Genetics and Genomics Commons^™

Genetic Variants Of Duffy And Hemoglobin S Genes In An Afrodescendent Population From Columbia, Diana C. Ortega, Heiber Cardenas, Guillermo Barreto

Human Biology Open Access Pre-Prints

Malaria is an endemic disease in a large part of Colombia, and the city of Buenaventura reports one of the highest malaria infection rates. Some genetic variants confer resistance to malaria, such as the heterozygote for hemoglobin S (HbS) and the homozygous variant FYB^ES/FYB^ES of the Duffy gene. The aim of this work was the molecular characterization of these genes in an afrodescendent population from the urban area of Buenaventura. A total of 819 individuals from a stratified random sampling in each of the 12 communities of this city were analysed. Molecular analysis was performed using PCR-RFLP, …

Complexity, Genetic Causation, And Hereditarianism, Charles Roseman

Human Biology Open Access Pre-Prints

Hereditarians have claimed that recent advances in psychological and psychiatric genetics support their contention that individual and group socially important aspects of behavior and cognition are largely insensitive to environmental context. This has been countered by anti- hereditarians who (correctly) claim that the conclusion of genetic ineluctability is false. Anti- hereditarians, however, sometimes use problematic arguments based on complexity and the ignorance that comes with complexity and a demand for mechanistic, as opposed to variational, explanations for the ways in which genes affect phenotype. I argue here, as a committed anti-hereditarian, that the complexity gambit and the demand for mechanisms …

Ontogenesis Of The Sella Turcica Among Egyptians: Forensic And Radiological Study, Wafaa Mohamed El-Sehly, Fatma Mohamed Magdy Badr El Dine, Mohamed Samir Shaban

Human Biology Open Access Pre-Prints

Introduction: The sella turcica has gained importance as a stable bony landmark in cephalometric studies.
Aim of the work: The aim of the work was to explore the changes that accompany postnatal ontogeny of the sella turcica until full development, and to verify its contribution in age estimation and sexual assignment among Egyptians.
Subjects and methods: Six selected measurements of the sella turcica of 215 Egyptian patients were assessed using Multidetector Computed Tomography (MDCT). The patients represented different ages and were referred to the Radiodiagnosis and Intervention Department. The gathered data were then subjected to statistical analysis including correlation and …

Pleasantview Hills Aspen Stand Diversity Project: Environmental Assessment, Pocatello Field Office

Aspen Bibliography

The Bureau of Land Management (BLM) Pocatello Field Office (PFO) has prepared this Environmental Assessment (EA) to analyze the environmental impacts of implementing treatments on aspen stands in the Pleasantview Hills area. This EA discloses the direct, indirect, and cumulative environmental effects that would result from implementation of this proposal as required by the National Environmental Policy Act (NEPA) of 1969. This EA will determine whether to prepare an Environmental Impact Statement (EIS) or a Finding of No Significant Impact (FONSI) based on environmental impact context and intensity, thereby informing agency decision making. Guidance for EA organization is determined by …

Geographic Population Structure And Taxonomic Identity Of Rhinichthys Osculus, The Santa Ana Speckled Dace, As Elucidated By Nuclear Dna Intron Sequencing, Liane Raynette Greaver

Electronic Theses, Projects, and Dissertations

Rhinichthys osculus (Cyprinidae), the speckled dace, is the most widely distributed freshwater fish in the western United States. The southern California populations of R. osculus are identified as the Santa Ana speckled dace (SASD), though the SASD has not yet been formally recognized as a distinct taxon. Current mtDNA analysis performed in the Metcalf Lab has shown a reciprocally monophyletic relationship among three California regions; southern, central coast, and Owens Valley. Similarly, microsatellite genotyping has shown significant levels of geographic population structure. The purpose of this study was to provide nuclear DNA sequence data to determine the taxonomic status of …

Isolation Of Caldatribacterium (Op9) And Investigation Of Its Potential Interactions With A Novel, Co-Cultivated Thermodesulfobacterium Species, Toshio Alvarado

Electronic Theses, Projects, and Dissertations

Atribacteria (OP9), candidate phylum with no representatives in pure culture, is found in various anaerobic environments worldwide. “Caldatribacterium”, a lineage within Atribacteria that is predicted to be a strictly anaerobic sugar fermenter based on cultivation-independent genomic analyses, is currently being maintained in lab enrichment cultures with fucose as its sole growth substrate. Metagenomics and 16S rRNA gene tag sequencing indicated that the fucose culture was a co-culture of “Caldatribacterium” and an uncultivated member of the genus Thermodesulfobacterium. Due to failed attempts to isolate “Caldatribacterium” by dilution-to-extinction and plating, it was hypothesized that “Caldatribacterium” is dependent in some way on the …

Using Single-Cell Sorting, Fish And 13c-Labeling To Cultivate And Assess Carbon Substrate Utilization Of ‘Aigarchaeota’ And Other Novel Thermophiles, Damon Kurtis Mosier

Electronic Theses, Projects, and Dissertations

‘Aigarchaeota’, a deeply branching lineage in the domain Archaea with no cultivated representatives, includes both thermophilic and hyperthermophilic microorganisms that reside in terrestrial and marine geothermal environments. The ‘Aigarchaeota’ consists of at least nine proposed genus-level groups that have been confirmed via 16S rRNA sequencing, with ‘Aigarchaeota’ Group 1 (AigG1) being the focus of this study. Based on cultivation-independent genomic data available from several AigG1 members in Great Boiling Spring (GBS), NV, and Yellowstone National Park, 22 different types of growth media were designed and tested for their ability to support growth of AigG1. One of these cultures, G1-10, was …

Phylogenetic Trees And Networks Can Serve As Powerful And Complementary Approaches For Analysis Of Genomic Data, Christopher Blair, Cécile Ané

Publications and Research

Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). However, the MSC assumes no gene flow post divergence, calling for additional methods that can accommodate this limitation. Explicit phylogenetic network methods have emerged, which can simultaneously account for ILS and gene flow by representing evolutionary history as a directed acyclic graph. In this point-of-view we highlight some of the strengths and limitations …

Sudden Aspen Decline: A Review Of Pattern And Process In A Changing Climate, Jack A. Singer, Rob Turnbull, Mark Foster, Charles Bettigole, Brent R. Frey, Michelle C. Downey, Kristofer R. Covey, Mark S. Ashton

Aspen Bibliography

The American quaking aspen (Populus tremuloides Michx.) and its close relative, the Eurasian quaking aspen (Populus tremula L.), cover a realm that is perhaps the most expansive of all tree species in the world. In North America, sudden aspen decline (SAD) is a growing concern that marks the rapid decline of quaking aspen trees leading to mortality at the stand and landscape scale. Research suggests that drought and water stress are the primary causes of SAD. Predisposing factors (age, structure, and landscape position), as well as associated stressors (i.e., pests and pathogens), have been linked to mortality in affected stands. …

Impacts Of Climate And Insect Herbivory On Productivity And Physiology Of Trembling Aspen (Populus Tremuloides) In Alaskan Boreal Forests, Melissa A. Boyd, Logan T. Berner, Patricia Doak, Scott J. Goetz, Brendan M. Rogers, Diane Wagner, Xanthe J. Walker, Michelle C. Mack

Aspen Bibliography

Climate change is impacting forested ecosystems worldwide, particularly in the Northern Hemisphere where warming has increased at a faster rate than the rest of the globe. As climate warms, trembling aspen (Populus tremuloides) is expected to become more successful in northern boreal forests because of its current presence in drier areas of North America. However, large-scale productivity decline of aspen has recently been documented throughout the United States and Canada as a result of drought and insect outbreaks. We used tree ring measurements (basal area increment (BAI) and stable carbon isotopes (δ 13C)) and remote sensing indices …

Mixing It Up: The Impact Of Episodic Introgression On The Evolution Of High-Latitude Mesocarnivores, Jocelyn P. Colella

Biology ETDs

At high latitudes, climatic oscillations have triggered repeated episodes of organismal divergence by geographically isolating populations. For terrestrial species, extended isolation in glacial refugia – ice-free regions that enable terrestrial species persistence through glacial maxima – is hypothesized to stimulate allopatric divergence. Alternatively, upon glacial recession, divergent populations expanded from independent glacial refugia and often contacted other diverging populations. In the absence of reproductive isolating mechanisms, this biogeographic process may trigger hybridization and ultimately, gene flow between divergent taxa. My dissertation research aims to understand how these episodic periods of isolation and contact have impacted the evolution of high latitude …

Probability, Populations, Phylogenetics And Hominin Speciation, Niccolo Caldararo

Human Biology Open Access Pre-Prints

A number of recent articles have appeared on the hominin Denisova fossil remains. Many of them focus on attempts to produce DNA sequences from the extracted samples. Often these project mtDNA sequences from the fossil remains of a number of Neandertal fossils and the Denisovans in an attempt to understand the evolution of Mid Pleistocene human ancestors. These papers, introduce a number of problems in the interpretation of speciation in hominins. One concerns the degradation of the ancient DNA and its interpretation as authentic genetic information. Another concerns the idea of “species” versus that of “population” and the use of …

Guidelines For Aspen Restoration In Utah With Applicability To The Intermountain West, Stanley G. Kitchen, Patrick N. Behrens, Sherel K. Goodrich, Ashley Green, John Guyon, Mary O'Brien, David Tart

Aspen Bibliography

As highly productive and biologically diverse communities, healthy quaking aspen (Populus tremuloides; hereafter aspen) forests provide a wide range of ecosystem services across western North America. Western aspen decline during the last century has been attributed to several causes and their interactions, including altered fire regimes, drought, excessive use by domestic and wild ungulates, and conifer encroachment. Today’s managers need science-based guidance to develop and implement strategies and practices to restore structure, processes, and resilience to the full range of aspen functional types across multiple spatial scales. In these guidelines, we detail a process for making step-by-step decisions …

Drought And Freezing Vulnerability Of The Isolated Hybrid Aspen Populus X Smithii Relative To Its Parental Species, P. Tremuloides And P. Grandidentata, Nicholas J. Deacon, Jake J. Grossman, Jeannine Cavender-Bares

Aspen Bibliography

Aim

We assessed the vulnerability of an isolated, relictual Pleistocene hybrid aspen population of conservation interest (Populus x. smithii ) and the nearest populations of its parent species (Populus grandidentata and Populus tremuloides ) to springtime post‐bud break freezing and growing season drought stress. Response to these stressors in the three taxa was compared in terms of avoidance and tolerance.

Location

North American Midwest; USA.

Methods

Unique genets from the hybrid Niobrara River population and from the two parental populations were propagated in a common garden from rhizome cuttings. We tracked their phenology before and after bud break …

Frogs Hiding In Plain Sight: Phylogenetic Systematics Of Myanmar’S Occidozyga Species Complex, And The Identification Of A Novel Species, Allison Bogisich

Master's Theses

Different species can be difficult to distinguish from one another when they are morphologically similar. Such cryptic species are the reason many anuran species go undetected. For this study, the taxonomic identity of the Occidozyga complex across Myanmar was investigated. An integrated approach was used combining molecular, morphological and phylogeographic data to better assess its taxonomy. Results indicate the presence of three new candidate species within Occidozyga, and three evolutionarily significant unit (ESU) lineages. Two mitochondrial gene fragments (16S, COI) and one nuclear gene fragment (Rhodopsin) were examined from DNA isolated from forty-seven preserved specimens from the California Academy …

Phylogenetic Inference Of Multiscale Selection Pressures Using A Continuous State Birth-Death Process, Marco Hamins-Puertolas, David Rasmussen

Biology and Medicine Through Mathematics Conference

No abstract provided.

Warming Up: Climate Change Related Shifts Of Mycorrhizal Fungal Communities In High Latitude Ecosystems, Megan Rae Devan

Biology ETDs

This dissertation examines how climate change affects mycorrhizal fungal communities in boreal and arctic ecosystems. In chapter one, I revealed that increases in fire severity and related increases in deciduous tree dominance result in greater Ascomycota relative abundance (RA) and subsequent declines in Basidiomycota RA. In chapter two I analyzed the effects of post-fire mycorrhizal fungal communites on host growth. There were trends at the fungal genus level that were largely reflected at the guild level across all hosts; however, there were some fungal genera that had the opposite effect on different host species. In chapter three, I found host …

What Lies Beneath? Molecular Evolution During The Radiation Of Caecilian Amphibians, María Torres-Sánchez, David J. Gower, David Alvarez-Ponce, Christopher J. Creevey, Mark Wilkinson, Diego San Mauro

Neuroscience Faculty Publications

Background: Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. …

Beaver And Aspen: Synergy Among Keystone Species, Stephen N. Bennett, Nicolaas Bouwes, Paul C. Rogers

Aspen Bibliography

In the West, climate change is likely to increase the frequency, intensity, and duration of drought. Restoration of soils and water storage capacity can help create resilient uplands and riverscapes (i.e., streams and the valley bottoms). Over the past two centuries, common land uses, the removal of beaver and wood, straightening of streams, and damage to riparian areas have created simplified, structurally starved, riverscapes. Degraded streams are very efficient at transporting water, sediment, and nutrients downstream. Aspen forests are also biological hotspots that have been degraded by past land uses such as overbrowsing ungulates, land clearing, fire suppression, and outright …

Biodiversity Within Aspen Forests, Paul C. Rogers

Aspen Bibliography

Aspen have long been known for supporting lush vegetation and rich wildlife habitat. These features, alongside brilliant green and gold seasonal coloration, accompany a broadly appreciated aesthetic for aspen forests by the public-at-large. However, in earlier times timber producers in many locales considered aspen to have low value and actively eliminated them. More recent research has pointed out that relative moisture held within aspen communities facilitates a wide array of species – collectively, biodiversity – compared to surrounding vegetation types. Aspen groves in the Intermountain West, for example, are known to be second only to riparian forests is supporting the …

Role Of Wildfire And Topography In Shaping Aspen Regeneration After The Hayman Fire, Co, Usa, Arianna A. B. Porter

Aspen Bibliography

Unusually rapid and widespread mortality in Quaking aspen (Populus tremuloides) has been documented throughout the 21st century primarily as a result of warm, dry weather conditions. Although aspen are not drought-adapted, aspen are well adapted to wildfire. Increases in wildfire severity and extent as a result of climate change may provide opportunities for aspen regeneration, especially at mid- and high-elevation sites. Aspen's sensitivity to drought suggests that regeneration following fire might be constrained to cooler and wetter topographic locations on the landscape which reduce drought stress on vegetation. While aspen mortality is demonstrated to occur at low elevation sites, aspen …

Burn Severity And Fire History In The Northwestern Canadian Boreal Forest: Drivers And Ecological Outcomes, Ellen Whitman

Aspen Bibliography

Wildfire is the dominant stand-renewing disturbance in the northwestern Canadian boreal forest. Fires burn extensive areas in Canada, disturbing an average of 1.96 Mha yr−1, primarily in the boreal zone. Fires generally occur every ~30 – > 200 years in this region, due in part to a lack of fuel that allows young stands to resist reburning. Boreal understory plants and trees are adapted to stand-renewing wildfire through mechanisms such as serotiny, seed banking, and resprouting from roots and rhizomes of top-killed individuals. Such adaptations confer resilience to boreal forests, and post-fire vegetation communities generally resemble the pre-fire ones, following a …

Hiding In The Lianas Of The Tree Of Life: Molecular Phylogenetics And Species Delimitation Reveal Considerable Cryptic Diversity Of New World Vine Snakes, Robert C. Jadin, Christopher Blair, Michael J. Jowers, Anthony Carmona, John C. Murphy

Publications and Research

The Brown Vine Snake, Oxybelis aeneus, is considered a single species despite the fact its distribution covers an estimated 10% of the Earth’s land surface, inhabiting a variety of ecosystems throughout North, Central, and South America and is distributed across numerous biogeographic barriers. Here we assemble a multilocus molecular dataset (i.e. cyt b, ND4, cmos, PRLR) derived from Middle American populations to examine for the first time the evolutionary history of Oxybelis and test for evidence of cryptic lineages using Bayesian and maximum likelihood criteria. Our divergence time estimates suggest that Oxybelis diverged from its sister genus, Leptophis …

Phylogeny Of The Australian Solanum Dioicum Group Using Seven Nuclear Genes: Testing Symon’S Fruit And Seed Dispersal Hypotheses., Christopher T. Martine, Ingrid E. Jordon-Thaden, Angela J. Mcdonnell, Jason T. Cantley, Daniel S. Hayes, Morgan D. Roche, Emma S. Frawley, Ian S. Gilman, David C. Tank

Faculty Journal Articles

The dioecious and andromonoecious Solanum taxa (the “S. dioicum group”) of the Australian Monsoon Tropics have been the subject of phylogenetic and taxonomic study for decades, yet much of their basic biology is still unknown. This is especially true for plant-animal interactions, including the influence of fruit form and calyx morphology on seed dispersal. We combine field/greenhouse observations and specimen-based study with phylogenetic analysis of seven nuclear regions obtained via a microfluidic PCR-based enrichment strategy and high-throughput sequencing, and present the first species-tree hypothesis for the S. dioicum group. Our results suggest that epizoochorous trample burr seed …

Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney

Student Scholar Showcase

Pseudomonas putida GB-1 is a model organism for the study of manganese oxidation in bacteria, however, the frequency of co-localization of multiple known and suspected manganese oxidizing proteins, as well as their occurrence between species, is unknown. Eight different genes isolated from known manganese oxidizing bacteria (MnxG, MopA, McoA, PputGB1_2552, PputGB1_2553, MoxA, MofA, and Bacillus MnxG) were tested individually using BioPython and BLAST (Basic Local Alignment Search Tool) on multiple genomic databases. BLAST searches had an expect value cutoff of 1e-50, limiting gene homologs to those with high sequence similarity. The abundance of homologous genes across classes of proteobacteria point …

The Role Of Disease & Insects In Aspen Ecology, John C. Guyon Ii

Aspen Bibliography

Aspen is a keystone species in montane forests, and enhances a number of key resource values including wildlife habitat, water resources, and fire behavior. Recently, aspen forests have experienced episodes of dieback and decline across western North America (Worrall et al. 2010, Guyon and Hoffman 2011). A large proportion of the dieback and decline has been linked to drought stress or drought-prone locations (Hanna and Kulakowski 2012). However, insects and diseases are commonly found in declining aspen stands, leading to confusion about the role of insects and diseases in aspen ecology. Additionally, aspen has a reputation for being susceptible to …

Plant Mitochondrial Genome Evolution And Structure Has Been Shaped By Double-Strand Break Repair And Recombination, Emily Wynn

School of Biological Sciences: Dissertations, Theses, and Student Research

Plant mitochondrial genomes are large but contain a small number of genes. These genes have very low mutation rates, but genomes rearrange and expand at significant rates. We propose that much of the apparent complexity of plant mitochondrial genomes can be explained by the interactions of double-strand break repair, recombination, and selection. One possible explanation for the disparity between the low mutation rates of genes and the high divergence of non-genes is that synonymous mutations in genes are not truly neutral. In some species, rps14 has been duplicated in the nucleus, allowing the mitochondrial copy to become a pseudogene. By …

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in …

Surface Fire To Crown Fire: Fire History In The Taos Valley Watersheds, New Mexico, Usa, Lane B. Johnson, Ellis Q. Margolis

Aspen Bibliography

Tree-ring fire scars, tree ages, historical photographs, and historical surveys indicate that, for centuries, fire played different ecological roles across gradients of elevation, forest, and fire regimes in the Taos Valley Watersheds. Historical fire regimes collapsed across the three watersheds by 1899, leaving all sites without fire for at least 119 years. Historical photographs and quaking aspen (Populus tremuloides Michx.) ages indicate that a high-severity fire historically burned at multiple high-elevation subalpine plots in today’s Village of Taos Ski Valley, with large high-severity patches (>640 ha). Low-severity, frequent (9–29-year median interval) surface fires burned on the south aspects …

Meta-Analysis Of Characteristics In Upper Missouri River Fishes: Prediction Of Invasiveness, Steph Purcell

UNO Student Research and Creative Activity Fair

Invasive species are often considered a global threat due to their association with biodiversity loss and novel diseases. The Missouri-Mississippi River Watershed, including the Missouri River Basin, is particularly vulnerable to invasive species because of low species diversity following historic glaciation events. Management of invasive species is imperative in this watershed but continues to be challenging in that there are over 100 invasive species currently present in this region. The goal of this project is to identify characteristics associated with successful invasions that may assist in developing management strategies to reduce the negative outcomes caused by the establishment of invasive …