Ecology and Evolutionary Biology Commons^™

Bearpaw Reserve Wildlife Monitoring And Mapping With The Wildlands Conservancy, Hope Hansen

Scripps Senior Theses

For my Environmental Analysis Capstone, I worked in a small group to monitor and map the wildlife at Bearpaw Reserve. Bearpaw Reserve, located in Forest Falls, California, is a 600 acre tract of wilderness that is owned by The Wildlands Conservancy. Bearpaw is located about an hour from Claremont, in the San Bernardino Mountains. The Wildlands Conservancy makes management decisions about its reserves while applying conservation research to the real world.

My group’s task was to use trail cameras to gather data on the wildlife at Bearpaw, then visualize this information into a GIS map. We used a combination of …

Differential Equation Modeling For Sustainable Resource Management: A Steady-State Optimal Harvesting Approach, Iordanka N. Panayotova, Aleksei Talonov

CODEE Journal

Mathematical models based on differential equations provide a powerful framework for connecting real-world data to informed decision-making. In this work, we present a student-accessible project that uses an optimal-control framework to study the sustainable management of biological resources.

Motivated by fisheries management, we examine a predator--prey system in which harvesting decisions must balance ecological and economic considerations. The model is formulated as an optimal control problem that seeks to maximize the total discounted net revenue from harvesting. Rather than solving for the complete time-dependent harvesting trajectory, we restrict the analysis to positive controlled coexistence equilibria and characterize an interior stationary …

Indirect Effects Of Coral Bleaching On Tursiops Truncatus Diet And Foraging Behavior In Bocas Del Toro, Panama, Annabel Fiero

Scripps Senior Theses

Indirect effects, where another species or factor mediates the effects of a given species, are critical to ecosystem structure and resilience. Shifts in fish community structure, as a result of rapidly declining coral reefs in the Caribbean due to warming-induced bleaching, pose a threat to apex predators like Tursiops truncatus (bottlenose dolphins). Branching corals create habitat niches for numerous fish species. These fish rely on coral for food and habitat, and in turn provide food for upper trophic levels. Prior research has highlighted how coral bleaching will disrupt Acroporid reef building corals and fish community structure, but the effects of …

How Semiflightless Birds Adapt: A Survey From Barú, Costa Rica, Eli P. Laloudakis

Scripps Senior Theses

When we think of birds, we think of flight. Because of this, scientific research often focuses on how birds evolved flight and how their wings function during flight. However, not all birds can fly or fly well, as wings wax and wane on developmental, seasonal, and evolutionary time scales (Dial and Heers 2021). Consequently, rudimentary wings can be found in developing birds, secondarily flightless or semiflightless birds, birds that undergo simultaneous molts, and extinct theropods with “protowings” (structures that preceded fully functional wings). Secondarily flightless and semiflightless birds often evolve where there is no/low predation, abundant year-round food supply, and …

Components Of Evolutionary Psychology Are Falsifiable, But Does That Make It A Good Theory? Commentary On Costello Et Al. (2025), David S. Moore

Pitzer Faculty Publications and Research

At the center of narrow evolutionary psychology’s theory lies the assumption that many human behavioral mechanisms evolved via natural selection. Although some components of this theory are falsifiable, its Lakatosian framework protects its core assumptions from falsifiability, even though most human behaviors probably do not require evolutionary explanations. Crucially, falsifiability is a necessary but insufficient quality of a good scientific theory, and the value of narrow evolutionary psychology (NEP) can be questioned on other grounds. NEP holds that only natural selection can create complex, functional adaptations, but natural selection is not a creative force; this process merely functions as a …

We Found Love In A Wetter Climate: The Impact Of Varying Climatic Conditions On The Prevalence Of A Fungal Endophyte In Elymus Virginicus Populations, Audrey Yung

Scripps Senior Theses

Epichloë is a genus of endophytes– symbiotic fungi residing within a plant’s tissue– that can provide mutualistic benefits to its host. The stress gradient hypothesis predicts that mutualism between species becomes stronger in conditions of high abiotic stress. We tested this idea by assessing how Epichloë prevalence in Elymus virginicus populations is affected by varying climatic conditions. We established plots of E. virginicus with known endophyte frequencies in the spring of 2023 at five sites across a precipitation gradient in Texas and Louisiana. We collected E. virginicus recruits in June and July 2024 at all field sites. To determine recruits’ …

The Chesapeake Pearl: A Proposal For An Environmental Public Art Installation, Samuel I. Reichard

Pitzer Senior Theses

In this thesis, I lay the foundation for an environmental art project along Chesapeake Bay. It includes an analysis of relevant literature and case studies, as well as a proposal for the project. The Chesapeake Pearl (working title) would be a 20-foot spherical aquarium that will visually display the water filtration capacity of eastern oysters and native seagrass, aiming to inspire curiosity around these organisms and the greater Chesapeake Bay ecosystem. The project exists at the intersection of environmental art and environmental education and seeks to promote learning and public engagement through visually demonstrating a scientific process, the water filtration …

If You Give A Tadpole A Chemosensory Stimulus: Detection Of Invasive Predatory Cues And Signs Of Conspecific Communication In Pseudacris Sierra Tadpoles, Faben Tesfazion

Scripps Senior Theses

Amphibians are at disproportionately higher risks of extinction than all other vertebrate classes, and a major causing factor is invasive predation. The American bullfrog (Lithobates catesbeianus), native to Eastern North America, is a notorious invasive species which preys on native Sierran treefrogs (Pseudacris sierra) in Northern and Central California. These treefrogs have yet to be placed on any Special Animals List, suggesting the presence of adopted behaviors against predation. Past studies have documented the importance of chemical sensing in anuran tadpoles as predator detection tools. This study tests if Sierran treefrog tadpoles can recognize invasive chemical …

“Nice To See You”: Addressing Plant Awareness Disparity With Locally Specific Ecological And Cultural Plant Education, Cecilia Muecke

Pomona Senior Theses

Plants form the basis of life on Earth. However, due to the phenomenon of plant awareness disparity, a self-perpetuating cycle whereby plants are overlooked on an individual and global level ensues. Lack of plant awareness leads to a lessened emphasis on plants in sustainability and conservation as well as biology education, resulting in negative impacts on biodiversity and food security. The severity of plant awareness disparity is dependent on cultural context, and Indigenous and/or traditional societies are less likely to experience plant awareness disparity because of they are typically more connected to plants for their everyday needs. Native plants are …

Crisis In The Current: A Proposed Study On The Impact Of Columbia River Basin Water Quality On Juvenile Chinook Salmon Survival, Olivia Buist-Thuillier

Pitzer Senior Theses

Salmon occupy a vital role in the ecosystem, economy, and indigenous culture of the Pacific Northwest of the United States, specifically within the Columbia River Basin. Of the five species of Pacific Salmon that live in the basin, Chinook salmon (Oncorhynchus tshawytscha) are the most widely commercially fished and are the largest. In recent years, Chinook Salmon populations have heavily declined from human influence. Rising temperatures from anthropogenic climate change, habitat destruction (dams, human presence), runoff from agricultural practices, and overfishing have all contributed to this decline. Because of their role as a keystone species and their cultural significance, there …

Behavioral Observations And Analysis Of Twix: The Cape Porcupine At The Lake Superior Zoo, Erin Davidson

Scripps Senior Theses

The three main goals of zoos are outlined as: education, conservation, and research. In our modern world, the focus of zoos has shifted away from simply housing animals, and towards how we can best promote proper animal welfare for individuals in human care. Animal welfare can be defined as the “mental health” of non-human species of fauna, and is greatly influenced by the stressors within the environment, as well as the option of choosing how to interact with and respond to the environment. Animals housed in zoos are presented with unique stressors that they often do not choose to experience, …

Assessing The Effects Of Wildfire Season Pm2.5 Exposure And Environmental Variables On Breeding Season Avian Body Condition, Cira Seyer-Ochi

Scripps Senior Theses

The increasing frequency and intensity of wildfires pose growing threats to wildlife, yet the indirect effects of wildfire smoke on avian populations remain largely unstudied. This exploratory study provides an initial assessment of how particulate matter 2.5 (PM2.5) associated with smoke pollution from the 2017 California wildfire season, in conjunction with precipitation and habitat type, influences the body condition of four resident bird species during the 2018 breeding season. Using bird banding data from 29 Monitoring Avian Productivity and Survivorship (MAPS) stations, I assessed the potential interactions between PM2.5 concentrations, precipitation, and habitat type with body condition for Song Sparrows …

The Effect Of Light Intensity On Wolf Spider Foraging, Julia Amoroso

Scripps Senior Theses

Light is of primary importance to most living organisms and most of the Earth’s natural processes. However, with rapidly expanding urbanization, humans have substantially impacted light metrics through the increase of artificial light. Artificial light pollution has been found to have a variety of behavioral and physiological effects on different organisms. However, less is understood about how light impacts community-scale interactions between different trophic levels. Here, we examined the influence of light exposure on nocturnal wolf spider (Schizocosa myccooki) foraging and interaction with red runner cockroach prey (Blatta lateralis). Of equal interest as the study …

Pcb Remediation In Transitional Floodplain Forests Along The Housatonic River, Soleil Laurin

Scripps Senior Theses

Human development affects natural environments in more ways than climate change, from the introduction of nonnative species and deforestation to pollution and urbanization. This is a case study examining the effects of PCB remediation on transitional floodplain forest along the Housatonic River in Western Massachusetts. The Housatonic River had previously been contaminated with PCBs and portions had been remediated. This study aims to determine the effects this remediation had on transitional floodplain forests, as well as provide a preliminary biodiversity assessment for sites that are planned to be remediated of PCBs by the Environmental Protection Agency. The study was carried …

Migration-Associated Variation In Blood Parasitism, Body Condition, And Stress In Gambel’S White-Crowned Sparrows (Zonotrichia Leucophrys Gambelii), Julianna Deibel

Scripps Senior Theses

Migration is a widespread behavior in animals which both causes and is motivated by fluctuations in nutrient availability. Migration is ecologically important, as it connects areas of differing primary productivities and carries pathogens over distance. The relationship between migration and disease is complex, sensitive to anthropogenic disturbance, and influenced by ecological cycles as well as host, vector and parasite life cycles. Four central migration-infection mechanisms have been proposed: migratory susceptibility, migratory exposure, migratory escape, and migratory culling. These mechanisms may yield increased or decreased infection post-migration, based on migration’s physiological tax and the concentration of pathogens along migratory pathways.

To …

Molecular And Systemic Epigenetic Inheritance: Integrating Development, Genetics, And Evolution, Robert Lickliter, David S. Moore

Pitzer Faculty Publications and Research

Currently, a central problem for theoretical biology is the integration of development with genetics and evolutionary theory. Through the late 20^th century, biologists held that animals resemble their ancestors strictly because of the transgenerational transmission of DNA. This view effectively wrote development out of evolutionary biology. However, many molecular and developmental biologists now understand that phenotypes—anatomical, physiological, and behavioral traits—are not determined by genes (i.e., DNA segments) alone; instead, they emerge epigenetically from developmental processes involving co-acting genetic factors, environmental factors, molecular epigenetic factors, and other non-genetic factors within organisms’ bodies. This insight forces a rethinking of biological inheritance. …

What Taking Development Seriously Means For Evolutionary Theory, David C. Witherington, Robert Lickliter, David S. Moore

Pitzer Faculty Publications and Research

Proponents of the Extended Evolutionary Synthesis (EES) emphasize the critical role that organisms and their development play in the process of evolution. This framework explicitly rejects the genocentric focus that once dominated interpretations of the Modern Synthesis in evolutionary theory. In place of genocentrism, EES highlights processes like niche construction, developmental constraint, and extragenetic inheritance as central to any understanding of evolutionary process. However, much more is at stake in adopting the EES than simply moving beyond the gene-dominant viewpoint of the Modern Synthesis. The EES, in fact, represents a fundamental challenge to the core of classic Darwinism itself by …

Restoring An Iconic Joshua Tree Forest: Natural Recovery, Restoration Success, And Soil Microhabitats On A Desert Burn Area, Riley Scaff

Pitzer Senior Theses

Wildfires are a novel disturbance type in the Mojave Desert, but have been increasing in size and frequency since the 1970s due to the proliferation of invasive grasses. Burned areas are more susceptible to invasion, which can lead to the establishment of a grass-fire cycle. For this reason, restoration is often necessary to facilitate natural plant community recovery, but the extreme desert climate makes returning native vegetation to burn areas challenging. Planting in nutrient-rich soil microhabitats could be a helpful tool to improve revegetation success, but has yet to be tested. This study surveyed natural postfire recruitment across two seasons …

Variation In Soil-Mediated Drought Response Traits Between Sympatric Species Of Mimulus, Anna Reitman

Scripps Senior Theses

The ‘time limitation hypothesis’ is an evolutionary theory regarding evolution in angiosperms. The theory attributes ephemeral drought stress to transitions from a perennial to annual life history and an animal- to self-pollinating mating style. The most influential edaphic parameter on water availability is soil texture (i.e. grain size) due to its controls on porosity. Adhesion weakens with coarseness allowing for expedited rates of water loss via evaporation and percolation. The potential implications of coarse soil textures on major transitions in angiosperms due to drought mediation as the ‘time-limitation hypothesis’ proposes has yet to be thoroughly examined. Here, we grew two …

An Analysis Of Water Quality At Orange County, California Beaches, Naomi Meurice

Pomona Senior Theses

Beaches in Southern California are highly recreated by residents and visitors, making beaches socially and economically important. Public health departments in coastal communities are in charge of measuring water quality and ensuring it is safe for users. Research in the past has indicated that beach water quality gets worse after storms, with bacteria levels jumping on the day of a storm and staying high for up to five days. Studies have shown these spikes in bacteria to be associated with storm runoff, with beaches closer to runoff discharge locations experiencing more impact. However, prior research has not considered the period …

Biogeography Of Special Metabolites Produced By Ant-Associated Bacteria, Katherine Hansen

Scripps Senior Theses

There is an urgent and growing need for novel antibiotics with the growing prevalence of antibiotic-resistant pathogens. Ecologically-guided discovery is a strategy that focuses on how and where specially evolved metabolites such as antibiotics are used in nature. This strategy reveals unique active molecules with potential for human use. An unexplored niche with great potential for antibiotic discovery exists with Southwestern fungus-farming Trachymyrmex ants and their Actinobacteria symbionts. In exchange for nutrients from the ant, the ants’ bacterial symbiont produces antifungal molecules that protect the ants’ fungal cultivar from invasion by pathogenic microorganisms. They also produce antibacterial molecules to protect …

Developmental Consequences Of Hatching Asynchrony In Boat-Tailed Grackles (Quiscalus Major), Emily Radner

Scripps Senior Theses

Boat-tailed grackles (Quiscalus major) typically lay clutches of three eggs and begin incubation before the clutch is complete, resulting in hatching asynchrony. To study the developmental consequences of hatching asynchrony on boat-tailed grackles, data loggers measured nest temperatures and were compared to ambient temperatures to see when incubation began, and it appeared to begin after the second egg is laid. The third laid egg had a significantly shorter lay to pip time and lay to hatch time than the first laid egg, highlighting the need to investigate the consequences of a shortened incubation time on development. To do …

How Deep Do We Have To Go To Rehabilitate Evolutionary Psychology? Reply To Bjorklund, Ellis, & Geary (2022), David S. Moore, David C. Witherington, Darcia Narvaez, Timothy I. Vandiver, Robert Lickliter

Pitzer Faculty Publications and Research

Disciplines like evolutionary-developmental psychology admirably focus on trying to rehabilitate Narrow Evolutionary Psychology (NEP) from within, by adding a developmental focus to NEP’s tenets of adaptationism and computationalism. We argue, however, that these tenets are fundamentally incompatible with taking psychology and its development seriously, and that the kinds of modifications introduced by evolutionary-developmental psychologists do not go deep enough to qualitatively change the non-developmental outlook of NEP.

Evolving Evolutionary Psychology, Darcia Narvaez, David S. Moore, David C. Witherington, Timothy I. Vandiver, Robert Lickliter

Pitzer Faculty Publications and Research

Which evolutionary theory can best benefit psychological theory, research, and application? The most well-known school of evolutionary psychology has a narrow conceptual perspective (a.k.a., “Narrow Evolutionary Psychology” or NEP). Proponents of NEP have long argued that their brand of evolutionary psychology represents a full-fledged scientific revolution, with Buss (2020) recently likening NEP’s scientific impact to that of a Copernican or Darwinian paradigm shift. However, NEP stands on two traditions that are now the subjects of serious debate and revision: the neo-Darwinian adaptationist framework within evolutionary biology, and the computationalist “mind-as-computer” framework within cognitive science. Although NEP calls itself revolutionary, the …

Effects Of Drought On Habitat Quality For Native Bees In Residential Gardens Of Claremont, Ca, Max Proctor

CMC Senior Theses

Over 1,500 of the 4000 bee species found in North America inhabit California. Native bees are declining however, largely due to climate change and agricultural intensification. Previous research shows that cities can sustain diverse bee communities, due to the diversity of ornamental flowers. Urban green space represents an opportunity for native bee conservation. Residential gardens provide lots of green space and are urban pollinator hotspots. Managing yards for increased floral resources and nesting habitat can benefit native bee communities. Turfgrass provides few floral or nesting resources and negatively correlates with bee diversity. The 2011-2017 California drought caused many homeowners to …

Understanding The Environmental Implications Of The Microbiome Of Canals In Bangkok, Thailand, Emma Tao

Scripps Senior Theses

The canals of Bangkok, Thailand hold significant economic and social value, yet the increasing urbanization of the city has resulted in increased water pollution. Agricultural runoff and urban waste contribute to the degradation of the water quality, which has impaired its safe usage by the people of the city. This study focused on analyzing the microbiome of the water in the canals in correlation with the surrounding environment, both in and out of the water. Ten sites along the Bangkok canals were analyzed. DNA was isolated for the sequencing of the 16s rRNA gene to determine the microbial diversity of …

Examining Soil Microbial Diversity In Transition Zones Between Corn Fields And Restored Prairie In The Upper Midwest, Anna M. Burns

Scripps Senior Theses

Prairies were once the largest ecosystem in North America, but agriculture and settlement has destroyed up to 99% of their pre-colonization extent. Prairie restorations are a strategy to recover the biodiversity and carbon sequestration functions of these grasslands, but typically occur in isolated strips between agricultural fields. My thesis analyzes how effective prairie restorations in the Liberty Prairie (northeastern Illinois) are at recovering the diversity of the prairie soil microbiome, focusing on verrucomicrobia abundance, alpha diversity, and soil physical characteristics.

Footprints On The Prairie: Examining The Interlocking Land Histories Of The Liberty Prairie Reserve, Illinois, Anna M. Burns

Scripps Senior Theses

This thesis begins with the local history of the Liberty Prairie, the land where I conducted the ecological field-work that I later discuss in my second thesis on soil microbiome diversity (“Examining Soil Microbial Diversity in Transition Zones Between Corn Fields and Restored Prairie in the Upper Midwest"). I examine the Indigenous histories of the land, and the conflicts between the Bodwéwadmi and Euro-American settlers that resulted in the land being farmed for cattle, corn, and soy for over a hundred and fifty years. I then take a step back and analyze the broader historical contexts of Midwestern Corn Belt …

Qualitative Analysis Of A Resource Management Model And Its Application To The Past And Future Of Endangered Whale Populations, Glenn Ledder

CODEE Journal

Observed whale dynamics show drastic historical population declines, some of which have not been reversed in spite of restrictions on harvesting. This phenomenon is not explained by traditional predator prey models, but we can do better by using models that incorporate more sophisticated assumptions about consumer-resource interaction. To that end, we derive the Holling type 3 consumption rate model and use it in a one-variable differential equation obtained by treating the predator population in a predator-prey model as a parameter rather than a dynamic variable. The resulting model produces dynamics in which low and high consumption levels lead to single …

The Intersection Between Black Hair And The Environment: Hair As A Site For Environmental Justice And Sustainability, Dafina Matiku

Scripps Senior Theses

Currently, we are facing several global crises that include but are not limited to climate change, food insecurity, pollution of the body and environment, as well as racial, gender, and class inequities. This thesis seeks to understand how the natural hair movement, which strives to omit toxic chemicals while embracing textured hair, can be a tool of reconnecting to nature. As humans we are intrinsically part of ecosystems and nature, we must find our niche in it instead of occupying and destroying our environment entirely. The methodology includes compiling a small array of experiences that show the nuance of hair …