Thesis defense by Mason Cole – November 6th Livestream


"Detecting Feeding and Estimating the Energetic Costs of Diving in California Sea Lions (Zalophus californianus) Using 3-Axis Accelerometers"
A Thesis Defense by Mason Cole

The Vertebrate Ecology Lab

MLML Live-Stream | November 6, 2020 at 12 pm

     There is written evidence that when Mason was in third grade he wanted to be an "adventure biologist!", which sounds like an awesome gig. He promptly forgot this dream and ended up pursuing a pre-med undergrad track (B.S. in General Biology from UCSD in 2010), only to change his mind again after graduating. Drawn by wilderness and adventure, and hoping to somehow stumble upon a fulfilling career choice, he booked it to Chilean Patagonia and wandered northward through mountains, diverse volunteer gigs in conservation biology, and his entire bank account before crawling reluctantly back to California. Two years later, armed with experience in both tough field work and poverty, he was ready to take on grad school!  Through hard work and perfect timing he ended up in Dr. McDonald's Vertebrate Ecology Lab, where he couldn't be happier. It was during this time (2015-2020) that Mason's 3rd grade "adventure biologist!" card was unearthed like a fossil from sedimentary layers of nostalgic keepsakes in his parents' home...COINCIDENCE? I think not.
     Mason's research interests currently include the foraging ecology and energetics of large predators, with ample room for broadening this horizon in the future. Mason is also passionate about scientific outreach, outdoor education, and active conservation (habitat conservation and restoration), and has worked (or is currently working) professionally in each of these avenues.

Thesis Abstract:

Knowledge of when animals feed and the energetic costs of foraging is key to understanding their foraging ecology and energetic trade-offs.  Despite this importance, our ability to collect these data in marine mammals remains limited.  In this thesis, I address knowledge gaps in both feeding detection and fine-scale diving energetic costs in a model species, the California sea lion (Zalophus californianus).  In Chapter 1 I developed and tested an analysis method to accurately detect prey capture using 3-axis accelerometers mounted on the head and back of two trained sea lions.  An acceleration signal pattern isolated from a ‘training’ subset of synced video and acceleration data was used to build a feeding detector. In blind trials on the remaining data, this detector accurately parsed true feeding from other motions (91-100% true positive rate, 0-4.8% false positive rate), improving upon similar published methods.  In Chapter 2, I used depth and acceleration data to estimate the changing body density of 8 wild sea lions throughout dives, and used those data to calculate each sea lion’s energetic expenditure during descent and ascent at fine temporal scales.  Energy expenditure patterns closely followed the influence of buoyancy changes with depth. Importantly, sea lions used more energy per second but less energy per meter as dive depth increased, revealing high costs of deep diving.  Combined, these chapters further our understanding of California sea lion foraging ecology and provide new methods to aid similar future studies.

Mason Cole Presents: Detecting Feeding and Estimating the Energetic Costs of Diving in California Sea Lions (Zalophus californianus) Using 3-Axis Accelerometers

Thesis Defense by Emily Pierce – April 17th Livestream


"Emanation and Decay of Environmental DNA from Three Molluscan Species"
A Thesis Defense by Emily Pierce

The Invertebrate Zoology and Molecular Ecology Lab

MLML Live-Stream | April 17, 2020 at 4 pm

Emily has loved marine invertebrates since visiting aquariums and tide pools as a young child. When she moved away from the ocean, she had pet snails so she could continue to learn about molluscs and slimy things, even though she lived in the desert. Emily received a B.S. in Biology from Pepperdine University, where she had a chance to work as an undergraduate researcher and teaching assistant for 3 years. Her research interests include invertebrate zoology and molecular biology, but she is also passionate about education and reaching underserved populations with marine biological knowledge. Emily will move on to a Ph.D. program in collaboration with the University of Maine, University of New England, and the Bigelow Laboratories under the Maine EPSCoR project to continue working with environmental DNA, this time searching for invasive species on the Maine Coast.

Thesis Abstract:

Environmental DNA (eDNA) is nucleic acids outside of living organisms found in air, soil, water, and ice. It is shed by organisms through waste and other bodily fluids, as well as cells sloughed off the outside of an organism. eDNA breaks down over time, especially when exposed to UV, heat, and bacteria. Scientists can analyze eDNA to identify organisms in an area, though the rate at which it is emanated and decayed seem to vary from organism to organism, complicating interpretation of results. The present study sought to quantify the rates of emanation and decay through a series of in vitro experiments for three species, Mytilus californianus (the California blue mussel), Haliotis rufescens (the red abalone), and Lottia scabra (the rough limpet). I found that eDNA emanation rates varied based on species, size, and activity level, and that rates of decay can be influenced by bacterial activity and time under treatment. This data can be used by scientists and managers to interpret eDNA signals of these commercially or ecologically important molluscs to help protect these species and the communities in which they belong.

Watch Emily’s Remote Thesis Defense Below:

Thesis Defense by Miya Pavlock-McAuliffe – January 27th

Drivers of Sub-Seasonal to Interannual Shoreline Change at Sunset State Beach in Monterey Bay, CA

A Thesis Defense by Miya Pavlock-McAuliffe

The Physical Oceanography Lab

Monday, January 27th, 2020 at 4pm

MLML Seminar Room

Thesis Abstract:

This study investigates the interrelationships between the shoreline, sandbar, and wave characteristics using twenty months of half-hourly video observations and five years of biannual survey observations. The relationship between sandbar and shoreline position was investigated to evaluate whether the sandbar buffers the shoreline from incoming wave energy. The shoreline varied by approximately 60 meters while the sandbar varied by approximately 100 meters in the cross-shore direction. The 95th percentile of nearshore significant wave height (1.7m) was required to significantly erode the shoreline at the onset of winter. The investigation of sandbar buffering was inconclusive but suggests that sandbar position plays a greater role in shoreline recovery than in shoreline erosion. Next, shoreline change models were used to test the influence of cross- and alongshore sediment transport on storm-scale to interannual shoreline evolution. An equilibrium shoreline change model was used to simulate shoreline change due to cross-shore sediment transport (RMSE = 6.4m). According to the equilibrium model, the accretion timescale at Sunset State Beach was nearly four times longer than the erosion timescale. Model performance was not significantly improved by the inclusion of shoreline change due to alongshore sediment transport but was likely degraded by temporally variable sediment supply, inferred from annual fluctuations of sandbar and shoreline position. Enhanced shoreline erosion corresponded with greater average winter wave heights and when wave energy approached from more shore-normal directions. Shore-normal wave approach did not necessarily correspond with El Niño periods, but did act to enhance alongshore wave energy gradients due to the irregular bathymetry of the Monterey Submarine Canyon. The results of this study emphasize the need for accurate projections of changing wave direction in addition to wave energy to accurately predict coastal change.

Miya Pavlock McAuliffe Presents: Drivers of sub-seasonal to interannual shoreline change at Sunset State Beach in Monterey Bay, CA

Thesis Defense by Brijonnay Madrigal – December 13th

Determining ecotype presence and the call repertoire of killer whales (Orcinus orca) from passive acoustic monitoring near Point Hope, Alaska in the Southeastern Chukchi Sea

A Thesis Defense by Brijonnay Madrigal

The Vertebrate Ecology Lab

Friday, December 13th, 2019 at 4pm

MLML Seminar Room

Brijonnay Madrigal is a master's student working under the co-advisement of Alison Stimpert and Birgitte McDonald in the Vertebrate Ecology Lab. She graduated from the University of Hawai’i at Mānoa in 2016 with a B.S. in Marine Biology and a B.A. in Communication. Prior to her time at Moss Landing, as an undergraduate and Ernest F. Hollings scholar, she completed a research internship at the NOAA Southeast Fisheries Science Center, where she determined sperm whale abundance from passive acoustic monitoring. She later worked as a research assistant for a project conducted in collaboration with both the U.S. Navy and the Hawai’i Institute of Marine Biology Marine Mammal Research Program, to assess dolphin presence through whistle detection at a sonar detonation sites off O'ahu, Hawai'i. Throughout her time at MLML, in addition to her thesis work, she conducted a passive acoustic study to determine acoustic behavior and repertoire composition of Risso's dolphin in the Monterey Bay. She enjoys education and outreach and has worked at the Monterey Bay National Marine Sanctuary as a volunteer coordinator and educator for more than three years. Driven by her passion for marine mammal acoustics she developed a K-12 program called "Listen up!" to educate kids about marine mammals and sounds in the ocean.

Thesis Abstract:
As apex predators, killer whales (Orcinus orca), can have large impacts on ecosystems through top-down predation. In the North Pacific, three genetically distinct ecotypes exist that differ in diet, range, morphology, and vocal behavior. Killer whales are known to occur in the Chukchi Sea but, few data exist regarding ecotypes present. Since killer whale ecotypes differ in vocal behavior, they can be distinguished based on call type, call rate, and bandwidth. An Autonomous Underwater Recorder for Acoustic Listening (AURAL) device was deployed 75 km off Point Hope, Alaska in the southeastern Chukchi Sea to identify which killer whale ecotypes were present in this region. A total of 1315 killer whale calls were detected on 38 days during the summers of 2013 to 2015. Calls were manually grouped into six categories based on the general call contours: multi-part, downsweep, upsweep, modulated, single modulation and tonal. The majority of detections were tonal calls (n = 607, 46%), and multi-part calls (n = 351, 27%) that contained high frequency and low frequency components. Comparison of the current call dataset with published literature showed similarities in peak frequency with other transient populations. These results indicate occasional presence of transient killer whales in the southeastern Chukchi Sea. This study provides the first comprehensive, catalogue of transient killer whale vocalizations in this region.

Brijonnay Madrigal Presents: Determining ecotype presence and the call repertoire of killer whales (Orcinus orca) from passive acoustic monitoring near Point Hope, Alaska in the Southeastern Chukchi Sea

Thesis Defense by Sharon Hsu – December 13th

Using stable isotopes to determine foraging areas of leatherback turtles: limitations of the isotope tracking technique in the western Atlantic Ocean

A Thesis Defense by Sharon Hsu

The Vertebrate Ecology Lab

Friday, December 13th, 2019 at 12pm

MLML Seminar Room

Sharon's love for the ocean started at a young age. She grew up playing in the tidepools and she has never lived far from the water. Sharon received her B.S. in Ecology, Behavior, and Evolution from UC San Diego, and then spent a number of years working abroad, first as a Peace Corps volunteer in the Republic of Vanuatu and later as a project coordinator for a sea turtle conservation group in Costa Rica and volunteer coordinator for various conservation projects. Her research interests include reproductive energetics of sea turtles and the use of stable isotopes to understand migration and foraging patterns. Sharon is currently working on establishing a collaborative project with biologists from Costa Rica.

Thesis Abstract:

Reproductive output has long been linked to habitat quality and resource availability. Individuals foraging in high-quality habitats with high resource availability will have better body conditions and higher survival rates, as well as greater reproductive output. Post-nesting, Western Caribbean leatherback turtles are known to migrate to at least two foraging regions: the western North Atlantic and Gulf of Mexico. This study had three objectives: [1] conduct a comprehensive review of existing stable isotope data and create a map of isotope values, or “isoscapes” to use as a reference for the western North Atlantic and Gulf of Mexico; [2] use stable isotope analysis (SIA) to examine bulk skin stable carbon and stable nitrogen as indicators of foraging region for nesting turtles in Parismina, Costa Rica; and [3] assess the differences of foraging region on female body size and reproductive output. Synthesized isoscapes showed substantial variation between taxa and sampling regions. Specifically for leatherbacks, stable carbon values were higher in the Gulf of Mexico than the western North Atlantic, but no other consistent trends were distinguishable. It was not possible to infer foraging region for skin samples collected in Parismina based on stable isotope values, nor was there a relationship between stable carbon values and reproductive output. This study highlighted the need for more stable isotope data and longer-term reproductive data collection. Although I was unable to validate it as a primary technique to study leatherback movements between nesting and foraging grounds, SIA still holds important conservation value for leatherbacks in conjunction with satellite tracking.

Sharon Hsu Presents: Using stable isotopes to determine foraging areas of leatherback turtles: limitations of the isotope tracking technique in the western Atlantic Ocean

Thesis Defense by Steven Cunningham – November 22nd

Physical and Biological Consequences of Giant Kelp (Macrocystis pyrifera) Removals Within a Central California Kelp Forest

A Thesis Defense by Steven Cunningham

The Phychology Lab

Friday, November 22nd, 2019 at 4 pm

MLML Seminar Room

Steven is a master's student under Dr. Michael Graham in the Phycology lab at MLML. Prior to MLML Steven obtained his bachelors in science at Humboldt State University. Steven also has three Associate degrees from College of the Redwoods in science, science exploration, and university studies. After completing his bachelor's degree, Steven volunteered at the RC lab at UCSC working on kelp forest ecosystem models and eventually became a scientific diver for the Partnership of Interdisciplinary Studies of Coastal Oceans (PISCO). Currently Steven works as a research technician at MLML's nutrient lab.

Thesis Abstract:

The giant kelp (Macrocystis pyrifera) is a well-studied foundation species that builds complex biogenic habitat and contributes fixed carbon to the base of food webs. Kelp forest systems are some of the most productive ecosystems in the world and can sustain high levels of species richness and abundance. It has long been debated whether these systems are rich due to the (1) complex habitat structure of the giant kelp or (2) the kelp’s high growth rates that provide an abundance of food for primary consumers. Giant kelp modifies its environment by creating shade with it’s surface canopy, slowing currents by surface drag, and adding habitat stratified through the water column. It has been debated if giant kelp or phytoplankton are more important to the stability of the food webs within kelp forest systems. Many studies have attempted to validate the importance of giant kelp to the associated community by kelp removal experiments, which are unable to separate physical from biological effects of kelp. I expand upon these studies here by creating artificial Macrocystis plots and measuring variables that are typically overlooked in kelp removal experiments such as, currents, POC/ PON, particle size distribution, temperature, turbidity, fluorescence, and phytoplankton concentration and carbon contribution. Three kelp beds were analyzed in Stillwater Cove, CA between June – October 2016. A randomized block design was used to test the differences in the measured variables among depth and treatments; control kelp, artificial kelp, and removed kelp. Each circular treatment plot was 10m in diameter and variables were measured weekly within blocks before (n=180) and after treatment (n = 216). There was no difference in POC/PON between control and kelp cleared treatments, indicating that a 10m plot is insufficient at reducing the ambient POC/PON. There was also no indication that the increased light in kelp cleared treatments increased phytoplankton concentrations to subsidize the missing kelp POC input, and the phytoplankton standing crop contributed very little (< 3%) to the standing POC pool. Particulates and POC/ PON were well mixed throughout kelp beds and clearings, with no benthic accumulation observed. Currents increased in speed within kelp removed plots, the velocity was still too slow for turbulent shearing. A subsequent dye tracing experiment with an acoustic doppler velocimeter showed that higher wave frequencies associated with turbulent shedding had higher energy levels within kelp beds compared to outside, and vertical velocities had higher variance within beds than outside. Furthermore, benthic dye release experiments showed that dye flowed further up in the water column inside kelp beds than outside and that dye detection duration was dependent on the presence of giant kelp and increased water velocities. These results indicate that waves have a higher impact on vertical mixing within kelp beds than currents within Stillwater Cove. Mixing in kelp beds blends particulates evenly through the water column and removal plots have no impact on total POC/PON but may change particle distribution.

Steven Cunningham Presents: Physical and Biological Consequences of Giant Kelp (Macrocystis pyrifera) Removals Within a Central California Kelp Forest

Thesis Defense by Cynthia Michaud-November 18th

Effects of Phytoplankton Composition and Biominerals on the Episodic Pulses of Particulate Organic Carbon to Abyssal Depths

A Thesis Defense by Cynthia Michaud

The Physical Oceanography Lab

Monday, November 18th, 2019 at 3pm

MLML Seminar Room

Cynthia is a master’s student under the guidance of Colleen Durkin and Tom Conolly in the Physical Oceanography lab. She received her B.S. from the University of Rhode Island in Marine Biology and Geological Oceanography in 2017. She arrived at MLML in the fall of 2017 and served as the student body treasurer her second year. She has presented her work on phytoplankton and biomineral contribution to the sequestration of carbon to the deep ocean at the recent Ocean Carbon and Biogeochemistry workshop at Woods Hole. She has also given talks to young students about being a scientist in hope of peaking the students’ interest in a marine science field. She hopes to continue her outreach along with staying in the research field.

Thesis Abstract:

The biological pump transports carbon to depth through physical mixing and gravitational sinking of organic particles. Carbon that sinks to the seafloor is consumed by benthic organisms who rely on the detrital particles as their source of food. Station M is a long-term deep-sea study site in the Northeast Pacific where large episodic pulses of particulate organic carbon (POC) sinking to the sea floor have been recorded for the past 30 years. The episodic pulses of POC have increased in frequency and magnitude over the past decade, driving a long-term increase in carbon export observed in sediment traps deployed at this location. The goal of this study is to resolve the role of phytoplankton in driving the high POC export pulses. Samples collected by sediment traps were analyzed by microscopy to determine phytoplankton community composition within sinking material. Sinking particles contain a different community composition during high flux events compared with before or after flux events. Particles sinking before or after high flux periods were relatively more enriched in phytoplankton cells compared to particles sinking during high flux events, but the phytoplankton cells are transporting the same amount of carbon between the two samples. Biogenic silica (BSi) and particulate inorganic carbon (PIC) were measured in the particles to test whether mineral ballasting may be driving the large pulses of POC sinking to depth. There was a stronger correlation between BSi and POC than PIC and POC showing that BSi may be playing a bigger role at Station M. Phytoplankton are relatively less enriched in high flux events, but we discovered that large diatoms including Rhizosolenia are sinking relatively more in the high flux events. Large cells may be driving this high flux event because they contain more carbon than 1 small cell and also contain more BSi making aggregates that they are a part of denser and sink more quickly. We have evidence that BSi is ballasting the cells more so in high flux events, while PIC is not following as close a relationship as BSi. These high flux events seem to be increasing because upwelling events and turbulence can be a cause for large cell disruption causing them to sink more when they are not in an ideal growing situation. The turbulence happens during upwelling which is affected by climate change.

Cynthia Michaud Presents: Effects of phytoplankton composition and biominerals on the episodic pulses of particulate organic carbon to abyssal depths

Thesis Defense by Elizabeth Ramsay – August 9

Morphological variability within Dictyoneurum californicum and Dictyoneurum reticulatum along a wave exposure gradient on the Monterey Peninsula

A Thesis Defense by Elizabeth Ramsay

The Phycology Lab

Friday, August 9th, 2019 at 10am

MLML Seminar Room

Elizabeth Ramsay is a Masters graduate from the Phycology Lab under Dr. Michael Graham. She graduated from California State University Monterey Bay in 2015 with a B.S. in Marine Science with a concentration in Marine and Coastal Ecology. During her time at Moss Landing Marine Labs, Elizabeth had the opportunity to travel and conduct research focused on marine algal species and the ecosystems they support in Baja and Chile. She also had hands on experience with marine aquaculture systems through the MLML aquaculture seminar and her part-time work at the Monterey Bay Seaweeds farm. During her time at MLML, Elizabeth also interned with Stanford Center for Ocean Solutions, where she worked as a scientific communicator, collaborating with researchers and policy makers. Elizabeth is currently seeking out a career in the marine science field with hopes to continue her work with research, science communication, and education.

Thesis Abstract:

The ability of kelps to change the physical characteristics of their thallus in response to their environment can be both functionally and ecologically important to the individual and their local surroundings, especially relative to variability in wave exposure. For decades, Dictyoneurum reticulatum and Dictyoneurum californicum have been studied independently along the Monterey Peninsula, where there is a well-studied wave exposure gradient. Recent genetic work has shown that these two species are genetically indistinct from one another. However, there is a deficit in the knowledge and understanding of the morphological variety within Dictyoneurum and role that wave exposure may play in determining characteristics used to distinguish species. This study tested for morphological variability within the Dictyoneurum genus to document the range of morphological traits and to determine whether or not the morphological traits were genetically fixed or plastic. Year-long observational surveys were conducted in tandem with common garden experiments along a well-established wave exposure gradient on the Monterey Peninsula. I found that depth and wave exposure determined the presence of the characteristic midrib trait, where individuals with midribs were significantly more likely to be found at sheltered sites or only at deeper depths at the exposed sites. Individuals that grew in clumps were also significantly more likely to lack a midrib and split completely through the lamina versus individuals that grew solitarily, that more likely had a midrib and did not split at all. The results based on midrib and splitting presence were most significant at the intermediate sites, whereas the two extreme sites did not show that much diversity in morphological traits. There was no significant difference in growth or morphological characteristics throughout the common garden experiment, suggesting that the morphological characteristics of the midrib and splitting were not genetically fixed. The results of my study suggest that the morphological characteristic of the midrib that is currently used to distinguish between D. californicum and D. reticulatum is plastic and therefore, should no longer be used for species identification for this genus.

Watch Elizabeth’s Thesis Defense Below:

Thesis Defense by Katie Harrington-July 11th

Seasonal time-energy allocation of an island-restricted Falconid, the Striated Caracara, using a low-cost, open-source inertial movement GPS logger

A Thesis Defense by Katie Harrington

Vertebrate Ecology Lab

Thursday, July 11th, 2019 at 12 pm

MLML Seminar Room

Katie began research on striated caracaras in 2015 and has since took over leadership of a long-term research site begun by Hawk Mountain Sanctuary in 2010. Along with overseeing and implementing the expansion of a banding program and educational outreach to farmers and schoolchildren in the islands, Katie’s research has focused on striated caracaras’ seasonal movements, feeding ecology, and energy use. Katie is currently collaborating with researchers in mainland South America to study the population genetics of striated caracaras within and beyond the Falklands, and to support and encourage research into their little-known populations in Chilean and Argentine Tierra del Fuego.


Thesis Abstract:

According to life history theory, animals should have adaptive strategies to cope with seasonal fluctuations in resource availability. However, the introduction of human settlements to natural landscapes can affect the spatial and temporal patterning of resources and disrupt the naturally occurring resource variation to which an animal is adapted. Human subsidies impact animal populations by affecting their density, population growth rate, and abundance. Research has shown that island species dependent on human subsidies are more prone to population declines and local extirpations. While population level effects are known, little research has been aimed at individual level behavior and energy allocation effects. Here, I investigate the time-energy allocation and activity budgets of striated caracaras (Phalcoboenus australis), a scavenging and predatory Falconid in the Falkland Islands, a highly seasonal and human-subsidized environment. I developed the Tapered Wings Logger, a low-cost, lightweight inertial movement GPS logger, and made the logger design available for researchers and applicable across many systems. I deployed the loggers on caracaras to examine seasonal differences in time-energy allocation and activity budgets. The acceleration data were used to calculate overall dynamic body acceleration (ODBA, gravitational g), a proxy for energy expenditure, and to estimate behavioral state using hidden Markov models. I combined the GPS data with ecological knowledge of the species and study sites to help validate model results. Additionally, I investigated space use with daily distances traveled and home range kernel density estimates. My results suggest that on a daily scale, caracaras overwintering at a farm settlement worked 20% harder than in summer (24-hr ODBA: winter 2848.07 ± 577.26 g; summer 2380.85 ± 435.65 g [x̄ ± SD]). During daytime, hourly ODBA rates were nearly two times higher in winter compared to summer (winter 239.50 ± 51.61 g; summer 127.92 ± 26.01 g). Caracaras exhibited more intense activity in winter, spending twice as long in the high activity state compared to summer (winter 99.0 ± 45.2 min, summer 44.1 ± 26.1 min). In addition, during winter, caracaras traveled greater cumulative daily distances (winter 23.75 ± 7.50 km, summer 10.94 ± 3.29 km) and daily ranges were 13 times larger (95% KDE: winter 8.34 ± 11.04 km2, summer 0.64 ± 0.49 km2). This study emphasizes that even with human subsidies to cope with seasonal food availability, caracaras work harder in winter than in summer to obtain enough energy to meet daily requirements. Many island-restricted species will likely face increased variation in resource availability in response to environmental change and human population expansion. I suggest conservation managers consider these results for how to target their efforts to maximize the benefit during a critical life stage of a near threatened species.