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- Creator:
- Chen, Jei-Ying
- Description:
- Postulated by Bayer (1955), the calcaxonian gorgonians may have close affinity to the pennatulaceans based on the resemblance of axial structure observed under polarized light microscopy. To further confirm the phylogenetic relationship between the two groups of octocorals, this study applied both polarized light microscopy and scanning electron microscopy to examine the extinction patterns of sclerites and axial skeletons in macro- to ultrastructural scale from the total of thirteen genera of calcaxonian octocorals and nineteen genera of sea pens. The results show significant similarities between calcaxonian gorgonians and sea pens on scleritic crystal orientations and organization of axial structures, together with the inferred phylogeny of forty-six taxa (seventeen gorgonians and twenty-nine pennatulaceans) using ND2 mtDNA sequence data, all strongly support Bayer’s postulation and reveal the sister group relationship between the Ellisellid calcaxonian gorgonians and the pennatulaceans. The X-ray microanalysis was also carried out for inter-family comparison of the axial chemical composition between calcaxonian gorgonians and sea pens for the implication of phylogeny, however the results shown that the axial chemical composition is largely determined by ambient seawater instead of biologically intrinsic differences, therefore it did not provide much resolution to gain plausible phylogenetic implication in consequence.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Manugian, Suzanne Camille
- Description:
- Pacific harbor seals (Phoca vitulina) within San Francisco Bay (SFB) have been described as stable compared with those in coastal northern California, like Tomales Bay (TB). Historical data (1970s - early 2000s) indicated an overall increase in adults and pup production. Recent data, however, revealed SFB and TB adult counts decreased while pup production increased. There is a paucity of life history data, such as survival rates, for northern California harbor seals. For 32 radio-tagged adult females, survival was 98.2% over 20 months 2011 through 2013, constant between bays and influenced by an individual’s axillary girth. Movement between bays supported this survival estimate. Lower resight probability in SFB compared with TB was likely due to multiple factors including sampling bias and haulout quality and area. These are the first adult/subadult survival and resight estimates for harbor seals in California, and suggest the stable SFB population is due to some reason other than poor adult female survival (e.g. emigration, poor pup survival).
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Mohan, Abigail Taylor
- Description:
- Mangrove ecosystems are at continued risk of degradation and deforestation through anthropogenic activity. Mangroves once covered 75% of tropical coastlines, and only 30 - 50% of this habitat currently remains. These ecosystems provide important benefits for the local communities, including supporting livelihoods and providing resources. Through the long-term sequestration of carbon, mangroves are essential to global goals of reducing greenhouse gas emissions. Although mangrove conservation and restoration are often recognized community or government goals, the lack of data and resources can hamper success. By analyzing approaches used across pilot conservation and restoration sites in Madagascar and Ecuador, lessons learned can highlight successful approaches that can be replicated and scaled up. This research analyzes how the influence of top-down (government or policy driven) and bottom-up (community-led) approaches impacted project outcomes. This case study comparison uses interviews with key experts, along with the Driver. Pressure, State, Impact and Response framework, to better understand the role national and local entities play in mangrove conservation and restoration. The most effective approach considers the underlying drivers of mangrove loss and includes a multidirectional approach to align government goals and community needs.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Gallagher, Cara Alyse
- Description:
- The occupation of an ecosystem by a new top predator could affect the stability of a food web. In San Francisco Bay (SF Bay), there is evidence for a multi-decadal disappearance of harbor porpoises {Phocoena phocoena) that spanned from the 1940’s to the early 2000’s. Understanding the energetic role of this predator in the food web, in addition to the conditions that allowed for occupation of the Bay, is crucial to shedding light on the possible impacts of this species and on the state of the ecosystem. Here two modelling approaches were used in order to assess the energetics of harbor porpoises in SF Bay. The first model presented was an equation-based, velocity-dependent energy budget of harbor porpoises. As harbor porpoises have been shown to reproduce on an annual calving cycle in some regions, the minimum cost of transport was found for each possible reproductive state (non-pregnant, non-lactating (NPL)=1.6 J k g 'W ; pregnant (P)=1.8 J k g 'W ; lactating (L)=3.1 J k g 'W 1; and pregnant and lactating (PL)=3.2 J k g 'W 1). The total daily costs, in terms of carbon uptake, were then estimated for a NPL porpoise and a PL porpoise (NPL=341.3 g; PL=756.4 g) and when compared using a one-way ANOVA test, the difference was significant (F=15,797, d /= l, p<0.001). The second model presented was an agent-based, ecophysiological model of porpoise foraging in central SF Bay. Energy expenditure was estimated using the swimming speed and the reproductive status of the porpoise agent and energy intake was dependent on foraging success, measured by the capture of anchovy agents in SF Bay. The total daily energetic costs of each reproductive state were found (NPL=8060.4 kJ; P=8776.3 kJ; L= 19269.6 kJ; and PL=19985.6 kJ). The marginal value theorem was used as a test of habitat optimum for harbor porpoises in SF Bay and using the model, it was found that foraging success was more dependent on the number of anchovy schools than the number of anchovies per school. The number of schools that allowed for foraging levels higher than found for wild porpoises for a population of 50 animals foraging inside SF Bay was 41 schools of anchovies. When estimating total energy sequestration by differing numbers of harbor porpoises foraging in SF Bay, competition emerged as a factor influencing foraging success. For 33 and 165 porpoises foraging in SF Bay, total carbon consumed during a 6-hour foraging bout was estimated at 17,111.5 ±1 096.0 and 74,273.5 ± 8171.4 grams of carbon, respectively. As an upper-tropic level species that has recently increased its spatial habitat, it is crucial to investigate the possible impacts of harbor porpoises in San Francisco Bay and these two modelling platforms have allowed for the thorough investigation of the questions proposed.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Rodriguez, Jessica
- Description:
- Groundwater sustainability is at the forefront of resource management. In light of climate change and growing populations, meeting future water needs must be met with planning and innovation. This is particularly challenging in cities where recharge is often limited by impervious surfaces and runoff is contaminated by urban pollutants. Low impact development (LID) is a design strategy that mimics the natural hydrologic cycle and is usually implemented as an alternative to the traditional stormwater system. Examples of LID best management practices (BMPs) include rain gardens, bioswales, infiltration trenches, rooftop gardens, and permeable pavement. LID BMPs delay and decrease peak runoff flows and improve water quality, and there is a growing number of studies investigating LID’s effect on groundwater. Understanding potential recharge under LID BMPs and identifying the design features influencing recharge can serve an important role in the move toward groundwater sustainability and management. In this study, I used HYDRUS-1D to model five LID BMPs (two rain gardens, two bioswales, one infiltration trench) from 1948-2099 with observed historic climate data and 9 global climate models (GCMs) at representative concentration pathways (RCP) of 4.5 and 8.5. Mean recharge ranged from 1725-3458 mm/yr under the LID BMPs, with the highest recharge rates occurring under the infiltration trench. Though simulated recharge from historic, 4.5 and 8.5 RCP showed no statistically significant changes in recharge over time, runoff is predicted to increase significantly, indicating that current LID BMPs should be redesigned to store increased inflow expected from climate change. Recharge efficiency during heavy rainfall events such as El Nino can be improved by increasing the loading ratio of a BMP. Results of a one-at a time (OAT) method sensitivity analysis showed that the hydraulic conductivity of the soil underlying a LID BMP has the most influence on recharge and suggested that location is critical for optimizing or minimizing recharge.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Richard, Heather
- Description:
- Plastic debris in aquatic environments can accumulate ions from the surrounding water, potentially altering the fate of trace metals in these ecosystems. Mechanisms driving this process are poorly understood, and may be attributed to organic matter fouling the plastic’s surface. In this study, two types of pristine plastic pellets as well as glass pellets were suspended in the San Francisco Bay and biomass and metal accumulation were measured at various time intervals up to 28 days. At each time point, increasing biomass was positively correlated with metal accumulation on plastic pellets. Glass accumulated significantly higher levels of Zn compared with plastic materials regardless of biofilm growth. For other metals that showed an affinity for glass, the importance of biomass as a predictor of metal concentration increased and the differences between glass and plastic decreased over time and as biofilm increased. Future studies should account for the effect of biofilms when estimating contaminant sorption and desorption potential on plastic debris relative to other types of debris materials.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Patten, Melissa Virginia
- Description:
- Morphological variations in widely distributed plants may be driven by phenotypic plasticity or by underlying genetic differences. In the brackish open water region of the San Francisco Estuary (SFE), a population of sago pondweed, (Stuckenia pectinata) shows at least two distinct growth forms, which are so different that they were previously thought to be two species. This study confirmed the S. pectinata species identity for all morphologies through sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region. I investigated phenotypic plasticity in response to flow variations in a common garden, and found that morphological traits are plastic but distinct morphotypes did not converge. I then used four microsatellite loci to investigate differentiation between the two morphotypes at three sites within Suisun Bay and the western Sacramento-San Joaquin Delta, and two populations from other central California sites for comparison. I found very few multilocus genotypes (unique combinations of alleles across two or more loci), which could be a reflection of low levels of clonal diversity, or a byproduct of low resolution in my methods. Lastly, I investigated the influence of plant morphology on the ecologically important invertebrate epibiont community. I found a positive relationship of plant surface area, leaf count, and leaf density with invertebrate abundance only at the more saline of the two sites sampled, which had a different invertebrate assemblage than the fresher site. Results of this study suggest that the two growth forms may provide different ecosystem functions and services, which could influence management and restoration decisions in the region.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
8. Relating benthic microorganism communities and processes to nutrient variability in tidal wetlands
- Creator:
- Lee, Tricia Louise
- Description:
- This study examined the benthic zone of tidal habitats in the San Francisco Estuary (SFE) in order to characterize this understudied part of the ecosystem. Microbial community composition was evaluated in relation to nutrient flux rates from the sediment across the SFE in June 2014. These values are some of the first of their kind and yield insight into the basic biology of the shallow water ecosystems in the SFE and how the benthos relates to overall biogeochemical functioning. Additionally, the benthic microalgae are key players in the carbon cycling of shallow systems of the SFE. Therefore an evaluation of the relative contribution of carbon fixation by these populations in comparison to water column microalgae was also conducted from February to October, 2015 in two historic marshes at China Camp, San Rafael, CA and Rush Ranch, Suisun City, CA, to better understand the overall role that single celled algae play in shallow tidal habitats of the SFE.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Nadel, Miko Rain Abraham
- Description:
- A systematic monograph of the lichen genus Usnea from the remote, under-explored islands of Sao Tome and Principe (ST&P) in tropical West Africa is presented, treating 11 species representing 2 subgenera, Usnea and Eumitria. Ten of the 11 species are reported as new for ST&P, including U. firmula, U. baileyi, U. pectinata, U. aff. flammea, U. sanguinea, U. picta, U. krogiana and three undetermined, potentially new species, Usnea species A, B and C. Usnea articulata is confirmed for the main island of Sao Tome. Determinations were made using morphological data, chemistry via thin layer chromatography, and a molecular phylogeny based on nDNA Internal Transcribed Spacer (ITS) sequences. Usnea baileyi, U. pectinata, U. articulata and Usnea species C represent species complexes consisting of two or more morphotypes each. Comprehensive descriptions, photographs, and a dichotomous key to the species are provided.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Kalmbach, Andrew James
- Description:
- The Amazon River Plume (ARP) is a productive region of the Atlantic Ocean where riverine nutrients drive particulate productivity. A portion of the carbon produced by phytoplankton is released as dissolved organic carbon (DOC); this research investigated the effects of the ARP on the extracellular release (ER) of DOC. Particulate production (PP) and ER were measured during two cruises to the region, and were contrasted with salinity, dissolved nitrogen, and phytoplankton taxa and size. Chlorophyll normalized PP and ER were unaffected by size, and assemblages dominated by Trichodesmium sp. released a greater percentage of fixed carbon as DOC than sites mainly composed of diatoms. Salinity and total dissolved nitrogen (TDN) did not affect ER, but phytoplankton released a larger fraction of their total productivity at low TDN and high salinity. Particulate production correlated with total dissolved nitrogen, there was no effect of dissolved inorganic nitrogen on PP or ER, suggesting that the phytoplankton utilize the organic nitrogen pool in lieu of ammonium and nitrate.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology