Population 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 …

A Genetic Analysis Of The Rare Endemic Astragalus Ripleyi Barneby, Juan Antonio Jaramillo-Chico

Master's Theses

Astragalus ripleyi Barneby is a rare endemic species found in the San Luis Valley of the southern portions of the Rocky Mountains in Colorado and New Mexico. Though not federally listed as endangered, the species is on the Bureau of Land Management’s Sensitive Species List, warranting protection and continued management. This study aims to provide information about the genetic health of the species to inform conservation efforts and provide updated management recommendations. A genetic health analysis was conducted investigating the levels of diversity present in the species, how genetic diversity is structured across the known range of the species and …

From Genes To Streams: Mitochondrial Approaches To Population Monitoring Of The Santa Ana Sucker Catostomus Santaanae, Mariana Antonio

Electronic Theses, Projects, and Dissertations

This study was developed to use aquatic environmental DNA (eDNA) as a tool to detect the presence of the Santa Ana sucker (Catostomus santaanae), a federally threatened fish species, across the Santa Ana River in Southern California. Environmental DNA is any genetic material that an organism sheds into the environment. We can get an idea of what aquatic species are present when sampling water at a given site. We sequenced the complete mitochondrial genome (mitogenome) of the Santa Ana sucker and designed custom DNA primers to improve eDNA detection accuracy. These primers were selected based on high genetic …

Influence Of Genetic Relationships On The Spatial Distribution Of Breeding Eastern Wild Turkeys (Meleagris Gallopavo Silvestris) In West-Central Louisiana, Rachel D. Price

LSU Master's Theses

Eastern wild turkeys (Meleagris gallopavo silvestris) have a complex social system influenced by dominance hierarchies and exhibit seasonal variation in gregarious behaviors. Previous work has examined the influence of kin relationships on interactions between same sex conspecifics and flock associations, but information on how genetic relatedness influences interactions between individuals remains lacking. We constructed a dyad-based social network using high-resolution GPS data from 179 female and 68 male wild turkeys in west-central Louisiana during the 28-day period before a females’ 1^st nest initiation to quantify interaction probability based on genetic relatedness and age. Our findings suggest that …

Pickleweed In The Disappearing Marsh: Population Genetics & Metal Accumulation In Salicornia Depressa, Alice Kaisla

Graduate Doctoral Dissertations

Salicornia is a genus of succulent halophytes found in salt marshes around the world. Salicornia species have a remarkably high tolerance for heavy metal pollution and have been shown to accumulate high concentrations of heavy metals in their tissue under experimental conditions. As a result, they are both a useful system for studying evolution in polluted coastlines and a potential candidate for use in phytoremediation. My research focuses on Salicornia depressa, known as pickleweed, a species commonly found in marshes along the heavily urbanized and industrialized New England coast. I investigate genetic diversity and population structure in S. depressa populations …

Adapting Population Genetics, Practice, And Policy For Plant Conservation In A Changing World, Cooper M. Kimball-Rhines

Graduate Doctoral Dissertations

Biodiversity conservation is an inherently interdisciplinary goal that requires effective collaboration among academics, ecosystem managers, policymakers, and other stakeholders. Codesigning research with these groups ensures experiments are useful and improves adoption of policy and practice recommendations while advancing our understanding of basic science. This dissertation explores the power of codesigned research in shaping plant conservation strategies using stakeholder engagement, causal inference, demographic modeling, and multi-omic sequencing techniques. In chapter 1 I discuss the history of New England ecosystems and the need for research-driven changes to plant conservation policy and practice in the face of global change. In chapter 2, I …

Investigating Cryptic Diversity In The Hawaiian Endemic Plant, Psychotria Mariniana (Rubiaceae), Uyen Thi Hoang Nguyen

Master's Theses

Islands, with their isolation and steep environmental gradients, serve as natural laboratories for studying speciation. Molecular phylogenetic and population genetic methods utilizing Next-Generation Sequencing (NGS) have revolutionized our ability to document patterns of genetic divergence and diversity. Cryptic diversity, genetically distinct populations that were previously unrecognized as unique, and cryptic speciation, where divergent genetic populations may be deserving of status as unique species, have been observed in many taxa. The Hawaiian Islands provide an ideal setting for studying divergence and speciation due to their extreme isolation, known ages, and volcanic origin. Previous work has investigated the evolutionary relationships of the …

Quantifying Genetic Diversity In Nematode Feeding Rate, Jacob King

Honors Theses

Understanding how populations persist under changing environmental conditions is a central question in ecology and evolutionary biology. Variation in traits related to resource acquisition may play a key role in determining population survival when resources are limited or fluctuate over time. In this study, I investigated how variation in feeding-related traits influences population persistence using a combination of computational modeling and laboratory experiments. I developed a stochastic, individual-based consumer–resource model to simulate population dynamics across varying levels of trait variance and resource regimes. Across 60,000 simulated populations, increased trait variation consistently reduced extinction risk and extended persistence time, although the …

Morphological Variation Of Lingual Glands In Wild American Alligator (Alligator Mississippiensis) Populations, Benjamin Angalet

Master's Theses

American alligators (Alligator mississippiensis) inhabit diverse aquatic ecosystems including freshwater wetlands, swamps, and estuarine rivers. As apex predators, their physiological resilience has implications for ecosystem stability and long-term conservation. With projected sea-level rise and increasing saltwater intrusion into coastal freshwater habitats, understanding the osmoregulatory capacity of alligators is increasingly important. Unlike marine-tolerant crocodilians such as the saltwater crocodile (Crocodylus porosus), which possess specialized salt-secreting lingual glands in addition to renal and cloacal mechanisms, the morphology and physiological significance of lingual glands in wild American alligators remain poorly understood. This study examined lingual gland morphology and plasma …

Contrasting Roles Of Downed Wood And Leaf Litter In Structuring Aphaenogaster Ants And Other Forest-Floor Arthropod Communities, Danielle E. Dolan

Great Lakes Center Masters Theses

Forest floors are dynamic and spatially heterogenous landscapes characterized by differing amounts of light, temperature, and moisture. Bounded substrates, like downed wood and leaf litter, add further complexity to this landscape. Specifically, downed wood is noted for its ability to retain a higher moisture level than the surrounding environment, and as such can serve as an ideal microhabitat for desiccation intolerant organisms (e.g., salamanders and eusocial insects). Here, I attempt to disentangle the relationship between forest floor arthropods and microhabitat selection (i.e., downed wood vs leaf litter) on a northeastern forest floor. The ant, Aphaenogaster picea, was chosen as my …

Enhancing Walleye (Ogaa) Recruitment: Evaluating Assisted Reproduction As A Mitigation Strategy, Douglass Keiser

Biology Graduate Theses

Over the past several decades, cold- and cool-water fish populations across the Upper Midwest, including Minnesota and Wisconsin, have shown troubling signs of decline. Among the most affected is the walleye/Ogaa (Sander vitreus), a species deeply embedded in the ecological balance, cultural identity, and economic vitality of the region, and central to the lifeways, treaty-reserved rights, and resource stewardship of Tribal Nations, including Ojibwe communities across the Upper Midwest. Despite ongoing stocking efforts and harvest regulations, many lake systems have experienced persistent declines in natural recruitment, prompting resource agencies to investigate the underlying causes. One such system is …

How Pollinator Populations Can Impact Chronic Disease Risk, Kylee Cubbison

Honors Projects

This project investigates how pollinator populations can impact chronic disease risk. Pollinator populations are declining, which can have serious implications for human health. Declining pollinator populations can limit healthy food production and affordability. Poor nutrition is a major risk factor for most chronic diseases. Less healthy food available for people to consume can negatively impact diets and increase the risk of developing chronic diseases. This project aims to address a potential gap in research existing on this specific topic regarding pollinator populations and human chronic disease risk. A brochure targeted towards educating the general public on this topic was created …

Singing Not To Sing: The Interplay Of The Environment And Behavior On The Reproductive Success Of Forest Breeding Migratory Birds, Miranda Bliss Zammarelli

Dartmouth College Ph.D Dissertations

Habitat selection is a key behavior that has consequences for fitness, which can shift with environmental variation. The environment can affect reproductive success indirectly by shaping behavior or via direct impacts. Many forest breeding migratory birds choose a habitat by establishing territories. To understand the interplay of environment and behavior on the reproductive success of forest breeding migratory birds, I leveraged long-term data and newly collected species-specific data from Hubbard Brook Experimental Forest, New Hampshire, USA. I analyzed over 50 years of territory maps from seven species occupying a 10-ha plot to understand how birds distribute themselves in a habitat. …

Hidden Diversity In A Clonal Endemic: Insights Into Clematis Socialis From A Population Genetics Perspective, Joanna M. Lapoint

Theses

Clematis socialis (Kral) is a rare, federally endangered perennial species restricted to a small number of fragmented populations in Alabama and Georgia. The species exhibits extensive clonality and limited sexual recruitment, characteristics that complicate expectations regarding genetic diversity and population connectivity. Despite its conservation significance, genome-wide assessments of population structure have been lacking. We used genotyping-by-sequencing (GBS) to generate a genome-wide SNP dataset for 170 individuals sampled from six natural populations. Population structure and genetic differentiation were evaluated using Bayesian clustering, analysis of molecular variance (AMOVA), pairwise FST estimates, and network-based visualization. Analyses revealed strong genetic structuring among populations and …

Testing The Intermediate Disturbance Hypothesis On Anthropogenic Pressure In Central Alabama, Gavin Terrell

Theses

Biodiversity is fundamental to maintaining ecosystem structure and function globally. Prior to the late 20th century, ecological theory generally predicted that biodiversity would be highest in systems experiencing minimal disturbance. However, Joseph H. Connell challenged this view with the Intermediate Disturbance Hypothesis (IDH), which posits that species diversity peaks at intermediate levels of disturbance and declines under conditions of both low and high disturbance. Although widely cited, the applicability of the IDH to natural systems remains debated, particularly in the context of anthropogenic disturbances and when diversity is measured beyond species richness alone.

This study evaluated the predictions of the …

Alabama Prairie Reconstruction: Comparing Management Pathways For A Southeastern Landscape, Cecelia R. Geyer

Theses

Southeastern prairies are highly biodiverse yet increasingly threatened by land-use change, fire suppression, and habitat fragmentation. These disturbance-dependent systems rely on periodic fire and grazing to maintain plant diversity and ecosystem function. This study evaluates prairie restoration strategies by testing predictions from the Intermediate Disturbance Hypothesis and the Patch Mosaic Burn Hypothesis. The study site was divided into three treatments: prescribed burned only (B), prescribed burned with mowing (BM) to simulate grazing, and an undisturbed control (C). A standardized mix of native plant seeds was broadcast across all treatments. Ecosystem health and function were evaluated using plant community diversity and …

Emerald Bowfin Amia Ocellicauda Ecology In Three Minnesota Lakes: Abundance, Age Analysis, Diet Composition, And Stable Isotope Food Web, Griffin Blegen

Biology Graduate Theses

The Emerald Bowfin Amia ocellicauda is a predatory fish species native to Minnesota that has often been discriminated against. This research expands ecological knowledge of Bowfin in Minnesota and provides population data to guide future management. Bowfin were sampled in the spring of 2024 and 2025 and a multi-census mark–recapture model was used to estimate abundance in three lakes. Estimated populations were 196 individuals in Little Toad Lake (95% CI: 116, 242) or 4.4 fish/littoral ha (95% CI: 2.7,5.7), 657 in Lake Sarah (95% CI: 436, 1014) or 4.2 fish/littoral ha (95% CI: 3.0, 6.7), and 612 in Gun Lake …

Trophic Structure And Mercury Bioaccumulation In Walleye And Yellow Perch In The Upper And Lower Red Lake Basins, Marissa Pribyl

Biology Graduate Theses

Mercury is a persistent global contaminant that biomagnifies through aquatic food webs, with dietary and environmental factors serving as the primary drivers of accumulation in fishes. Trophic structure and methylmercury dynamics in Walleye (ogaa; Sander vitreus) and Yellow Perch (asaawens; Perca flavescens) were investigated in the Upper and Lower Red Lake basins in Red Lake, Minnesota, during 2024-2025. Diets of Walleye and Yellow Perch were assessed through stomach dissections, and tissue samples from both species were analyzed for total mercury concentrations. Additional analyses included shiners (gigoozens; Notropis spp., Hudsonius spp.) along with a variety of freshwater fish and …

Decoupling Of Reproduction And Lifespan Trade-Off In Caenorhabditis Elegans Through Microbial Programming, Nora M. Villafuerte

LSU Master's Theses

The microbiome is increasingly recognized as a major regulator of host physiology. Using the Caenorhabditis elegans model, we investigated how natural commensal bacteria modulate host reproduction and lifespan through internal egg hatching, a phenotype in which retained embryos hatch within the maternal body. Screening strains from the CeMbio collection identified four focal strains Ochrobactrum BH3, Lelliottia JUb66, Pantoea BIGb0393, and Enterobacter CEent1 that significantly increased internal egg hatching during the late reproductive period. This contrasts with pathogenic bacteria, which induce early-onset internal egg hatching. Across the focal strains, worms exhibited reduced total brood size but an expanded reproductive window relative …

Assessing Localized Recovery And Synchrony Of An Endangered Wetland Species., Aiyana Reissman

Theses

The state and federally endangered light-footed Ridgway’s rail (LFRR; Rallus obsoletus levipes) is central to regional conservation, yet the drivers of its population fluctuations remain poorly understood. The fragmented nature of coastal wetlands in Southern California is threatening the existence of endemic species like the LFRR. Tidal inundation, severe storms, and overpredation threaten the survival of LFRR. This study addresses population fluctuations by analyzing the spatial and temporal drivers of LFRR populations to inform effective, site-specific management.

To do this, a 45-year (1980–2024) LFRR census data set across 16 wetlands throughout its range in California was synthesized. A multi-faceted …

Coho Salmon (Oncorhynchus Kisutch) Response To Habitat Restoration Through Space And Time: Monitoring Growth, Survival, And Movement In A Restored Habitat Network, Carter Perez Adamson

Cal Poly Humboldt theses and projects

Despite the decline of coho salmon (Oncorhynchus kisutch), Prairie Creek, a tributary of Redwood Creek in northern California, remains a coho salmon stronghold. The restoration of juvenile coho rearing habitat was identified as a recovery objective in this watershed by the National Marine Fisheries Service. Among the restoration projects addressing this objective are an ongoing project on Prairie Creek and its tributary Skunk Cabbage Creek, and a prior effort on Strawberry Creek (a tributary of Redwood Creek’s estuary). Standard monitoring methods for assessing project success have limitations and may be improved by measuring salmon use of restored habitats …

Geographic Variation In Proteomic Responses To Ocean Acidification In A Cold-Water Coral (Balanophyllia Elegans), Keana A. Richmond

Cal Poly Humboldt theses and projects

In the face of a rapidly changing climate, assessing organismal responses to future stressors in the context of current, natural exposure to stress could provide key insights to understanding marine ecosystem resilience. I used Balanophyllia elegans, a cold-water, solitary, azooxanthellate coral as a model to better understand how varying oceanographic conditions across its geographic range have shaped its ability to tolerate and potentially adapt to current and future ocean acidification conditions. I collected B. elegans individuals from four sites across 2,500km of their range and subjected them to two pH treatments to investigate site-specific protein expression in response to …

A Frog, A Toad, And A Salamander Walk Into A Forest: How Timber Harvest And Environmental Conditions Impact Amphibian Species Abundance In The White Mountain National Forest, William T. Brandenburg

Honors Theses and Capstones

Balancing the needs of humans and wildlife is one of the primary goals of conservation. Understanding how species respond to resource extraction is essential to achieve long-term population stability. This is especially relevant for amphibians, which are particularly sensitive to environmental disturbances due to habitat loss and degradation. As such they are often used as indicator species. This study leverages 20-years of amphibian abundance data from surveys in different silvicultural treatments to understand how American toads (Anaxyrus americanus), wood frogs (Lithobates sylvaticus), and red-backed salamanders (Plethodon cinereus) respond to changes in forest structure, weather, …

Current And Historical Occurrences Of Rare Coastal Plants In The Hampton Falls Salt Marshes, Liliana T. Chirichella

Honors Theses and Capstones

A botanical survey of two sites in the Hampton Falls saltmarshes was conducted to document the occurrences of a list of eleven endangered and threatened coastal plants listed in the Natural Heritage Bureau’s NH Rare Plant List. This survey was conducted in fulfillment of the NH Native Plant Protection Act to highlight and identify target species in an area where restorative runneling is to be implemented in order to restore proper hydrology and prevent further expansion of mega-pools in the Little River and Depot Road salt marsh sites, which have been subject to historical ditching and are a part of …

Managing Multi-Drug Resistance: An Evolutionary Game Theory And Optimal Control Approach, Shukhrat Nasrulloev

Theses and Dissertations

Multi-drug resistance is an evolutionary process in which treatment eliminates sensitive cells, allowing resistant clones to dominate. This thesis investigates this process using a framework integrating population dynamics, evolutionary game theory, and optimal control theory. We develop a two-population logistic growth model describing competition between drug-sensitive and drug-resistant cells under treatment, construct dose-dependent payoff matrices and replicator dynamics to characterize evolutionary competition, and derive a critical drug level D_crit = (r_S - rR)/(dS - d_R) at which resistant cells gain a fitness advantage. An optimal control problem is formulated via Pontryagin's Maximum Principle to identify schedules …

Mapping The Distribution Of The Common House Mosquito (Culex Pipiens) In The City Of Spokane: Mosquito Breeding Sites And Blood Meal Analysis, Oluwapelumi Hannah Sonoiki

EWU Masters Thesis Collection

Mosquitoes in the genus Culex are the primary vectors of West Nile virus (WNv) in the United States, with Culex pipiens and Culex tarsalis serving as the dominant species in Spokane. In urban environments, catch basins and other artificial water bodies that collect stagnant and polluted water provide favorable breeding habitats for Culex pipiens. This study aimed to assess the spatial distribution and seasonal dynamics of Culex larvae in Spokane. We examined 303 randomly selected catch basins in the summer of 2025, and at each site we recorded the presence or absence of water, water depth, and mosquito larval …

False-Positive Detections In Avian Auditory Surveys: Effects Of Song Number And Directionality In A Calibration-Based Immersive Sound Environment, Katia Elena Chavez

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Detection-based surveys are widely conducted to monitor wildlife populations and provide data for estimating density and abundance. Avian count surveys are especially common because birds respond quickly to habitat degradation and restoration, making them effective indicator species. However, these detection-based surveys rely heavily on human observers and are prone to errors. If left unaddressed, these errors can bias estimates of species occurrence, and abundance, leading to misleading ecological inferences and management decisions. False-positive errors have received limited attention, in part because they are difficult to identify without independent confirmation of true species. To investigate false-positive rates in a controlled setting, …

Long-Term Banding And Encounter Patterns Of Cinnamon Teal Banded In Utah (1960-2025), Gracie A. Henrie

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Utah is a valuable breeding and nesting ground for a number of waterfowl species, largely because of the Great Salt Lake, which supports over 400,000 acres of wetland habitat (Ducks Unlimited, n.d.). The Utah Division of Wildlife Resources manages 24 wildlife management areas (WMAs) with the purpose of creating high quality waterfowl habitat in these wetlands that can be enjoyed by hunters, recreators, and birds alike (Wildlife/Waterfowl Management Areas (WMAs), 2025). Effective management is supported with an understanding of the movement and demographic patterns of the waterfowl species the WMAs are designed to support. Bird banding is one tool managers …

Equid Major Histocompatibility Complex (Mhc) Evolution & Genome Organization, Lauren C. Johnson

Theses and Dissertations--Veterinary Science

The evolution of modern horses has a well-documented fossil record and has long been of interest to the genetics community. Although non-caballine equids (e.g. zebras, donkeys, and asses) can hybridize with horses, the resulting offspring are typically infertile. Despite these reproductive barriers, genomic analyses reveal regions of high sequence similarity among equid species. This dissertation investigates the role of historical introgression in the evolution of modern Equus species. The first chapter re-evaluates earlier findings derived from a limited horse population and a single reference genome. The variants of the identified regions were pushed through Ensembl’s Variant Effect Predictor to assess …

Using Camera-Based Unmarked Spatial Capture-Recapture Modeling To Estimate Reintroduced Elk (Cervus Canadensis) Population Parameters And Distribution In Southeastern Kentucky, Claire Marie Muia

Theses and Dissertations--Forestry and Natural Resources

Estimation of population parameters is important for wildlife management decisions. Elk reintroduced to southeastern Kentucky experienced early irruptive population growth and are currently monitored using a statewide harvest-based statistical population reconstruction model (SPR) across the Kentucky Elk Restoration Zone (KERZ). Because the SPR model is spatially coarse and difficult to scale to the smaller management units comprising the KERZ, we conducted a spatially explicit capture-recapture study using a clustered camera-trapping array deployed for 10 weeks from June–August 2024 to estimate elk population parameters within Management Unit 4. Due to a lack of resights of GPS-marked elk, population parameters were estimated …