Genetics and Genomics Commons^™

The Role Of Historical And Contemporary Processes On Phylogeographic Structure And Genetic Diversity In The Northern Cardinal, Cardinalis Cardinalis, Brian T. Smith, Patricia Escalante, Blanca E. Hernandez-Banos, Adolfo G. Navarro-Siguenza, Sievert Rohwer, John Klicka

Ornithology Program (HRC)

Background

Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, Cardinalis cardinalis …

Molecular Evolution And Historical Biogeography Of New World Birds, Brian T. Smith

UNLV Theses, Dissertations, Professional Papers, and Capstones

Deciphering the patterns of how biodiversity has evolved across time and space has remained a fundamental objective for biologists for the last 200 years. Researchers are faced with the challenge of interpreting the complexity of evolutionary patterns that have been generated over the deep history of the Earth. The advancement of DNA sequencing technology has yielded a new and powerful genetic toolkit that has allowed biologists to address novel evolutionary questions. For my dissertation research, I used molecular genetics and a statistical framework to study the evolution and historical biogeography of birds distributed in North and South America. My dissertation …

Oral Presentation: Plant Genes And Drought Tolerance, Norris Lam

Festival of Communities: UG Symposium (Posters)

Research has shown that a gene from C3 xerophyte Larrea tridentata (creosote bush), LtWRKY21, is involved in pathways governing creosote bush’s high tolerance to environmental stress. By understanding the way in which creosote bush adapts to drought, crop plants can be engineered to be more drought tolerant during times of imminent global climate change. To study the underlying mechanisms of creosote bush drought response, the LtWRKY21 gene was mobilized into the model organism Arabidopsis thaliana. Chlorophyll degradation, cellular electrolyte leakage, and water content in leaves will serve as indicators of drought tolerance in LtWRKY21-transgenic A. thaliana after treatment in chemically …

Stationary Phase Mutagenesis In Bacillus Subtilisis Independent Of Genome Replication, Mark Upchurch, Holly Martin, Eduardo Robleto

Festival of Communities: UG Symposium (Posters)

Stationary phase mutagenesis is defined as cellular mechanisms that produce genetic diversity in cells experiencing conditions of stress. These processes are associated with many biological phenomena, including those that produce the formation of cancers in animal cells and other degenerative diseases. Also, these mechanisms are associated with the accumulation of beneficial mutations in bacteria, but follow stochastic processes and are controlled by genetic factors. The current models explaining the generation of stress-induced mutations are predicated on the formation of DNA replication intermediates that are formed during the repair of damaged DNA or during DNA replication and transcription encounters. Here we …

Draft Genome Of The Red Harvester Ant Pogonomyrmex Barbatus, Chris R. Smith, Christopher D. Smith, Hugh M. Robertson, Martin Helmkampf, Aleksey Zimin, Mark Yandall, Carson Holt, Hao Hu, Ehab Abouheif, Richard Benton, Elizabeth Cash, Vincent Croset, Cameron R. Currie, Eran Elhaik, Christine G. Elsik, Marie-Julie Favé, Vilaiwan Fernandes, Joshua D. Gibson, Dan Graur, Wulfila Gronenberg, Kirk J. Grubbs, Darren E. Hagen, Ana Sofia Ibarraran Viniegra, Brian R. Johnson, Reed M. Johnson, Abderrahman Khila, Jay W. Kim, Kaitlyn A, Mathis, Monica C. Munoz-Torres, Marguerite C. Murphy, Julie A. Mustard, Rin Nakamura, Oliver Niehuis, Surabhi Nigam, Rick P. Overson, Jennifer E. Placek, Rajendhran Rajakumar, Justin T. Reese, Garret Suen, Shu Tao, Candice W. Torres, Neil D. Tsutsui, Lumi Viljakainen, Florian Wolschin, Jürgen Gadau

Department of Entomology: Faculty Publications

We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in …

Drafting Human Ancestry: What Does The Neanderthal Genome Tell Us About Hominid Evolution? Commentary On Green Et Al. (2010), Michael Hofreiter

Human Biology

Ten years after the first draft versions of the human genome were
announced, technical progress in both DNA sequencing and ancient DNA
analyses has allowed a research team around Ed Green and Svante Pa¨a¨bo to
complete this task from infinitely more difficult hominid samples: a few
pieces of bone originating from our closest, albeit extinct, relatives, the
Neanderthals. Pulling the Neanderthal sequences out of a sea of contaminating
environmental DNA impregnating the bones and at the same time
avoiding the problems of contamination with modern human DNA is in itself
a remarkable accomplishment. However, the crucial question in the long …

Leaf Number Indicates Salt Tolerance Of Young Seedling Families Of European Aspen (Populus Tremula L.) Growing In Different Soils, Lu-Min Vaario, Kim Yrjälä, Matti Rousi, Timo Sipila, Pertti Pulkkinen

Aspen Bibliography

Soil salinity limits plant productivity and quality. We evaluated the response of 12 aspen (Populus tremula) families to salt stress in two different soils irrigated for 4-weeks with 0, 80 or 160 mM saline solution. Easily measurable characteristics such as shoot height, leaf number, dry mass as well as the distribution of sodium (Na+) ions were measured in 5-month-old aspen seedlings raised in controlled greenhouse conditions on two different soils. Growth among families varied significantly, and the interaction between family and soil type was significant. From 2–5 months, leaf number correlated with that of the first month and salin-ity tolerance. …

Reduced Mhc And Neutral Variation In The Galápagos Hawk, An Island Endemic, Jennifer Bollmer, Joshua Hull, Holly Ernest, José Sarasola, Patricia Parker

Biology Department Faculty Works

BackgroundGenes at the major histocompatibility complex (MHC) are known for high levels of polymorphism maintained by balancing selection. In small or bottlenecked populations, however, genetic drift may be strong enough to overwhelm the effect of balancing selection, resulting in reduced MHC variability. In this study we investigated MHC evolution in two recently diverged bird species: the endemic Galápagos hawk (Buteo galapagoensis), which occurs in small, isolated island populations, and its widespread mainland relative, the Swainson's hawk (B. swainsoni).ResultsWe amplified at least two MHC class II B gene copies in each species. We recovered only three different sequences from 32 Galápagos …

Multicentury Fire And Forest Histories At 19 Sites In Utah And Eastern Nevada, Emily K. Heyerdahl, Peter M. Brown, Stanley G. Kitchen, Marc H. Weber

Aspen Bibliography

Our objective is to provide site-specific fire and forest histories from Utah and eastern Nevada that can be used for land management or additional research. We systematically sampled fire scars and tree-recruitment dates across broad gradients in elevation and forest type at 13 sites in Utah and 1 in eastern Nevada to characterize spatial and temporal variation in historical fire regimes as well as forest structure and composition. We collected similar data non-systematically at five additional sites in Utah. These 19 sites include a broad range of forest types (from pinyon-juniper woodlands to spruce-fir forests) and fire regime types. In …

Variation, Systematics, And Relationships Of The Leptodactylus Bolivianus Complex (Amphibia: Anura: Leptodactylidae), W. Ronald Heyer, Rafael O. De Sá

Biology Faculty Publications

Heyer, W. Ronald, and Rafael O. de Sá. Variation, Systematics, and Relationships of the Leptodactylus bolivianus Complex (Amphibia: Anura: Leptodactylidae). Smithsonian Contributions to Zoology, number 635, viii + 58 pages, 21 figures, 20 tables, 2011.—The Leptodactylus bolivianuscomplex has been considered to consist of one or two species, L. bolivianus alone or L. bolivianus and L. insularum. Detailed morphological analyses were undertaken to evaluate variation in the complex, which ranges from Costa Rica through Panama, across northern South America in the river valleys draining to the Caribbean, and throughout much of the Amazon basin with southern limits in Bolivia. Members of …

Population And Conservation Genetics Of Crawfish Frogs, Lithobates Areolatus, At Their Northeastern Range Limits, Schyler O. Nunziata

Online Theses and Dissertations

Crawfish Frogs (Lithobates areolatus) are state endangered in Indiana and Iowa, with populations in decline throughout their range. I studied populations of Crawfish Frogs on local and statewide scales at their northeastern range limits to (1) assess the level of genetic diversity within populations (2) estimate fine-scale genetic structure, and (3) estimate genetic differentiation between populations at the state level. Crawfish Frogs breed in temporary pools and wetlands, and have high breeding-pond fidelity; therefore I predicted to find genetic differences between ponds at small geographic scales. I used 10 microsatellite loci to genotype frogs collected from three primary populations in …

Oregon Aspen Project, Forest Restoration Partnership

Aspen Bibliography

The Oregon Aspen Project was initiated in response to the decline of aspen groves in Oregon and throughout the Western United States, and the lack of information to guide managers interested in stewardship to enhance this resource. There were three central goals and accompanying objectives for this project which are listed below. The project accomplishments are provided below each bulleted objective

Phenotypic And Genetic Characterization Of Wildland Collections Of Western And Searls Prairie Clovers For Rangeland Revegetation In The Western Usa, Kishor Bhattarai

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Western prairie clover [Dalea ornata (Douglas ex Hook.) Eaton & J. Wright] is a perennial legume that occurs in the northern Great Basin, Snake River Basin, and southern Columbia Plateau, whereas Searls prairie clover [Dalea searlsiae (A. Gray) Barneby], also a perennial legume, occurs in the southern Great Basin and surrounding areas. Understanding the genetic and ecotypic variation of these prairie clovers is a prerequisite for developing populations suitable for rangeland revegetation in the western USA. DNA sequences of internal transcribed spacer (ITS/5.8S) and trnK/matK were used to study the phylogeny of these species. The species were distinguished …

Reconstructing Species Responses To Past Climatic Changes Using Niche Modeling And Genetic Data, Tereza Jezkova

UNLV Theses, Dissertations, Professional Papers, and Capstones

Glacial – interglacial cycles have a pronounced impact on species distributions and genetic structure. Many species shift their distributions to lower latitudes and altitudes during the colder glacial periods and expand northwards and up the elevation during warmer interglacial periods. Some species however are capable of adapting to changing environment which allows them to persist in place despite climatic changes. I explored how climatic changes after the last glacial maximum (LGM) effected two species inhabiting the deserts of western North America: one mammal (Chisel-toothed Kangaroo Rat, Dipodomys microps) and one reptile (Desert Horned Lizard, Phrynosoma platyrhinos). I used …

Micrornas Reveal The Interrelationships Of Hagfish, Lampreys, And Gnathostomes And The Nature Of The Ancestral Vertebrate, Alysha M. Heimberg, Richard Cowper-Sal{Middle Dot}Lari, Marie Semon, Philip C. J. Donoghue, Kevin J. Peterson

Dartmouth Scholarship

Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish and lampreys as closest relatives). Here, we show through deep sequencing of small RNA libraries, coupled with genomic surveys, that Cyclostomata is monophyletic: hagfish and lampreys share 4 unique microRNA families, 15 unique paralogues of more …

Evolutionary Rates And Gene Dispensability Associate With Replication Timing In The Archaeon Sulfolobus Islandicus, Kenneth M. Flynn, Samuel H. Vohr, Philip J. Hatcher, Vaughn S. Cooper

Molecular, Cellular & Biomedical Sciences

In bacterial chromosomes, the position of a gene relative to the single origin of replication generally reflects its replication timing, how often it is expressed, and consequently, its rate of evolution. However, because some archaeal genomes contain multiple origins of replication, bias in gene dosage caused by delayed replication should be minimized and hence the substitution rate of genes should associate less with chromosome position. To test this hypothesis, six archaeal genomes from the genus Sulfolobus containing three origins of replication were selected, conserved orthologs were identified, and the evolutionary rates (dN and dS) of these orthologs were quantified. Ortholog …

Plastic And Genetic Determination Of Population, Community, And Ecosystem Properties In Freshwater Environments, Leigh C. Latta Iv

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The hierarchy of biological organization, from molecules to ecosystems, describes the relationships among various biological systems. Of particular interest is assessing how the factors that primarily determine the nature of one hierarchical level also have transcendent qualities that affect the ecology and evolution of higher hierarchical levels. The goal of this dissertation was to use a bottom-up approach to examine the transcendent effects of two factors that strongly determine the nature of their associated level of biological organization. The first, phenotypic plasticity, is a primary factor that determines the phenotype of an individual. The second factor, genetic diversity, largely determines …

Genomic Perspectives On Evolution In Bracken Fern, Joshua P. Der

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The fern genus Pteridium comprises a number of closely related species distributed throughout the world. Collectively they are called bracken ferns and have historically been treated as a single species, Pteridium aquilinum. Bracken is notorious as a toxic weed that colonizes open fields and poisons livestock. Bracken is also easily cultured and has become one of the most intensively studied ferns. Bracken has been used as a model system for the study of the fern life cycle, fern gametophyte development, the pheromonal mechanism of sex determination, toxicology, invasion ecology, and climate change. This dissertation places bracken within a global …

An Entrepreneurial Approach To Librarianship, Flora Shrode, Jennifer Duncan, Wendy Holliday

Library Faculty & Staff Publications

Librarians from Utah State University explain recent efforts to encourage subject librarians to take a more holistic view of their roles. We are shifting from a traditional emphasis primarily on collection development and refocusing on natural connections between collections, instruction, liaison, and reference service. The poster provides background about Utah State University’s situation and explains our approach to analyzing local needs and culture to inform development of a new organizational structure. We describe our vision of subject librarianship, the process by which we assessed librarians’ ideas and goals for performing as subject librarians, and the actions we are taking to …

Damage Agents And Condition Of Mature Aspen Stands In Montana And Northern Idaho, Brytten E. Steed, Holly S.J. Kearns

Aspen Bibliography

No abstract provided.

Genetic Variation At Nuclear Loci Fails To Distinguish Two Morphologically Distinct Species Of Aquilegia, Elizabeth A. Cooper, Justen B. Whittall, Scott A. Hodges, Magnus Nordborg

Biology

Aquilegia formosa and pubescens are two closely related species belonging to the columbine genus. Despite their morphological and ecological differences, previous studies have revealed a large degree of intercompatibility, as well as little sequence divergence between these two taxa [1,2]. We compared the inter- and intraspecific patterns of variation for 9 nuclear loci, and found that the two species were practically indistinguishable at the level of DNA sequence polymorphism, indicating either very recent speciation or continued gene flow. As a comparison, we also analyzed variation at two loci across 30 other Aquilegia taxa; this revealed slightly more differentiation among taxa, …

Sex, Mixability, And Modularity, Adi Livnat, Christos Papadimitriou, Nicholas Pippenger, Marcus W. Feldman

All HMC Faculty Publications and Research

The assumption that different genetic elements can make separate contributions to the same quantitative trait was originally made in order to reconcile biometry and Mendelism and ever since has been used in population genetics, specifically for the trait of fitness. Here we show that sex is responsible for the existence of separate genetic effects on fitness and, more generally, for the existence of a hierarchy of genetic evolutionary modules. Using the tools developed in the process, we also demonstrate that in terms of their fitness effects, separation and fusion of genes are associated with the increase and decrease of the …

Phylogeographical Patterns Of Neobalanocarpus Heimii (Dipterocarpaceae) For The Evolutionary History And Chain Of Custody Certification., Tnah Lee Hong

Student Works (2010-2019)

Tectonic movement and climatic oscillations during the Cenozoic have had dramatic effect on the biota of the tropical rain forest. This study aims to reveal the phylogeography and evolutionary history of a Peninsular Malaysian endemic tropical timber, Neobalanocarpus heimii (Dipterocarpaceae), based on chloroplast DNA (cpDNA) variation. Fifteen haplotypes were identified from 10 intraspecific variable sites of five non-coding cpDNA regions: trnL intron, trnS-trnG spacer, trnG intron, trnK intron and psbK-trnS spacer. Two major genealogical cpDNA lineages of N. heimii were elucidated: a widespread southern and a northern region. The species is predicted to survive in multiple refugia during climatic oscillation: …

Ecology And Genetics Of Philodina Megalotrocha (Rotifera, Bdelloidea) From Chihuahuan Desert Populations, Lina Kamel Hamdan

Open Access Theses & Dissertations

The Chihuahuan Desert is a unique region with high biodiversity. There is a high degree endemism of freshwater biota, but relatively few studies have been focused on zooplankton. Bdelloid rotifers are one component of these ecosystems and often dominate very temporary habitats. Bdelloids are usually assumed to be cosmopolitan species due to their potentially high dispersal rates. Distribution records of the bdelloid P. megalotrocha extend from North America to New Zealand. However, little is known about its ecology or genetics. The aims of this study are to: 1) determine whether the distribution of P. megalotrocha in the Chihuahuan Desert is …

Systematics Of The Genus Ptychadena Boulenger, 1917 (Anura: Ptychadenidae) From Democratic Republic Of The Congo, Katrina Marie Weber

Open Access Theses & Dissertations

This thesis increases the scope of previous phylogenetic analyses that revealed high levels of genetic differentiation within the anuran genus Ptychadena. Herein, I increase sampling of Central African populations of Ptychadena by over six times to examine their relationships to other African populations and to search for cryptic species. This study represents the most comprehensive molecular phylogeny of Ptychadena to date. A total of three mitochondrial (12S, 16S, and cyt b) and two nuclear (RAG1 and rhodopsin) genes were sequenced for 67 specimens of Ptychadena. Maximum parsimony, maximum likelihood, and Bayesian analyses were conducted. These analyses revealed …

Identification Of Eurycea Using Cytochrome B, Karis A. Myers

Senior Honors Theses

Genomic sequencing is a powerful tool that has many applications for research, one of which is in the field of taxonomy and the identification of species. This thesis discusses the mitochondrial gene cytochrome b and its utility in population genetics and identification of larval amphibians. The development of the Polymerase Chain Reaction and primers are an integral part of the modern DNA sequencing process. The Polymerase Chain Reaction is used to amplify a target DNA sequence, and the protocol for this procedure must be optimized for the specific sequence of target DNA. Primers must also be designed and modified for …

Attempted Cloning Of A Wnt Gene From Botrylloides Violaceus, Manasa Chandra, James Tumulak

Biological Sciences

Botrylloides violaceus is a colonial ascidian with the ability to undergo sexual and asexual reproduction as well as regeneration. The canonical pathway starts with the extracellular protein Wnt and ends with β-catenin, a transcription factor, which also functions in cell adhesion. The Wnt signaling pathway is involved in embryogenesis and regeneration in a variety of other species. In our studies we attempt to isolate and sequence both a Wnt gene and from Botrylloides via degenerate primer design and PCR. Using bioinformatic methods we aligned sequences from other organisms, as the Botrylloides genome has not yet been sequenced. Using mouse, Ciona, …

Aspen In Scotland: Biodiversity And Management, John Parrott, Neil Mackenzie

Aspen Bibliography

No abstract provided.

It's Not Too Late For The Harpy Eagle (Harpia Harpyja): High Levels Of Genetic Diversity And Differentiation Can Fuel Conservation Programs, Heather R. Lerner, Jeff A. Johnson, Alec R. Lindsay Ph. D., Lloyd F. Kiff, David P. Mindell

Faculty Works

Background: The harpy eagle (Harpia harpyja) is the largest Neotropical bird of prey and is threatened by human persecution and habitat loss and fragmentation. Current conservation strategies include local education, captive rearing and reintroduction, and protection or creation of trans-national habitat blocks and corridors. Baseline genetic data prior to reintroduction of captive-bred stock is essential for guiding such efforts but has not been gathered previously.

Methodology/Findings: We assessed levels of genetic diversity, population structure and demographic history for harpy eagles using samples collected throughout a large portion of their geographic distribution in Central America (n = 32) and South America …

Assessment Of The Endangered Species Podarcis Carbonelli On A Microgeographic Scale: A Molecular, Morphological And Physiological Approach, Maria Clara Figueirinhas Do Amaral

Masters Theses & Specialist Projects

The lizard Podarcis carbonelli is an endangered species endemic to the Iberian Peninsula. One location where this species occurs is at the Berlengas Natural Preserve, an Atlantic archipelago off the coast of Portugal. These island populations are geographically separated from nearby mainland populations. The fundamental question is, are these insular individuals distinct from the mainland populations? Four localities were chose for comparison: two island populations and two nearby coastal populations. We assessed this question using three distinct approaches: molecular, morphological and physiological approach. We sequenced the 12S RNA, the mtDNA Control Region and the 7th intron of the !-fibrinogen gene …