Biology Commons^™

Beetle Tree Of Life Project, Dr. Michael Whiting

Journal of Undergraduate Research

Funding was received from the BYU ORCA mentorship program during 2010 to support undergraduates performing research in my lab, under the mentorship of postdoctoral researchers, graduate students, and myself. During 2010, this funding provided direct support for 8 undergraduates who are in various stages of completing research projects. The following report focuses on undergraduate achievements, but also provides summary data for graduate students and other lab participants.

Plant Diversity At Home And Abroad, Dr. Leigh Johnson

Journal of Undergraduate Research

This award supported a multifaceted mentoring environment for students with a focus on plant biodiversity. The objectives were to provide support for two students participating in a focused, study abroad program sponsored by an NSF Partnerships in Research and Education award for which the PI is a participant, and support for multifaceted research that includes training in herbarium curation and contemporary plant systematics. The goal for all participants was to provide training and skills useful for successful graduate study or employment. Because the project was extended beyond one year, this mentoring award serviced more students than originally anticipated. Beyond the …

Patagonian Field Study: An International, Cross-Cultural Mentoring Experience, Dr. Jerry Johnson

Journal of Undergraduate Research

This mentoring environment grant was awarded in 2008. The purpose of the project was twofold: (1) to help support BYU undergraduate students to participate in our Patagonia PIRE international field study program in Argentina and Chile; and (2) to support undergraduate participation in research on evolution of fishes in Mexico. Here I report on the outcomes of this project, specifically addressing the five points requested by the ORCA for MEG final reports.

Mitochondrial Genetics Of Alzheimer's Disease And Aging, Perry Gene Ridge

Theses and Dissertations

Mitochondria are essential cellular organelles and the location of the electron transport chain, the site of the majority of energy production in the cell. Mitochondria contain their own circular genome approximately 16,000 base pairs in length. The mitochondrial genome (mtDNA) encodes 11 protein-coding genes essential for the electron transport chain, 22 tRNA genes, and two rRNA genes. Mitochondrial malfunction occurs in many diseases, and changes in the mitochondrial genome lead to numerous disorders. Multiple mitochondrial haplotypes and sequence features are associated with Alzheimer's disease. In this dissertation we utilized TreeScanning, an evolutionary-based haplotype approach to identify haplotypes and sequence variation …

Orientocreadium Batrachoides Tubangui, 1931 (Orientocreadiidae): The Only Trematode Parasite Of Clarias Gariepinus (Burchell, 1822) (Clariidae) From The Asi River (Southern Turkey), Tayha Tepe, Mehmet Cemal Oğuz, Mark C. Belk, Remzi Özgen

Faculty Publications

Objective: Some information is available about the parasite fauna and incidence for Clarias gariepinus in Turkey, but digenean parasites have received little attention. The purpose of the study is to contribute to the parasite fauna of Turkey.

Methods: From 2007 to 2008, a total 63 Clarias gariepinus that were caught in the Asi River were purchased from the fish market in Hatay and brought on ice to the Parasitology Research Laboratory at Atatürk University. The fish were dissected. The obtained parasites were fixed with AFA, dyed with Mayer’s Carmalum, and mounted with Canada Balsam.

Results: Forty-eight fish were infected with …

A Tree Theory Case Study In Steinernema, Camille Eileen Finlinson Porter

Theses and Dissertations

It is widely assumed that current phylogenetic methods are fairly accurate at recovering the evolutionary relationships among different species, but evaluating the relative success of this enterprise is a difficult task. This study addresses some fundamental questions associated with generating phylogenetic trees. The complete genomes of five species of Steinernema were sequenced and assembled. Genes were predicted in AUGUSTUS and orthologous genes were found from those data using OrthoMCL. I aligned 3890 genes in MAFFT and eliminated poorly aligned positions with GBlocks. I created individual trees for each gene as well as a supermatrix tree in PAUP*, using a closely …

Characterization Of Sterile Tassel Silky Earl: A Homeotic B-Class Gene Involved In Specification Of Floral Organ Identity In Zea Mays, Steven Keith Williams

Theses and Dissertations

Specification of floral organ identity in angiosperm flowers is accomplished by the coordinated activity of A-, B-, C-, and E-class MADS-box genes. In the eudicots, B-class genes specify petal and stamen identity. This eudicot B-class function depends on the simultaneous expression of genes from two paralogous B-class lineages (the DEFICIENS/APETALA3 lineage and the GLOBOSA/PISTILLATA lineage). Proteins produced by genes from these two lineages interact as obligate heterodimers and together regulate the transcription of various downstream targets. These obligate heterodimers also positively regulate the transcription of the B-class genes themselves, thereby mediating a unique B-class autoregulatory feedback loop. There is compelling …

Evaluating The Performance Of Computational Approaches For Identifying Critical Sites In Protein-Coding Dna Sequences, Matthew Lewis Bendall

Theses and Dissertations

The ability to link a particular phenotype to its causative genotype is one of the most challenging objectives for biological research. Although the genetic code provides an explicit formula for determining the sequence of amino acid phenotypes produced by a given nucleotide sequence, identifying specific residues that are functionally important remains problematic. Many computational approaches have been developed that use patterns observed in DNA sequences to identify these critical sites. However, very few research studies have used empirical data to test whether these approaches are truly able to identify sites of interest.In most empirical studies, the actual protein function and …

Stoneflies Of Unusual Size: Population Genetics And Systematics Within Pteronarcyidae (Plecoptera), John S. Sproul

Theses and Dissertations

Chapter 1. The family Pteronarcyidae (Plecoptera) is a highly studied group of stoneflies and very important to a wide variety of aquatic studies. Several phylogenies have been proposed for this group recent decades, however there is little congruence between the various topologies. The present study revises the phylogeny of the group by combining molecular data from mitochondrial cytochrome oxidase subunit II, ribosomal subunit 12S, ribosomal subunit 16S, and nuclear loci ribosomal subinit 18S and Histone H3, with published morphological data in a parsimony-based total evidence analysis. The analysis produced a well-supported phylogeny with novel relationships within the genus Pteronarcys. …

Diversification And Conservation In The South American Dry Biomes: Distribution Modeling And Multilocus Lizard Phylogeography, Fernanda Werneck

Theses and Dissertations

The understanding of diversification of intraspecific lineages can shed light on speciation processes and ultimately biogeographic patterns across multiple spatial and temporal scales. In this dissertation I investigated the geographical and ecological factors promoting diversification across the South American dry diagonal biomes (i.e. Cerrado, Chaco, and Seasonally Dry Tropical Forests - SDTFs), through a coupled approach between multilocus phylogeographic and geospatial methods, in the larger context of interpreting the consequences of the resulting patterns for the conservation of biodiversity and evolutionary processes. In Chapter 1 I evaluate biogeographic hypotheses previously proposed and emphasize that the dry diagonal biomes are particularly …

Testing Crayfish Evolutionary Hypotheses With Phylogenetic Methods, Jesse W. Breinholt

Theses and Dissertations

This dissertation focuses on increasing the understanding of the evolution processes that have contributed to the diversification of freshwater crayfish. Chapter one estimates the divergence time of the three crayfish families and tests the hypothesis that diversification is tied to the break-up of Pangaea, Gondwanna, and Laurasia. I find that the families of crayfish diverged prior to or in association with the break-up of the three super continents. Chapter two addresses the evolutionary history of the genus Cambarus, using molecular data to test hypotheses of relationships based on chela and carapace morphology. The results provide evidence that the morphology used …

Dispersal Behavior Correlates With Personality Of A North American Fish, Josh E. Rasmussen, Mark C. Belk

Faculty Publications

The process of dispersal is determined by the interaction of individual (intrinsic) traits and environmental (extrinsic) factors. Although many studies address and quantify dispersal, few evaluate both intrinsic and extrinsic factors jointly. We test the relative importance of intrinsic traits (exploration tendency and size) and extrinsic factors (population density and habitat quality) on dispersal of a medium-sized western United States minnow, southern leatherside chub Lepidomeda aliciae. A generalized linear model with a binomial response was used to determine the probability of individuals dispersing one year after tagging. Medium-sized individuals that were more prone to explore novel environments were 10.7 …

The Phylogeography Of The Mountain Sucker [Catostomus (Pantosteus) Platyrhynchus], Nina Johanna Laitnen

Theses and Dissertations

Pantosteus, a subgenus of Catostomus, includes the mountain sucker (Catostomus playthyrnchus), whose speculated older origins in the Miocene/Pliocene can provide insight into the ancient geographical events of western North America. We believe that major geologic events influencing the diversification of mountain suckers include the rise of the Colorado Plateau, the connections between the ancient Snake River system and the Lahontan system and subsequently the connection of the Snake River system to the Columbia Basin, dispersal of mountain suckers across the continental divide, as well as the Pleistocene Bonneville flood. If this is true, we should see …

Effects Of Predation Environment And Food Availability On Somatic Growth In The Livebearing Fish Brachyrhaphis Rhabdophora (Pisces: Poeciliidae), Brittany Herrod Gale

Theses and Dissertations

Variation in somatic growth rates has interested biologists for decades because of the relationship between growth and other fitness-determining traits (i.e. fecundity, survival, and body size), and the corresponding effect of somatic growth on production of organisms humans use for food. The interaction between genetic variation in growth rates and environmentally induced variation in growth rates shows the pattern of growth across multiple environments (i.e. the reaction norm) that clarifies the history and potential future of evolutionary change in growth rates among populations. Theoretical predictions suggest variation in predator-induced mortality rates can influence mean growth rates and the shape of …

Phylogenetics Of Thysanoptera (Insecta: Paraneoptera), Rebecca S. Buckman

Theses and Dissertations

The order Thysanoptera (Insecta: Paraneoptera), commonly known as thrips, includes organisms that exhibit a wide range of social and feeding behaviors that are of particular interest in evolutionary studies. These studies within thrips have been inhibited by the lack of knowledge of thrips relationships. The recognized classification scheme strives to reflect evolutionary relationships and is based upon morphology. Molecular data is next as morphology alone is not enough to resolve relationships. Few molecular studies have been conducted and all were limited in their taxon sampling and genetic sampling. To provide a foundation of future evolutionary studies, the objectives of this …

A Floristic Survey Of The Lichens Of The Spring Mountains, Nevada, Usa, Monica W. Proulx

Theses and Dissertations

This thesis is the culmination of a graduate research project involving a floristic survey of the lichens of the Spring Mountain National Recreation Area (SMNRA), Humboldt-Toiyabe National Forest, Nevada. The project was based on extensive collections made between 1997 and 2007 as part of an air pollution biomonitoring program and a baseline established by Larry St. Clair (BYU). The Spring Mountains are a sky island mountain range in the Mojave Desert located less than an hour northwest of Las Vegas. A floristic survey of the lichen communities in the Spring Mountains represents a major addition to our understanding of the …

An Invasive Species Reduces Aquatic Insect Flux To Terrestrial Food Webs, Steven S. Merkley

Theses and Dissertations

Although it is well documented how introduced species can negatively affect native species, we only poorly understand how they may alter ecosystem functions. We investigated how an invasive fish affected the flux of aquatic insects to terrestrial food webs using mesocosms in a desert spring ecosystem. We compared aquatic insect emergence between alternative community states with monocultures and polycultures of two native species of fish, least chub (Iotichthys phlegethontis) and Utah chub (Gila atraria) plus, introduced western mosquitofish (Gambusia affinis). We tested three hypotheses: (1) aquatic insect biomass will be greater than terrestrial insect …

Changes In Life History Within An Individual's Lifetime, Eric J. Billman

Theses and Dissertations

A central goal of life history theory is to understand the selective factors that generate the diversity of reproductive patterns observed in nature. Within lifetime changes in reproductive investment will determine an organism's fitness; however, this area of life history theory has received less attention than comparisons among population that characterize life history traits as a single population mean. Reproductive allocation can be affected by multiple cues; the integration of these cues across an organism's lifetime generates the diversity in life history strategies observed in nature. Life history studies should examine the interacting effects of multiple cues on life history …

Multiplicity: An Organizing Principle For Cancers And Somatic Mutations, Lewis J. Frey, Stephen R. Piccolo, Mary E. Edgerton

Faculty Publications

Background: With the advent of whole-genome analysis for profiling tumor tissue, a pressing need has emerged for principled methods of organizing the large amounts of resulting genomic information. We propose the concept of multiplicity measures on cancer and gene networks to organize the information in a clinically meaningful manner. Multiplicity applied in this context extends Fearon and Vogelstein’s multi-hit genetic model of colorectal carcinoma across multiple cancers.

Methods: Using the Catalogue of Somatic Mutations in Cancer (COSMIC), we construct networks of interacting cancers and genes. Multiplicity is calculated by evaluating the number of cancers and genes linked by the measurement …

Morphological Convergence During Pregnancy Among Predator And Nonpredator Populations Of The Livebearing Fish Brachyrhaphis Rhabdophora (Teleostei: Poeciliidae), Jeff S. Wesner, Eric J. Billman, Adam Meier, Mark C. Belk

Faculty Publications

Predation can drive morphological divergence in prey populations, although examples of divergent selection are typically limited to nonreproductive individuals. In livebearing females, shape often changes drastically during pregnancy, reducing speed and mobility and enhancing susceptibility to predation. In the present study, we document morphological divergence among populations of nonreproductive female livebearing fish (Brachyrhaphis rhabdophora) in predator and nonpredator environments. We then test the hypothesis that shape differences among nonreproductive females are maintained among reproductive females between predator and nonpredator environments. Nonreproductive females in predator environments had larger caudal regions and more fusiform bodies than females in nonpredator environments; …

Species Trees And Species Delimitation With Multilocus Data And Coalescent-Based Methods: Resolving The Speciation History Of The Liolaemus Darwinii Group (Squamata, Tropiduridae), Arley Camargo Bentaberry

Theses and Dissertations

The inference of species boundaries and phylogenetic relationships are fundamental for evolutionary, ecological, and conservation studies. The resolution of species boundaries and the inference of phylogenetic relationships among species are required to define the units of analysis and to find the most closely related units for evaluating alternative models of speciation. I highlight lizards as model organisms for ecological and evolutionary studies, emphasizing their contributions to advances in understanding linkages between phylogeography and speciation. In this dissertation, I focus on the phylogenetic relationships of the lizards in the Liolaemus darwinii group, and the species boundaries of a nested clade within …

Gene Flow And Dispersal Of The Flatworm, Polycelis Coronata: A Multiscale Analysis, Jeffrey N. Moore

Theses and Dissertations

We determined genetic variance and gene flow across multiple scales (reaches, headwater segments, and catchments) to examine the dispersal ability of the flatworm Polycelis coronata along the Wasatch Mountains of Utah. Multiple models predict patterns of genetic differentiation in stream invertebrates based on dispersal traits and the spatial connectivity of the habitat. The stream hierarchy model predicts genetic differentiation to be low and gene flow to be high between reaches nested in segments, moderate among segments within catchments, and differentiation to be highest and gene flow lowest among catchments, whereas the headwater model predicts the greatest differentiation between headwater segments. …

Antimicrobial And Anticancer Activity Of Essential Oils From Guatemalan Medicinal Plants, Andrew B. Miller

Theses and Dissertations

Guatemalan medicinal plants were collected and screened for the presence of essential oils using steam distillation. Oil was found in 63 species from 24 families and was tested in tube dilution assays for activity against Escherichia coli, Staphylococcus aureus, Streptococcus mutans, Lactobacillus acidophilus and Candida albicans. Several essential oils were highly active with 20 instances of oils inhibiting the microbes at an MIC of 0.31 µl/ml. Oils were also tested against cancerous and established cell lines using a 15% (v/v) agar-media which was developed to improve essential oil solubility. Assays were performed against three cancer lines: …

Predicting The Distribution Of Air Pollution Sensitive Lichens Using Habitat Niche Modeling, Gajendra Shrestha

Theses and Dissertations

Usnea hirta and Xanthoparmelia cumberlandia are commonly used as bio-monitors of air quality. In order to more accurately and efficiently determine the distribution of these two sensitive indicator species, we have developed a probabilistic distribution map as a function of 9 macroclimatic and topographic variables for the White River National Forest, Colorado using Non-Parametric Multiplicative Regression (NPMR) analysis. Furthermore, we also developed a logistic regression (LR) model for X. cumberlandia in order to evaluate the strengths and limitations of the NPMR model. The best model for U. hirta included four variables - solar radiation, average monthly precipitation, average monthly minimum …

Model Detection Based Upon Amino Acid Properties, Kit J. Menlove

Theses and Dissertations

Similarity searches are an essential component to most bioinformatic applications. They form the bases of structural motif identification, gene identification, and insights into functional associations. With the rapid increase in the available genetic data through a wide variety of databases, similarity searches are an essential tool for accessing these data in an informative and productive way. In our chapter, we provide an overview of similarity searching approaches, related databases, and parameter options to achieve the best results for a variety of applications. We then provide a worked example and some notes for consideration. Homology detection is one of the most …

Genomic Analysis Of Nematode-Environment Interaction, Bishwo Adhikari

Theses and Dissertations

The natural environments of organisms present a multitude of biotic and abiotic challenges that require both short-term ecological and long-term evolutionary responses. Though most environmental response studies have focused on effects at the ecosystem, community and organismal levels, the ultimate controls of these responses are located in the genome of the organism. Soil nematodes are highly responsive to, and display a wide variety of responses to changing environmental conditions, making them ideal models for the study of organismal interactions with their environment. In an attempt to examine responses to environmental stress (desiccation and freezing), genomic level analyses of gene expression …

A Correlation Of Teacher Understanding Of The Nature Of Science (Nos) With Student Understanding, David G. Kent

Theses and Dissertations

This is a study of how a teacher's understanding of the nature of science (NOS) correlates to student understanding of the nature of science. Participants are in semester long seventh grade science classes in a suburban school district. Seven strands of the nature of science were identified in the literature. Four strands were analyzed in this study. Teachers were ranked according to their understanding of the nature of science and compared to their corresponding students' average gain. There was no definitive pattern between the teacher's and corresponding students' gain. When broken down by strand, there still was no definitive pattern …

Investigation Of Potential Trapping Bias In Malaise Traps Due To Mesh Gauge, In Two Habitats, David Jensen Betts

Theses and Dissertations

Malaise traps are a common tool for collecting insects used by many researchers. Although there have been variations in the models and materials used for Malaise traps, the potential for sampling bias due to mesh gague has been explored inadequately. This study compared coarse and fine mesh Townes model Malaise traps in two habitats on the Grand Staircase-Escalante National Monument. The two habitats next to the Lick Wash trailhead were defined by dominant vegetation type – sagebrush and grasses or Piñon-Juniper. We collected from three sites per habitat type, over three consecutive days in June in both 2006 and 2007. …

Assessing Traditional Morphology- And Chemistry-Based Species Circumspections In Lichenized Ascomycetes: Character Evolution And Molecular Species Delimitation In Common Western North American Lichens, Steven Leavitt

Theses and Dissertations

Accurate species delimitation has critical implications for ecological and conservation studies; and for understanding factors driving diversification. However, a growing body of evidence indicates that morphology-based species circumspection in lichenized ascomycetes often fails to accurately represent the number of fungal species. The use of molecular data in lichen systematics provides an important alternative to traditional morphological characters for identifying natural groups and assessing evolutionary histories in challenging lichen taxa. In this work, I examined two common lichen-forming genera in western North America, Rhizoplaca and Xanthoparmelia, as models for investigating character evolution, species delimitation in morphologically and chemically diverse species, …

Landscape-Scale And Macrohabitat-Scale Variation In Growth And Survival Of Young June Sucker (Chasmistes Liorus) In Utah Lake, Joshua Daniel Kreitzer

Theses and Dissertations

The spatial scales at which ecological phenomena are viewed constrain the results of interactions between species and their environments. In lake ecosystems, important dynamics have been identified at the landscape scale and the macrohabitat scale. To determine if landscape-scale effects and macrohabitat-scale effects are important in survival and growth of young June suckers, we compared variation among sites in Utah Lake. Large semi-permeable cages were used to house June suckers in situ at five sites representing landscape-scale variation and two sites representing macrohabitat-scale variation in Utah Lake. We compared survival and growth among sites and related it to resource availability …