Thesis Defenses

Thesis Abstract

Global climate change is causing increasing ocean acidification (OA) and deoxygenation (hypoxia) of coastal oceans. Along the coast of California, where upwelling is a dominant seasonal physical process, these environmental stressors often co-occur and are intensified in nearshore ecosystems. For juvenile nearshore fishes, who spend a crucial developmental life stage in coastal kelp forests during the upwelling season, these stressors are experienced concurrently and may have large implications for fitness. Environmental stress can set off an endocrine response, which impacts physiology, energy allocation, growth, and behavior. To test the effects of climate change on juvenile blue rockfish, I measured the endocrine response to single and combined stressors of OA and hypoxia after one week of exposure. Assays of cortisol and IGF-1 hormone responses, served as proxies for stress and growth, respectively. Full organismal effects of environmental stressors were evaluated using a scototaxis (i.e., light/dark anxiety) behavior test, and measures of physiological changes in maximum metabolic rate (MMR) and body condition (i.e., Fulton’s K condition index). I found that peak (~1 hour) cortisol levels were highest in the single stressor low pH (7.3 pH), followed by the combined stressor (7.3 pH and 2.0 mg/L O2) and then the single stressor hypoxic treatment (2.0 mg/l O2). This high peak cortisol associated with low pH may indicate the role of cortisol in acid-base regulation. Only the low DO (dissolved oxygen) group did not exhibit a recovery of cortisol levels by the end of one week. There was no observable difference in IGF-1 in juvenile blue rockfish after a week of exposure to any of the pH or DO stressors. When cortisol levels were high, the same fish had low levels of IGF-1, and when cortisol levels were lower, the same fish had highly variable levels of IGF-1. At one-week of exposure, cortisol exhibited a positive relationship with MMR, such that higher stress levels were associated with greater oxygen consumption by the fish. MMR values themselves were highest in the low DO fish, which subsequently also had slightly higher cortisol levels at one-week. Juvenile blue rockfish were largely robust to any behavioral changes associated with stress across treatments. Hypoxic treatment fish had significantly lower body condition than fish from treatments with ambient DO levels after one week. Overall, the results indicated that pH levels influenced hormonal stress physiology, while DO levels contributed to observed differences in metabolism, body condition, and behavioral anxiety in juvenile blue rockfish. I was unable to tease apart and classify whether OA and hypoxia work in an additive, antagonistic, or synergistic way. Continued research should include more experimental stressor treatment levels of varying intensity of both individual and combined treatments as well as upwelling/relaxation fluctuating treatment levels. Elucidating the effects of climate change on fish endocrine response and physiology is important for fish population management and can help inform stock assessment models of blue rockfish in a rapidly changing ocean.

Thesis Abstract

Thesis Abstract

Alternative feeds for finfish aquaculture are critical for the sustainable expansion of the aquaculture industry. Fish that are farmed for human consumption are often carnivorous; therefore, the industry uses wild-caught forage fish as a primary ingredient in farmed fish feeds in the form of fish meal (FM) and fish oil (FO). With the aquaculture industry expanding, alternative ingredients are needed to safeguard fisheries' sustainability and future aquaculture development. While some alternative feed ingredients have been identified, it is necessary to improve the existing options and identify alternative ingredients with higher concentrations of omega-3 polyunsaturated fatty acids (PUFAs). This study was designed with six feed treatments to test a microalga, Schizochytrium sp., as an alternative feed ingredient for sablefish (Anoplopoma fimbria). The two fish ingredient control diets are called +FM+FO (contains both FM and FO) and -FM+FO (contains FO). The fish-free diets completely replace FO with flax oil (FF Flax) or a combination of flax oil and low, moderate, or high inclusion of Schizochytrium sp. (FF LowSc, FF ModSc, and FF HighSc) in the feeds. After a five-month feeding trial, sablefish condition metrics, whole-body proximate composition, and apparent digestibility coefficients were not different across diet treatments. In contrast, sablefish growth was influenced by treatment, with the high microalga-inclusion diet (FF HighSc) performing as well as the fish-ingredient controls. Fillet fatty acid profiles were also influenced by diet treatment, generally reflecting the fatty acid profiles of the feed. Total PUFAs were higher in the fish-free diets than in the controls. These results suggest Schizochytrium sp. can increase PUFA concentrations in fish fillets, while not compromising fish health and growth, making it a viable ingredient for alternative sablefish feeds.

Bio

Alora Yarbrough is a graduate student in the Ichthyology Lab at Moss Landing Marine Labs (MLML). She received her BA in Biology from Pepperdine University in 2017. While there, she completed an undergraduate honor's thesis researching the effects of variable incubation conditions on the development of the California grunion which she presented at the Western Society of Naturalists Annual Meeting, the Joint Meeting of Ichthyologists and Herpetologists, and the Society for Integrative and Comparative Biology's Annual Meeting. After graduating, she completed internships with Heal the Bay at the Santa Monica Pier Aquarium and with Disney World's Animal, Science, and Environment Program in Florida. She then accepted a position in Dr. Scott Hamilton's lab at MLML in the fall of 2018.

For her Master's thesis, Alora examined how climate change affects the stress response, reproduction, and offspring fitness of blackeye gobies, a demersal reef fish common off the west coast of the United States and Mexico. In addition to her master's work, Alora joined the MLML IT department as a Help Desk Technician in 2019 through which she implemented projects such as the Student Life Website and headed the first media committee for the annual Open House fundraiser. In April 2022, Alora returned to southern California to join the Yelon Lab at the University of California, San Diego (UCSD) as a staff research associate supporting research investigating cardiac development in zebrafish.

Bio

Rachel graduated from the University of Oregon in December of 2018 with a B.S. in Marine Biology. While she was there, she spent three semesters at the Oregon Institute of Marine Biology (OIMB) exploring the tidepools, catching fish, and searching for whales. She also joined the Everblue team, a nonprofit organization that uses social media to share the latest marine science research, and spent a semester in the Maslakova lab working on a Nemertean DNA barcoding project. After graduating, she worked as a Teaching Assistant and joined the Pacific Shark Research Center in the fall of 2019.

For her thesis, Rachel analyzed the morphology of three Data Deficient species of guitarfish from the Southwestern Indian Ocean in order to revise their species descriptions. She presented this research at the American Elasmobranch Society International Wedgefish and Guitarfish Symposium, which she also co-organized, and the Northeast Pacific Shark Symposium. While at MLML, Rachel also helped with several student thesis projects including the surf zone Marine Protected Area (MPA) monitoring project and understanding salmonid environmental DNA (eDNA) movement in rivers. When she's not working, Rachel enjoys hiking, painting, and caring for her many plants. After graduation, Rachel is looking forward to moving back to the Pacific Northwest to ski, prepare for a PhD program, and get married.

Thesis Abstract

The shark-like rays (Rhinopristiformes) are found worldwide and are among the most threatened species of cartilaginous fishes. The guitarfishes (Rhinobatidae) are one of five families in this order, with many species being assessed as vulnerable, endangered, or critically endangered by the International Union for Conservation of Nature (IUCN). Current fisheries and conservation efforts are limited, however, due to unresolved taxonomic issues and poor species descriptions. Presently, there are three described species of Rhinobatos from the Southwestern Indian Ocean: Rhinobatos austini, R. holcorhynchus, and R. nudidorsalis. These three species of Rhinobatos are often mistaken for one another and are assessed as Data Deficient (DD). Until its description in 2017, R. austini was misidentified with the poorly defined, offshore occurring R. holcorhynchus. Rhinobatos nudidorsalis was described from a single specimen caught near the Mascarene Ridge in 2004, but may have been previously misidentified as R. holcorhynchus. The issue of misidentification is also often amplified by the lack of consistency in terminology and measurements for the Rhinopristiformes. Since the descriptions of R. austini and R. nudidorsalis, additional specimens have become available. Thus, a redescription of these three species is needed to clarify their taxonomic status. In addition, a guide to guitarfish morphology is needed to standardize measurements for this group by clarifying techniques and minimizing error across research groups.

            Several Rhinobatos species descriptions and FAO (Food and Agricultural Organization of the United Nations) catalogs for cartilaginous fishes were reviewed to describe and define guitarfish measurements. Morphometrics from four congener species of Rhinobatos from the Indian Ocean that have been assessed by the IUCN were analyzed and served as comparative material for the three DD species. In addition to the traditional morphological analyses used to distinguish guitarfish species, morphometrics from all seven species were analyzed using three multivariate statistics: a Non-Metric Multidimensional Scaling (nMDS), a Principal Component Analysis (PCA), and a Linear Discriminant Analysis (LDA). Results from the LDA show distinct clusters for species of Indian Ocean Rhinobatos and indicate that the oronasal region is effective in differentiating Southwestern Indian Ocean species. In addition, R. austini, R. holcorhynchus, and R. nudidorsalis are confirmed as distinct species and redescribed based on new material. These redescriptions provide taxonomic clarity for Southwestern Indian Ocean guitarfishes and will aid in species-specific identification, leading to improvements in conservation and fisheries monitoring and management.

Bio

Lauren Cooley is a graduate student in the Vertebrate Ecology Lab at Moss Landing Marine Labs (MLML). She received her BS in Animal Science from Cornell University in 2016 and completed internships at the Alaska SeaLife Center and Florida Fish & Wildlife Conservation Commission. After two years working as a marine mammal and sea turtle stranding technician at the Institute for Marine Mammal Studies in Gulfport, Mississippi, Lauren moved to California to join Dr. Gitte McDonald's lab group in 2018. Her research interests include the ecology, physiology, and conservation of marine mammals and sea turtles with a focus on animal welfare.

For her master's thesis, Lauren investigated the effects of research handling activities on stress levels in juvenile northern elephant seals using hormone, blood parameter, and heart rate data. She also worked as the Data Manager and later Stranding Coordinator for the MLML Marine Mammal & Sea Turtle Stranding Network. In addition to her research work, Lauren is passionate about science communication and served as MLML Social Media Coordinator, Editor of the MLML Drop-In Blog, and Outreach Chair for the Vertebrate Ecology Lab. In February 2022, Lauren moved back east to Cape Cod, Massachusetts to begin a new job as a Stranding Biologist with the International Fund for Animal Welfare (IFAW). She looks forward to a long career in the always exciting marine mammal stranding field and is very thankful for the opportunity to use her fieldwork and research skills in this new conservation-focused role.

Thesis Abstract

Wildlife researchers must balance the need to safely capture and handle their study animals to sample tissues, collect morphological measurements, and attach dataloggers while simultaneously ensuring their results are not confounded by stress artifacts caused by handling. To determine the physiological effects of research activities including chemical immobilization, transport, instrumentation with biologgers, and overnight holding on a model marine mammal species, I collected hormone, blood chemistry, hematology, and heart rate data from 19 juvenile northern elephant seals (Mirounga angustirostris) throughout a translocation experiment. Across my six sampling timepoints, cortisol and aldosterone data revealed a moderate hormonal stress response to handling that was accompanied by minor changes in hematocrit, blood glucose, and blood lactate, but not ketone bodies or erythrocyte sedimentation rate. I also performed the first assessment of heart rate as a stress indicator in this species and found that mean heart rate, interbeat interval range, and apnea-eupnea cycles were influenced by handling. However, by the time seals were recaptured after several days at sea, all hormonal and hematological parameters had returned to baseline levels and 95% of study animals were resighted in the wild up to two years post-translocation. Together these findings suggest that while northern elephant seals exhibit mild physiological stress responses to handling activities in the short term, they recover rapidly and show no long-term deleterious effects, making them a robust species for ecological and physiological research.

Juliana graduated from the University Honors Program at the University of California, Davis in spring 2018 with a B.S. in Biological Sciences. While there, Juliana participated in undergraduate research in the Grosberg Lab, where she assisted with a project on population genetics of symbionts hosted by sea anemones, and conducted an independent research project on symbiont photosystem performance for her undergraduate honors thesis. She also spent a semester studying abroad at the University of Queensland in Australia. After graduation, Juliana took a gap year, which included work in environmental education and volunteer work in museum education, before beginning her M.S. in Marine Science in the Logan Lab at CSUMB and the Ichthyology Lab at MLML in fall 2019. 

For her thesis, Juliana investigated physiological responses to hypoxia in juvenile flatfishes to determine the implications of hypoxic events in their important nursery habitat in Elkhorn Slough. She presented this research at the SACNAS National Diversity in STEM conference, the Western Society of Naturalists Annual Meeting (where she was awarded “Best Graduate Poster”), and the Ocean Sciences Meeting, in addition to presenting this research in the inaugural “Grad Slam” (3-minute thesis) competition at CSUMB, where she won first place. 

Juliana worked as a teaching associate at CSUMB during her first year of graduate school, before beginning a position as a program assistant for the Coastal and Marine Ecosystems Program (CMEP) at CSUMB. In that role, Juliana helps plan, run, and evaluate all of the educational programs within CMEP, including the Research Experience for Undergraduates (REU) program and the annual Sea Lion Bowl. She also works as a naturalist on a whale watching boat in Moss Landing. When not working, Juliana enjoys spending time with her pets, hiking, photography, and art - mostly watercolor painting and digital illustration. Following graduation, Juliana will be starting an Alaska Sea Grant State Fellowship at the Alaska Fisheries Science Center.

Thesis Abstract:

Estuaries serve numerous important ecosystem roles, including providing critical nursery habitat for juvenile fish. However, due to eutrophication and climate change, estuaries experience highly variable dissolved oxygen (DO) levels and hypoxic conditions. Though hypoxia negatively impacts juvenile fish, there are physiological compensatory mechanisms fish utilize to prevent tissue-level hypoxia. This study examines the effects of hypoxia on two ecologically and economically important flatfish species in Elkhorn Slough on California’s central coast: juvenile English sole, Parophrys vetulus, and juvenile speckled sanddabs, Citharichthys stigmaeus. I measured metabolic rate, ventilation rate, and hematocrit, as well as biochemical indicators of hypoxia (HIF-1a and L-lactate) and oxidative stress (superoxide dismutase), following an acute, six-hour exposure to six DO levels ranging from ambient to severely hypoxic: 8.0, 6.0, 4.0, 3.0, 2.0, and 1.5 mg/L O2. I found that both standard metabolic rate (SMR) and maximum metabolic rate (MMR) in English sole decreased as DO level decreased. A more significant change in MMR compared to SMR also led to a significant decrease in aerobic scope (the ability to increase metabolic rate over resting levels) with decreasing DO levels. For both species, ventilation rate increased as DO level decreased, likely as a mechanism to increase oxygen supply. Both species also exhibited a significant increase in anaerobic activity (increased lactate in muscle tissue) at low DO levels (1.5 mg/L O2 for English sole and 2.0 mg/L O2 for speckled sanddabs). English sole also experienced a significant increase in oxidative stress (as measured by SOD in gill tissue) at 1.5 mg/L O2. Overall, all of these factors can lead to or indicate decreased survival and fitness of juvenile flatfish in hypoxic conditions, with decreased survival potentially reducing population size and fishery success. Evaluating thresholds for tolerance of hypoxia may allow us to predict these changes, as well as determine areas of suitable nursery habitat and targets for estuarine restoration. Since many responses to hypoxia were only observed only at very low DO levels (i.e., 2.0 or 1.5 mg/L O2), these flatfish species appear to have a higher tolerance for hypoxic conditions than other teleost fishes and may be able to withstand many of the environmental hypoxia events observed in Elkhorn Slough, as long as DO levels do not drop below lethal thresholds. Species-specific differences were also found. For two metrics measured, ventilation rate and L-lactate, speckled sanddabs exhibit a nonlinear response, with highest values at mid DO levels, in contrast to a more linear response for English sole, with highest values at low DO levels, suggesting responses to hypoxia may be employed at different DO thresholds for the two species. Additionally, an oxidative stress response was only present in English sole, and not in speckled sanddabs, potentially indicating that speckled sanddabs are better able to withstand hypoxic conditions compared to English sole. If English sole are less tolerant of hypoxic conditions, suitable nursery habitat for this species could be reduced more significantly than for speckled sanddabs, potentially altering the relative distribution and abundance of the two species. 

Gammon graduated from the University of Miami (UMiami) in the Spring of 2019 with a BS in Marine Science and Biology. His research career started with Dr. Diego Lirman's Benthic Ecology and Coral Restoration Lab at UMiami and the citizen science based, coral restoration program Rescue a Reef. His primary research project with the lab was investigating the most effective outplanting methods for microfragmented massive corals. He presented his findings at the Reef Futures 2018 conference in the Florida Keys and published the results in the PeerJ scientific journal. Gammon joined the Ichthyology Lab in the Fall of 2019.

During his time at MLML, Gammon helped lead the efforts for the surf zone marine protected area (MPA) monitoring program which is a project studying the effects of MPAs on California's sandy beaches. The project is a collaborative effort through the University of California – Santa Barbara and Humboldt State University in addition to MLML to sample beaches throughout the state. The project started in 2019 and has continued during the summer every year since. Gammon used this project as inspiration for his thesis by expanding on it to focus on the seasonal changes within the surf here in central California. Through his thesis, he also recorded a rare species of guitarfish that has never been observed north of southern California. With his fellow lab mate, Rachel Aitchison, they published this range extension in the Journal of the Ocean Science Foundation.

When not doing research, you might find Gammon in one of the exhibits at the Monterey Bay Aquarium as a volunteer SCUBA diver helping to keep the inside of the tanks clean. Gammon also works part-time for the California Department of Fish and Wildlife (CDFW) in the geographic information systems (GIS) lab of the Marine Region Department, helping with the California Recreational Fishermen Survey project run by the CDFW. After graduating, Gammon is looking forward to starting a career combining data and policy to help conserve the ocean's resources.

Thesis Abstract:

The surf zone is an important and highly dynamic ecosystem situated at the land-sea interface; however, it is relatively understudied in California. Beaches are one of the most, intensely used coastal resources by humans (e.g., recreation, fishing, development), and can be altered by human impacts, potentially affecting the species that reside there. In addition, oceanographic conditions such as upwelling, temperature, and storm-generated waves have a predictable seasonality that may drive shifts in species assemblages throughout the year. This study investigated the factors influencing spatial and temporal changes in surf zone communities at four beaches in central California from July 2020 to June 2021, testing seasonal trends, the effects of marine protected areas (MPA), and associations with environmental conditions. Each site was sampled eleven times, roughly once a month, for the sampling window using replicated (n = 6 per sampling day) horizontal baited remote underwater video stations (BRUVS). The MaxN statistic (i.e., the maximum number of individuals of the same species observed in a single frame of the video), was calculated for fish and invertebrates on each sampling day, while the relative abundance of drift algae was extracted from still frames using percent cover estimation techniques. Environmental data were obtained from in situ observations on the day of sampling (e.g., water temperature, salinity, wind speed, wave height and period) or weather station sources (e.g., wind and wave direction). Fish and invertebrate abundance and community composition were analyzed separately due to differences in relative abundance and behavior. The results indicated that fish assemblages exhibit seasonality. Species like the barred, calico, and walleye surfperch and leopard shark were far more common in the winter and spring and the speckled sanddab was more common in the summer. Other species like the silver surf perch, thornback ray, dwarf perch, and black-and-yellow rockfish were common throughout the year. There were no impacts on seasonality on invertebrate assemblages, but the system was dominated by the purple dwarf olive snail, Pacific sand crab, slender crab, and red rock crab species. Marine protection inside MPAs had a significant impact on the community structure of fish species, with species such as the reef perch, black perch, kelp rockfish, black-and-yellow rockfish, striped surfperch, rainbow surfperch, señorita, cabezon, and pile perch being observed more commonly within MPAs and other species such as the thornback ray, grass rockfish, barred surfperch, and walleye surfperch being more common at reference sites. There were no effects of MPA status on the invertebrate species diversity or community assemblage. Significant environmental variables for both fish and invertebrate species included wave height and visibility with the former being the dominant driver of surf zone assemblage. Fish species like the barred, calico, and walleye surfperch and leopard shark and invertebrate species like the Dungeness crab, purple dwarf olive snail, and Pacific sand crab were more common during larger wave events while most other species were more abundant on calmer days. Future studies should continue monitoring the surf zone to gather additional years of sampling and sample additional MPA sites to determine if there are greater impacts of MPAs on surf zone species. This study is one of the first to study the temporal trends of central California surf zone. The seasonal trends identified and association of species with MPAs provide key insight into the species that inhabit the surf zone and can be used to help inform management decisions on fishing regulations for these species.

Thesis Abstract:

The partitioning of solar radiation entering the upper ocean in the presence of sea ice during the Arctic summer is essential to predicting future ice retreat.  This study compares predicted incoming heat with upper ocean density and thermal structure by constructing a simple, one-dimensional vertical heat budget around drifting buoy clusters deployed as part of the Stratified Ocean Dynamics of the Arctic experiment. Model reanalysis surface heat flux estimates were used with Synthetic Aperture Radar (SAR) and satellite radiometer derived open water fraction (OWF) estimates to construct an incoming surface heat flux budget.   The incoming solar radiation forced upper-ocean heat gains, either stored locally or contributing to ice melt, through open water and the thinning ice cover.  The estimated seasonal heat input directly through SAR-determined open water is roughly 44 MJ m^-2, and the measured heat sinks total 104 MJ m^-2 for mixed layer heat gain, basal melting, and basal conductance.  Given the lack of sizeable advective heat sources, these results suggest that the residual heat source is through-ice transmittance.  A transmission parameter was estimated from the residual heat flux and comparable to previous in situ observations of ice transmittance.  These results suggest that through-ice transmittance is the dominating heat source around the observation site during the summer 2019 melt season.