Biology Commons^™

From Olfaction To Immunity: Characterization Of Nasal Immunity In Bony Fish, Ali Sepahi

Biology ETDs

The olfactory system is a common route pathogen entry in vertebrates. As a consequence, the nasopharynx-associated lymphoid tissue (NALT) needs to rapidly clear infections without compromising the sense of olfaction. NALT is present in teleost fish but its cellular and molecular mechanisms of action have not been investigated to this date. This dissertation focuses on three aims: 1. investigating the role of CCL19-like as a primordial chemokine in vertebrate nasal immunity, 2. determining the presence of tissue microenvironments within the olfactory organ (OO) of rainbow trout, and 3. understanding the immune contributions of olfactory sensory neurons (OSNs) in teleosts against …

Investigations On The Role Of The Immune System In Mammary Development And Maternal Immunity In The Marsupial, Monodelphis Domestica, Bethaney D. Fehrenkamp

Biology ETDs

All newborn mammals are highly dependent upon milk for nourishment and immune protection. This is especially true for marsupials, a lineage of mammals with a short gestation, limited placental development, and an increased reliance on an extended lactation period. Most newborn marsupials do not receive passive maternal immunity in utero and therefore are entirely dependent upon factors within the milk for immune protection until capable of mounting their own response. In this project we seek to characterize the complex lactation program utilized by marsupials, and seek greater understanding of the maternal role in the establishment of the developing immune system …

Genomic Signatures Of Adaptive Evolution, Jessica A. Weber

Biology ETDs

Comparative genomics has revolutionized virtually all fields of biology including the study of evolution. In this dissertation, I used next-generation sequencing to explore the evolutionary histories and adaptive evolution of a diverse set of taxa. Comparisons ranged across time scales, from population-level genetic diversity studies to questions spanning the deepest branches of the metazoan lineage. Whole genome sequencing of 50 unrelated Korean individuals revealed that Koreans have a distinct genetic history from the Chinese and Japanese populations. Our Korean-specific variome database was used to identify novel disease-causing variants in the Korean population, highlighting the value of high-quality ethnic variation databases …

Soil Properties Explain Changes In Soil Microbial Enzyme Activity With Depth In A Piñon-Juniper Woodland, Amanda B. Sacks

Biology ETDs

Semi-arid ecosystems play a major role in the global carbon cycle. These ecosystems, including piñon-juniper (PJ) woodlands, are experiencing extreme drought. As such, it is vital to characterize both above and below-ground processes in these systems in order to understand their vulnerability to future drought and other changes in climate.

Soils microbial communities play a critical role in nutrient cycles, as well as carbon storage, within PJ woodlands. More specifically, microbes aid the decomposition and mineralization of key nutrients, including carbon, nitrogen and phosphorus, through the use of extracellular enzymes. Measuring microbial enzyme activity, therefore, can provide insight into how …

Systematics And Diversification Of The Pantropical Avian Order Coraciiformes, Jenna Merle Mccullough

Biology ETDs

How and why species diversify is a central theme of evolutionary biology. Species-rich, morphologically diverse, pantropical clades provide rare opportunities to explore questions about drivers of diversification in the tropics. Here, we present the first complete species tree of Coraciiformes (6 families, ~177 species of kingfishers, motmots, bee-eaters, and allies), produced with thousands of ultraconserved elements. We recovered a well-supported tree which shows that there are two clades within Coraciiformes: 1) bee-eaters sister to rollers + ground- rollers and 2) todies sister to motmots + kingfishers. We estimated the biogeographical history of the group, explored bill shape evolution with a …

Rodent Responses To Drought In The Southwestern United States: Resource Utilization Strategies And Effects To Keystone Resources, Charles L. Hayes Iv

Biology ETDs

The role of abiotic and biotic factors in regulating community and population dynamics is a central question of ecological inquiry. In the southwestern United States, the North American monsoon supplies vital pulses of moisture to Sonoran desert, arid grassland, and montane communities. I evaluated abiotic limitation in prairie and montane populations of Gunnison’s prairie dog (Cynomys gunnisoni) using stable isotope analysis to quantify foraging niche widths. Niche widths declined under periods of drought stress. Prairie dogs in montane habitats exhibited seasonal shifts in dietary niche width during favorable growth periods for more nutritious plants using the C_{3 …}

Schistosomiasis In The Wild: A Transcriptomics Perspective On Field-Derived Biomphalaria Pfeifferi And Schistosoma Mansoni, And Their Interactions, Sarah K. Buddenborg

Biology ETDs

Schistosomiasis, caused by trematodes in the genus Schistosoma, is a widespread neglected tropical disease with the species S. mansoni infecting over 100 million people. We aimed to better understand the snail host and parasite responses during intramolluscan stages of infection by performing dual RNA-Seq on field-collected snails with natural infections from western Kenya. We collected uninfected Biomphalaria pfeifferi, B. pfeifferi with a patent cercariae-producing S. mansoni infection, and B. pfeifferi exposed to field-collected S. mansoni at 1 and 3d (days post infection).

We first created a high-quality B. pfeifferi transcriptome to identify the snail response to S. mansoni infection. …

Linking Climate Change And Mortality In Piñon-Juniper Woodlands, From Leaf To Ecosystem, Amanda I. Liebrecht

Biology ETDs

As global climate changes, the Southwestern US is predicted to experience more frequent and intense drought events. Extreme droughts can drive decreases in both physiological and ecosystem function, and can result in widespread tree mortality. Piñon-juniper (PJ) woodlands are a prevalent ecosystem in the region, co-dominated by two tree species, piñon (Pinus edulis) and juniper (Juniperus monosperma). Drought-induced piñon mortality has occurred over the past few decades, coinciding with outbreaks of a piñon-specific bark beetle. Piñon and juniper have different hydraulic strategies (isohydry and anisohydry, respectively) that should affect the way each species responds to drought. …

Understanding Patterns Of Diversity And Evolution In Mainland Anolis Lizards, Levi Nathaniel Gray

Biology ETDs

Patterns of organismal diversity and evolution are often difficult to interpret with a high level of confidence. The number of mechanisms and processes that contribute to shaping patterns of diversity is extensive and is reflected in the many methods researchers have used to infer causation. Taxonomic groups that are well-studied can offer more precise interpretation of pattern and process due to the considerable amount of research addressing ecology, natural history, and behavior of the organisms.

In this dissertation, I explore patterns of phylogenetic and phenotypic variation in Anolis lizards (anoles) by testing hypotheses that could have led to the observed …

Revealing Biotic Diversity: How Do Complex Environments Influence Human Schistosomiasis In A Hyperendemic Area, Martina Rose Laidemitt

Biology ETDs

Human schistosomiasis is one of the great neglected tropical diseases (NTDs) of our time with more than 206 million individuals infected and more than 90% of those infected reside in Sub-Saharan Africa (WHO 2017). Chemotherapy based control programs play an essential role in contributing to the elimination of human schistosomiasis; however, there is an increasing consensus that chemotherapy needs to be supplemented by other means if interruption of transmission and elimination are to be achieved. Given this situation, the focus of this dissertation was to better understand transmission dynamics in a hyperendemic setting in western Kenya and to find alternative …

Prevalence Of Artemisinin Resistance Associated Single Nucleotide Polymorphisms In Kenyan Isolates, Elizabeth M. Glenn

Biology ETDs

Malaria has had an unspeakable toll on human economy and wellbeing. Every year, there are approximately 212 million malaria infections caused by Plasmodium falciparum leading to 429,000 deaths, the vast majority of which occur in sub-Saharan Africa where the parasite is endemic. Decades of widespread use, and probable misuse, of antimalarial drugs has created extraordinary selective pressure on the parasite and made many formerly effective drugs ineffective. Currently, artemisinin and artemisinin derivatives are the most effective treatment available but resistance to dihydroartemisinin (DHA), the active ingredient, is emerging. Continued monitoring for genetic mutations linked with resistance is vital to global …

Seasonal Shifts In C3 And C4 Resource Use By A Small Mammal Community Under Changing Precipitation Regimes, Alaina Dianne Pershall

Biology ETDs

In light of climate change and projections of increasing temperatures and aridity in the North American southwest, it is essential to understand how consumer populations will respond to changes in the resource landscape. Rainfall varies in timing and intensity and therefore the timing, proportion, phenology, and abundance of C₃ and C₄ plant resources vary seasonally and annually. Here we examine rodent resource use in the Chihuahuan desert and focus on two distinct precipitation pulses in this system, where spring C₃ plants increase production in response to winter rains and C₄ plants respond to summer monsoons. We …

Using Δ13c, Δ15n, And Δ2h To Better Understand The Ecology Of Green Sea Turtles, Laura Pagès Barceló

Biology ETDs

Many green sea turtle populations are slowly recuperating from a recent severe decline due to anthropogenic factors including human consumption and mortality related to the fishing industry. Despite being charismatic animals that have been extensively studied, there is still a limited understanding of their feeding strategies and diet plasticity. This research explores the use of hydrogen isotopes in marine ecosystems to better understand green sea turtle ecology. This study is presented in two chapters: I first examined the trophic discrimination factor (D²H_NET) for hydrogen isotope (d²H) as a tool to correct hydrogen isotope data …

Comparison Of Bacterial And Archaeal Communities In The Subsurface Versus Surface: Implications For Nitrogen Cycling, Jason Cody Kimble 5059801155

Biology ETDs

Arid-land caves are thought to be extremely nitrogen-limited, but almost nothing is known about how microbes in subsurface arid-land environments obtain this essential element to meet cellular demand. The depth of caves beneath the surface may represent a critical factor affecting microbial nitrogen cycling in these environments. Percolation of water and nutrients from a precipitation pulse event would affect deep arid-land carbonate caves at a much slower rate. To obtain nitrogen in deep, carbonate caves, microorganisms could use fixed N in the host rock for assimilatory biochemical pathways or for a respiratory electron acceptor. However, the latter process leads to …

Forage Selection And Habitat Architecture As Drivers Of Small Mammal Community Dynamics In An Arid, Nutrient Limited, Highly Stochastic Ecosystem, Jennifer Darby Noble

Biology ETDs

In the Northern Chihuahuan desert, grassland and shrubland co-occur as separate stable states under similar climatic conditions. In this bottom up (resource driven) system, the magnitude and timing of precipitation events drives primary production which varies from year to year and season to season. Climate change is predicted to alter precipitation regimes, and increase aridity, facilitating shrub encroachment which results in increased landscape heterogeneity and a decrease in plant biodiversity. These changes will likely result in a restructuring of small mammal communities.

We used long-term data on precipitation, primary production, and abundances of small mammals in adjacent grassland and shrubland …

Bacterial Siderophore Production In Lechuguilla And Spider Caves, Carlsbad National Park (Ccnp) Carlsbad, New Mexico, Tammi R. Duncan

Biology ETDs

Lechuguilla and Spider caves, Carlsbad Caverns National Park, contain a rich microbial diversity. Despite oligotrophic conditions, the microorganisms in these caves have developed strategies to acquire essential nutrients. I hypothesized that cave bacteria use siderophores, a ferric iron chelating compound, to acquire iron for essential life processes. To understand the backdrop against which the cave bacteria would produce siderophores, I examined the bacterial physiological characteristics, determined whether cave bacteria have an ability to produce siderophores, and investigated a possible correlation between iron and manganese concentrations in cave deposits and siderophore production by bacteria cultured from the same site. I carried …

Dynamics Of Community Composition And Ecological Processes In Mesic And Semiarid Grasslands, Sydney K. Jones

Biology ETDs

Grassland communities change in response to disturbance and chronic resource alterations. Temporal community dynamics were examined within mesic tallgrass prairie at Konza Prairie in northeastern Kansas, and semiarid desert grassland and shrubland in central New Mexico. In both grasslands, producer and consumer communities changed over time in response to fire frequency and shrub encroachment. Directional change was driven by changes in abundances of species already in the community, rather than turnover in species composition. Despite directional change, species richness was highly stable, making species abundance rather than richness a better indicator of future community change. Species reordering also occurred during …

The Impact Of Climate And Elevation On The Growth And Mortality Of Piñon Pine, Alice M. Fretz

Biology ETDs

The Southwestern United States is currently experiencing severe drought, resulting in the mortality of many tree species. Piñon-juniper woodlands are an extensive biome in the Southwest, and are highly vulnerable to extended periods of drought that lead to tree mortality. Specifically, Pinus edulis populations are decreasing due to increasingly arid conditions. I used dendrochronology to investigate how tree growth rings of Pinus edulis reflect severe drought in living and dead trees. I also investigated how severe drought affects Pinus edulis along an altitudinal gradient. Tree core samples were taken from currently living and dead trees, as well as from trees …

Nutrient Additions Alter Semi-Arid Grassland Response To Fire, Alec A. Carrigy

Biology ETDs

Knowledge of how multiple global change drivers interact to affect community structure is critical for predicting future community states, especially when community structure drives ecosystem function. Disturbances such as fire and nutrient additions often shift communities away from their mean composition, but less is known about how disturbances affect spatial variation among local patches of the community over time (spatiotemporal dispersion). Dispersion may increase (local communities diverge in composition), stay the same, or decrease (communities converge) in response to disturbance. We compared patterns of spatiotemporal dispersion and temporal trajectories in community composition across three sites in a northern Chihuahuan Desert …

Diet Specialization Does Not Explain Occupancy Or Abundance In A Test Of The Resource Breadth Hypothesis In A Small Mammal Community, Deborah R. Boro

Biology ETDs

The abundance-occupancy relationship (AOR) is a recurrent pattern in ecology and biogeography, in which species with expansive distributions are locally common while those with restricted distributions are locally rare. Despite occurring across a wide variety of taxa and spatial scales, the mechanisms underlying AORs are not well understood. I tested two such mechanisms regarding dietary generalism in a guild of 8 small, herbivorous African mammals: (1) the degree to which diet was explained by food availability, and (2) population-level diet breadth. I expected that food availability would better predict diet for abundant, widespread species than rare, restricted species. Additionally, I …

Genetic Approaches To Population Ecology And Conservation Of The Sacramento Mountain Salamander, Samantha Jo Nicole Cordova

Biology ETDs

Aneides hardii (Sacramento Mountain salamander) is restricted to high-elevation habitat that is fragmented by low-elevation piñon-juniper woodland. Aneides hardii is a species of conservation concern in New Mexico, in part, because disease and climate change endanger its long-term persistence. In this study, we use sequence data from the mitochondrial cytochrome b gene and a microsatellite locus of A. hardii to addresses the timing and scale of population subdivision. We also calculated genetic diversity measures and compared them among mountain ranges to explore demographic history of A. hardii. Twenty-six haplotypes and three genetically distinct lineages were identified, and each haplotype …

Dengue Vaccination Modulates The Dengue-Zika Viral System Via Immunogenic Cross-Talk, Noah Joseph Bernard Silva

Biology ETDs

A vaccine for dengue, a viral disease which is a major driver of morbidity and mortality in tropical and subtropical regions, has recently been approved by eleven countries. While vaccination has the potential to reduce disease burden, the approved vaccine faces challenges due to the interactions between the four serotypes of dengue virus (DENV1-4) and the potential interactions with Zika virus (ZIKV), a related flavivirus. In this study, we propose a mathematical model incorporating both DENV and ZIKV in order to investigate the effects of viral competition on dengue vaccine performance, the potential for change in incidence of Zika due …

Evaluating The Relationship Of Temperature And Growth Of A Larval Colorado River Catostomid, C. Latipinnis, Through Otolith Aging And Stable Isotopes (Δ18o), Adam Lawrence Barkalow

Biology ETDs

Knowledge of early life history strategies and ecological dynamics of larval fish growth and development is invaluable for effectively managing and conserving common and endangered fish species. Isotopic analysis of otoliths (bony structures of the inner ear) from larval Flannelmouth Suckers Catostomus latipinnis obtained from the Colorado River in Grand Canyon could greatly facilitate understanding of thermally-regulated growth rates, thermal preferences, and ontogenetic habitat use by these fishes. Colorado River water temperatures in the Grand Canyon are highly modified from projected historic water temperatures present before closure Glen Canyon Dam. Cold water as result of Glen Canyon dam and hypolimnetic …

Phylogeography And Population Dynamics Of North American Wolverines (Gulo Gulo Luscus) In Alaska And Western Canada, Dianna M. Krejsa

Biology ETDs

The circumboreal wolverine (Gulo gulo sp.) is ideal for studying responses to environmental perturbation in the North due to a history of persistence in glacial refugia and subsequent glacial recolonization. Wolverines are also excellent indicators of human influence on the environment due to their close association with remote areas and cold, snowy climes. Through the use of genetic tools (i.e., nuclear microsatellite loci and mitochondrial sequences), I examined population structure of wolverines in Alaska and western Canada to identify signatures of glacial refugia, bottlenecks, and distinctive populations, sex-biased dispersal, gene flow, and source and sink population dynamics. I identified genetic …

Natural History And Evolution Of An Elevational Generalist, The Cinereous Conebill (Conirostrum Cinereum), Andrea N. Chavez, Chandresekhar Natarajan, Jay F. Storz, Angela Fago, Christopher C. Witt

Biology ETDs

Elevational generalism is relatively rare in the tropical Andes Mountains, likely owing to the inherent requirements of enduring a high degree of climatic zonation and coping with hypoxic stress. The Cinereous Conebill (Conirostrum cinereum) appears to be an exception, and inhabits a continuous elevational distribution that spans over 4,500 m. Two subspecies, cinereum and fraseri, are restricted to high elevations and may be isolated, whereas the third and most widespread, littorale, occurs continuously along the western slope of the Andes from 0 to over 4,500 m. First, we aim to characterize the morphology, genetics, and climatic …

Immunology Of The Gray Short-Tailed Opossum During Pregnancy And Prenatal Development, Victoria L. Hansen

Biology ETDs

Vertebrate species that bear live young have overcome the evolutionary challenge of maintaining both a functional adaptive immune system and viviparous life cycle. In normal pregnancy, viviparous mothers are able sustain and nourish a fetus that is genetically half non-self without mounting an immunological attack. In 1953 Sir Peter Medawar brought attention to the “enigma of the fetal graft” and immunologists have been puzzling out the intricacies of fetal tolerance ever since. Although viviparity has evolved in all jawed vertebrate lineages aside from Aves, the vast majority of reproductive immunology research has been limited to eutherian mammals. There are insights …

The Effects Of Atmospheric Pressure On Inter-Specific Competition And The Morphological And Hematological Characteristics Of Elevational Distributions Of Hummingbirds, Ariel Marie Gaffney

Biology ETDs

Species diversity in mountainous regions is strongly influenced elevational range limits of species, but it is generally not known which abiotic or biotic factors maintain these limits. Using Black-chinned and Broad-tailed Hummingbirds, species with offset but overlapping elevational ranges in the southwestern USA, we investigate the role barometric pressure plays in influencing these limits. In chapter one, we used a hypobaric chamber to test the effects of variable air pressures on interspecific competitive dominance. We sequenced the genes that encode the two adult isoforms of haemoglobin and measured the O₂-binding affinity of each isoform. In chapter two, we …

Precipitation Patterns And Fungal Community Succession In A Seasonally Dry Secondary Tropical Savanna, Sara R. López-Rodríguez

Biology ETDs

In the northwestern part of South America, seasonally dry forests have undergone extensive conversion to savannas to support ranching and agriculture. The combination of fire and vegetation removal employed for clearing, together with extensive agricultural practices, often lead to loss of soil fertility. This results in land that is no longer useful for agriculture and on which historical forests are unable to regenerate. This study examined the effects of common agricultural practices on soil fungal communities by simulating the effects of fire followed by plant removal. The goal was to determine whether common practices have rapid effects on soil communities, …

Plant-Microbial Interactions Are Strong Determinants Of Plant Population And Community Dynamics, Yan-Yi Anny Chung 9485698

Biology ETDs

Plant-microbial interactions are ubiquitous and yet the consequences of these interactions on plant population and community dynamics are relatively unknown. Here, we used two different classes of plant-microbial interactions to examine their effects on key plant population and community characteristics such as commonness and rarity, competition and coexistence, as well as community stability.

Vertically-transmitted endophytes had stage-dependent effects on the population growth of two grass species Poa sylvestris and Poa alsodes, and generally increased host population growth rates. However, it was the intrinsic demographic advantage of P. sylvestris that allowed its population to grow at a much faster rate …

Pattern And Process In The Radiation Of Ground-Dwelling Squirrels, Bryan Stephen Mclean

Biology ETDs

What causes biological diversity to be unevenly apportioned across the Tree of Life? The pattern is widespread and well-characterized; but our understanding of processes underlying the taxonomic, phenotypic, and ecological disparities of clades remains incomplete. At least some of this disparity is due to clade-specific differences in the ability to respond to ecological opportunity, whereby access to, and exploitation of, different resources in ecological time drives evolutionary divergence and adaptive radiation. However, not all clades respond equivalently to ecological opportunity, and considerable heterogeneity therefore exists in diversification patterns across radiations.

This dissertation focuses on patterns and processes of diversification in …