tue, 23 Jan 2018 00:00:00 +0000 Takada, Miji T https://escholarship.org/uc/item/020740qq Expectations and adaptation to environmental risks https://escholarship.org/uc/item/020740qq Tue, 23 Jan 2018 00:00:00 +0000 Shrader, Jeffrey https://escholarship.org/uc/item/0tn745pm The Effects of 4-nonylphenol on the Immune Response of the Pacific oyster, Crassostrea gigas, Following Bacterial Infection (Vibrio campbellii) https://escholarship.org/uc/item/0tn745pm Thu, 1 Sep 2016 00:00:00 +0000 Hart, Courtney E https://escholarship.org/uc/item/1nr8r16n CREATION AND UTILIZATION OF NOVEL GENETIC METHODS FOR STUDYING AND IMPROVING MANAGEMENT OF CHINOOK SALMON POPULATIONS https://escholarship.org/uc/item/1nr8r16n Tue, 28 Oct 2014 00:00:00 +0000 Clemento, Anthony https://escholarship.org/uc/item/26394160 Phytoplankton samples were collected off the Monterey Municipal Wharf II at a single location (36º 36’ N and 121º 53’ W) weekly from June 2003 to March 2010. The contribution of five algal groups to total chlorophyll a (chl a) was derived using CHEMTAX from biomarker pigment measurements made via HPLC analysis. The purpose of this study was to specifically define the relative abundances of diatoms and dinoflagellates on a seasonal and interannual basis. Spearman’s rho (ρ) correlation coefficients were calculated to determine the strength of the relationship between the diatoms and dinoflagellates and two environmental variables; sea surface temperature (SST) and upwelling indices (UI). During the summer of 2004 and until the end of 2006, previous studies had suggested that the typical diatom-dominated bay shifted to a dinoflagellate-dominated system resulting from global warming effects on mixed layer stability. The high-resolution (weekly), long-term (2003-2010) sampling regime... https://escholarship.org/uc/item/26394160 Mon, 9 Jun 2014 00:00:00 +0000 Keating, Kelene https://escholarship.org/uc/item/01g8c0ck The Chinese mitten crab, Eriocheir sinensis, has a history of invasions in numerous countries. In 1992, the Chinese mitten crab was introduced to the San Francisco Bay/Delta system. Since its invasion in the San Francisco Bay, it has become an aquatic nuisance species. Little is known about the population dynamics of the megalopa stage of the Chinese mitten crab in the San Francisco Bay estuary, particularly the megalopa stage. Light traps are often used to sample marine larvae and can provide measures for relative abundance of larvae between sampling locations. As part of an ongoing study to monitor mitten crab larvae in the San Francisco Bay, light trap and plankton tow samples were analyzed formitten crab megalopae and zoeae. In order to implement low cost sampling devices for mitten crab megalopae such as light traps, it is necessary to be able to identify their larvae in collected samples. Thus, the main objective of this work was to develop a means to distinguish mitten... https://escholarship.org/uc/item/01g8c0ck Mon, 9 Jun 2014 00:00:00 +0000 Gonzales, Vanessa Alexandra https://escholarship.org/uc/item/1g8542m8 <p>This dissertation addresses the role that dynamic flow characteristics play in shaping the potential for significant ecosystem benefits from floodplain restoration. Mediterranean-climate river systems present challenges for restoring healthy floodplains because of the inter and intra-annual variability in stream flow, which has been dramatically reduced in an effort to control flooding and to provide a more consistent year-round water supply for human use. Habitat restoration efforts require that this reduced stream flow be altered in order to recover more naturally dynamic flow patterns and reconnect floodplains. This thesis defines and takes advantage of an eco-hydrology modeling framework to reveal how the ecological returns of different hydrologic alterations or restoration scenarios—including changes to the physical landscape and flow dynamics—influence habitat connectivity for freshwater biota. A method for quantifying benefits of expanding floodplain connectivity can... https://escholarship.org/uc/item/1g8542m8 Mon, 2 Jun 2014 00:00:00 +0000 Matella, Mary https://escholarship.org/uc/item/0j06b65p Phenology is the study of seasonal, biological events and how they are influenced by climate. Climate change has prompted an earlier arrival of spring in numerous ecosystems. It is uncertain whether such changes are occurring in coastal upwelling ecosystems, because these regions are subject to decadal climate oscillations and regional climate models predict later seasonal upwelling. To answer this question, chapter 1 investigated decadal changes in the phenology of 43 larval fish species in southern California. The first principal component of this dataset showed a progression towards the earlier appearance of larvae, although 18% of phenological events exhibited seasonal delays. These changes were best explained by a secular trend towards earlier warming of surface waters. Species with earlier phenology were characterized by an offshore, epipelagic distribution, while fishes with delayed phenology were more likely reside in coastal, demersal habitats. Chapter 2 focused on improving... https://escholarship.org/uc/item/0j06b65p Thu, 22 May 2014 00:00:00 +0000 Asch, Rebecca https://escholarship.org/uc/item/3t79n0d9 <p>Geophysical and geological approaches were employed to understand sediment dispersal systems and their response to various forcing functions (i.e., sea level member marine environments were studied; one with high precipitation and sediment discharge (Gulf of Papua, Papua New Guinea) and the other with low precipitation and sediment discharge (Oceanside Littoral Cell). The high-sedimentation rate in the Margins Source-to-Sink (S2S) program, we acquired CHIRP and core data across the GoP continental shelf that complemented onshore and offshore research in the region. CHIRP seismic data imaged three Holocene sedimentary lobes. The older Central lobe is downlapped by two younger lobes to the north and south. Sediment analysis showed that the older Central lobe has an elemental signature similar to the younger Northern lobe with both sourced from the Purari River watershed and lobe migration appears to be climatically controlled. The Southern lobe has elemental signatures more consistent... https://escholarship.org/uc/item/3t79n0d9 Wed, 17 Apr 2013 00:00:00 +0000 Johnstone, Elizabeth Anne Carruthers https://escholarship.org/uc/item/0sx0n5tt <p>Cryptosporidium and Giardia are important disease agents for both humans and animals worldwide. Unlike many pathogens, their capacity for surviving in soil and water for extended periods of time enables environmental transmission. Both parasites replicate within warm-blooded vertebrate hosts and are excreted as an environmentally resistant oocyst or cyst, respectively. New hosts become infected through ingestion of oocysts or cysts in contaminated water, food, or soil. The objective of this thesis work was to utilize an epidemiologic approach to identify environmental factors associated with the prevalence of Cryptosporidium and Giardia spp. in California coastal wetlands, as well as to ascertain the prevalence and identify potential transmission pathways within the animal community in the Virunga Massif, Rwanda.</p><p>Because Cryptosporidium and Giardia are waterborne parasites, key factors in wetland ecology were examined for their impact on parasite levels in water. First,... https://escholarship.org/uc/item/0sx0n5tt Fri, 22 Mar 2013 00:00:00 +0000 Hogan, Jennifer Nicole https://escholarship.org/uc/item/7hp692zp Hydrologic systems are vulnerable to anthropogenic and natural environmentalchanges. When these changes impair a system’s ability to function and serve as aresource, then restoration or mitigation may be needed. Successful management offreshwater resources requires a quantitative understanding of hydrologic processes and dynamics, and an assessment as to how hydrologic systems may respond to futurechanges. Some systems are sufficiently large or complex so as to defy direct control or restoration, but people can still benefit from understanding that will allow more reliable and thoughtful resource use, as part of a comprehensive management approach. The three chapters presented in this thesis examine hydrologic system response to a variety of environmental changes, including: (1) a recovering riparian wetland located downstream of a dam, (2) an overdrafted and seawater intruded coastal groundwater basin, and (3) a region experiencing an increase in the intensity of extreme precipitation... https://escholarship.org/uc/item/7hp692zp Tue, 27 Nov 2012 00:00:00 +0000 Russo, Tess A. https://escholarship.org/uc/item/7507v28b <p>Dispersion of planktonic propagules connects shoreline populations of many marine species, and considerable effort has been directed at understanding this process. However, gaps in knowledge persist. In particular, relatively little information has been available regarding transport over the innermost portions of the continental shelf and its impacts on larval distributions and population connectivity. I quantified velocity in nearshore waters at 5 sites along the California coast and investigated characteristics relevant for dispersing larvae. Mean depth-averaged velocities increased with distance from shore at all sites. This repeated and consistent “coastal boundary layer” (CBL) pattern exhibits a logarithmic profile that resembles that associated with the “law of the wall” of smaller-scale turbulent boundary layers, despite differences in spatial dimension and governing physics. A tentative scaling of dominant terms in an alongshore momentum balance suggests nontrivial... https://escholarship.org/uc/item/7507v28b Tue, 27 Nov 2012 00:00:00 +0000 Nickols, Kerry Jean https://escholarship.org/uc/item/9jf1j3mv <p>In the Central Valley of California, <em>Populus fremontii</em> ssp. <em>fremontii</em>, <em>Salix</em> <em> gooddingii</em>, and <em>Salix exigua</em> dominate the near-river forests. Historically, seedling recruitment for these disturbance-adapted species coincided with spring floods. Changes in flow timing and magnitude due to river regulation have decreased the success of seedling cohorts and contribute to the decline of pioneer riparian tree populations.</p><p>In order to address gaps in our understanding of these species and their potential restoration strategies, I rigorously quantified and field-calibrated a conceptual model of seedling recruitment using field and laboratory studies. Results indicate that these species do not maintain a seed bank and that vegetation competition does not limit seedling recruitment in the first year. Abundance was correlated with soil moisture and with low bank elevation. However, overwinter mortality was nearly complete.</p><p>Results... https://escholarship.org/uc/item/9jf1j3mv Fri, 16 Nov 2012 00:00:00 +0000 Stella, John Christopher https://escholarship.org/uc/item/9tx3r1sm <p>A general survey of trace metal content in Ulva spp. (Linnaeus) around Moss Landing, California was carried out. The next objective was to evaluate whether tissue nitrogen or media nitrate affects metal uptake (As, Pb, Mn, Zn) by Ulva spp. under eutrophic conditions. Additionally, the role of metal burden in the invertebrate <em>Idotea resecata</em> as a function of metal content in its diet was examined. Mean trace metal concentrations in Ulva differed significantly among sites in Moss Landing, California. Laboratory measurements using samples from 15 sites along the central California coast revealed a significant positive correlation between Ulva spp. tissue nitrogen and both arsenic and manganese uptake. No relationship was found between tissue nitrogen and lead or zinc, but a significant positive correlation with the relative change in manganese and lead was observed. Though statistically insignificant, a regression analysis revealed a logarithmic relationship between media... https://escholarship.org/uc/item/9tx3r1sm Tue, 30 Oct 2012 00:00:00 +0000 Sankaran, Sonya Meenakshi https://escholarship.org/uc/item/1w92g8pt <p>Comprehensive primary productivity measurements of the impact of invasive species are important environmental indicators. This study obtained measurements of the impact of invasive <em>Spartina densiflora</em> on the primary productivity of a Humboldt Bay (California) salt marsh using above and belowground biomass measurements coupled with paired closed-chamber carbon dioxide flux measurements. Compared to samples dominated by native vegetation, samples dominated by <em>S. densiflora</em> displayed higher aboveground net primary productivity, lower belowground net primary productivity, lower net primary productivity, and lower net ecosystem exchange measurements; thus, <em>S. densiflora</em> colonization reduced primary productivity. Benthic macroalgal cover was a strong predictor of net ecosystem exchange. In plots dominated by <em>S. densiflora</em>, less benthic macroalgae was present and less photosynthetically active radiation reached the substratum. Therefore, increased... https://escholarship.org/uc/item/1w92g8pt Mon, 13 Aug 2012 00:00:00 +0000 Lagarde, Luc A. https://escholarship.org/uc/item/0165g8wb <p>Compound-specific isotope (CSI) analysis is rapidly growing tool in the field of ecology to assess the trophic position and foraging behavior of an animal. Only a handful of studies have examined the values and patterns of carbon and nitrogen amino acid isotopes ( δ 13C-AA and δ 15N-AA), and have primarily been done on plankton and other low trophic position organisms. Since AA data separate into unique biochemical groupings, much more detailed information is revealed than the widely used bulk isotope technique - such as source of diet (offshore vs. coastal), base of the food web, trophic positions, and an animals physiology. To examine the usefulness and power of the CSI method, we tested how  δ 13C-AA and  δ 15N-AA patterns and values appear in several populations of harbor seals (<em>Phoca</em> <em>vitulina</em>) off the California coast, primarily comparing seals from San Francisco Bay (SFB) and the Channel Islands (CI).</p><p>In Chapter 1, we compared bulk isotopes... https://escholarship.org/uc/item/0165g8wb Thu, 9 Aug 2012 00:00:00 +0000 Roland, Leslie https://escholarship.org/uc/item/0t66215v Nearshore concentrations of fecal indicator bacteria (FIB) are controlled by a complex array of physical and biological processes. The studies herein evaluate the contribution of several such process to coastal FIB dynamics using laboratory studies, mathematical modeling, and fieldwork. Two field sites are discussed; Border Fields State Beach (BFSB) and Huntington Beach, both sites of chronic FIB contamination in Southern California. At Huntington Beach field measurements of alongshore currents and horizontal diffusion were used to parameterize a suite of individual based particle tracking models. These models were used diagnostically to evaluate the contribution of physics and mortality to FIB dynamics. Advection and diffusion were found to explain a significant fraction of surfzone FIB decay, but played a lesser role offshore, suggesting that offshore FIB loss may be dominated by mortality rather than physics. No single mechanism was identified that best-explained FIB mortality... https://escholarship.org/uc/item/0t66215v Wed, 8 Aug 2012 00:00:00 +0000 Rippy, Megan Anjuli https://escholarship.org/uc/item/4w62j72c <p>From May 2003 to February 2005,20 female leopard sharks (78 -140 cm TL) were tagged with acoustic transmitters in Elkhorn Slough, California, and their movements and habitat use were examined using acoustic tracking techniques. Nine sharks were manually tracked for 20-71.5 h, and 11 sharks were monitored for 4-443 d using an array of acoustic receivers. Use of different regions in Elkhorn Slough by tagged sharks changed seasonally and was associated with changes in temperature, salinity, and dissolved oxygen. Sharks used Elkhorn Slough National Estuarine Research Reserve (ESNERR) extensively throughout the year, but especially during the spring and summer. ESNERR appeared to be important as both a foraging and nursery area, likely due to the abundance of intertidal mudflats. Movements and habitat use were tidally influenced, and likely were related to the distribution of important prey items in Elkhorn Slough.</p> https://escholarship.org/uc/item/4w62j72c Wed, 11 Jul 2012 00:00:00 +0000 Carlisle, Aaron B. https://escholarship.org/uc/item/3030r26r <p>Movements of 30 lingcod (<em>Ophiodon elongatus</em>) tagged with acoustic transmitters were monitored over one year using an array of acoustic receivers in Carmel Bay, California. For all tagged lingcod, residence times in the array varied from 3.8 to 100%of their respective days at liberty. On average, lingcod spent 42.5 ± 17.9 (SE) consecutive days in and 8.1 ± 1.5 (SE) consecutive days out of the array. Residency significantly decreased with total length for female lingcod, while a significant relationship was not exhibited for male lingcod. Large female lingcod, at lengths &gt; 90% maturity, spent the least amount of time in the array but were present during the fall spawning season and briefly during the spring. There was an observed decline in residency in April for males and small female lingcod, the timing of which coincided with the post nest-guarding dispersal period for males and with the return of large females into the array. Large female lingcod were recorded... https://escholarship.org/uc/item/3030r26r Wed, 11 Jul 2012 00:00:00 +0000 Greenley, Ashley P. https://escholarship.org/uc/item/7328g533 <p>Late  Holocene stratigraphy representing  rapid episodic subsidence is found in synclines of Humboldt Bay, California. These synclines are associated with the Cascadia subduction zone fold and thrust belt, which bends eastward in Northern California. In the axes of the synclines, repeated sequences of intertidal muds overlying saltmarsh to lowland peat deposits represent episodes of rapid submergence followed by gradual emergence. Observations of the contacts between the peats and overlying muds are abrupt (&lt;1 cm). The rapid submergence most likely represents coseismic subsidence associated with large magnitude earthquakes. The evidence for these submergence events is found within both the northern Freshwater syncline and the southern South Bay syncline.</p><p>Radiocarbon dating indicates at least eight rapid episodic subsidence events during the past 3500 years. Rapid episodic events have occurred for the following age ranges:  0-300, 500-800, 1050-1350 (2 events), 1600-1900,... https://escholarship.org/uc/item/7328g533 Tue, 3 Jul 2012 00:00:00 +0000 Valentine, David Wade https://escholarship.org/uc/item/5ts3008d <p>Adult female Dungeness crabs (<em>Cancer</em> magister) can be inseminated only while in a soft-shell condition immediately after molting. Population modelers have therefore assumed that all adult female Dungeness crabs undergo an annual molt. Based on this assumption, a tag-recovery project was initiated in northern California to determine demographic statistics of the adult female stock. Of 12,037 adult female crabs tagged and released, recoveries of 492 crabs in the commercial fishery showed that a large proportion of adult female Dungeness crabs fail to molt annually and that extrusion of viable eggs does not require annual molting and mating.</p><p>A size-specific annual molting probability estimator was developed which accounts for commercial gear selection biases. Estimates using this technique showed that annual molting probabilities decline with increasing adult female size and become zero above 155 mm. Therefore, size and age are weakly correlated. Size-related population... https://escholarship.org/uc/item/5ts3008d Tue, 3 Jul 2012 00:00:00 +0000 Diamond, Nancy https://escholarship.org/uc/item/4kh5w74h <p>The spawning behavior of unmanipulated groups of tagged and untagged chinook salmon was observed during three spawning seasons on Bogus Creek, Siskiyou County, California. Individually recognizable male and female chinook salmon were observed daily throughout their lives on the spawning grounds. Male chinook salmon were observed to compete for access to females.  Larger than average sized males were observed to be in primary (dominant) status with females much more often (44 percent of observations) than smaller males (8 percent). In 35 observed spawnings, primary males always appeared to spawn, and entered the nest first or at the same time as the first satellite male in 27 of the 29 spawnings involving more than one male. Individual large males were observed to spawn as a primary male on three occasions, and may have spawned as a primary male on up to 12 occasions.</p><p>Female chinook salmon exhibited significantly more aggressive behavior toward smaller males and more courting... https://escholarship.org/uc/item/4kh5w74h Tue, 3 Jul 2012 00:00:00 +0000 Baxter, Randall D. https://escholarship.org/uc/item/2pm4k9d8 <p>Dungeness crab (<em>Cancer magister</em>) fisheries of the eastern Pacific, from Alaska to central California, have a minimum size limit, measured as carapace width (CW), to ensure that all harvested males have had the opportunity to participate in at least one mating season as sublegal-sized crabs. Dependable indicators of female mating activity have been revealed, but mating activity of males has only been indirectly inferred through examination of  so-called "mating marks", presumably created  during the premating embrace between a male and female. Previous researchers found that mating marks were present on a higher percentage of sublegal-sized males than on legal-sized males, leading to implications that in a fished population large females may go unmated, and cause a reduction in overall egg production. I present results from laboratory experiments designed to discover the process of mating mark formation, along with at-sea observations documenting the occurrence of mating... https://escholarship.org/uc/item/2pm4k9d8 Wed, 13 Jun 2012 00:00:00 +0000 Ainsworth, Justin C. https://escholarship.org/uc/item/0rc2w7wt <p>Wild juvenile chinook salmon appear to spend an extended period of time in the estuary of the Smith River, California. Based on recovery patterns of freeze-branded juveniles released from June through August, 2000, mean estuarine residence time ranged from 8.3-13.8 d during June and July, and increased to an estimated 38.3 d for fish marked and released in August.  Based on computer simulations of the process of estuarine entrance and exit, and on evidence of estuarine growth of juvenile Chinook salmon, it appears that these estimates of mean residence times were negatively biased. True mean residence times calculated in other studies may also be considerably longer than those estimated using existing published methods.</p><p>Rowdy Creek Hatchery rears large numbers of chinook salmon and many are released as fingerlings into the Smith River estuary during May–June. In 1999, about 13% of Rowdy Creek fingerlings were marked with a left maxillary clip, whereas in 2000 about 22%... https://escholarship.org/uc/item/0rc2w7wt Wed, 13 Jun 2012 00:00:00 +0000 Zajanc, David https://escholarship.org/uc/item/4zr31050 A large body of work has established a link between endocrine disrupting compounds (EDCs) and physiological abnormalities in fishes. EDCs, which include pesticides such as pyrethroids, can mimic, synergize or antagonize the effects of endogenous hormones. Both theory and empirical data confirm that EDCs can also cause fish population decline. However, to date few studies have attempted to link realistic environmental EDC mixtures with responses at multiple tiers of the biological hierarchy, including population level impacts. Additionally, although EDCs currently areknown to impact a wide array of fishes, most studies continue to use a few standardlaboratory denizens. A need exists for an estuarine model fish, particularly consideringthat estuaries are utilized by many fish species for part of their lives and are subject to many EDC inputs. Silversides (Menidia spp.) are well appointed for this role.Furthermore, the San Francisco Bay (SFB) estuary, home to introduced silversides,represents... https://escholarship.org/uc/item/4zr31050 Mon, 7 May 2012 00:00:00 +0000 Brander, Susanne Marie https://escholarship.org/uc/item/08t52207 The scattering of light in the atmosphere by aerosols has significant implications to the measurement of ocean color by satellite. Determining the effects of this scattering by measuring aerosol optical thickness (ζ_a) and sky radiance requires a Sun Photometer. The COOPS Sun photometer was designed and constructed using a commercially available two channel CCD spectrometer, tracking telescope, and Gershun Tubes fabricated at Moss Landing Marine Laboratories. The instrument was then calibrated using the high altitude Langley method. The performance of COOPS was evaluated using an industry standard CIMEL CE 318N (serial #59) as a reference. Measurements of ζ_a by both instruments were compared and the results how deviations as a function of wavelength, channel, and day of measurement. COOPS was accurate to within 2% for select sequences of measurements at 440 nm while measurements at the longer wavelengths of 675 and 870 nm showed potential for similar accuracy.... https://escholarship.org/uc/item/08t52207 Wed, 2 May 2012 00:00:00 +0000 Beatman, Luke Valentine https://escholarship.org/uc/item/2vn1333q <p>This dissertation is based on a bioinformatics approach to study microbiology, ecology, evolution, marine biology and secondary metabolites. Comparative genomics was applied to identify the similarities and differences between two marine Actinobacteria<em> Salinispora tropica</em> and <em>S. arenicola</em>. The first step in this analysis was to identify orthologous genes between the two species and create a gene-by-gene alignment of the genomes in order to identify synteny of orthologs. The second step was to identify all secondary metabolite gene clusters and mobile genetic elements followed by a thorough analysis of the evidence for horizontal gene transfer. The first two steps reveal that the main differences between these species lie on genomic islands that harbor secondary metabolites and mobile genetic elements. The Salinispora genomes were used as the basis for comparison against other Actinobacteria to identify possible marine adaptation genes. Several marine adaptation... https://escholarship.org/uc/item/2vn1333q Tue, 1 May 2012 00:00:00 +0000 Penn, Kevin Matthew https://escholarship.org/uc/item/0m56t6cc <p>In an era of increasing governmental protection of marine resources and accelerating climate change, knowing how benthic populations of marine organisms are connected is of paramount importance. However, little is known about connectivity in the nearshore environment, particularly at ecologically and demographically relevant scales. Because the dispersive larval stage is the key to understanding population connectivity, my dissertation focused on developing a new technique for tracking larvae and determining how larval swimming behaviors can influence their cross-shelf distributions in the dynamic upwelling environment of northern California. This information is relevant not only to the applied fields of invasive species management, stock assessment, and marine protected area establishment, but also to the academic pursuit of understanding how life evolved in the sea.</p><p>In Chapters 1 and 2, I focused on investigating the role of swimming behavior in regulating larval transport... https://escholarship.org/uc/item/0m56t6cc Mon, 30 Apr 2012 00:00:00 +0000 Miller, Seth Haylen https://escholarship.org/uc/item/1bg1z47b <p>The order Rajiformes, or skates, is a morphologically conservative group that exhibits a wide range of life history characteristics. This inter-species variability warrants species-specific research. This study investigates the age, growth, reproduction, and habitat of the Starry Skate, <em>Raja stellulata</em>, which is endemic to the U.S. West Coast. Age and growth parameters were determined using two preparation techniques: gross sectioning and histological sectioning. The assumption that gross sections deposit one band pair a year was indirectly validated with centrum edge analysis and marginal increment ratio. It was not indirectly validated with histological sections. Age estimates from gross sections ranged from 0 to 11 years, and growth was best described by the two parameter von Bertalanffy growth function in which L_∞ = 865 mm TL and k = 0.15. Age estimates from histological sections ranged from 0 to 15 years, and growth was best described by the Gompertz... https://escholarship.org/uc/item/1bg1z47b Thu, 26 Apr 2012 00:00:00 +0000 James, Kelsey https://escholarship.org/uc/item/0nd3g6hk <p>This dissertation describes collaborative fisheries research (CFR) on Californiaspiny lobster (<em>Panulirus interruptus</em>) at the Santa Barbara Channel Islands (SBCI).The research goals addressed in this work include: (1) establishing a collaborativeapproach to gathering fisheries data for assessments and management; (2)assessment of marine reserves at SBCI; (3) estimating mortality rates of lobsterspopulations throughout the SBCI marine reserve network; and (4) construction offisheries models that provide context for interpreting mortality rates I estimated.</p><p>CFR enhanced assessment of marine reserves established in 2003 at the SBCIin terms of their impact in P. interruptus population structure and fisheryinteractions. After six years of reserve protection, there was a four to eight-foldincrease in trap yield, a 5–10% increase in the mean size (carapace length) of legal sized lobsters, and larger size structure of lobsters trapped inside versus outside of three replicate... https://escholarship.org/uc/item/0nd3g6hk Fri, 23 Mar 2012 00:00:00 +0000 Kay, Matthew Curry https://escholarship.org/uc/item/6jb3j28w <p>Methods for determining and confirming age for Sebastes rufus from otoliths were examined. The periodicity of growth zone formation and of calcium deposition in otoliths was studied to verify ages estimated from counts of otolith growth zones;    results were inconclusive.</p><p>Pb-210/Ra-226 activity ratios were measured in otoliths to confirm ages estimated from counts of otolith growth zones. Radiometric ages agreed well with growth zone counts, giving substantial validity to them and suggesting longevity of 50 years or more <em>Sebastes rufus</em>.</p><p>Otolith length, width, area, perimeter and weight were evaluated as criteria for determining age. All parameters were highly correlated with growth zone counts, with otolith weight showing the most promise as an age predictor.</p> Von Bertalanfy growth parameters were L _∞ <p>=488, K=0.048, t₀=-8.372 for 81 males and L _∞ =594, K=0.039, t0=-6.96 for 86 females. <em>Sebastes... https://escholarship.org/uc/item/6jb3j28w Fri, 16 Mar 2012 00:00:00 +0000 Watters, Diana L. https://escholarship.org/uc/item/2kn6v4mz <p>A number of molecular mechanisms have been implicated in biological tolerance of marine environmental stress. Among the best characterized of these is the heat shock response, which has been shown to play an important role in determining the distribution of marine invertebrates along natural gradients of stress (eg. thermal stress in the intertidal). The heat shock response also appears to play a critical role in determining the susceptibility of invertebrates to anthropogenic stress. In a parallel context, it has been proposed that multidrug resistance may play an important role in determining the survival of invertebrates along natural and anthropogenic gradients of toxic organic compounds.</p><p>This study characterized the role of both of these systems in the tolerance of natural stressors in model marine invertebrate systems. ln the first section of the dissertation I demonstrated that, although Pacific oysters are capable of significant adaptive regulation of heat shock... https://escholarship.org/uc/item/2kn6v4mz Thu, 15 Mar 2012 00:00:00 +0000 Hamdoun, Amro M. https://escholarship.org/uc/item/2gz6m0sv <p>Residual flow and exchange along a channel connecting an embayment with the coastal ocean are examined experimentally, using direct observations of currents and scalar concentrations across the mouth of San Francisco Bay. The study encompasses separate experiments during each of three "seasons": winter/spring runoff (March 2002), summer upwelling (July 2003), and fall relaxation (October 2002). Within each experiment, transects across the channel were repeated approximately every 12 minutes for 25 hours during both sprilng and neap tides. Velocity was measured from a boat-mounted acoustic Doppler current profiler. Scalar concentrations were measured at the surface and from a tow-yoed SeaSciences Inc. Acrobat.</p><p>Several sources of residual circulation were isolated: baroclinic flow, tidal pumping, and frictional phasing. We further isolated a portion of tidal pumping as tidal trapping of a headland eddy during flood tide. Density-driven flow is complicated by a dramatic... https://escholarship.org/uc/item/2gz6m0sv Thu, 15 Mar 2012 00:00:00 +0000 Fram, Jonathan Peter https://escholarship.org/uc/item/1kq4f5jq <p>Chemical communication between sperm and eggs is ubiquitous in organisms with widely divergent reproductive strategies. Sperm attractants are found in marine taxa that broadcast their gametes into the sea, as well as terrestrial organisms with internal fertilization, such as humans. Chemosensory-mediated behavior thus is a key component in sperm-egg interactions and fertilization. Despite nearly a century of research, the mechanisms controlling fertilization remains one of the least understood biological processes. For example, waterborne egg-factors that attract sperm are thought to be ecologically meaningful for increasing gamete encounters, or evolutionary significant by maintaining species barriers, but the contributions remains unknown. In this study, I (i) developed analytical and behavioral techniques to establish the reproductive consequences of sperm attractants, and (ii) examined the biological processes controlling fertilization success in the red abalone, <em>Haliotis... https://escholarship.org/uc/item/1kq4f5jq Thu, 15 Mar 2012 00:00:00 +0000 Riffell, Jeffrey Allan https://escholarship.org/uc/item/9jb5301w <p>The natural history and ecology of the California Crayfish, <em>Pacifastacus leniusculus</em> (Dana}, was investigated in a portion of subalpine Lake Tahoe from March 1974 through February 1975. Three specific areas of the lake were chosen for study because of their variability in bottom contour, substrate type and primary production. Population estimates in these areas ranged from 16,561 to 192,448 crayfish with almost equal distribution of sexes. Mean standing crop and annual production of the population were estimated at 99.77 and 30.56 g/m² respectively.</p><p>Both sexes matured in their fourth year, mating took place from late Sep­tember through October, and hatching occurred in July. Reproductive performance was 78% of the potential capacity.</p><p>Age structure of the crayfish population varied in the three areas. The avnilable cover in one of these areas was identified as the limiting factor responsible for slower growth rate and smaller mean size at onset... https://escholarship.org/uc/item/9jb5301w Wed, 14 Mar 2012 00:00:00 +0000 Flint, Robert Warren https://escholarship.org/uc/item/6j8457z5 Marine invertebrates are exposed to endocrine disrupting compounds (EDCs) and must utilize defense mechanisms to survive and reproduce; however, little is known about the effects of EDCs on marine invertebrates. Using the sea urchin developmental model, we ascertained that embryos were sensitive at environmentally relevant concentrations to estradiol, ethynylestradiol, 4-octylphenol, tributyltin and <em>o,p</em>-DDD in a stage-specific manner with early embryos being the most sensitive.  Incubation with tamoxifen, a selective estrogen receptor modulator, 'protected' the embryos from estrogenic toxicity suggesting a receptor-mediated mechanism of toxicity.  Estradiol is produced during gastrulation and binds to a low-capacity, low-affinity receptor. Maternal exposure to EDCs altered embryo sensitivity and the expression of mRNA of a steroid receptor in the oocyte in a treatment and dose-dependent manner demonstrating that maternal EDC exposure in invertebrates may directly effect... https://escholarship.org/uc/item/6j8457z5 Wed, 14 Mar 2012 00:00:00 +0000 Roepke, Troy Adam https://escholarship.org/uc/item/3wh820qs <p>A Markov Decision Process model is developed for analyz­ ing the socially optimal allocation of a replenishable or non replen­ ishable resource over time. The resource is managed by choosing the rate of extraction in each period to maximize the discounted stream of expected social returns. Elements of uncertainty enter the analysis in three ways:                                                                                (1) Uncertainties may exist about the current size of the resource, either because of difficulties in observing the stock, as in the case of a fishery, or because of the possibilities of finding new reserves th:rough exploration, as in the case of minerals and oil.  (2) The market value of the resource and the cost of extracting it may be random, due to varyingeconomic conditions. (3) Unpredictable changes in the environ­ ment may perturb the natural rate of growth or deterioration of the resource, as well as the effective rate of depletion by man.</p><p>The... https://escholarship.org/uc/item/3wh820qs Mon, 12 Mar 2012 00:00:00 +0000 Lewis, Tracy Royal https://escholarship.org/uc/item/1ck8r5z3 <p>Large volume, gravity  structures  are used as storage tanks in offshore  development. To design these gravity structures,  the understanding  of major environmental loadings  are needed. In seismic areas, one of  these  loadings  is due to earthquakes.    The pressure distributions associated with hydrodynamic inertia  forces acting on large structures during earthquakes are important while the drag forces  may be neg]ected.</p><p>A closed form solution of hydrodynamic pressure acting on rigid cylindrical tanks, surrounded by incompressible water and subjected to horizontal  ground excitation, was given  by Jacobsen^1*many years ago. Later, Petrauskas², Chandrasekaran, et  a1³ investigated  the influence of response interaction  between flexible cylindrical columns or towers and fluid pressures.  Chandrasekaran also investigated the effect  of water compressibility on hydrodynamic  pressure.</p><p>These closed form solutions are, however, limited... https://escholarship.org/uc/item/1ck8r5z3 Mon, 12 Mar 2012 00:00:00 +0000 Nilrat, Fukij https://escholarship.org/uc/item/8zz3s6w8 <p>Microbial inhabitants of the marine environment are poorly understood in terms of chemical interaction. Tremendous taxonomic diversity exists among these microorganisms, encompassing adaptations to the wide range of physical parameters found in marine habitats. Production of secondary metabolites has been studied in several marine bacteria and fungi, primarily isolated from shallow, near-shore sediments. However, most resources for the discovery of new natural products from marine microorganisms remain unexploited, and little is known of the function of microbial secondary metabolites in situ.</p><p>The study described in  this dissertation had two major goals: 1) to identify novel compounds produced by microbial isolates from extreme marine environments, and 2) to identify antibiotic compounds which might act in situ. The first investigation resulted in the isolation and structure elucidation of several novel compounds from deep-sea isolates of the genus<em> Bacillus</em>.... https://escholarship.org/uc/item/8zz3s6w8 Fri, 9 Mar 2012 00:00:00 +0000 Trischman, Jacqueline A. https://escholarship.org/uc/item/8fz5z4f9 This thesis describes a novel approach to remote and synoptic surface flow measurements in small bodies of water; it also includes an investigation to determine the practicality of this technique. The approach is based on imaging monochromatic wavetrains, of known frequency, propagating ovel'surface flows. The thesis shows that the wavelength and direction of two monochromatic wave trains of known frequency, at a region of interest, carry all the necessary information to determine the surface flow in that region. Experimental tests, conducted both in a wavetank and in a lagoon, utilizing inexpensive and readily available equipment, are described as well. These tests have shown the viability of this remote and synoptic surface flow measurement. Practical aspects of the measurements, such as vertically nonhomogeneous flow profiles, data processinof the aerial photos via 20 Fourier transforms, and the measurement of wavelength by photography of specular reflection of sun light from... https://escholarship.org/uc/item/8fz5z4f9 Fri, 9 Mar 2012 00:00:00 +0000 Sheres, David https://escholarship.org/uc/item/8172g7tv <p>The objective of motion understanding is to provide computers with the ability to identify motions captured by video cameras. The definition of what is a motion varies across applications. For example, in a dance application the motions could be the possible movements (plie, pirouette, etc.) in ballet. A characteristic of motions that does extend across applications is the fact that they occur in the spatiotemporal do­ main where both the evolving shape and the trajectory of the object can be expressed. Motion understanding differs from the classical problem of object tracking in that for tracking, the output of the system is a trajectory defining the position of the object in time. The output of a motion understanding system is a sequence of semantic labels (typically verbs) describing the motions identified in the video sequence. Motivating the development of motion understanding is the possibility of applications such as computerized sports analysis, immersive entertainment,... https://escholarship.org/uc/item/8172g7tv Fri, 9 Mar 2012 00:00:00 +0000 Schlenzig, Jennifer https://escholarship.org/uc/item/2mv030bm <p>Stable carbon isotopes and pollen analysis provide a multiproxy record of vegetation change in four tidal marshes in Northern San Francisco Bay Estuary, including two island marshes in Suisun Bay, a pocket marsh at Benicia State Park in the Carquinez Strait and a salt marsh at China Camp State Park on the western edge of San Pablo bay. Marsh vegetation responds to changes in physical conditions in the Estuary, particularly salinity. The 0¹³C value of plants occupying the marsh is preserved in the organic sediments, providing a permanent record of vegetation change, with some residual differences which are discussed. Marsh pollen types are easily identified in the sediments and provide another, complementary, record of vegetation change in the marshes around the Estuary. Combining these two methodologies, a record of late Holocene vegetation change can be reconstructed, and interpreted in terms of changes in the salinity of the San Francisco Estuary.</p><p>Near surface... https://escholarship.org/uc/item/2mv030bm Fri, 9 Mar 2012 00:00:00 +0000 Malamud-Roam, Frances P. https://escholarship.org/uc/item/1gg65842 I investigated the spatiotemporal dynamics of plant communities on islands in the Aleutian archipelago, Alaska, using small scale plots and landscape level remote sensing. Islands of the Aleutian archipelago are a model system for vegetation studies: there is no significant variation in island size, geology, soil type, or plant composition for hundreds of islands spanning 1600km of longitude. There is variation in two important factors: nutrients and climate. Past fox introductions onto some of the islands substantially reduced seabird populations that formerly vectored nutrients from the sea to land. Previous field studies have documented significant differences in vegetation composition and biomass between fox­ infested and fox-free islands using small scale field measurements. I examined the landscape level vegetation response to nutrient subsidies on individual islands and to a regional climate gradient across the entire archipelago. There was also evidence of a climate gradient... https://escholarship.org/uc/item/1gg65842 Fri, 9 Mar 2012 00:00:00 +0000 Danner, Eric M. https://escholarship.org/uc/item/2385g2q7 <p>Methods for determining and confirming age for Sebastes rufus from otoliths were examined. The periodicity of growth zone formation and of calcium deposition in otoliths was studied to verify ages estimated from counts of otolith growth zones;     results were inconclusive.</p><p>Pb-210/Ra-226 activity ratios were measured in otoliths to confirm ages estimated from counts of otolith growth zones.  Radiometric ages agreed well with growth zone counts, giving substantial validity to them and suggesting longevity of 50 years or more <em>Sebastes rufus</em>.</p><p>Otolith length, width, area, perimeter and weight were evaluated as criteria for determining age. All parameters were highly correlated with growth zone counts, with otolith weight showing the most promise as an age predictor.</p><p>Von Bertalanfy growth parameters were L =488, K=0.048, t0=-8.372 for 81 males and L00 =594, K=0.039, t0=-6.96 for 86 females.<em> Sebastes rufus</em> are long-lived, slow growing and reach... https://escholarship.org/uc/item/2385g2q7 Thu, 8 Mar 2012 00:00:00 +0000 Watters, Diana L. https://escholarship.org/uc/item/7gs5h8c9 <p>The marine sediment-derived Streptomyces spp. CNQ-525 and CNQ-766 were recently characterized by the Fenical laboratory as a new group of marine sediment-derived actinomycetes, tentatively named the MAR4s. These bacteria are prolific producers of hybrid isoprenoids, including the meroterpenoid (polyketide-terpene) antibiotics that are rarely encountered from bacteria. Structural inspection of the meroterpenoid antibiotics belonging to the napyradiomycin family of chlorinated dihydroquinones suggests that the biosynthetic cyclization of their terpenoid subunits is initiated via a chloronium ion, which exists as hypochlorous acid. The vanadium-dependent haloperoxidases that are known to catalyze such reactions are distributed in fungi and marine algae and have yet to be characterized from bacteria.</p><p>The MAR4 strain Streptomyces sp. CNQ-525 was used as a source for identifying novel halogenating enzymes. The cloning and sequence analysis of the 43-kb napyradiomycin biosynthetic... https://escholarship.org/uc/item/7gs5h8c9 Tue, 6 Mar 2012 00:00:00 +0000 Winter, Jaclyn Marie https://escholarship.org/uc/item/8d6275gr This study was performed to determine the variation and reliability among and between traditional methods of otolith ageing, and a new computer-aided technique designed for this project using the rockfish, <em>Sebastes rufus</em>. As expected, break-and-burn and thin-sectioning traditional ageing method using whole otoliths produced the fewest counts. The generated von Bertalanffy growth curve indicated a slower growth rate than previous studies. This study also incidcated a faster growth rate for females than males. The computer-aided method tended to undercount the number of bands when compared to a manual count. The computer-aided method was also markedly faster in producing multiple counts and produced less variability between counts. However, since the computer-aided method required thin-sectioning of otoliths, the overall time to produce counts was greater for the computer-aided method than traditional methods. https://escholarship.org/uc/item/8d6275gr Mon, 5 Mar 2012 00:00:00 +0000 King, Aaron Everet https://escholarship.org/uc/item/0xf7s380 Longevity estimates for the Pacific grenadier, <em>Coryphaenoides acrolepis</em>, range from 6 to greater than 60 years. Age estimates in this study using growth increments in otolith sections indicate the Pacific grenadier is long-lived. Prior to this study, traditional ageing of this fish was not validated. In this study, the radioactive disequilibria of ²¹⁰Pb and ²²⁶Ra in otolith cores from Pacific grenadier were used to validate age estimates. Accuracy of radiometric ageing using²¹⁰Pb: ²²⁶Ra disequilibria in otoliths was improved using ion-exchange chromatography and thermal ionization mass spectrometry (TIMS) to measure ²²⁶Ra. Because TIMS counts atoms, the accuracy and precision of the technique is superior to a-spectrometric methods. This procedure was applied to otoliths from three other fish species. Results indicate the procedure reduced sample size and processing time, and increased accuracy. Radiometric ages for... https://escholarship.org/uc/item/0xf7s380 Mon, 5 Mar 2012 00:00:00 +0000 Andrews, Allen Hia https://escholarship.org/uc/item/8nx1670x <p>The application of genetic markers to investigate evolutionary and ecological questions about white sturgeon, <em>Acipenser</em> <em>transmontanus</em>, has been limited due to the species’ highly duplicated nuclear genome. Here, polysomic microsatellite markers were used to 1) examine the ancestral level of genome duplication in white sturgeon, 2) examine genetic diversity and patterns of population structure within and among drainages across the species’ range, and 3) provide genetic monitoring for a conservation aquaculture program sustaining an endangered white sturgeon population. In the first chapter, we followed the inheritance of eight microsatellite markers in 15 families of white sturgeon from a commercial caviar farm to determine whether white sturgeon (~250 chromosomes) should be classified as tetraploid or octoploid. The eight microsatellite loci were detected predominantly in four or eight copies, with one locus observed in &gt;8 copies. Numbers of alleles... https://escholarship.org/uc/item/8nx1670x Mon, 13 Feb 2012 00:00:00 +0000 Schreier, Andrea Marie https://escholarship.org/uc/item/3ff3q032 Fossil data from multiple locations indicates that Atlantic elkhorn coral, <em>Acropora</em> <em>palmata</em>, formed shallow reefs throughout the Caribbean Sea since the Pleistocene. Beginning in the 1980s <em>A. palmata</em> has declined to a small fraction of its formerly vast extent throughout the region. In 2006, elkhorn coral was the first coral, along with its sister species, staghorn coral (<em>Acropora</em> <em>cervicornis</em>), to be included on the U.S. Endangered Species List. We used size-based matrix modeling to parameterize annual <em>A. palmata</em> population dynamics in Florida, over the course of one severe hurricane year (2005) and six calm years (2004, and 2006-2010), incorporating environmental stochasticity as inter-annual variability. We predicted that benthic cover would remain at current levels (4%) for the foreseeable future (until 2030) and beyond (until 2100), suggesting a lack of resilience following the 2005 hurricanes. Standard metrics... https://escholarship.org/uc/item/3ff3q032 Thu, 9 Feb 2012 00:00:00 +0000 Vardi, Tali https://escholarship.org/uc/item/1c35d8ww The extent to which exploitation may alter marine life population structure anddynamics is incompletely understood because past research overwhelmingly relies on time series that date back less than 30 years and begin long after the onset ofexploitation. This study seeks to partially fill this gap with respect to the Californiaspiny lobster, <em>Panulirus interruptus</em>, by fitting a recently developed Bayesian sizestructuredmodel to a newly assembled 120-year historical time series of catch and effort to quantify the effects of fishing on the population’s size-structure and dynamics. In a little over a century, as fishing effort increased, the abundance andproportion of large-sized lobster (&gt; 100mm carapace length) progressively declined.Severely reducing the lobster's average lifespan and size has increased thepopulation's short-term variability, potentially diminishing the resilience of thespecies and the kelp forest ecosystem by compounding the effects of ‘fishing downthe... https://escholarship.org/uc/item/1c35d8ww Tue, 7 Feb 2012 00:00:00 +0000 McArdle, Deborah Ann https://escholarship.org/uc/item/8cn120s9 <p>I developed two conceptual models addressing fishery questions in the Monterey Bay motivated by 1) the California Market Squid (<em>Loligo opalescens</em>) and 2) marine reserves as a recovery and management tool. The model for California Market Squid incorporates the close ties between environmental variability and squid life history. Inclusion of environmental factors in the model provides a biological mechanism contributing to the large fluctuations that occur in the fishery. Furthermore, I predict that removal of 30% of the unspawned SSB may drive the population to extinction within 30 generations.</p><p>Reserves are generally agreed to be good for habitat and ecosystem conservation; however, specific measures of success, such as increases in yield or size at age have been difficult to generalize across reserves. I identify density dependent body growth and displaced fishing effort as potential explanations for the variable outcomes. I predict that density dependent body... https://escholarship.org/uc/item/8cn120s9 Fri, 3 Feb 2012 00:00:00 +0000 Ish, Teresa Lin https://escholarship.org/uc/item/9x72c5g9 <p>Assigning categorical labels to objects in images has proven to be a significantchallenge for automated systems. As cameras rapidly proliferate our society, however, we will necessarily depend more heavily on computers to help us label andsort our images. This work addresses the problem of trying to assign categorical labels to images. We contend that to do this task effectively, we should consider also which part of the image contains the object.</p><p>We examine the sensitivity of feature detection to nuisances and propose a new feature detector based on a tree of segmentations. When a detector is notrequired, we describe a fast adaptation that extracts a popular descriptor (SIFT) on a dense grid on the image. Next, we show that a dictionary constructed for the task of categorization can be both smaller and more accurate than one constructed to represent the data alone. We explore splitting descriptors along segmentation boundaries, and show that knowing which part of an... https://escholarship.org/uc/item/9x72c5g9 Thu, 12 Jan 2012 00:00:00 +0000 Fulkerson, Brian Daniel https://escholarship.org/uc/item/2pq8d3dc Since the 1980s total landings for protogynous California sheephead have doubled and their abundances have declined. This study used histology to determine sexual type (immature, female, transitional or male) of sheephead collected from nine southern California populations. Fecundity was estimated for all active females and reproductive potential was assessed for each population. In five populations sheephead were undergoing sexual transition (i.e. reproductively non-functional) during the summer breeding season. The proportions of the populations in transition ranged from 2.4% at San Nicolas to 25% at Santa Catalina Island. Northwestern populations had greater reproductive potential than southeastern populations and the greatest reproductive potential was observed in the most remote population (San Nicolas Island) and at two marine protected areas (MPA). Multivariate analysis of biological variables and explanatory variables found that sea surface temperature best explains trends... https://escholarship.org/uc/item/2pq8d3dc Wed, 11 Jan 2012 00:00:00 +0000 Loke, Kerri https://escholarship.org/uc/item/4m2446t9 <p>Elk Kelp, <em>Pelagophycus porra</em>, is commonly observed in deep (20-30 m) water along the outer edge of Giant Kelp, <em>Macrocystis</em> <em>pyrifera</em>, beds in southern California, USA and northern Baja California, MEX, but rarely occurs in shallower water or within beds of M. pyrifera. Due to the nature of <em>P. porra</em>’s heteromorphic life history that alternates between a macroscopic diploid sporophyte and a microscopic haploid gametophyte, investigations of both life history stages were needed to understand <em>P. porra</em>’ apparent inability to encroach into <em>Macrocystis</em> beds along the southern California coast.</p><p>Juvenile <em>P. porra</em> sporophytes were transplanted (1)within the <em>Pelagophycus</em> zone along the offshore edge of the <em>M. pyrifera</em> bed at 20 m, (2) within the center of the <em>M. pyrifera</em> bed at 15 m and (3) along the inshore edge of the <em>M. pyrifera</em> bed at 8 m. Transplanted <em>P. porra</em>... https://escholarship.org/uc/item/4m2446t9 Thu, 5 Jan 2012 00:00:00 +0000 Fejtek, Stacie Michelle https://escholarship.org/uc/item/0nr9z2dt <p>Coral reefs support an abundance of organisms despite being surrounded byoceanic waters characterized by low nutrient levels. Over more than a century ofresearch, scientists have debated whether life on coral reefs is self-sustaining orwhether reef organisms extract nutrients from the open ocean that in turn subsidizeorganic production within the reef system. This dissertation focuses on one guild ofcoral reef consumers - fish that feed on zooplankton from the water column. Pairingtwo independent metrics of fish diet - gut content analysis and stable isotope analysisfollowed by a mass-balance mixing model - I provide direct evidence that zooplankton from the open ocean comprise a significant proportion of the diet of fish inhabitingboth offshore and nearshore reefs.</p><p>In a study of feeding behavior of the planktivorous fish <em>Dascyllus flavicaudus</em>,I document that this species feeds selectively on certain taxa within the zooplankton assemblage. Oceanic copepods (Oncaeidae... https://escholarship.org/uc/item/0nr9z2dt Tue, 13 Dec 2011 00:00:00 +0000 Hanson, Katherine Mary W. https://escholarship.org/uc/item/9x3272ww <p>The overall aim of this project was to understand the mode of sex determination mechanism operates in chondrostean species. The following hypotheses were tested: i) white sturgeon has a genetic sex determination system, ii) one of the sexes in sturgeon is heterogametic, and iii) sex-specific DNA polymorphisms exist between the sexes.</p><p>Several experimental approaches derived from the fields of transmission, molecular, and cytogenetics were used to examine the nature of the sex determination process.</p><p>In the first series of experiments (Chapter 2) ploidy manipulation techniques were used  to produce gynogenetic and polyploid white sturgeon. A novel random amplified polymorphic DNA (RAPD)-based technique was developed to rapidly assess the overall success of treatments designed to induce gynogenesis, and measuring erythrocyte nuclei size with a Coulter Counter was found to be a rapid and accurate technique for ploidy analysis in sturgeon. Both sexes were observed in... https://escholarship.org/uc/item/9x3272ww Mon, 28 Nov 2011 00:00:00 +0000 van Eenennaam, Alison Louise https://escholarship.org/uc/item/8tw6m1wx <p> A numerical model has been developed to determine the large amplitude motions of a vessel subjected to severe wave conditions, including those that may lead to capsizing. The aim was to numerically identify different modes of capsizing, and to study relevant  mechanisms and conditions. The theory is  based on a combination of potential and viscous flow approaches in the time domain, where large displacements, the instantaneous free surface and memory effects are considered.</p><p>Reasonable agreement was found between predicted motions and experimental results for a variety of wave conditions. A number of capsizes, observed experimentally, were simulated successfully using the numerical model.</p><p>An investigation has been carried out to determine the sensitivity of th roll response to changes in the force components. The Froude-Krylov forces were found to be always of importance, irrespective of the wave conditions. Generally, the relative importance of the various components depends... https://escholarship.org/uc/item/8tw6m1wx Mon, 28 Nov 2011 00:00:00 +0000 de Kat, Jean Otto https://escholarship.org/uc/item/79g8r03s Over the past decade the consumption of planktivorous northern anchovies containing the diatom-produced neurotoxin, domoic acid (DA), has been responsible for severe neurologic illness and mass mortality events involving hundreds of sea birds and marine mammals in Monterey Bay, California. This research characterizes the dynamics of DA transfer, accumulation, and neurotoxicity in this pivotal and dangerous DA vector fish species. Chapter one documents aDA-poisoning event in which dozens of California sea lions died as a result of consuming DA-contaminated anchovies in Monterey Bay. DA levels in sea lion feces and anchovies were attained using HPLC-UV and microplate receptor binding assays, with absolute confirmation by tandem mass spectrometry. The presence of toxic <em>Pseudo-nitzschia</em> frustules in sea lion feces and anchovy gut contents was determined using scanning electron microscopy. Chapter two presents data from an intracoelomic injection study in which anchovies were... https://escholarship.org/uc/item/79g8r03s Mon, 28 Nov 2011 00:00:00 +0000 Lefebvre, Katherine Ann https://escholarship.org/uc/item/65h7t5r3 <p>Airway mucus gel plays a vital role in maintaining the integrity of mucosal epithelia and protecting respiratory health. Such defensive mechanism stems primarily from a constant clearance of mucus-entrapped inhaled pathogens and particulates by mucociliary transport. The success in removing mucus-entrapped harmful substances relies heavily on proper mucus rheology. It is well established that hydration is the single most important determinant of mucus rheological properties. In a healthy condition, the body precisely controls the degree of mucus hydration through modulating physiological parameters of various ionic concentrations in the nascent microenvironment which bathe the mucus. On the contrary, inadequate mucus hydration and abnormal mucus hypersecretion seem to be the major causal factors underlying pathological states involving the accumulation of highly viscous mucus plugs, obstructive airflow, chronic infection and inflammation. These symptoms are characteristic of... https://escholarship.org/uc/item/65h7t5r3 Mon, 28 Nov 2011 00:00:00 +0000 Chen, Eric https://escholarship.org/uc/item/5q8498kw Krill of the California Current play a crucial role in the transfer of primary production up to many commercially important higher trophic levels. Understanding the short time scale (weeks to seasonal) and long time scale (decadal) variability in abundance, condition, and spatial patterns that results from changes in ocean conditions is critical if we hope to manage the fishery of any higher trophic levels from more than a single species approach. I have coupled a suite of models in an attempt to understand the impacts of changing ocean conditions on this important prey item. The coastal ocean was simulated with a commonly used oceanographic model (Regional Ocean Modeling System) coupled with an ecosystem model (Nutrient, Phytoplankton, Zooplankton, Detritus). The coastal ocean was simulated from Newport, OR to Point Conception, CA over an 18-year period (1991–2008). These model results were used to force a 3-dimensional individual based model (IBM) that was parameterized to represent... https://escholarship.org/uc/item/5q8498kw Mon, 28 Nov 2011 00:00:00 +0000 Dorman, Jeffrey G. https://escholarship.org/uc/item/4gw285v2 <p>During the last three decades, tropical marine cyanobacteria have emerged as an extraordinarily prolific source of promising biomedical natural products (NPs). Creative endeavors have been used to explore this novel chemical diversity, but lagging behind is the recognition and description of the biological diversity responsible for these NPs. Instead of being recognized as unique taxa, tropical marine NP-producing groups have been identified, with few exceptions, based on classification systems tied to morphospecies of terrestrial and freshwater specimens from temperate regions. This lack of proper classification systems is primarily due to the fact that tropical marine cyanobacteria have only recently been explored. As a result, our current perspective of the taxonomic origin and distribution of NPs in marine cyanobacteria is extraordinarily incomplete.</p><p>A major aspect of this thesis research has focused on providing a better understanding of how NPs are distributed among... https://escholarship.org/uc/item/4gw285v2 Mon, 28 Nov 2011 00:00:00 +0000 Engene, Niclas https://escholarship.org/uc/item/424497vt The work of this dissertation is the culmination of five years of research in the field of marine natural products chemistry. It involves the investigation of halogenated constituents isolated from Indo-Pacific marine sponges associated with cyanobacterial symtionts. The primary goal in the UCSC research group is to seek out novel and interesting secondary metabolites produced by marine organisms, specifically marine sponges, isolate and elucidate their chemical structures and determine their biological activity against cancer. https://escholarship.org/uc/item/424497vt Mon, 28 Nov 2011 00:00:00 +0000 Clark, William David https://escholarship.org/uc/item/3hk1d1sf <p><em>Pseudo-nitzschia</em> is a cosmopolitan marine diatom which can cause the poisoning of humans, marine mammals, and birds through the production of the neurotoxin domoic acid and subsequent contamination of the marine food web. Severe poisoning events are induced when environmental conditions allow: (1) the rapid proliferation ('bloom') of resident toxic species of <em>Pseudo-nitzschia</em>, and/or (2) their enhanced toxin production, and (3) the conveyance of the toxin into prey items. The introduction of domoic acid into the food web was recognized as a public health concern along the coast of California following a <em>Pseudo-nitzschia</em> bloom and seabird mortality event in the Monterey Bay area in 1991, and blooms of <em>Pseudo-nitzschia</em> have since been observed in the region with regularity. Since the recognition of the public health concern posed by these recurrent harmful algal bloom (HAB) events, the California Department of Public Health (CDPH) has been... https://escholarship.org/uc/item/3hk1d1sf Mon, 28 Nov 2011 00:00:00 +0000 Quay, Jenny Elisabeth https://escholarship.org/uc/item/2562b0gb Rhodoliths are free-living coralline algae (Rhodophyta) that form large beds on the seafloor. Rhodolith beds are globally widespread and biologically diverse shallow marine habitats. Beds are ecologically sensitive, disturbed by humans, and in Europe are protected by law. While rhodolith beds have been found in California waters at Catalina Island, no literature exists regarding their distribution or ecological significance. This study sought to (1) map the distribution and characterize the rhodolith beds around Catalina, (2) determine the seasonal growth rates, and (3) investigate the effect of common sources of disturbance. A systematic search of shallow subtidal (0-40 meters) areas revealed seven beds. These were mapped by divers using SCUBA. Living and dead rhodolilths and rhodalgal sediments covered approximately 22,900 and 42,696 square meters of seafloor, respectively. Percentage cover, and mean size of living rhodoliths varied across beds. Growth rates varied seasonally... https://escholarship.org/uc/item/2562b0gb Mon, 28 Nov 2011 00:00:00 +0000 Tompkins, Paul Anthony https://escholarship.org/uc/item/4h27m0nq <p>Environmental factors influencing the cultivation of many economically important marine algae are not well understood. Cultivation problems are being encountered in the growing of various algae in artificial algal beds or on man-made farming structures. It is necessary to study these cultivation problems under controlled conditions in order to understand and solve them. Aspects of Eucheuma uncinatum as a model organism for cultivation were studied in the laboratory and in a greenhouse. Gradients of different environmental factors, such as light, temperature, salinity, and nutrients, were created in the laboratory and in outdoor water tanks. Plants were exposed both to single gradients and cross qradients and their qrowth and morphology were monitored. Plants with different morpholoqies developed under different experimental conditions. High light levels (1500 uEm-2 sec -1) caused large light yellow-brown plants to develop, which became dark red when light levels were... https://escholarship.org/uc/item/4h27m0nq Tue, 1 Nov 2011 00:00:00 +0000 Polne-Fuller, Miriam https://escholarship.org/uc/item/04k9k8x3 <p>Field and laboratory tests were conducted for the kelp crab, Pugettia producta (Randall) and for the California spiny lobster, Panulirus interruptus (Randall) to determine the role of chemical stimuli in food search. Sensitive chemoreceptors were identified in gill chambers of Pugettia capable of inducing reflex cardiac inhibition. The gill chamber has not previously been described as a major chemoreceptive site in marine decapods. Stimulation of the branchial chamber with amino acids and sugars evoked cardiac inhibition that was significantly greater than that induced by sea-water controls, and chemical sensitivities were correlated with the natural diet of the animal. Primarily homolateral leg and claw food-orienting behavior were observed to follow stimulus injections into branchial chambers; however, stimuli were not strictly confined to this region. Consequently, unmistakable correlates have yet to be established between branchial chamber chemoreception and food... https://escholarship.org/uc/item/04k9k8x3 Tue, 1 Nov 2011 00:00:00 +0000 Zimmer-Faust, Richard K. https://escholarship.org/uc/item/6w39c74z <p>The roles of life history and behavior in the dynamics of dispersal, recruitment and population maintenance were investigated for a dense infaunal polychaete assemblage on the Kendall-Frost mudflat in Mission Bay, California. Polychaete life history features provided the framework for investigations of (1) the relevant scales and mechanisms of dispersal, (2) response to disturbance, and (3) the spatial and temporal predictability of species abundances in the plankton, during recruitment, and in the benthos. Field and laboratory studies of the Kendall-Frost polychaete species Pseudopolydora paucibranchiata Okuda, Polydora ligni Webster, Rhynchospio arenicola Hartman, Streblospio benedicti Webster, Exogone lourei Hartman, Fabricia limnicola Hartman and Capitella capitata Fabricius, revealed many shared life history traits which limit the spatial extent of dispersal. These include annual life cycles, small size, brood protection, small brood size and reduced or facultative... https://escholarship.org/uc/item/6w39c74z Mon, 31 Oct 2011 00:00:00 +0000 Levin, Lisa A. https://escholarship.org/uc/item/3qv250bs <p>Propagule supply is fundamental in regulating the strength of demographic and genetic interactions in natural populations. In marine systems, recent studies focusing on benthic fish and invertebrate species with long planktonic durations have found that propagule production and supply are de-coupled by physical transport processes. Most benthic marine populations therefore have been considered demographically open, whereby recruitment is driven by remote propagule production. Few studies have focused on species with shorter planktonic durations (e. g., seaweeds). I developed techniques for in situ sampling and identification of kelp zoospores and used them to study coupling between giant kelp (Macrocystis pyrifera) zoospore production and supply in the Point Loma kelp forest during 1999. The techniques were based on instrumentation for (1) concentrating and isolating planktonic particles from sea water and (2) obtaining absorption spectra from individual kelp zoospores. Absorption... https://escholarship.org/uc/item/3qv250bs Mon, 31 Oct 2011 00:00:00 +0000 Graham, Michael H. https://escholarship.org/uc/item/3f64f393 <p>Iridaea cordata, including varieties cordata (Turner) Bory and splendens (Setchell and Gardner) Abbott, has a geo­graphic distribution that rims the north Pacific basin from Honshu, Japan to northern Mexico with its major populations from central California to southern Oregon (Abbott, 1972). Morphological and cytological descriptions of the life history stages have been reported (Setchell and Gardner, 1903; Kylin, 1928; Smith, 1938; Norris and Kim, 1972; Fralick and Cole, 1973; Kim, 1976) and the taxonomy of the genus has been reviewed (Abbott, 1971; Kim, 1976). The life history described (Kylin, 1928), involves the alternation of morphologically similar haploid and diploid generations. I. cordata is a source of the polysaccharide carrageenan and sporadic commercial harvesting of natural populations of this plant has occurred in northern California (Tseng, 1947) and Washington (Silverthorne and Sorensen, 1971). Some quantitative work on the population biology of Iridaea spp.... https://escholarship.org/uc/item/3f64f393 Mon, 31 Oct 2011 00:00:00 +0000 Hansen, Judith E. https://escholarship.org/uc/item/26j8768b <p>I investigated the movements of the olive rockfish, Sebastes serranoides, off Santa Barbara, California, using both mechanical and parasite tags. Movements were very restricted over shallow reefs though somewhat less so around deeper oil platforms. Limited movements may contribute to over fishing, as comparisons of olive rockfish size frequencies between two reefs indicates that fishing pressure has reduced olive rockfish populations to almost all prereproductive individuals on the more heavily fished site. I discuss movements of other rockfish and suggest potential management problems and solutions.</p><p>Age and growth relations, reproduction and food habits of the olive rockfish were also studied. Olive rockfish grew at a faster rate off Avila than Santa Barbara. Evidence from laboratory studies indicate this differential may be due to ambient temperature. Females grew at a faster rate and attained a larger maximum size than males. Off Avila, spawning took place from December... https://escholarship.org/uc/item/26j8768b Mon, 31 Oct 2011 00:00:00 +0000 Love, Milton S. https://escholarship.org/uc/item/9v33t9gx <p>Wave kinematics are involved in most processes that coastal engineers study. Knowledge of fluid velocities and accelerations are necessary for the study of wave loading of structures through the use of the O'Brien-Morison equation. Knowledge of the kinematics near the sea bed are necessary for studies of sediment transport processes. For this reason, it is important that wave measurements be interpreted as accurately as possible.</p> https://escholarship.org/uc/item/9v33t9gx Thu, 27 Oct 2011 00:00:00 +0000 Barker, Christopher H. https://escholarship.org/uc/item/93r3k3vh <p>In this dissertation I address how open ocean plankton populations can diverge genetically, and ultimately form new species. Research focuses on the oceanic calanoid copepod family Eucalanidae. A global phylogenetic study of the Eucalanidae revealed substantial cryptic diversity at the species level. Genetic data from both mitochondrial and nuclear gene loci support 13 new genetic lineages within the Eucalanidae. These new lineages range from 1.6% to 23.2% divergent from their closest relatives (16S rRNA, p-distances) suggesting that although some diverged relatively recently, other represent quite ancient speciation events. Rhincalanus nasutus was found to be a cryptic species complex, with at least 7 genetically distinct, predominantly allopatric populations worldwide. A molecular phylogeny for the family supports monophyly of the Eucalanidae, all four eucalanid genera, and the 'pileatus' and 'subtenuis' species groups.</p><p>A distinct genetic form of Eucalanus hyalinus... https://escholarship.org/uc/item/93r3k3vh Thu, 27 Oct 2011 00:00:00 +0000 Goetze, Erica https://escholarship.org/uc/item/17f1b6km <p>The following thesis presents results from several investigations of marine natural products. It is divided into 5 chapters consisting of an introduction, three chapters examining the metabolites of tropical sponges. and a final chapter which discusses the chemical profile of a marine derived fungal culture. Chapter 1 is a brief survey of some of the most promising bioactive marine metabolites discovered to date. Furthermore, the first chapter includes some history and perspective pertaining to the field of marine natural products and natural products in general. Chapter 2 is an analysis of sponge metabolites derived from several Indo-Pacific collections of Diacarnus cf spinopoculum. A series of new terpenes of the nuapapuin class (norditerpene peroxides) and muqubilin class (norsesterterpene peroxides) were isolated, along with the new dinorditerpenone muquketone. When these and other related isolates were screened for in vitro cytotoxicity, the diterpenes nuapapuin A... https://escholarship.org/uc/item/17f1b6km Thu, 27 Oct 2011 00:00:00 +0000 Sperry, Samuel https://escholarship.org/uc/item/6jh755fc <p>The application of system reliability methodology for offshore structural problems is investigated. The emphasis is on wave-load modeling and its implications with respect to system reliability analysis of fixed offshore structures. In addition, probabilistic and deterministic measures of "system effects" are proposed.</p><p>The wave loading in system reliability analysis is usually modeled as a fixed spatial pattern of nodal forces scaled by a random intensity factor. In this work, the change of spatial pattern of the mean nodal wave forces with increasing wave height is accounted for by using the so-called "fragility approach" to systems analysis. The change of the relative importance of different member-failure sequences with wave loads corresponding to different wave heights is studied for a fixed offshore jacket in 140 feet of water. Results from simplified "fixed-pattern" analyses are calibrated against the "fragility" analysis.</p><p>The nodal wave forces are implicitly... https://escholarship.org/uc/item/6jh755fc Wed, 26 Oct 2011 00:00:00 +0000 De, Rabi S. https://escholarship.org/uc/item/4b73h2f7 <p>Bioengineering parameters were determined for California halibut in a marine recirculating system under farm-like conditions. California halibut studied ranged in size from 1 to 400 g. Bio-engineering parameters studied were relative swimming velocity; stocking density; oxygen consumption rates; ammonia and urea excretion rates; and feces and uneaten feed settling velocities.</p><p>California halibut were reared at a relative swimming velocity between 0.5 and 1.5 body length per second (bl/s). It was determined that a velocity up to 1.0 bl/s was adequate to achieve maximum fish growth. Stocking densities between 100 and 300 percent of coverage area (PCA) were tested. It was found that maximum fish growth was maintained at densities up to 200% PCA. Daily average oxygen consumption rates ranged from 0.31 to 1.40 g O2 / g feed, ammonia as N (TAN) excretion rate values ranged from 4.3 to 8.5 mg TAN I g feed, and urea as N (urea-N) excretion rate values ranged from 0.8 to 1.8... https://escholarship.org/uc/item/4b73h2f7 Wed, 26 Oct 2011 00:00:00 +0000 Merino Araneda, German E. https://escholarship.org/uc/item/491653vx <p>A series of laboratory experiments have been conducted that reveal significant insights into the nature of oscillatory flow bedload sediment transport. The 730 data runs represent 170 combinations of flow field, sedi­ment size, and bed slope.</p><p>An analysis of two grain sizes (440 and 1100 µm) shows that at high velocities, the bedload transport rate is independent of grain size. However, below a threshold which is a function of grain size, velocity and period, the transport rate is found to be inversely proportional to the grain size though the exact relationship is not well constrained. Observationally, this change occurs when the top layer of sediment becomes fully mobilized to an approximate depth of one to two grain diameters. These two types of transport occur in what has been tradition­ally termed the bedload regime, and this analysis indi­cates that it is more appropriate to consider bedload as two regimes which should be modeled with different equa­tions.</p><p>While... https://escholarship.org/uc/item/491653vx Wed, 26 Oct 2011 00:00:00 +0000 King, David B., Jr. https://escholarship.org/uc/item/29f9b1zj <p>The shells of living marine gastropods are often colonized by other organisms. However, host and site specificity varies among epibionts. Notably, only one species, the newly discovered sabellid worm Terebrasabella heterouncinata, settles in the aperture of gastropods. I examined intrinsic susceptibility of 15 California marine gastropods to this apertural fouling organism by exposing them to conditions highly favorable to sabellid infestations (Chapter I). Intrinsic susceptibility was significantly different among species, being partially associated with phylogeny, but not habitat. This suggested that species-specific characteristics may influence sabellid settlement. As T. heterouncinata is native to South Africa, identification of adaptive mechanisms of native California hosts would illustrate general, not co-evolved, adaptations that preclude apertural fouling by all other epibionts.</p><p>Because many marine invertebrate larvae settle in association with certain substrates... https://escholarship.org/uc/item/29f9b1zj Wed, 26 Oct 2011 00:00:00 +0000 Culver, Carolyn S. https://escholarship.org/uc/item/9t4444q8 <p>The marine Bacillus sp. strain SG-1 produces dormant spores that catalyze the oxidation of soluble Mn(II) to insoluble Mn(IV) oxides. The Mn(ll)-oxidizing activity was localized to the ridged outermost spore layer, which could be physically removed and retain activity. MnxG, the product of the most downstream gene in the previously identified mnx gene cluster, is a multicopper oxidase believed to be the Mn(II) oxidase. MnxG was immunologically localized to the outermost layer of wild-type spores but was absent in non-oxidizing mutants within the mnx cluster, suggesting that MnxG may be the only protein directly involved in Mn(II) oxidation.</p><p>To explore the phylogenetic diversity of marine Bacillus strains capable of producing Mn(II)-oxidizing spores, 16S rRNA and mnxG sequences were PCR-amplified from 14 Mn(II)-oxidizing spore-formers isolated from coastal marine sediments. Phylogenetic trees based on both genes revealed extensive diversity of Mn(II)-oxidizers within the... https://escholarship.org/uc/item/9t4444q8 Tue, 25 Oct 2011 00:00:00 +0000 Francis, Christopher A. https://escholarship.org/uc/item/94f2k0vx <p>It is shown theoretically that surface waves incident on a beach from deep water can excite edge waves. In particular, a monochromatic wave train normally incident and reflected on a beach of constant gentle slope is found to transfer energy to edge waves through a weak resonant interaction resulting from an instability of the incident wave with respect to perturbation by edge waves. The analysis is based on the shallow water approximation and ignores the earths rotation and consequently applies only to relatively low mode, high frequency waves. Coupling coefficients. frequencies and longshore wave numbers of the excited waves are given. In accord with Hasselmann's (1967) rule, only edge waves with frequencies lower than the incident wave are excited by this mechanism. Viscous effects suggest that an edge wave with mode number zero and frequency one-half that of the incident wave (a subharmonic edge wave) is preferentially excited. The minimum incident wave amplitudes... https://escholarship.org/uc/item/94f2k0vx Tue, 25 Oct 2011 00:00:00 +0000 Guza, Robert T. https://escholarship.org/uc/item/7ww5k7ht <p>Bioluminescence (BL), light produced by organisms, is a diverse and widespread marine phenomenon. yet little studied by researchers. Major contributors to sea surface BL displays are dinoflagellates, which produce rapid BL flashes upon fluid motion; mechanical stimulation triggers a 200-ms flash within 20 ms, representing one of the most rapid sensor-effector transduction systems described. In some dinoflagellate species the sensor-effector link is not constant throughout a 24-hour period. Mechanical agitation during day phase produces no BL, even in cells kept in constant lighting conditions, indicating that BL is controlled by a circadian rhythm. The mechanism of this day-phase BL reduction is the subject of this thesis. Pyrocystis fusifonnis, has circadian­ controlled BL,. punctate intracellular BL sources (microsources), and is a sensitive fluid shear sensor. In this species, BL microsources and chloroplasts appear to migrate bidirectionally twice daily, and up to 500 µm.</p><p>An... https://escholarship.org/uc/item/7ww5k7ht Tue, 25 Oct 2011 00:00:00 +0000 McDougall, Carrie A. https://escholarship.org/uc/item/0789w222 <p>Disputes over tuna have highlighted international fisheries affairs since World War II. The underlying legal and policy question has been whether tuna should be subject to exclusive coastal state jurisdiction, or, instead, subject to multilaterally agreed measures that apply throughout their migratory range. The "juridical position" of the United States on this question-in both domestic law and international practice-has played a major role in this history. Until 1990, the United States maintained, consistent with the interests of the U.S. distant water tuna industry and traditional "freedom of the seas" principles, that tuna should not be subject to exclusive coastal state jurisdiction. To this day, the United States has insisted that tuna fishing be subject to measures prescribed by international and regional organizations that are applied consistently to the species throughout its range, both within and beyond exclusive economic zones. The U.S. juridical position was reflected... https://escholarship.org/uc/item/0789w222 Tue, 25 Oct 2011 00:00:00 +0000 Carr, Christopher J. https://escholarship.org/uc/item/028959vr <p>The high productivity and diversity of giant kelp forests have long attracted the attention of biologists. After observing the kelp forests of Tierra del Fuego, Charles Darwin (1860, p. 227-229) wrote: "There is one marine production, which from its importance is worthy of a particular history. It is the kelp, or Macrocystis pyrifera…The number of living creatures of all Orders, whose existence intimately depends on the kelp, is wonderful…I can only compare these great aquatic forests of the southern hemisphere, with the terrestrial ones in the intertropical regions. Yet if in any country a forest was destroyed, I do not believe nearly so many species of animals would perish as would here, from the destruction of the kelp."</p><p>Along the coast of California, forests of giant kelp also harbor rich and complex communities of marine plants and animals. The environmental conditions and species composition of these forests vary, but they all have one factor in common: the... https://escholarship.org/uc/item/028959vr Tue, 25 Oct 2011 00:00:00 +0000 Gerard, Valrie A. https://escholarship.org/uc/item/8nx8c53f <p>Seacliff erosion and retreat in California threatens public and private property, coastal infrastructure, transportation corridors, and public safety. Seacliffs also contribute sediment to California beaches, which drive the coastal tourism economy. Thus, understanding the processes which govern seacliff erosion is paramount in protecting the coast and mitigating erosional issues. This research effort, focused on the Oceanside Littoral Cell, builds upon past projects and provides new insight into seacliff morphological processes.</p><p>This study utilized airborne and terrestrial LIDAR (Light Detection And Ranging) and GIS (Geographic Information System) analysis to quantify short-term seacliff morphology and the effectiveness of erosion control methods. Additionally, the stability of cantilevered seacliffs was also explored using finite element analysis and elastic beam theory. Numerous field investigations and photographic surveys also provided indispensable information... https://escholarship.org/uc/item/8nx8c53f Mon, 24 Oct 2011 00:00:00 +0000 Young, Adam P. https://escholarship.org/uc/item/8k0006ch <p>Homologous molecular probes were used to examine in vivo molecular chaperone and polyubiquitin gene expression patterns in the American lobster, Homarus americanus, an ectothermic marine crustacean. Following long-term laboratory acclimation to temperatures experienced during overintering in nature, juvenile lobsters failed to elicit the classical "heat-shock response'' when subjected to an acute 13°C thermal stress. Levels of mRNA coding for molecular chaperones (HSC70, HSP70, and HSP90) and polyubiquitin were not induced during thermal stress or recovery in cold-acclimated animals. These results contrasted with those for lobsters acclimated to ambient Pacific Ocean temperatures that experienced an acute stress over an equivalent thermal interval. Ambient-acclimated lobsters displayed significant inductions in the mRNA levels for both molecular chaperones and polyubiquitin. Hyper- and hypo-osmotic stress were found to significantly induce HSP90 and polyubiquitin mRNA levels... https://escholarship.org/uc/item/8k0006ch Mon, 24 Oct 2011 00:00:00 +0000 Spees, Jeffrey L. https://escholarship.org/uc/item/82r7m2jv <p>The processes that shape present day distributions of marine organisms have remained a central topic in evolutionary biology, conservation biology, and ecology. In this thesis, genetic data from mitochondrial and nuclear genes were used to create a phylogenetic hypothesis for the groupers of the subfamily Epinephelinae as a means of evaluating the current taxonomy of the group and the geography of speciation in marine organisms.</p><p>The molecular phylogenetic hypothesis presented in Chapters I and IV identifies several genera that are paraphyletic. New taxonomic considerations, including the resurrection of the genus Hyporthodus Gill, are discussed. We identify four main radiations: Cephalopholis, Epinephelus, Hyporthodus, and Mycteroperca. These lineages each represent a unique pathway of colonization to the New World and patterns of evolutionary radiation.</p><p>In Chapter II, the phylogenetic relationships among the genera Alphestes and Dermatolepis are discussed based... https://escholarship.org/uc/item/82r7m2jv Mon, 24 Oct 2011 00:00:00 +0000 Craig, Matthew T, https://escholarship.org/uc/item/6wn46905 <p>To evaluate how terrestrially descended, marine-living tetrapods have adapted their vision for life in the ocean environment, the rod and cone visual pigments of diving turtles, birds, and mammals were examined. Genetics was used primarily. When possible, in situ electroretinography (ERG) was also used.</p><p>Of the three visual pigments possessed by most mammals, cetacean rod and middle/long-wavelength sensitive (M/L) cone visual pigments had previously been shown to be shifted towards the wavelengths (λ) of light that predominant in marine habits, λ~475 nm. The genetic sequences of the short-wavelength sensitive (S) cones of numerous cetaceans were examined from nuclear DNA. The distribution of mis­-sense mutations found in their S cone opsin genes indicates that all members ofthe cetacean order lack S cones. Genetic evaluation of the retinal mRNA of seven pinniped species revealed that these mammals also lack S cones. The convergent loss of S cones in pinnipeds and cetaceans... https://escholarship.org/uc/item/6wn46905 Mon, 24 Oct 2011 00:00:00 +0000 Levenson, David H. https://escholarship.org/uc/item/2v29q9tc <p>This dissertation compares the reproductive ecology of three species of intertidal barnacles in the context of their life histories. Emphasis is placed on the patterns of repro­duction shown by similar species exploiting different but overlapping ranges of the intertidal zone. The intertidal environment imposes stringent gradients of greater physical stress in the high range of tidal exposure and increasing biological complexity at the low range of tidal exposure. Selection for differing adaptive modes of reproduction, re­cruitment, growth, and survivorship may be expected in species occupying different positions along these environmental gradi­ents. Ideally, the problem is not just to measure how partic­ular aspects of these modes differ between species facing vary­ing degrees of environmental stress, competition, and preda­tion but it is also to examine how components of the reproduc­tive ecology of the species interact with important parameters of growth and demography... https://escholarship.org/uc/item/2v29q9tc Mon, 24 Oct 2011 00:00:00 +0000 Hines, Anson H., Jr. https://escholarship.org/uc/item/1q25p72j <p>The goal of this research is to investigate the biochemistry of solitary ascidians, with particular focus on the hemocytes (blood cells). Styela plicata and Ciona intestinalis have a high local abundance and their hemocytes are easily isolated, making them an appropriate model for histochemical studies. Because ascidian hemocytes mediate host defense reactions and accumulate specific metals, they are a potential source of novel antimicrobial and metal binding agents. Acid soluble peptides from ascidian hemocytes were investigated to determine their antimicrobial properties. Chapter II of this thesis presents a comprehensive review of marine invertebrate antimicrobial peptides. Chapter III describes the characterization of plicatamide, a modified octapeptide from hemocytes of the ascidian S. plicata. Chapter IV investigates the molecular origins of plicatamide and Chapter V describes attempts to generate a polyclonal antibody to plicatamide. Chapter VI presents, in detail, the... https://escholarship.org/uc/item/1q25p72j Mon, 24 Oct 2011 00:00:00 +0000 Tincu, John A. https://escholarship.org/uc/item/737485ms <p>Iron is required for growth of nearly all microorganisms. While iron is the fourth most abundant element on the earth’s surface, iron is only sparingly soluble in the aerobic, near neutral conditions under which most microorganisms grow. Therefore, microorganisms experience iron limitation in nearly every environment where they grow, from infection of a mammalian host (where iron is highly controlled by protein complexation) to aquatic and marine environments (where iron is relatively insoluble or is complexed by organic ligands). Bacteria, fungi, and other microbes have developed complex strategies to compete for iron under these conditions. Specifically, many microbes produce low molecular weight, iron binding compounds called siderophores to acquire iron from the environment. Siderophores are secreted by microorganisms and then are taken back into the cells as the ferric complex to promote microbial growth.</p><p>The siderophores produced by marine α-proteobacterium Ochrobactrum... https://escholarship.org/uc/item/737485ms Fri, 21 Oct 2011 00:00:00 +0000 Martin, Jessica E. https://escholarship.org/uc/item/6xc5t2zm <p>Marine protected areas (MPAs) can potentially impact food web dynamics by increasing the density of predatory fishes within their borders. Such increases in density can cause shifts in the prey use of generalist predators. This study investigated the effects of increased conspecific density on the diet of Gopher Rockfish (Sebastes carnatus) at a 35-year-old MPA at Point Lobos and four newly established central California MPAs at Año Nuevo, Point Lobos, Piedras Blancas, and Point Buchon. Analysis of 710 stomachs collected in 2007-2009 indicated the most important overall prey were crabs, especially the family Pisidae and genus Cancer, as well as brittle stars and mysids. Diets did not differ inside versus outside the old Point Lobos MPA in terms of prey richness, evenness, composition, or Gopher Rockfish trophic level. Individual specialization, however, was greater outside the MPA. No consistent differences in these metrics were observed inside versus outside the four new... https://escholarship.org/uc/item/6xc5t2zm Fri, 21 Oct 2011 00:00:00 +0000 Loury, Erin K. https://escholarship.org/uc/item/5ft0r5tf <p>This work examines the molecular population genetics of hybrid breakdown in the harpacticoid copepod Tigriopus californicus. The aim of this work was to use classical population genetic analysis of natural populations together with molecular genetics to characterize the genetic basis of reduced F2 hybrid fitness. Each of the chapters of this dissertation makes a unique contribution to our understanding of the genetic consequences of hybridization. In Chapter II, I combine time series data from natural populations with DNA sequence polymorphism data to characterize the extent of population exchange among local T. californicus populations. A primary result from this work is that gene flow among local populations is likely higher than previous data suggested. This has implications for our understanding of local population differentiation and the consequences of hybridization between T. califomicus populations. Chapters III and IV, I investigated two transcription systems, RNA... https://escholarship.org/uc/item/5ft0r5tf Fri, 21 Oct 2011 00:00:00 +0000 Flowers, Jonathan M. https://escholarship.org/uc/item/3ft93223 <p>In this thesis the evolution of the sghC1q gene family is explored throughout the metazoan lineage and within the zebra�fish (Danio rerio) genome. This involved novel bioinformatic analyses, extensive synthesis of the literature, development of a bioinformatic tool, and the transcriptional assessment of the full complement of sghC1q genes within D. rerio during infection and early development.</p><p>The secreted globular head C1q (sghC1q) genes can be characterized as a family of genetic loci each encoding a signal peptide followed by a complement component 1q globular (gC1q) motif. Members of this family have been referred to as precerebellin-like (cblnl), C1q-like or ovary speci�c C1q-like factors. Previous studies have found gene family members in multiple organisms with varying numbers of copies within a species. The genes are known to be transcribed in response to infection and/or during development.</p><p>The domain of the C1q globular head (gC1q or ghC1q) appears to... https://escholarship.org/uc/item/3ft93223 Thu, 20 Oct 2011 00:00:00 +0000 Carland, Tristan M. https://escholarship.org/uc/item/9v46r9f8 <p>Connectivity at relevant scales for management and conservation of many marine species occurs through dispersal of larvae. The goal of this study was to assess dispersal and connectivity among populations of depth-limited rockfish using a combination of indirect and direct methods. In one component of the dissertation, kelp rockfish populations were examined for evidence of genetic structure using 8 coastal and 5 island locations from central California to Baja using seven microsatellite loci. Although no significant population structure was detected with all populations treated separately, significant differences were found when populations were pooled based on hydrographic regions identified using average sea surface temperature as a proxy for hydrography at the time of spawning and pelagic dispersal (Fst = 0.002). This structure appeared to be driven by an isolation by distance pattern of gene flow among coastal and nearshore island comparisons (Mantel Test, p = 0.01).... https://escholarship.org/uc/item/9v46r9f8 Thu, 6 Oct 2011 00:00:00 +0000 Taylor, Cynthia A.