Thesis Defenses

"The Influence of Maternal Size/Age Effects On the Physiological Responses of Adult Female Gopher Rockfish (Sebastes carnatus) to Ocean Acidification and Hypoxia"

A Thesis Defense by Dylan Sarish

MLML Ichthyology

Live-Stream | May 1st, 2025 at 4:00 pm PDT

Abstract

Climate change is rapidly reshaping the chemistry of the ocean. Fishes living in California coastal waters experience ocean acidification, elevated pCO₂, and hypoxia (OAH) in response to upwelling of deep water, and this process may increase in frequency and intensity with climate change. Nearshore rockfish may be particularly threatened by increasingly frequent OAH conditions due to their long lifespans and late maturation. Maternal effects, whereby larval condition is influenced by non-genetic components of the maternal phenotype (e.g. size, age) or environment, is one process that may allow rockfish to rapidly adapt to climate change. To understand the physiological effects of OAH on pregnant rockfish during gestation, adult female gopher rockfish, Sebastes carnatus, were collected and exposed to four different combined OAH stress treatments, from fertilization to parturition. A second group was exposed to two combined OAH stress treatments. Routine metabolic rate (RMR), maximum metabolic rate (MMR), blood chemistry, including hematocrit (Hct), hemoglobin (tHb), pCO₂, HCO₃^-, ions (Na⁺, K⁺, Cl^-), and metabolites, were measured to assess physiological responses to OAH stress. Ovarian oxygen levels were measured to examine the potential capacity of females to buffer their developing broods against changing ocean chemistry. Fish exposed to higher OAH stress displayed elevated Hct and tHb, higher blood pCO₂ and HCO₃^-, and decreased MMR, indicating they attempted to compensate for low pH and hypoxia exposure. Only partial compensation was achieved as blood pH was not always maintained near ambient levels. Fish showed signs of buffering their ovaries against hypoxia under OAH exposure. Lastly, pregnancy altered Hct and MMR under OAH exposure and size/age did not have a consistent effect on maternal physiology. By evaluating the responses of maternal physiology to OAH stress, which directly impact larval physiology, we can better understand how climate change affects, fecundity, larval condition, and survival which will influence the management of nearshore fisheries in an ever-changing climate.

Bio

Dylan earned her B.S. in Marine Biology with a minor in Environmental Science from UC San Diego in 2019. While at UCSD, when not practicing as a member of the varsity fencing team, she volunteered for Dr. Andrew Nosal, where she helped with the tagging of sevengill sharks in La Jolla cove, and was in charge of the care and feeding of a tank of juvenile horn sharks in the Scripps Institute of Oceanography’s experimental aquarium. She was also a member of the Coral Ecology Lab under Dr. Stuart Sandin, where she contributed to the 100 Island Challenge. After graduating, Dylan spent some time working for the California Department of Fish and Wildlife, where she contributed to the California Recreational Fisheries Survey (CRFS) as a sampler, assisting with the mission to collect fishery-dependent data on California’s marine recreational fisheries and to accurately estimate catch, effort, and stock.

Dylan joined the Ichthyology lab in Fall of 2022, and examined the effects of ocean acidification and hypoxia on the reproductive success of female gopher rockfish. In her spare time, Dylan enjoys being around animals, baking, and traveling

"DRIVERS OF RHYTHMIC CONTRACTIONS IN THE TEMPERATE DEMOSPONGES TETHYA CALIFORNIANA AND HYMENIACIDON PERLEVIS"

A Thesis Defense by Keenan C. Guillas

MLML Invertebrate Ecology

Live-Stream | May 1st, 2025 at 2:00 pm PDT

Abstract

Sponges (Phylum Porifera) are suspension feeders whose water filtration is important to benthic ecosystems because of their conversion of large amounts of dissolved carbon and nitrogen into particulate waste available for detritivores. Sponges filter water by drawing it through a complex aquiferous system of canals and pores. Rhythmic contractions of tissue, which temporarily constrict canals and reduce body size, can diminish filtration rates and therefore affect ecosystem services; however, the physiological function of rhythmic contractions is not completely understood. I recorded long-term time-lapses of the demosponges Tethya californiana and Hymeniacidon perlevis to determine the endogenous and environmental factors that influence rhythmic contractions. I found that contractions occurred simultaneously in the osculum, ostia, and whole body in T. californiana. In H. perlevis, contractions originated and spread between many different oscula, with no evidence of cohesive whole-body behaviour. In T. californiana, duration of rhythmic contractions were significantly correlated with body size, oceanographic season, and dissolved oxygen. Both species reduced contraction frequency and increased total time expanded in seawater enriched with Rhodomonas sp. microalgae. This thesis provides support for rhythmic contractions in sponges as products of both endogenous and environmental factors, improving our understanding of the complexity of behaviours in early-diverging aneural metazoans.

Bio

Keenan earned his BSc in 2018 from the University of Alberta, where he worked with Dr. Sally Leys investigating the ecology of glass sponge reefs in Hecate Strait, British Columbia. At MLML his research focused on drivers of rhythmic contraction behaviours in the marine demosponges Tethya californiana and Hymeniacidon perlevis. He used time-lapse photography and microscopy to improve our understanding of sponge coordination, behaviour, and resilience. He was also student body vice president and an active member of the MLML community. He is now a research technician in the Marine Structural Biology unit at Okinawa Institute of Science and Technology in Japan. He is also a coffee enthusiast and a fiction writer.

" A COST EFFECTIVE MULTIBEAM SYSTEM YIELDS HIGH TEMPORAL AND SPATIAL RESOLUTION BATHYMETRIC MAPS OF THE MONTEREY CANYON HEAD"

A Thesis Defense by Marcel Peliks

MLML Geological Oceanography

Live-Stream | February 7th, 2025 at 9:30 am PST

Abstract

The coastal environment is a dynamic and complex system constantly in flux. A comprehensive understanding of the nearshore system is crucial for habitat management, modeling impacts of climate change, as well as managing economic resources. Studying nearshore bathymetric environments through mapping has traditionally been challenging due to high surveying costs and adverse environmental conditions. The Monterey Canyon Head offshore of Moss Landing, California exemplifies a complex nearshore feature with significant impacts on the local environment. Previous studies have identified the canyon head as the primary sand sink for two littoral cells: the Santa Cruz and Southern Monterey Bay cells. Nevertheless, the spatial and temporal trends of sediment accretion and erosion in the canyon head remain poorly understood. To address this, a cost- effective multibeam system for high-resolution mapping of complex seafloor topography in shallow water has been assembled, enabling high-frequency repeat mapping of the canyon head. Preliminary testing demonstrates that the system is capable of mapping seafloor features at 1 m resolution at depths up to 60 m, with increasingly finer resolutions achievable at shallower depths. Tests conducted at the canyon head showed repeatable mapping surveys with a root mean square error (RMS) of 10 cm in back-to- back surveys. The greatest differences were observed on steep (>50°) canyon walls and in deeper water (>35 m). A total of seven test surveys were completed between October 2021 and January 2022 resulting in an average survey frequency of twice per month. Comparison maps of these surveys reveal a complex sedimentary cycle characterized by frequent sediment deposition, movement, and failure in the northern tributaries of the canyon head, and minor deposition and bedform migration in the southern tributaries.

Bio

Marcel earned a B.S. in Earth Science from the University of California, Santa Cruz, which laid the foundation for his early career as a geologist. Drawn by a passion for instrumentation, geospatial analysis, and geology, he transitioned into the M.S program at MLML - finding his niche in the seafloor mapping field. Since embarking on this path, Marcel has immersed himself in Hydrography and Ocean Exploration, working as a mapping technician aboard NOAA's Okeanos Explorer, contracting private dredging surveys, and most recently working for the Office of Coast Survey to qualify bathymetric data for use in the National Bathymetric Source (NBS). Outside of work, Marcel enjoys spending time in the ocean and mountains, with his closest friends, and by going on extended trips abroad.

"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