Biology Commons^™

The Evolution Of Regulatory Architectures Underlying Phenotypic Plasticity, Shweta Agarwal

Biology ETDs

Phenotypic plasticity refers to a mechanism where a single genotype results in distinct phenotypes in response to distinct environments, making it a key mechanism for persistence under environmental change. Phenotypic plasticity can arise from two distinct regulatory architectures: epistatically regulated plasticity or environmentally sensitive loci. The evolutionary forces shaping these architectures remain unclear. I use the recombination modifier framework to explore how the regulatory architecture of plasticity evolves across a range of selection regimes, including the rate of environmental change and the costs and benefits of plasticity. I find that the evolution of the regulatory architecture of phenotypic plasticity requires …

Scale-Dependent Drivers Of Demographic Change For American Pikas (Ochotona Princeps) In Glacier National Park, Montana: Local Habitat Characteristics Vs. Regional Climate Trends, Danielle M. Owens

Biology ETDs

Climate change is shifting thermal environments globally, driving range contractions, upslope movement, and poleward shifts across taxa. However, these changes are not uniform: microclimates, shaped by topography, can amplify or decouple operative temperatures from regional trends. The American pika is an ideal model for studying climate-driven population change given its strong site fidelity and thermal sensitivities. We re-surveyed 173 sites in Glacier National Park, originally surveyed in 2007-2010, using an AIC-based model selection to test competing local and regional hypotheses driving three demographic processes: persistence, colonization, and within-patch density change. Pika occupancy increased over the 15-year period, with a net …

Finding Fish Families: Movement And Demography Of Loach Minnow (Tiaroga Cobitis) Inferred From Gt-Seq-Enabled Kinship Analysis, Patrick C. Baca

Biology ETDs

River fragmentation poses major threats to freshwater biodiversity by reducing connectivity and limiting persistence of imperiled desert fishes. Connectivity in streams is impaired by anthropogenic changes, including road crossings, prompting the installation of engineered fish passage structures at low-water road crossings and raising questions about the dispersal of aquatic species across these structures. This thesis investigates the movement of the threatened Loach Minnow (Tiaroga cobitis) by applying a close-kin mark-recapture (CKMR) framework in a restored stream (including a fish passage) and a stream without rehabilitation efforts. We developed and optimized a GT-seq panel for relatedness analysis and used it to …

Using Temporal Genomic Data To Uncover Patterns Of Genetic Diversity And Signatures Of Selection For Management Of A Threatened Minnow Species, Erika A. Dunn

Biology ETDs

The Little Colorado River (LCR) spinedace persists only in three isolated watersheds within the LCR Basin in Arizona. This imperiled minnow faces ongoing pressure from habitat alteration, climatic shifts, and invasive non-native predators. Over the past two decades, managers have translocated spinedace within watersheds to increase abundance and expand habitat occupancy. We sequenced a reference genome and analyzed single nucleotide polymorphisms (SNPs) from 475 individuals over their geographic range. DNA samples were obtained from a previous study in the mid-1990s and compared with samples from 2024 and 2025, allowing us to track genetic diversity, effective population size, population structure, and …

Autotrophic And Heterotrophic Contributions To Soil Co2 Fluxes And Variability In A Chihuahuan Desert Grassland, Savannah B. Sanchez

Biology ETDs

Drylands are major drivers of interannual variability in the global terrestrial carbon sink, and their influence is expected to increase as climate change promotes the expansion of hotter and drier regions. Predicting the consequences of these shifts remains challenging because ecosystem models are largely developed for mesic systems, which differ from drylands in water and nutrient availability, decomposition rates, respiration dynamics, and microbial communities. Improving our understanding of carbon cycling in drylands is therefore critical. This research focuses on soil CO₂ efflux, a major pathway of terrestrial carbon release driven by plant root respiration and microbial decomposition. I investigated the …

How To Measure A Carnivore: Understanding The Scaling Of Cranial And Postcranial Elements With Body Mass, Marina Casiano Ruiz

Biology ETDs

Body size is a fundamental predictor of ecological function, life history, and population dynamics in mammals. However, direct measurements of body mass remain unavailable for many rare or extinct species, particularly within the order Carnivora. Allometric relationships between skeletal dimensions and body mass provide a tractable solution; however, previous studies have been limited in their taxonomic scope or trait diversity. Here, we quantify the scaling of 82 cranial and postcranial traits across 97 species from 11 carnivoran families spanning four orders of magnitude in body mass (20g to >500kg). Additionally, we examine the influence of phylogenetic relatedness, dietary specialization, and …

The Concept 'Pollination' And Bee Pan-Trap Color And Uv Reflectance Determine The Taxonomic Compositions Of Bee Taxa Captures Across An Elevation Gradient And Seasons In The Jemez Mountains Of New Mexico, Esther A. Burton, Kelly B. Miller, Paul J. Watson, David C. Witherington, Steven Poe, David Lightfoot

Biology ETDs

This thesis examines the pollinator concept and tests how sampling methods shape bee communities. Chapter 1 provides a conceptual and philosophical analysis, arguing that pollination is a process and that pollinators are context-dependent functional roles rather than fixed taxonomic categories. It traces the concept’s development from natural history to ecological theory, introduces a dual-goal model separating plant reproduction from visitor foraging, and proposes a classification framework based on evidentiary certainty and pollination potential to resolve ambiguity in pollination research.

Chapter 2 applies these ideas empirically by evaluating how pan-trap color and ultraviolet (UV) reflectance influence bee assemblages across elevation and …

From Cranes To Clinics: Genomic Epidemiology At The Human-Animal Interface, Sarah Shrum

Biology ETDs

Emerging infectious diseases represent a significant, increasing threat to human life, economic stability, and global security. The One Health framework, which promotes human health and wellness through the understanding that animal, environmental, and human health are interwoven, is critical to understanding pathogen emergence and transmission. This is underscored by the fact that roughly 60% of all human pathogens and 75% of emerging infectious disease are zoonotic, meaning they are transmitted from animals to humans.

The work presented in this dissertation integrates genomic epidemiology, ecological analysis, and One Health Surveillance approaches to characterize cross-species circulation of opportunistic yeast pathogens (Candida …

Investigating Changes In The Stable Isotopic Composition Of Juniperus Osteosperma Over 34,000 Years Of Climatic Shifts, Lisa S. Garcia

Biology ETDs

Isotopic compositions of plants from the past provides empirical evidence for paleoclimatic shifts and plants physiologically response. This study used Neotoma paleomiddens (fossilized debris piles) collected from Death Valley National Park, which contained preserved abundant plant materials. These middens range from modern to >35,000 years and capture different climatic events in Earth history. Employing Juniperus osteosperma (Utah Juniper) leaves found in middens, I investigated variation in carbon and nitrogen stable isotopic composition. To help interpret paleomidden results, we used modern field and herbaria samples of Juniperus from a spatial gradient stretching across their geographic range. Results showed δ ¹³C …

Reassembling Riparian Ecosystems: Stream Restoration Effects On Vegetation, Arthropods, And Aquatic-Terrestrial Connectivity, Katelyn P. Driscoll

Biology ETDs

Riparian areas exist at the aquatic-terrestrial interface and provide disproportionate ecosystem services, yet multiple stressors have degraded these zones globally. Stream restoration seeks to reverse degradation, but rigorous evaluation of treatment effectiveness remains limited. I conducted a before-after-control-impact (BACI) study in the southern Rocky Mountains to evaluate two stream restoration treatments—beaver dam analogs (BDAs) and plug-and-ponds (P&Ps)—across three dimensions of riparian ecosystem response. Using Bayesian analysis, I quantified treatment effects on functional diversity and composition of riparian plant communities. Using generalized linear mixed models, I evaluated restoration effects on riparian arthropod abundance, richness and guild composition across lateral gradients and …

Energy Management And Water Balance In Migrating Hummingbirds, Shayne R. Halter

Biology ETDs

Small body size and rapid metabolism make annual migrations challenging for North American hummingbirds. Many of these birds make annual journeys of over 10,000 km. During migrations, hummingbirds use stopover sites, where they remain for several days to accumulate body fat. At these stopovers, they often encounter uncertainties in food resources, competition, and weather. To save energy, hummingbirds sometimes enter nocturnal torpor. My dissertation uses respirometry data, lipid measurements from Quantitative Magnetic Resonance, and feather hydrogen stable isotopes to understand how energy levels, migration patterns, torpor use, and water balance interact in four species of migrating hummingbirds. I discovered lipid …

Biological Soil Crusts: Effects Of Environmental Change On Dryland Microbes, Mariah T. Patton

Biology ETDs

Climate change is increasing rainfall variability, altering nutrient availability, and causing warming in drylands, which comprise approximately ~36% of Earth's terrestrial surface. These expanding ecosystems contribute the most to interannual variability in the global carbon cycling. Biological soil crusts (biocrusts)—often called the "skin of the Earth"—are critical components of dryland surfaces, consisting of successional microbial communities dominated initially by Cyanobacteria and later by a more diverse composition with other bacteria, archaea, lichen, fungi, and algae. These communities play essential roles in soil aggregation, erosion prevention, and carbon and nitrogen cycling. However, our ability to predict biocrust responses to environmental change …

Synteny To Snps: Comparative And Population Genomics Of Endemic Gila River Fishes, Alexander C. Cameron

Biology ETDs

Population genomic data are becoming an essential component of the best available science used by conservation professionals to make management decisions to preserve biodiversity in a rapidly changing world. The proliferation of high-throughput sequencing technologies has made generating genome scale data feasible for non-model organisms that are of conservation concern. In addition to applicability in conservation science, genomic data enable the exploration of basic questions related to species evolution. To that end, this body of research exemplifies the applied and basic utility of genomic data and is focused on two federally-protected minnows endemic to the Gila River basin, Loach Minnow …

Drivers Of Ecosystem Respiration In The Middle Rio Grande Floodplain Aquifer, Eva Tipps

Biology ETDs

Little is known about carbon flux and ecosystem metabolism in river floodplains, despite their potentially large and dynamic contributions to carbon storage and loss. We hypothesized that the region of intermittent saturation (ROIS), which is the subsurface interface between terrestrial and aquatic ecosystems, is a biogeochemical ‘hotspot’ for ecosystem respiration and carbon transformation. Groundwater depth and variability in the ROIS facilitate interactions between aquatic and terrestrial processes, but their role in carbon fluxes is poorly understood. We developed a novel method utilizing high-frequency sensors in groundwater wells to capture biogeochemical ‘hot moments’ of ecosystem respiration in the ROIS of the …

Assessing The Ecological Drivers And Consequences Of Partial Migration In Hudson River Striped Bass Over Three Decades, Caitlin Egan Zimmer

Biology ETDs

Climate change and shifts in human land use have caused extensive impacts to the connectivity, structure, and resilience of aquatic populations. Partial migration (PM), where only some individuals from a population migrate while the rest remain resident, can mitigate population-level responses to environmental stressors. However, little is known of the underlying mechanisms promoting variation in migration and whether these shift over time. In the Hudson River Estuary, striped bass (Morone saxatilis) are known to exhibit anadromous PM behavior. Here, I measured carbon isotopes (δ¹³C) of essential amino acids in striped bass scales to determine variation in …

The Island Biogeography Of Mangrove-Dwelling Vertebrates: Isolation, Specialisation, And Extinction, Jian Xiong David Tan

Biology ETDs

Mangroves are highly dynamic ecosystems that are widely distributed across the coastlines of the tropics and subtropics. Despite their low plant diversity, mangroves host a disproportionately high number of terrestrial vertebrate taxa. However, mangrove specialists — taxa that only occur in mangrove habitats — exhibit a global distribution that is incongruous with the broader background distribution patterns of mangrove-associated fauna, exhibiting higher diversity in Australia and Southeast Asia. This dissertation therefore aims to assess how the diversity and distribution of mangrove specialist fauna may have been shaped by the historical biogeography of mangroves, and the effects of mangrove specialisation on …

Plant Reproductive Strategies Shift In Response To Restoration Using Beaver Dam Analogs, Laurel F. Martinez

Biology ETDs

As riparian communities become increasingly degraded, restoration treatments are being implemented in streams to recover ecosystem functions. In the Jemez Mountains, beaver dam analogs (BDAs) are used to restore degraded streams by connecting the floodplain and increasing the extent of anoxic soil conditions. These environmental disturbances are expected to alter how riparian plants recruit, particularly their allocation to seed-based and vegetative regeneration strategies. We investigated whether BDAs and associated changes in soil water filled pore space (WFPS) affected riparian plant recruitment. We investigated the number of flowering stems as a proxy for seed-based regeneration and rhizome length and mass as …

Ecoimmunology Of Dirty Physella Acuta Snails, Kevin Arthur Mcquirk

Biology ETDs

Research on Physella acuta, an invasive freshwater snail, reveals insights into its parasitology, fitness, and molecular biology. Morphological and molecular analyses revealed two distinct mitogenomic lineages, local (B) and invasive (A) strains of native P. acuta, both having comparable trematode infection rates, suggesting that the low infection rates observed from A in invaded regions result from "enemy release" rather than immune incompatibility. Fitness assessments showed that while lineages A and B performed similarly under laboratory conditions, rewilding experiments revealed significantly higher fitness in lineage A. Transcriptomic profiling supported these differences, with A snails showing greater immune-related gene expression and …

The Nature Of Anthropogenically Driven River Drying: Spatiotemporal Causes And Consequences, Eliza Inez Gilbert

Biology ETDs

Streambed drying naturally occurs in over 60% of rivers and streams worldwide. Climate change and human regulation of surface and groundwater have increased drying in naturally intermittent systems and caused perennial systems to transition to intermittency, impacting water security, water quality, and biodiversity. To understand human-induced drying dynamics, we used 12 years of daily drying data along a 154-km regulated reach of the Rio Grande. We conceptualized river drying as a regime analogous to the natural flow regime paradigm and quantified drying magnitude, rate of change, and duration. Although linear models predicting drying magnitude and rate of change were uninterpretable, …

Nitrogen Addition Additively Boosts Climate-Driven Salsola Tragus (Russian Thistle) Invasion Into Southwestern Usa Grasslands, Melissa A. Bacigalupa

Biology ETDs

Effective management of invasive, non-native plants requires understanding key drivers of invasion, including nitrogen enrichment from atmospheric deposition and agriculture. Long-term studies are essential for capturing complex invasion dynamics yet remain uncommon. We used 22 years of observations and 14 years of nitrogen experiments to examine invasion by Salsola tragus (Russian thistle) into three semi-arid grasslands of central New Mexico. Invasion patterns varied, with rapid expansion in Chihuahuan Desert grassland and the Desert-Plains ecotone but stability in Plains grassland. Under ambient nitrogen, precipitation most strongly correlated with Russian thistle biomass and high native grass biomass was associated with Russian thistle …

Genetic Gain And Loss In The Evolution Of Amniote T Cell Receptor And Immunoglobulin Genes, Jordan M. Sampson

Biology ETDs

The immune system of most jawed vertebrates consists of three major cell types: αβ T cells, γδ T cells, and B cells. Every species evaluated contains the loci that encode the highly conserved αβ T cells, however, γδ T cells are less conserved and have been lost in squamate reptiles. The loci that encode the B cell receptor have also varied across evolution. Seven immunoglobulin (Ig) heavy chain isotypes have been identified in amniotes: IgM, IgD, IgY, IgG, IgE, IgO, and IgA. Some are found in most species (IgM and IgD) and others only in specific lineages (IgY or IgG). …

A Floristic Study Of The Vascular Flora Of The Brokeoff Mountains, Southcentral New Mexico, Bryana L. Olmeda, Harpo Faust, Hannah E. Marx

Biology ETDs

The vascular flora detailed here describes 438 km² (169 mi²) of the Brokeoff Mountains of southeastern New Mexico. The Brokeoffs are part of the northern extent of the Chihuahuan Desert, the largest desert in North America and one of the ecoregions least represented in botanical collections. Prior to 2023, only 254 plant collections were known from the study site, representing roughly 1.5 collections per 2.59 km² (1 mi²), despite strong research interest in its neighboring Guadalupe Mountains. Over two field seasons, 1920 plant collections were made, over 81 days of field work conducted, in …

Life After Death: Investigating The Resistance And Recovery Of Fungal Communities To Foundation Tree Mortality, Jessie F. Marlenee

Biology ETDs

Tree mortality can have cascading effects on the composition and resilience of interacting fungal communities. Yet, little is known about the impact tree mortality, distinct from abiotic drivers (i.e., drought), has on these communities. This dissertation focuses on the resilience of fungal communities to experimental tree mortality in a piñon-juniper woodland. In chapter one, I found that piñon mortality reduced piñon fine root biomass and piñon mycorrhizal fungal diversity, whereas juniper mycorrhizal fungi were unaffected by juniper mortality. In chapter two, I revealed that piñon mortality altered the composition and spatial structure of mycorrhizal and saprotrophic fungi in the soil, …

Forest Response To Increasingly Frequent Fire And Drought Disturbances, Kevin G. Willson

Biology ETDs

Changes in fire regimes and drought intensity have increased fire and drought severity in southwestern forests, decreasing forest resilience to recent changes in climate. As tree response and regeneration after disturbance are critical for forest persistence, this dissertation assesses ponderosa pine regeneration patterns after high-severity fire, tree growth response to the reintroduction of frequent-fire, and tree growth response to multiyear droughts in fire-maintained and fire-excluded forests. We found that high-severity patch locations were more likely to regenerate when positioned downwind, downslope, and near intact forest. Trees had similar growth responses to first-entry fires and reburns following long-term fire-exclusion. After experiencing …

Human Impacts On Mammal Diversity From The Pleistocene To The Present, Carson P. Hedberg

Biology ETDs

Humans have fundamentally altered the planet’s biodiversity. It is critical to characterize these changes, but also to understand how they impact the structure and function of modern ecosystems. This dissertation investigates how anthropogenically mediated species losses and/or introductions influence ecological function and community structure in mammals across multiple temporal and spatial scales. We found that selective loss of large-bodied mammals over the Late Quaternary has led to severe losses in functional diversity in modern ecosystems, suggesting megafaunal mammals contribute distinct ecological functions. These changes to mammal diversity and distribution over millennia have altered both global patterns in functional diversity and …

The Role Of Elevation In The Migration, Physiology, And Genomic Diversification Of Birds, Jessie L. Williamson

Biology ETDs

Elevational gradients cause profound eco-climatic variation across short distances. Partial pressure of oxygen (PO₂) is a severe challenge that organisms face at high elevations; due partly to specialization on PO₂, most Neotropical bird species have narrow elevational ranges. However, a small fraction are elevational generalists that span sea level to high elevations, and a subset undertake extreme migratory journeys from low to high elevations biannually. My dissertation combines diverse approaches across levels of biological organization to understand how elevation impacts the ecology, evolution, physiology, and migration of montane birds. I examined ‘extreme’ elevational …

Host-Microbiome Interactions In The Teleost Brain, Amir Mani Varnoosfaderani

Biology ETDs

This dissertation investigates host-microbial interactions within the teleost brain, previously considered sterile. Reviewing current literature highlights significant gaps in understanding teleost brain immunity, despite prevalent neurotropic diseases. We mapped the immune profiles of rainbow trout brains and meninges, revealing the olfactory bulbs as the immune effector part of the brain and the optic tectum as a nod2 expression hub. High il6 and il10 levels were noted in the telencephalon. A persistent bacterial community within healthy salmonid brains shares diversity with gut and blood microbiota. Brain bacterial isolates exhibit genomic signatures for brain colonization and polyamine biosynthesis. The microbiota shifts across …

Support For Climate Shaping The Mitochondrial Dna Contact Zone In The Audubon's Warbler, Kyana Nina Montoya

Biology ETDs

Mitochondrial introgression has potential consequences for physiology and adaptation, but its causes are poorly understood. The Audubon’s Warbler (AUWA; Setophaga coronata auduboni) provides a case study to examine those causes as mitochondrial introgression has swept through part of the range. The northern mitochondrial genome (mtDNA) introgressed from the Myrtle Warbler (MYWA; S. c. coronata) and is 4% divergent from the southern mtDNA. Incomplete introgression suggests discordant AUWAs conferred a selective advantage in the north; it was hypothesized that energetic demands associated with migration formed this advantage. We tested two hypotheses to explain partial introgression and the mtDNA distribution …

Ponderosa Pine Plant Community Response To High-Severity Wildfire In The Jemez Mountains, Samantha Brodley

Biology ETDs

Climate change related temperature increases, and precipitation shifts, along with an increase in fuel loads have rendered large areas of the Southwest more prone to high-severity fire for longer periods of time throughout each year. Fire adapted forests that experience high-severity, stand replacing fires are not consistently experiencing dominant tree species regeneration, and appear, in some cases, to be shifting into novel systems. We collected and analyzed up to 11 years of understory plant community data in ponderosa pine (Pinus ponderosa) forests in the Jemez Mountains, New Mexico, to address early forest regeneration after high and low severity …

Conservation Genomic Investigation Of A Threatened Trout Species Endemic To The Gila River, David Thomas Camak

Biology ETDs

Climate change is a looming threat to the persistence of species, especially aquatic, imperiled species. Species native to desert streams are at a particular disadvantage, as many species already face drought, floods, wildfires, and threats from nonnative species, all of which are thought to be exacerbated by climate change. Species such as the threatened Gila Trout (Oncorhynchus gilae) already have small ranges and persist in fragmented and isolated habitats that limits gene flow between populations. Therefore, it is important to understand the current genomic status of such populations to be able to predict the future effects of climate …