Thesis Defenses

"Population genetic analysis informs dispersal capacity in representative marine trematodes"

A Thesis Defense by Randi Barton

MLML Invertebrate Ecology

Live-Stream | November 15th, 2024 at 3:00 pm PST

Abstract

In marine and terrestrial systems, life history drives the distribution of organisms and informs the spatial scale of population connectivity. Nearly all bony reef fishes and invertebrates have a bipartite life cycle with a planktonic larval stage, which increases the organism’s dispersal capacity, and concludes with a relatively non-dispersive adult phase. While many studies have identified the relevant spatial scale for studying population structure in fishes and invertebrates, few have done the same for parasitic taxa, which have even more complex life histories with a higher diversity in the range of dispersal strategies they use. Parasite taxa differ in (1) life cycle complexity, (2) host specificity, and (3) the types of hosts they can infect. All variables are likely to have both independent and synergistic effects on dispersal capacity. This research investigates dispersal capacity using population genetics in two complex life cycle parasites- marine trematodes from Family Microscaphidiidae and Family Paramphistomatidae. We examined the population structure of adult microscaphidiids across the Northern Line Islands and found significant, high genetic structure, suggesting low gene flow. We also examined the population structure of adult and larval paramphistomes across the islands of French Polynesia, and found evidence of cryptic species. Overall, this study supports the idea that parasite life history contributes to their dispersal capacity, and highlights current issues associated with parasite genetic research such as the lack of biodiversity knowledge and the need for more studies on wild populations of parasites in natural systems.

Bio

I graduated from CSU, Monterey Bay in 2020 with my B.S. in Biology. During my undergraduate I became interested in population genetics, and began working with Dr. Alison Haupt on a project to better understand marine parasite dispersal using population genetics. This project evolved into my master’s thesis work at MLML, where I am co-advised by Dr. Alison Haupt and Dr. Amanda Kahn. In 2022, I began working at Granite Canyon Marine Pollution Studies Laboratory as a Lab Assistant alongside my studies. Now, I am a Staff Research Associate and oversee lab operations and lead field collections of sediment for a statewide monitoring program. After I graduate from MLML, I hope to incorporate my molecular experience into the toxicology work conducted at Granite Canyon, to enhance our understanding of how pollutants are affecting biological systems in both freshwater and marine ecosystems. Outside of school and work, I love being outside and doing activities such as hiking, backpacking, and tidepooling. I also love a good nap with my two cats.

"Swim Bladder Morphology Influences the Responses of Nearshore Rockfishes to Barotrauma"

A Thesis Defense by Molly Alvino

Fisheries and Conservation Biology Lab

Live-Stream | May 20th, 2024 at 4:00 pm PDT

Abstract

Rockfishes (Sebastes spp.) are ecologically and economically important fishes in the continental shelf and slope regions of the Eastern Pacific Ocean. All species within the Sebastes genus have a buoyancy organ, the swim bladder, which is sensitive to rapid changes in pressure that occur when fish are caught and brought up to the surface. Although all rockfishes have swim bladders, pressure-related injuries (barotrauma) affect rockfish species differently. To determine if swim bladder morphology can explain differences in barotrauma among rockfishes, semi-pelagic (Blue rockfish, S. mystinus and Olive rockfish, S. serranoides) and benthic (Gopher rockfish, S. carnatus and Vermilion rockfish, S. miniatus) species were captured via hook-and-line and manually recompressed using a hyperbaric chamber. Decompressed fish were sacrificed and seven different swim bladder morphological features were quantified and related to external barotrauma injuries observed at the time of capture. Benthic Vermilion rockfish displayed a greater incidence of barotraumatic injuries and had thicker swim bladder membranes with a higher tearing threshold than the semi-pelagic species. Conversely, the swim bladders of Blue rockfish were significantly thinner and more elastic than Vermilion rockfish, and experienced fewer barotraumatic injuries than both benthic species. Despite occupying different habitat zones and responding differently to barotrauma, many swim bladder measurements were similar between Olive and Gopher rockfish. Additionally, the number and severity of barotraumatic injuries significantly decreased as total length increased in Blue rockfish, consistent with a significant increase in tearing threshold and swim bladder membrane thickness with total length. This research furthers the understanding of pressure-related injuries among different rockfish species, while informing fishery managers of the swim bladder morphology directly impacting interspecific discard mortality rates.

Bio

Molly grew up in and around the water, and once she was introduced to SCUBA diving in high school, she knew it was what she wanted to do with her life. Following this passion, Molly went on to graduate from Northeastern University in 2020 with a B.S. in Marine Science. Wanting to explore the West Coast, she packed up and moved to California to attend Moss Landing Marine Laboratories within the Fisheries and Conservation Biology Lab. At MLML, Molly has worked on a number of different research projects including the California Collaborative Fisheries Research Program (CCFRP), Shallow Water Mini Landers, Benthic Observation Survey System (BOSS), Surf Zone sampling, and Rockfish Ocean Acidification. When she's not at the lab, you can find Molly doing Crossfit, trying out new food spots, or playing with her cat, Crouton.

"Observations of Currents, Waves, and Turbulence within a Giant Kelp Forest in Stillwater Cove, Carmel, California"

A Thesis Defense by Logan Grady

Physical Oceanography Lab

Live-Stream | March 25th, 2024 at 12:00 pm PDT

Abstract

Giant kelp (Macrocystis pyrifera) forests are hydrodynamically complex regions of enhanced drag that rely on turbulence for nutrient distribution and propagule dispersal. Currently, there are no in-situ measurements of turbulence within giant kelp forests and studies of driving mechanisms for turbulence are limited to controlled flume experiments. This study investigates relationships between currents, surface gravity waves, and turbulence within a kelp forest through deployment of moored instrumentation and kelp surveys in Stillwater Cove, California from July 22 to August 30, 2022. Oceanographic conditions during this time period are primarily driven by coastal upwelling and semi-diurnal internal tides, which likely originate from the Carmel Submarine Canyon. During rising tides, these internal waves are associated with cooling events and enhanced onshore velocity within the kelp forest. Estimates of gradient Richardson numbers and kelp Reynolds numbers indicate that cooling events are likely not associated with shear instabilities in the bottom layer, while enhanced bottom velocities could consistently generate turbulent kelp wake. Turbulent kinetic energy dissipation rate (ε) was calculated using data from an acoustic Doppler velocimeter, spanning a range of 1.9 x 10 -8 to 8.0 x 10 -7 m 2 /s 3 . Onshore velocities associated with cooling events are positively correlated with ε, while offshore velocities are not. This asymmetrical pattern implies a directional relationship triggered by cooling events, which may generate turbulence through interactions with dense kelp and rough bottom substrate. Models of submerged vegetation wake production and bottom boundary layer production of turbulent kinetic energy are compared to observed values of ε to assess hypothetical kelp and bed drag coefficients.

Bio

Logan graduated from the University of California Santa Cruz in 2020 with a B.S. in Environmental Science and a passion for scientific SCUBA diving in Monterey Bay. With an interest in ocean physics and the native kelp forests, he went on to attend Moss Landing Marine Laboratories under the advisorship of Dr. Tom Connolly. His current project investigates how nearshore currents, waves, and turbulence are influenced by giant kelp forests. In his free time, Logan can be found mountain biking, watching Formula 1, or at various trivia nights around Santa Cruz.

"Multi-Tissue Analysis of Combined Fluctuating Environmental Stressors in Juvenile Copper Rockfish, Sebastes caurinus"

A Thesis Defense by Arie Dash

Ichthyology Lab

Live-Stream | January 29th, 2024 at 2:30 pm PDT

Abstract

Global ocean chemistry has been affected by historic and ongoing anthropogenic carbon emissions. These changes are expected to intensify and subject species normally tolerant to fluctuating, stressful environments, such as those in Eastern Boundary Upwelling Systems (EBUS) like the California Current Ecosystem to increasingly more extreme conditions. Specifically, dissolved oxygen (DO) and pH are both expected to fall in upwelled waters below the extremes currently experienced. To investigate the effects of these projected changes on the physiology and gene expression of potentially vulnerable nearshore rockfish, I utilized tissues samples from juvenile copper rockfish (Sebastes caurinus) subjected to fluctuating combined pH/DO stressors designed to mimic the upwelling pulses normally experienced in the field. Over 13 weeks, fish were exposed to alternating 8-day cycles of stressor (“upwelling”, pH 7.3, 2 mg/L DO) and ambient (pH 8.0, 8 mg/L DO) conditions. Two cohorts experienced fluctuating conditions and were sampled at the end of either an upwelling phase or an ambient phase. A third cohort was kept at static ambient conditions for the duration of the experiment as a control. At the end of the experiment, brain, gill, liver, and muscle tissue was collected for RNA sequencing and compared to physiological responses of the same individual fish. A de novo metatranscriptome that combined expression of all tissues was constructed and used as a reference for differential gene expression. Recently, falling costs of sequencing have made genomes much more prevalent for nonmodel species, and so to investigate the differences between transcriptome and genome references I performed all analyses again with a copper rockfish genome reference. Overall, I found that the genome reference led to similar but generally less noisy results than the metatranscriptome. I also did not detect evidence for a conserved stress response, because although I found significantly differentially expressed genes (DEGs) (p < 0.05) in all tissues, no DEGs were shared between all tissues. In fact, each tissue appeared to leverage specialized responses to the stressors rather than relying on a general stress response, which could be a result of adaptation to the chronic exposure in this experiment or a reflection of evolutionary tolerance to upwelling stressors. Brain and muscle tissue appeared to recover during the relaxation phase of the fluctuating cycle, indicating that transcriptomic resilience is an important mechanism of stress tolerance in these tissues. On the other hand, gill and liver tissue appeared to exhibit lingering effects, indicating that mechanisms such as frontloading (i.e., constitutive expression of stress response genes) may be more important for these tissues. To overcome some of the limitations of gene expression alone, a separate analysis correlating expression of novel gene networks to physiological and behavioral traits from the same fish was performed. These results largely mirrored those seen in the differential gene expression analysis, increasing confidence that patterns seen in the gene expression data reflect relevant physiological effects. Analyzing gene expression from multiple tissues under environmentally realistic fluctuating stressors highlights tissue specific environmental stress responses and allows for a more holistic understanding of predicted future upwelling conditions on a potentially vulnerable lifestage of copper rockfish, an important nearshore fish within the California EBUS.

Bio

Arie graduated from the University of Pittsburgh in 2020 with a B.S. degree in Microbiology and Computer Science. He went on to attend Moss Landing Marine Laboratories and study gene expression in juvenile copper rockfish under the co-advisorship of Dr. Cheryl Logan and Dr. Scott Hamilton. He is very interested in the confluence of marine science, bioinformatics, and public health, and intends to continue working at the Monterey Public Health Laboratory after graduating. In his free time, Arie can be found camping, hiking, cooking, or playing video games.

"Seasonal dynamics of the introduced sponge Hymeniacidon perlevis in the Elkhorn Slough, California, USA"

A Thesis Defense by Jackson Hoeke

Invertebrate Ecology Lab

Zoom | Live-Stream | December 15th, 2023 at 12:00 pm PDT

Abstract

Hymeniacidon perlevis is a cosmopolitan non-native sponge with a seasonal life cycle that has been introduced to the Elkhorn Slough in central California, USA. This study investigated seasonal and interannual dynamics of H. perlevis in Elkhorn Slough estuary, explored correlations between sponge cover and environmental conditions, and estimated how the potential scale of change H. perlevis has on its environment could vary across its seasonal life cycle. Successful recruitment is currently restricted to the upper estuary and while it varies annually, the frequency and density of sponge recruits have generally increased over time from 2007 to 2023. Prior observations have recorded seasonal patterns in other populations, and data from this study in Elkhorn Slough demonstrates a seasonal pattern variation with sponge cover peaking in October and declining to a minimum from March to May. Time-lagged Spearman-ranked cross-correlations suggest that sponge cover is correlated with increased temperature and lower dissolved oxygen at all sites, with a lag of 2-4 months. Precipitation from severe storms in 2023 also coincided with declines in sponge cover. Over the course of a year, the estimated rate of water filtered by H. perlevis and biomass accumulated are greatest in fall-corresponding with peak cover, and weakest to nonexistent in the spring. Understanding the seasonal and interannual dynamics of this population can inform future approaches to manage or mitigate its ecological impacts.

Bio

Jackson graduated from the University of Oregon in 2020 with a B.S. in Marine Biology. During that time, he studied at the Oregon Institute of Marine Biology and conducted a survey of native and introduced hydroids in Coos Bay, Oregon. Jackson is fascinated by the ever more frequent introductions of marine invertebrate species around the globe and their growing impact on the communities they establish themselves in. His current project focuses on the seasonal drivers and impacts of the introduced sponge Hymeniacion perlevis in the Elkhorn Slough next to MLML. During his free time, he can often be found reading, hiking, listening to music, or painting marine life.

"Into the Deep: Impacts of Natural and Artificial Substrates in the Deep Sea"

A Thesis Defense by Sydney Mcdermott

Invertebrate Ecology Lab

Zoom | Live-Stream | December 13th, 2023 at 10:00 am PDT

Abstract

With increasing maritime activities, man-made structures such as oil platforms, wind farms, and lost shipping containers are becoming ubiquitous in the oceans. These structures serve as substrates for marine organisms. There is evidence that unique communities develop on some man-made structures; however, the effects of substrate type vary, and are often confounded with geography and depth. Man-made objects lost in shallow water have a better chance of being retrieved than those in the deep sea, resulting in the deep sea becoming a semi-permanent repository. We studied invertebrate communities on a lost shipping container found at 1.3 km depth and deployed experimental substrates at 200 m depth to assess whether colonization and succession differ between natural and artificial substrates in the deep sea. The community on the lost container changed over time, becoming more similar to the communities on naturally occurring substrate in the Monterey Bay Submarine canyon with dominance by echinoderms, cnidarians, poriferans, and small mollusks. Communities on the experimental artificial substrates were similar to those found on experimental natural substrates, with no significant difference in diversity, richness, or evenness based on substrate type. There was a significant difference across all experimental substrates over time, indicating that the substrates may have undergone successional changes at similar rates with a major shift after 5 years. Lost objects may serve as substrates for communities mostly similar to those that form on naturally occurring hard substrates, making anthropogenic pollutants a potential subject of future monitoring efforts.

Bio

Sydney received her B.S. in marine science from the University of Maine in 2020 before attending Moss Landing Marine Laboratories. She has worked on a variety of projects across different marine habitats, from studying the microbiome of an east coast intertidal alga, to monitoring harmful algal blooms in the Pacific Northwest, to investigating the changes in sea sponge populations in the Bering Sea over the past 5 million years. Her research at MLML under the guidance of Dr. Amanda Kahn focuses on the impact of lost anthropogenic objects in the deep sea, specifically lost shipping containers. Sydney also began a PhD in ecology and evolution at the University of Louisiana at Lafayette in the fall of 2023.

"The Feeding Habits and Selectivity of Siphonophores in Monterey Bay"

A Thesis Defense by Alex Lapides

Invertebrate Ecology Lab

Zoom | Live-Stream | November 27th, 2023 at 12:00 pm PDT

Abstract

Gelatinous zooplankton are historically understudied and we have much to learn about how they fit into the larger food web.  Of gelatinous zooplankton, siphonophores are especially known to have broad diets and to select for a wide variety of prey.  In this study we investigated siphonophore feeding habits using a long-term remotely operated vehicle video dataset from the Monterey Bay, CA.  In addition, we quantified the degree of specialization for each siphonophore-prey pair, and we investigated the relationship between genetic distance and specialization differences.  We found siphonophores tended to belong to one feeding guild and in some cases fed exclusively on one prey.  Siphonophores also selected strongly for a few specific prey.  We found a slight relationship between genetic distance and siphonophore specialization.  Overall, this study upholds previously known trends about siphonophore diet, selectivity, and phylogenetic patterns and expands our knowledge of the midwater food web.

Bio

Alex received her B.S. in Ecology and Evolution from UC Santa Cruz in 2018 before coming to MLML in the Fall of 2020.    She has held a variety of technician positions ranging from research vessel operations to molecular lab work to machine learning, and has studied a variety of habitats ranging from salt marshes to the deep sea.  Overall, she is most interested in problems concerning the open ocean that leverage large datasets and statistics to make inferences about the environment, and is most content behind a computer playing in R.  In her free time, Alex likes to perform aerial silks, spin fire, and play Magic: the Gathering

"Drivers of intertidal purple sea urchin (Strongylocentrotus purpuratus) reproductive capacity and the implications for kelp forest recovery"

A Thesis Defense by Isaak Haberman

Invertebrate Ecology Lab

| Live-Stream | December 8th, 2023 at 3:00 pm PDT

Abstract

Kelp forests are integrally important ecosystems along eastern Pacific coastlines, sequestering carbon, reducing wave erosion, and increasing biodiversity in coastal marine communities. However, kelp forest coverage in central California has experienced major decline in the past decade, being replaced with unproductive urchin barren habitats. The factors affecting the establishment and persistence of urchin barrens have been extensively researched in the subtidal, but the influence of intertidal sea urchin populations is unknown. Moreover, intertidal populations are likely connected to subtidal communities via larval dispersal, so an understanding of intertidal urchin reproductive dynamics is important. I collected urchins and biological and environmental data from nine sites along the Monterey Peninsula in central California with varying algal communities, urchin densities, and wave exposures. I weighed and extracted the gonads from urchins at each site to measure gonadal somatic index (GSI%), a representation of reproductive capacity proportional to urchin size. I found that intertidal urchin reproductive capacity is unrelated to coralline algae cover or urchin density; contrary to what is seen in the subtidal. There is a weak positive relationship between fleshy algae coverage and reproductive capacity. Moreover, urchins collected from sites that had higher drift algae presence exhibited higher reproductive capacities. This indicates that urchins in the intertidal are resilient to poor fleshy algae coverage where they are living because drift algae is continually deposited into intertidal environments for them to consume. Therefore, the intertidal can support higher densities of healthy sea urchins that may represent an important contribution of urchin larval supply to subtidal urchin barrens. Kelp restoration efforts must be amended to include intertidal areas - especially those of high urchin densities - in order to maximize their efficacy.

Bio

I am a graduate student at CSUMB and MLML advised by Alison Haupt and co-advised by Amanda Kahn. I completed my undergraduate degree at the University of British Columbia where I studied marine biology and did research on the caloric value of different seaweed species. My thesis at CSUMB focuses on the reproductive capacities of intertidal populations of purple sea urchins (Strongylocentrotus purpuratus) and how these populations are important to consider for kelp forest restoration techniques. My research interests are nearshore community ecology, applied ecology, and generally how species interactions and habitat shape the species composition of different nearshore areas. After I graduate, I will be teaching at CSUMB in the spring. In my spare time I like doing crossword puzzles, going camping and climbing, and watching the Packers.

"Habitat-mediated efficacy of 360 degree diver-operated video for quantitative surveys of California reef fishes"

A Thesis Defense by Kameron Strickland

Ichthyology Lab

Zoom | Live-Stream | November 13th, 2023 at 3:00 pm PDT

Abstract

Temperate rocky reefs feature a mosaic of complex macrohabitat features which host a variety of demersal fish species. Giant kelp forests add considerable vertical structure to rocky reefs, including macrohabitats extending from the reef to the upper water column. Much of what we know about temperate communities derives from shallow SCUBA surveys in which divers record observations using underwater visual census (UVC) techniques. Increasingly, these communities are being studied with video techniques first utilized in deeper water. While UVC provides immediate data on fish communities and requires no additional technology either for data collection or post-processing, imagery captures the fine-scale associations between fish specific habitat features that elude UVC techniques. While traditional video cameras constrain the field of view available to a UVC diver, 360˚ cameras record everything in all directions, eliminating the need to selectively survey one direction underwater. However, questions remain as to how data derived from 360˚ video transects compare to the more well-established UVC transects, particularly in complex environments. My primary research objective was to examine the trade-offs associated with 360˚ video and UVC when quantifying attributes of the demersal fish community across multiple sites and macrohabitat types. I performed SCUBA dives at four sites around the Monterey Peninsula in central California. Pairing UVC and 360˚ video, I recorded fish counts along 30 meter demersal transects. Richness, diversity, abundance, and density of fishes from UVC and 360˚ video were compared statistically with two-way analysis of variance (ANOVA) and non-metric multidimensional scaling (NMDS). Results indicate that within fish-habitat guilds, counts of species were similar between methods at all macrohabitats and most sites. 360˚ video and UVC produced similar results with respect to species richness and diversity. Differences between the methods arose by looking at density at any scale, as well as total count per meter of all fishes. These results suggest that with some caveats, 360˚ video transects can be incorporated into temperate subtidal reef monitoring without compromising data quality.

Bio

Kameron graduated with his B.S. in Marine Science from CSU Monterey Bay in 2019. There, he was heavily involved in the SCUBA program, both volunteering for courses and diving for his personal capstone project. Early discussion of Kameron's thesis project was already in progress when he joined the Ichthyology lab in 2020. After learning to create 360˚ video SCUBA dives, Kameron wanted to put the technology through trials and see how 360˚ video transects surveyed kelp forest fish compared to SCUBA divers. During his time at MLML Kameron performed video analysis for the Fisheries and Conservation Biology Lab's BOSS video lander project at San Clemente Island, became a SCUBA Instructor, started a marine consulting job, and even worked as a long-term substitute teacher across multiple grade levels. In his free time, Kameron enjoys wildlife photography and can be found taking cameras precariously close to seawater.