Biology Commons^™

Threatened Fishes Of The World: Percilia Irwini (Eigenmann 1927) (Perciliidae), Evelyn Habit, Mark C. Belk

Faculty Publications

Common name: Carmelita de Concepcion (Spanish).

Biological Status Of Leatherside Chub: A Framework For Conservation Of Western Freshwater Fishes, Mark C. Belk, Jerald B. Johnson

Faculty Publications

Outside of anadromous salmonids and a few endangered species, biology of native freshwater fishes of western North America is poorly known. What do we need to know to effectively manage native species and avoid decline and extinction? A recent analysis of the role of science in the Pacific salmon controversy outlines a clear framework for biological evaluation and management of native species. This framework has three components: (1) determine status of populations based on genetic and ecological variation, (2) identify and quantify threats to populations, and (3) determine actions to alleviate threats and promote conservation of populations. We use our …

Evolution In Neotropical Herpetofauna: Species Boundaries In High Andean Frogs And Evolutionary Genetics In The Lava Lizard Genus Microlophus (Squamata: Tropiduridae): A History Of Colonization And Dispersal, Edgar Benavides

Theses and Dissertations

In this collection of papers I have summarized my investigations into the field of evolutionary genetics and more specifically into patterns of biodiversity and evolutionary processes. The lizards (and frogs) studied here share common features in that they are largely present in unique environments, which are also regions that are biologically understudied. Most of these taxa show high degrees of endemism, interesting natural history characteristics, and each group manifests distinctive adaptations of general evolutionary interest. My work in the genus Telmatobius has been a progressive approach that began in my MS program, and it first focused on alpha taxonomy, morphological …

Genetic Considerations For The Conservation And Management Of Yellowstone Cutthroat Trout (Oncorhynchus Clarkii Bouvieri) In Yellowstone National Park, David J. Janetski

Theses and Dissertations

A key component to conservation is an accurate understanding of genetic subdivision within a species. Despite their ecological and economic importance, relatively little is understood about the genetic structuring of Yellowstone cutthroat trout in Yellowstone National Park. Here, we use traditional (Fst, Rst, Nm, and AMOVA) and modern (Bayesian assignment tests, coalescent theory, and nested clade analysis) analytical approaches to describe the population genetic subdivision of cutthroat trout spawning populations in Yellowstone Lake and to identify genetically distinct population segments throughout Yellowstone National Park. Evidence for restricted gene flow between spawning populations within Yellowstone Lake was detected using nested clade …

Phylogeographic Analyses Of Obligate And Facultative Cave Crayfish Species On The Cumberland Plateau Of The Southern Appalachians, Jennifer Elizabeth Buhay

Theses and Dissertations

Cave systems and their unique biota are widely viewed as highly endangered, yet very little is known about basic life history, ecology, distributions, habitat requirements, and evolutionary relationships of subterranean species. The crux of the problem in cave studies is the assumption that traditionally defined morpho-species represent distinct evolutionary lineages. Convergence is exhibited in the morphologies of many animal groups, vertebrate and invertebrate, which leads to confusion in diagnosing species' boundaries, geographic distributions, gene flow routes, and imperilment. This dissertation research includes phylogeographic analyses of freshwater cave-dwelling crayfishes in the Southern Appalachians, a global hotspot of subterranean biodiversity. By examining …

Delimitating Species Boundaries Within The Liomys Pictus- Spectabilis Complex (Rodentia: Heteromyidae), Victoria L. Vance

Theses and Dissertations

Previous studies based on morphological, allozymic and mitochondrial sequence data have indicated that Liomys pictus is paraplyletic relative to L. spectabilis. The purpose of this study was to determine the species boundaries that exist within this complex. I estimated phylogenetic relationships within this complex using sequence data from 1,140 bp of the mitochondrial DNA cytochrome b gene and two nuclear introns from engrailed protein (190 bp) and myosin heavy chain (254 bp) genes for approximately 712 individuals representing 82 localities across the range of L. pictus and L. spectabilis. Maximum parsimony, maximum likelihood, and Bayesian analyses suggest that there are …

The Dogma Of The 30 Meter Riparian Buffer: The Case Of The Boreal Toad (Bufo Boreas Boreas), Michael C. Goates

Theses and Dissertations

We tested the adequacy of standard 30 m riparian buffers for semi-aquatic vertebrate species, using the boreal toad (Bufo boreas boreas) as an example. We monitored toad populations in south-central Utah using radio telemetry during the summers of 2003 and 2004. We found 30 m buffers inadequate for protecting boreal toads and suggest this is likely true for other species as well. Managers must consider several factors when constructing buffers: (1) Buffer requirements may vary by time of year. While we located toads most often in wet habitats, toads commonly utilized upland habitats in late summer, occasionally at distances greater …

A Hydrothermal After-Ripening Time Model For Seed Dormancy Loss In Bromus Tectorum L., Phil S. Allen, Necia B. Bair

Faculty Publications

After-ripening, the loss of dormancy under dry conditions, is associated with a decrease in mean base water potential for germination of Bromus tectorum L. seeds. After-ripening rate is a linear function of temperature above a base temperature, so that dormancy loss can be quantified using a thermal after-ripening time (TAR) model. To incorporate storage water potential into TAR, we created a hydrothermal after-ripening time (HTAR) model. Seeds from two B. tectorum populations were stored under controlled temperatures (20 or 30° C) and water potentials (400 to 40MPa). Subsamples were periodically removed from each storage treatment and incubated at 15 or …

Patterns Of Habitat Use By Bats Along A Riparian Corridor In Northern Utah, Duke S. Rogers, Mark C. Belk, Malinda W. González, Brent L. Coleman

Faculty Publications

We examined patterns of habitat use within a community of bats along the Provo River in Heber Valley, Utah. The landscape was divided into 5 habitat categories: riparian forest, wetland, agricultural field, edge, and a habitat restoration site. We used Anabat II bat detectors to record the number of echolocation calls per night within each habitat type as an index of bat activity. Echolocation calls were classified into foraging guilds based on acoustic traits, and we analyzed activity by entire community and by the 4 guilds related to habitat type and environmental variables. Activity was not significantly related to moon …

Applications Of Phylogenetics To Issues In Freshwater Crayfish Biology, Keith A. Crandall

Faculty Publications

Freshwater crayfish have served as model organisms for over 125 years in scientific research, from areas such as neurobiology and vision research to conservation biology and evolution. Recently, evolutionary histories in the form of phylogenies have served as a critical foundation for testing hypotheses in such diverse research areas as well. In this article, I review the amazing diversity of freshwater crayfish, especially in a phylogenetic context and explore how these evolutionary histories have informed crayfish biology and can be used powerfully in the future to guide research in a diversity of areas. Throughout the article, I draw on examples …

Phylogeny And Biogeography Of Ice Crawlers (Insecta: Grylloblattodea): Evidence From Six Molecular Loci, Karl J. Jarvis

Theses and Dissertations

Ice crawlers (Insecta: Grylloblattodea) are rarely encountered insects that consist of five genera representing 26 species from North America and Asia. Asian grylloblattids are the most diverse, but North American ice crawlers (genus Grylloblatta) are known for their adaptation to cold conditions. Phylogenetic relationships among grylloblattid species and genera are not known. Late Pleistocene glaciations had a major effect on the current Grylloblatta distribution, because their specific habitat requirements restrict them to small geographical areas. Six genes were sampled in 37 individuals for 18S rRNA, 28S rRNA, histone 3, 12S rRNA, 16S rRNA, and cytochrome oxidase II (COII) from 27 …

Digestibility, Nitrogen Balance, And Blood Metabolites In Llama And Alpaca Fed Barley And Barley Alfalfa Forages., Heather Loree Davies

Theses and Dissertations

These projects were conducted to determine the digestibility of forage diets with differing CP levels in llamas and alpacas. The Utah study was designed to compare llama and alpaca nutritional parameters to determine if nutritional recommendations for llamas can be directly extrapolated to alpacas. The first study evaluated the effects of forage quality on blood metabolites and nitrogen balance in mature, intact male llamas (n = 4, 36 ± 4.4 months, 87 ± 17 kg) at high altitude in Letanias, Bolivia (4,267 m = aprox.14,000 ft above sea level). A second experiment was conducted with eight adult gelded camelids (n …

Phylogenetic Relationship Of Forest Spiny Pocket Mice (Genus Heteromys) Inferred From Mitochondrial And Nuclear Markers With Implications For Species Boundaries, Malinda Wallentine Gonzalez

Theses and Dissertations

I constructed a best estimate phylogeny based on congruence of multiple data sources. In recent years molecular data has been used both to construct phylogenies of taxonomic groups and to aid in the delimitation of new species. I generated and analyzed sequence data for forest spiny pocket mice (Genus Heteromys) for the mitochondrial gene cyt b (1143 bp) and two nuclear gene segments MYH2 (252 bp) and EN2 (189 bp). I used maximum parsimony and Bayesian analyses to infer relationships among species and to provide a framework for using a species delimitation method to investigate the possibility of multiple …

Vegetation Response Of A Wyoming Big Sagebrush (Artemisia Tridentata Ssp. Wyomingensis) Community To 6 Mechanical Treatments In Rich County, Utah, Daniel David Summers

Theses and Dissertations

In recent years, the importance of sagebrush to shrub-steppe ecosystems and associated plant and animal species has been recognized. The historical removal of herbaceous species by excessive and uncontrolled livestock grazing on many of our sagebrush ecosystems has resulted in a stagnant state where dense, competitive stands of sagebrush prevent herbaceous species from recovering. Most early research on sagebrush control was directed toward eradication to increase herbaceous forage for livestock production, rather than sagebrush thinning to improve shrub vigor and understory production for wildlife habitat and community diversity. Mechanical treatments have the ability to retain shrub and herbaceous components, while …

Phylogenetic History, Morphological Parallelism, And Speciation In A Complex Of Appalachian Salamanders (Genus: Desmognathus), Nathan D. Jackson

Theses and Dissertations

Understanding the mechanisms that generate shared morphologies across closely related taxa is important when identifying distinct evolutionary lineages using morphological characters. Desmognathus salamanders are an ideal group for testing hypotheses concerning the correlation between morphological similarity and genetic exchange within and among nominal species due to a pattern of high discordance between the two. Phylogeographic hypotheses are tested for populations of the D. quadramaculatus species complex throughout southern Appalachia by combining phylogenetic and population genetic methods with geographical information. Phylogenetic and phylogeographic inferences are then assessed in conjunction with morphological characteristics that have traditionally diagnosed taxonomic entities to understand the …

Biochemical And Molecular Nutrition Blocks As Dietary Supplements In Llamas (Lama Glama) In The Last Third Of The Gestation Period Of The Ceac, Janette Illanes Callejas

Theses and Dissertations

The present work consisted in the use of biochemical and molecular nutrition blocks (BMN) in llamas during the last third of the gestation period, at the Agricultural Experiment Center of Condori (CEAC), located 49 km north of the city of Oruro, and 12 km north of the Caracollo population, in the province of Cercado. For this research work, we used 20 pregnant llamas in the last third of their gestation period, between the ages of 2 and 3 years old, 10 of which belonged to the Khara breed, and 10 to the Thampulli breed. Two corrals of 7 x 7 …

Distribution Of Chemistry And Sexual Fecundity In The Lichenized-Fungi, Xanthoparmelia Cumberlandia And Xanthoparmelia Coloradoensis On Boulder Mountain, Aquarius Plateau, Ut, Heather Bird Jackson

Theses and Dissertations

Three aspects of Xanthoparmelia cumberlandia and Xanthoparmelia coloradoënsis populations found at two elevations are explored: clustering of secondary chemicals and the resulting implications for taxonomic distinctions, the usefulness of thallus size as an indirect measure of sexual fecundity, and the frequency of sexual reproduction.

First, we use clustering of 46 chemicals produced by X. cumberlandia and X. coloradoënsis to evaluate the adequacy of the current taxonomic distinction between them. Using principal components analysis and UPGMA, we find that the currently recognized species boundaries indicated by the presence of stictic acid in X. cumberlandia and salazinic acid in X. coloradoënsis are …

Neglected Taxonomy Of Rare Desert Fishes: Congruent Evidence For Two Species Of Leatherside Chub, Jerald B. Johnson, Thomas E. Dowling, Mark C. Belk

Faculty Publications

Conservation biologists rely heavily on taxonomy to set the scope for biological monitoring and recovery planning of rare or threatened species. Yet, taxonomic boundaries are seldom evaluated as falsifiable hypotheses that can be statistically tested. Here, we examine species boundaries in leatherside chub (Teleostei, Cyprinidae), an imperiled desert fish native to the Bonneville Basin and upper Snake River drainages of western North America. Recent molecular data hint that this fish could be composed of two distinct taxa that are geographically separated into northern and southern species. To formally test this hypothesis, we evaluated leatherside chub using several different categories of …

Density Effects On Growth, Survival And Diet Of June Sucker (Chasmistes Liorus): A Component Allee Effect In An Endangered Species., David Barrett Gonzalez

Theses and Dissertations

Density-dependence is considered one of the most important regulators of population growth, and it has been documented across a wide variety of species. Typically, population growth rate and components thereof decline with increasing density (i.e., negative density-dependence); however, in species that exhibit high population densities and social behavior, positive density-dependence (i.e., Allee effect) may occur at low density. June sucker, a federally endangered lake sucker endemic to Utah Lake, Utah, USA, occurred historically at high density, and it exhibits coordinated feeding behavior. These characteristics indicate a potential for the existence of an Allee effect at current low population densities. To …

Evolution And Phylogeny Of Basal Winged Insects With Emphasis On Mayflies (Ephemeroptera), Thomas H. Ogden

Theses and Dissertations

Ephemeroptera (mayflies) is a monophyletic group of semi-aquatic pterygote insects, comprising 3083 species, 376 genera, and 37 described families and are present on all continents, excluding Antarctica, being associated with freshwater and brackish water habitats. The order is unique among pterygote insects in possessing functional wings at the penultimate molt (subimago stage), prior to the full development of genitalia; in all other insects the presence of functional wings occurs only after the final molt. The purpose of this dissertation is to use molecular and morphological data, in order to investigate the position of the order Ephemeroptera among other insect orders, …

Testing Species Boundaries In An Ancient Species Complex With Deep Phylogeographic History: Genus Xantusia (Squamata: Xantusiidae), Keith A. Crandall, Elizabeth A. Sinclair, Robert L. Bezy, Kathryn Bolles, Jose L. Camarillo, Jack W. Sites

Faculty Publications

Identification of species in natural populations has recently received increased attention with a number of investigators proposing rigorous methods for species delimitation. Morphologically conservative species (or species complexes) with deep phylogenetic histories (and limited gene flow) are likely to pose particular problems when attempting to delimit species, yet this is crucial to comparative studies of the geography of speciation. We apply two methods of species delimitation to an ancient group of lizards (genus Xantusia) that occur throughout southwestern North America. Mitochondrial cytochrome b and nicotinamide adenine dinucleotide dehydrogenase subunit 4 gene sequences were generated from samples taken throughout the geographic …

Prevalence Of Teleological And Lamarckian Misconceptions Of Natural Selection Among College Students, Bryce T. Battisti

Theses and Dissertations

Science teachers and researchers note that students must correctly understand the role of natural selection in evolution to make sense of biology. The level of understanding of natural selection can be assessed using the Conceptual Inventory of Natural Selection (CINS) which is a 20-item multiple-choice test that incorporates student misconceptions as distractors. In the present study, Item Response Theory (IRT) was used to analyze the occurance of misconceptions on the CINS among 1192 students in an introductory non-majors biology course. The four most difficult topics in the CINS are: (a) how change occurs in a population; (b) origin of variation; …

Zapus Princeps, E. Blake Hart, Mark C. Belk, Eralee Jordan, Malinda W. Gonzalez

Faculty Publications

Zapus princeps Allen, 1893:71. Type locality “Florida, La Plata Co., Colorado.”
Zapus pacificus Merriam, 1897:104. Type locality “Prospect, Rogue River Valley, Jackson Co., Oregon.”
Zapus saltator Allen, 1899:3. Type locality “Telegraph Creek, British Columbia.”

The Impact Of Species Concept On Biodiversity Studies, Keith A. Crandall, Paul-Michael Agapow, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, Jonathon C. Marshall, Andy Purvis

Faculty Publications

Species are defined using a variety of different operational techniques. While discussion of the various methodologies has previously been restricted mostly to taxonomists, the demarcation of species is also crucial for conservation biology. Unfortunately, different methods of diagnosing species can arrive at different entities. Most prominently, it is widely thought that use of a phylogenetic species concept may lead to recognition of a far greater number of much less inclusive units. As a result, studies of the same group of organisms can produce not only different species identities but also different species range and number of individuals. To assess the …

Phylogeny Of The Polyneopterous Insects With Emphasis On Plecoptera: Molecular And Morpological Evidence, Matthew Dana Terry

Theses and Dissertations

Polyneoptera is an assemblage of eleven insect orders comprising the "orthopteroid" insects. It includes familiar insects such as grasshoppers, roaches, termites, earwigs and preying mantises; as well as the more obscure web-spinners, angel insects and ice-crawlers. We present a phylogenetic analysis of the polyneopteran orders based on 18S rDNA, 28S rDNA, Histone 3, and a coded morphology matrix for an extensive sampling of taxa. We investigate the use of congruence between separate datasets as an a priori measure of alignment quality. Our results support the paraphyly of Polyneoptera, the monophyly of Dictyoptera, sister taxon relationships between Embiidina + Phasmatodea and …

Phylogenetic Systematics And Evolution Within The Family Scincidae, Alison Swindle Whiting

Theses and Dissertations

Scincidae (skinks) comprise one of the largest families of lizards, and the more than 1300 species show great variation in body size and form, and are found worldwide in a diversity of habitats. The group presents many interesting questions ranging from the colonization of oceanic islands, to the evolution of limb loss, yet most of these and other questions remain understudied. The purpose of this dissertation is to use multiple mitochonidrial and nuclear DNA markers in connection with current cladistic methods to address evolutionary questions at many levels within Scincidae. In chapter one, a molecular phylogenetic study, based on six …

Threatened Fishes Of The World: Iotichthys Phlegethontis Cope, 1874 (Cyprinidae), Joseph H. Hanks, Mark C. Belk

Faculty Publications

Common name: least chub.

Multiple Domains Of The Co-Chaperone Hop Are Important For Hsp70 Binding, Gregory M. Nelson, Patricia E. Carrigan, Patricia J. Roberts, Jha'nae Stoffer, Daniel L. Riggs, David F. Smith

Faculty Publications

The Hop/Sti1 co-chaperone binds to both Hsp70 and Hsp90. Biochemical and co-crystallographic studies have suggested that the EEVD-containing C terminus of Hsp70 or Hsp90 binds specifically to one of the Hop tetratricopeptide repeat domains, TPR1 or TPR2a, respectively. Mutational analyses of Hsp70 and Hop were undertaken to better characterize interactions between the C terminus of Hsp70 and Hop domains. Surprisingly, truncation of EEVD plus as many as 34 additional amino acids from the Hsp70 C terminus did not reduce the ability of Hsp70 mutants to co-immunoprecipitate with Hop, although further truncation eliminated Hop binding. Hop point mutations targeting a carboxylate …

Epidemiology Of Ustilago Bullata Berk. On Bromus Tectorum L. And Implication For Biological Control, Toupta Boguena

Theses and Dissertations

The seedling-infecting pathogen Ustilago bullata Berk. is a naturally occurring biological control agent for cheatgrass (Bromus tectorum L.). The effects of temperature and nutrients on pathogen teliospore germination behavior and the effects of temperature on host seed germination were examined. The effects of temperature on sporidial proliferation, host infection in a temperature-controlled environment and in a field setting for eight populations were investigated. The infection success of Ustilago bullata on Bromus tectorum in cultivated fields as a function of seeding date, inoculation method, inoculum density, supplemental watering, and litter was also investigated. Teliospores germinated faster on potato dextrose agar than …

Evidence For Survival Of Pleistocene Climatic Changes In Northern Refugia By The Land Snail Trochoidea Geyeri, David Posada, Markus Pfenninger, Frederic Magnin

Faculty Publications

The study of organisms with restricted dispersal abilities and presence in the fossil record is particularly adequate to understand the impact of climate changes on the distribution and genetic structure of species. Trochoidea geyeri (Soos 1926) is a land snail restricted to a patchy, insular distribution in Germany and France. Fossil evidence suggests that current populations of T. geyeri are relicts of a much more widespread distribution during more favourable climatic periods in the Pleistocene. Results: Phylogeographic analysis of the mitochondrial 16S rDNA and nuclear ITS-1 sequence variation was used to infer the history of the remnant populations of T. …