Biology Commons^™

Diversity Of Understudied Archaeal And Bacterial Populations Of Yellowstone National Park: From Genes To Genomes, Daniel Robert Colman

Biology ETDs

Yellowstone National Park (YNP) thermal springs have been a crucial resource for the discovery and characterization of microbial biodiversity. The use of cultivation-independent methods has documented many new phyla of uncultured Archaea and Bacteria within thermal springs. Here, I describe the phylogenetic diversity and distribution of Archaea within the YNP thermal spring ecosystem and the phylogenetic and physiologic characterization of novel, uncultured hyperthermophilic bacterial lineages from metagenomic data. In chapter two, I evaluated the efficacy of commonly used, 'universal' archaeal-specific 16S rRNA gene PCR primers in detecting archaeal phylogenetic diversity. In chapter three, using the PCR primers that would provide …

The Gene Blistered Selectively Controls Muscle Type Differentiation In Drosophila Melanogaster, Ashley A. Deaguero

Biology ETDs

The muscle fiber is a structural unit of skeletal muscle in many organisms. Muscle fiber composition has been implicated in maintaining muscle longevity and controlling systemic energy homeostasis, however not much is known about how different types of muscle fibers are specified. The fruit fly Drosophila melanogaster provides a useful model to study specification and differentiation of different types of muscle fiber. In this study, the functional properties of the transcription factor blistered (bs) were explored. The gene bs is evolutionarily conserved and has a mammalian homologue, Serum Response Factor (SRF). When bs is genetically down-regulated in all muscles, only …

Schistosomes Of Nepal, Ramesh Devkota

Biology ETDs

Globally, digenetic trematodes called schistosomes (Family Schistosomatidae) have enormous public and veterinary health significance because they cause debilitating and chronic infections collectively called schistosomiasis. Schistosomes have a life cycle featuring a bird or mammal definitive host in which adult worms are found, and freshwater snail intermediate hosts in which larval stages are found and free-swimming cercariae are produced which infect the definitive host. Although schistosomes are known to be common in tropical and subtropical Asia, their presence in Nepal, a small south Asian country situated between India and China, was almost completely unknown at the beginning of this study. Consequently, …

Drying Events In The Rio Grande: Effects On Hydrology, Riparian Vegetation, And Arthropod Communities, Kimberly Lorraine Fike

Biology ETDs

1. Anthropogenic-induced river intermittency is an increasing global concern with far-reaching ecological consequences. Cessation of flow outside of a rivers natural regime can have cascading effects on aquatic and terrestrial community composition and structure. Water abstraction during summer months often leaves the Rio Grande below Isleta Diversion Dam dry. This research investigates differences in hydrology, riparian vegetation, and arthropod communities within the Rio Grande floodplain, known locally as the 'bosque,' between perennial and intermittent reaches of the river.

2. Despite the high degree of interannual variability, a spatio-temporal analysis of stream discharge revealed a trend of declining flow in both …

How Ants Turn Information Into Food, Tatiana Paz Flanagan

Biology ETDs

Animals constantly process information from their environment. In social organisms, information exchange among individuals allows for behaviors to be finely tuned to local environmental cues. Such is the case of foraging in ants, where sharing information about the distribution of resources can drive adaptive behaviors to exploit those resources. In a first study, we quantified how clustering of experimental seed baits significantly increased foraging rates of seed harvester ants. That study found that species with larger colonies were no better than species with smaller colonies at collecting clumped seeds. In a second study, we integrated computer simulations, information science and …

Constraints On Distributions And Diversity Of Birds And Mammals Over Variable Environments, Trevor S. Fristoe

Biology ETDs

The distributions of species are determined by intrinsic factors such as physiological tolerances as well as extrinsic factors of the environment such as the availability of resources. While physiological tolerances generally change over evolutionary time scales, changes in environmental productivity due to processes such as succession or seasonal progression often occur over ecological times. I address both physiology and resource availability as drivers of the distributions and diversity of endothermic birds and mammals using a macroecological approach and a metabolic perspective. Migratory birds, altering communities over seasonal cycles, provide a unique opportunity to investigate the drivers of distributions and diversity …

Unraveling The Mysteries Of Plant Mating Systems In Raphanus Sativus, Lindsey C. Kaufman

Biology ETDs

Plant mating systems include a variety of mechanisms that result in non-random success of self- and outcross pollen, pollen from different compatible mates, and pollen from the same or different species. Although some of these mechanisms have received considerable attention (i.e., Charlesworth et al. 2005; Pannell and LaBouche 2013), most previous study has been of only one of these mechanisms at a time. Further in the field, a plant might simultaneously receive pollen of several types; thus, it is likely that multiple mechanisms of sorting among pollen operate simultaneously. If these mechanisms interact in ways that alter sorting among mates, …

Conservation Genetics At The Interface Of Theory And Application, Tyler Jess Pilger

Biology ETDs

Understanding the ecological mechanisms responsible for patterns of spatial genetic structure and diversity is a central issue to evolutionary ecology and biodiversity conservation. The Anthropocene has seen a mass extinction only previously observed through geological records, and freshwater fishes of North America have not been spared owing to large-scale modification of freshwater habitats and introduction of nonnative species. Concomitant with reduced numbers of species is a rapid reduction in genetic diversity within species; this diversity that is required for species to adapt to rapidly changing environments of human dominated landscapes. However, understanding why species exhibit different patterns of spatial genetic …

Evolution Of Young Gene Duplicates In The Caenorhabditis Briggsae Genome, Lucille Boreal Packard

Biology ETDs

Gene duplication plays a significant role in the evolution of novel function. Investigations concerning the genomic features of young gene duplicates can enhance our understanding of the nature of gene duplicates at inception and their fates over evolutionary time. Previous analysis of young gene duplicates in Caenorhabditis elegans has revealed genomic features of evolutionarily young gene duplicates with respect to structure, span, location and orientation of paralogous genes. The analysis of young gene duplicate pairs in Caenorhabditis briggsae provides insight into the characteristics of gene duplication in another member of the genus Caenorhabditis. The identification of 376 evolutionarily young gene …

Pre-Industrial Melanism: The Origin, Maintenance, And Genetic Basis Of An Urban Melanic Morph Of The Vermilion Flycatcher, Carl Jonathan Schmitt

Biology ETDs

Industrial melanism is a celebrated evolutionary phenomenon because it demonstrates the efficacy of natural selection in response to anthropogenic environmental change. We investigated a potential instance of industrial melanism in a vertebrate, the vermilion flycatcher (Pyrocephalus rubinus). The species is strikingly bright red throughout its broad range, but a sooty brown morph is abundant in the heavily polluted city of Lima, Peru. We found that plumage morph is perfectly predicted by a single nucleotide polymorphism in the MC1R gene. We quantified genotype and allele frequencies in seven neighborhoods of Lima. Within neighborhoods, there were fewer heterozygotes than expected, and surveys …

Into The Tropics: A Quantitative Study Of Mammals In The Great American Biotic Interchange, Winifred S. B. Whiteman-Jennings

Biology ETDs

For almost 100 million years, North and South America were isolated from each other. This long period of geologic separation led to the evolution of strikingly different mammalian faunas: marsupials were prevalent in South America, while ecosystems in North America were composed of placental mammals. Roughly 3 Mya, a land bridge formed between the two continents leading to an accelerated exchange of mammalian fauna. The Great American Biotic Interchange (or GABI, as this has come to be called,) led to the successful colonization of many North American species, but few South American species. The highly asymmetrical nature of the faunal …

The Effects Of Ecology And Evolution On Avian Flight Morphology, Natalie A. Wright

Biology ETDs

The tendency for flying organisms to possess small genomes has been interpreted as evidence of natural selection acting on the physical size of the genome. Nonetheless, the flight-genome link and its mechanistic basis have yet to be well established by comparative studies within a volant clade. Is there a particular functional aspect of flight such as brisk metabolism, lift production, or maneuverability that impinges on the physical genome? I measured genome sizes, wing dimensions, and heart, flight muscle, and body masses from a phylogenetically diverse set of bird species. In phylogenetically controlled analyses, I found that genome size was negatively …

The Indirect Effects Of Climate Variability On The Reproductive Dynamics And Productivity Of An Avian Predator In The Arid Southwest, Corrie C. Borgman

Biology ETDs

The deserts of the Southwestern United States are experiencing rapid warming and climate models predict declining winter precipitation. The combined effects of higher air temperatures and drought are a reduction in productivity, which may importantly impact reproduction in consumers. Here, we investigate the effects of warming and drought on the reproductive timing and output in loggerhead shrikes (Lanius ludovicianus) in central New Mexico from 2007 to 2012. We found increases in air temperature of 3°C during the breeding season (March—July) and highly variable winter and annual precipitation. With increasing spring temperatures, shrikes advanced nesting phenology by 20 days over 6 …

Negative Effects Of Rapid Warming And Drought On Reproductive Dynamics And Population Size Of An Avian Predator In The Arid Southwest, Kirsten K. Cruz-Mcdonnell

Biology ETDs

Avian communities of arid ecosystems may be particularly vulnerable to global climate change due to the magnitude of model projected change for desert regions and the inherent challenges for species of resource limited ecosystems. How arid zone birds will be affected by rapid increases in air temperature and increased drought frequency and severity is poorly understood. To date, avian responses to climate change have primarily been studied in northern temperate regions in relatively mesic habitats. We studied the effects of increasing air temperature and aridity on a Burrowing Owl (Athene cunicularia) population in the southwestern USA from 1998-2013. Over 16 …

Root Associated Microbes: The Mediators Between Plants And Soil, Sarah Livingston Dean

Biology ETDs

Globally, increasing human populations have either caused or accelerated several types of environmental change. Symbiotic microbes have powerful effects on plant fitness, yet little study has been done on how microbial-plant relationships are affected by environmental changes. In two different ecosystems I explore how either nitrogen (N) pollution or drought can alter root associated microbe (RAM)-plant relationships using Next Generation Sequencing. In moist-meadow alpine tundra at Niwot Ridge, CO, I examine the relative contribution of host identity, N enrichment, and plant neighborhood on RAM diversity and community composition in two co-dominant plant species; Geum rossii and Deschampsia cespitosa. In New …

Multi-Scale Models Of Ovarian Cancer, Kimberly Rene Kanigel Winner

Biology ETDs

In ovarian cancer, disease and treatment can be examined across multiple spatial scales including molecules, cells, intra-tumor vasculature, and body-scale dynamics of circulating drugs. Survival of primary tumor cells and their development into disseminated tumors is related to adhesion between the cells, attachment, and invasion. Growth of new tumors depends on the delivery of nutrients, which depends on the tumor diameter and the tumors vasculature. Drug delivery also depends on tumor diameter and vasculature, and molecular- and gross-scale drug processes. A cellular Potts simulation integrated data at these multiple scales to model microscopic residual disease during relapse after a primary …

A Novel Family Of Major Histocompatibility Complex Class I Genes In Marsupials And Monotremes, Katina Krasnec

Biology ETDs

The Major Histocompatibility Complex (MHC) class I family of genes encode for molecules that have well-conserved structures, but have evolved to perform a diverse functions. The availability of an opossum genome from the grey, short-tailed opossum, Monodelphis domestica, has allowed for analysis of MHC class I genes in a marsupial. Traditional methods for gene discovery uncovered 13 MHC class I genes in the opossum. Utilization of a novel method to search for MHC domain structures discovered a family of 17 novel MHC class I genes. These genes, named ModoUT1-17, were located in a cluster on chromosome 1, unlinked to the …

Too Wet For Frogs, Too Dry For Lizards: Role Of Changing Precipitation On Tropical Frogs And Arid Lizards, Mason J. Ryan

Biology ETDs

During the course of the Anthropocene, humans have modified the landscape and atmosphere resulting in increased global temperatures and intensification of the hydrologic cycle over the last 100 years. Amphibians and reptiles are especially vulnerable to climate change because of their ectothermic physiology and sensitivity to changes in water availability. The role of moisture or precipitation in ectotherm responses to climate change has not been well studied, but moisture plays a vital role in all aspects of the lives of lizards and frogs. It is exceedingly difficult to study the ecological effects of changing precipitation patterns due the stochastic nature …

Bridging Structure And Function In Semi-Arid Ecosystems By Integrating Remote Sensing And Ground Based Measurements, Dan J. Krofcheck

Biology ETDs

The Southwestern US is projected to continue the current significant warming trend, with increased variability in the timing and magnitude of rainfall events. The effects of these changes in climate are already evident in the form of multi-year droughts which have resulted in the widespread mortality of woody vegetation across the region. Therefore, the need to monitor and model forest mortality and carbon dynamics at the landscape and regional scale is an essential component of regional and global climate mitigation strategies, and critical if we are to understand how the imminent state transitions taking place in forests globally will affect …

A Morphological Phylogenetic Analysis And Taxonomic Revision Of The Millipede Family Atopetholidae (Chamberlin) (Diplopoda: Spirobolida) With Descriptions Of New Species And The Conservation Status Of Comanchelus Chihuanus (Chamberlin 1947) (Diplopoda: Spirobolida: Atopetholidae), A Species Of Concern, Michael F. Medrano

Biology ETDs

The taxa of family Atopetholidae Chamberlin 1918 occurring in the southwestern US and Mexico, including Baja California, are revised with new records and species from collections that have never been evaluated. Five new genera, Aculeulus, Bajabolus, Choixulus, Pinnaulus and Tamaulus and twenty new species, Aculeulus monicae, Arinolus anahiae, Arinolus sequoiaensis, Arinolus shelleyi, Atopetholus lowreyi, Atopetholus milleri, Atopetholus westi, Bajabolus bernadinoensis, Bajabolus lapazensis, Choixulus valdezi, Eurelus alisonae, Eurelus isaiasi, Eurelus marisae, Pinnaulus fieldsi, Tamaulus brantleyae, Tamaulus justini, Tamaulus maribelleae, Tamaulus miae, Tamaulus wardae and Watichelus sheari are described using morphological data and 18 synonyms are proposed for a total fauna of …

Community Ecology, Climate Change And Ecohydrology In Desert Grassland And Shrubland, Matthew Daniel Petrie

Biology ETDs

This dissertation explores the climate, ecology and hydrology of Chihuahuan Desert ecosystems in the context of global climate change. In coming decades, the southwestern United States is projected to experience greater temperature-driven aridity, possible small decreases in annual precipitation, and a later onset of summer monsoon rainfall. These changes may have profound consequences for ecological systems in the Chihuahuan Desert, which are intensely water-limited and respond to even small pulses of moisture availability. The first chapter (Chapter 2) compares change in the properties of monsoon season precipitation from 1910-2010 in the northern Chihuahuan Desert region to local variability in monsoon …

Aret: A Novel Regulator Of Alternative Splicing In The Flight Muscle Transcripts In Drosophila Melanogaster, Sandy Thi Oas

Biology ETDs

Drosophila melanogaster has been used as a model organism for understanding muscle development. Drosophila flight and jump muscles are distinct functionally and biochemically. This distinction is due to differentially expressed genes and differentially spliced mRNA transcripts. The exact mechanism of alternative splicing in somatic muscles is not well characterized. Aret was previously shown to be a transcriptional repressor, and has been implicated in splicing regulation based upon literature analysis and preliminary work. This study aims to define the regulatory role of Aret and the impact of alternative splicing on determining muscle diversification and fiber choice. We indicate the importance of …

Bacteriophage Host-Range Expansion To Include Two Strains Of Clostridium Sporogenes, Kevin K. Crown

Biology ETDs

Bacteriophages are viruses that infect bacteria, which have been used to treat bacterial infections in people for decades. They are also now being used as FDA approved preservatives as a means to prevent the growth of spoiling bacteria in many ready-to-eat foods. Bacteriophages tend to infect a very narrow range of bacterial hosts, some only a single sub-strain. When used for therapeutics or food treatment however, it is desirable to use phages that are promiscuous in their host range. This has led to attempts to broaden the host range of the most useful phages. By passaging phages in co-cultures of …

The Effects Of Intestinal Sulfate-Reducing Bacteria On Cognitive Behavior And Intestinal Transit In Mice, Nathaniel Ritz

Biology ETDs

This research reports the effects of two metabolic groups of bacteria on physiological activity and cognitive function in C57BL/6 mice. In one experiment, the mice on a diet supplemented with red kidney bean for 24 hr were able to complete an eight-arm radial learning maze in a shorter time than mice on a diet without red kidney beans. The median time required for mice to complete the maze when fed red kidney beans was 118 sec while the median time for mice on standard diet to finish the maze was 270 sec. Based on the cycle threshold values when using …

Evaluating The Utility Of Natural History Collections In Research And For The Public, Bethany L. Abrahamson

Biology ETDs

Natural history collections (NHCs) are useful in many fields of study, but knowledge about how they are used in the modern day is poor. The first part of this study, focused on the collections data held by the Museum of Southwestern Biology (MSB), analyzes specimen-based publications, specimen loan records, and guestbook information to determine how NHCs have been used in scientific study over time. Using a novel methodology, I objectively sorted the publications into ten research subjects via particular phrases found in publication titles, places of publication, and keywords. I observed from this dataset the proportions of particular subjects for …

Diversification And Adaptation In The Andes: Insights From Phylogeography, Malaria, And Hemoglobin Of The House Wren (Troglodytes Aedon), Spencer C. Galen

Biology ETDs

The tropical Andes of South America represent a highly complex landscape characterized by physical barriers to dispersal and stark ecological gradients. The study of intraspecific genetic diversity in widespread Andean species has the potential to elucidate the historical biogeographic events that have driven diversification as well as the processes by which organisms have adapted to their environments in this region. The house wren (Troglodytes aedon) provides a convenient system for the study diversification and adaptation in the Andes, as it is distributed widely across both biogeographic barriers and heterogeneous environments. In chapter one, I utilize house wren and malaria parasite …

Population And Metapopulation Ecology Of Childhood Diseases, Christian E. Gunning

Biology ETDs

Researchers have long used mathematical models and empirical data to explore the population ecology of childhood diseases such as measles and whooping cough. These diseases have proven ideal model systems for studying population dynamics over space and time. Here we present a novel dataset of weekly measles and whooping cough case reports in pre-vaccine era U.S. cities and states, along with a previously- studied dataset of measles in England & Wales. We first estimate per-population disease reporting probabilities. We find that disease reporting is highly variable over space and between diseases, and correlated with socioeconomic covariates including ethnic composition and …

The Microbiome Of Rainbow Trout (Oncorhynchus Mykiss), Liam T. Lowrey

Biology ETDs

Commensal organisms are an integral part of all vertebrates, contributing heavily to development, pathogen defense, and metabolism. Commensals reside at different body sites within vertebrate animals creating unique and distinct communities that vary between locations. The human microbiome project has revealed distinct bacterial community compositions at the diverse range of body sites that have been sampled, providing evidence for different functional purposes of each microbiome. Rainbow trout, Oncorhynchus mykiss, serves as a model organism for the study of mucosal physiology and immunology. Teleost fish are evolutionarily important as one of the first jawed vertebrates with a dedicated adaptive mucosal immune …

Defining The Complexities Of Mef2 Function And Regulation In Drosophila, Tyanna L. Lovato

Biology ETDs

The development of cardiac and somatic muscle is coordinated by many factors that are highly conserved across species. Mutations in the coding or regulatory sequences of a gene can alter the structure, function or levels of expression of the protein it encodes. We have identified the genetic mechanism underlying the temperature sensitive mutation in MEF2 (myocyte enhancer factor 2), which is required for the differentiation of all muscle lineages. In addition, we have identified a regulatory element upstream of the Mef2 gene that directs its expression from stage fourteen through the end of embryogenesis which is activated by the NK-homeobox …

Living On The Edge: A Comparative Phylogeographic Study Of Refugial And Insular Fragmentation, Yadéeh Escobedo Sawyer

Biology ETDs

Pleistocene glacial-interglacial cycles resulted in population isolation that led to inter- and intra- specific genetic divergence in many North American species. The magnitude of isolation also influenced species response to these climatic changes and set the stage for contemporary gene flow. We can refine our understanding of species response to historical climate change by identifying regions of ice-free persistence and refugia during glacial maxima, and geographic locations and genetic dynamics of post-glacial secondary contact. This dissertation examines the role of glacial cover, geographic barriers, habitat fragmentation as a result of changes in sea level, and insularity on the contemporary genetic …