Biology Commons^™

Eight-Legged Encounters—Arachnids, Volunteers, And Art Help To Bridge The Gap Between Informal And Formal Science Learning, Eileen Hebets, Melissa Welch-Lazoritz, Pawl Tisdale, Patricia Wonch Hill

Eileen Hebets Publications

Increased integration and synergy between formal and informal learning environments is proposed to provide multiple benefits to science learners. In an effort to better bridge these two learning contexts, we developed an educational model that employs the charismatic nature of arachnids to engage the public of all ages in science learning; learning that aligns with the Next Generation Science Standards (NGSS Disciplinary Core Ideas associated with Biodiversity and Evolution). We created, implemented, and evaluated a family-focused, interactive science event—Eight-Legged Encounters (ELE)—which encompasses more than twenty modular activities. Volunteers facilitated participant involvement at each activity station and original …

Audiobook Of A World From Dust, Ben Mcfarland

Faculty Open Access Books

A World From Dust is a popular science book about the chemical sequence behind the evolution of creation.

It’s about how geology, biology, and chemistry worked together over billions of years, providing a hidden order under the random flow of genes and lava and water.

It’s about the chemical job that each element takes up in life, and how that job is predictable from its place on the periodic table.

It can be told as the story of many elements: how iron and sulfur gave a spark of life; how manganese was a key for oxygen; and how copper and …

Deciphering The Origin, Evolution, And Physiological Function Of The Subtelomeric Arylalcohol Dehydrogenase Gene Family In The Yeast Saccharomyces Cerevisiae, Dong Dong Yang, Gustavo M. De Billerbeck, Jin Jing Zhang, Frank Rosenzweig, Jean Marie Francois

Biological Sciences Faculty Publications

Homology searches indicate that Saccharomyces cerevisiae strain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). Yeast AAD genes are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes, AAD4 and AAD14, encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with the oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns. Other yeast AAD genes are undergoing pseudogenization. The 5' sequence of AAD15 has been deleted from the genome. Repair of an AAD3 missense mutation at the catalytically essential Tyr73 …

Identification Of Novel Mites (Miniature Inverted-Repeat Transposable Elements) In Coxiella Burnetii: Implications For Protein And Small Rna Evolution, Shaun Wachter, Rahul Raghavan, Jenny Wachter, Michael F. Minnick

Biological Sciences Faculty Publications

Background: Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature invertedrepeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. However, information regarding bacterial MITEs is limited.

Results: We describe two MITE families discovered during research on small non-coding …

De-Extinction And The Conception Of Species, Leonard Finkelman

Faculty Publications

Developments in genetic engineering may soon allow biologists to clone organisms from extinct species. The process, dubbed “de-extinction,” has been publicized as a means to bring extinct species back to life. For theorists and philosophers of biology, the process also suggests a thought experiment for the ongoing “species problem”: given a species concept, would a clone be classified in the extinct species? Previous analyses have answered this question in the context of specific de-extinction technologies or particular species concepts. The thought experiment is given more comprehensive treatment here. Given the products of three de-extinction technologies, twenty-two species concepts are “tested” …

A Closer Look At The Items Within Three Measures Of Evolution Acceptance: Analysis Of The Mate, I-Sea, And Gaene As A Single Corpus Of Items, William L. Romine, Amber Todd, Emily M. Walter

Biological Sciences Faculty Publications

Background

Current direct Likert measures for evolution acceptance include the MATE, GAENE, and I-SEA. Pros and cons of each of these instruments have been debated, and yet there is a dearth of research teasing out their similarities and differences when they are used together in a single context beyond the fact that their measures tend to be highly correlated. We administered these to 452 college students in non-major biology classes at two research-intensive universities from the Midwestern and Western United States to investigate the measurement properties of the items within these instruments when combined as a single corpus.

Results

Factor …

Biodiversity And Evolution In The Guiana Shield, South America, Andrew Michael Snyder

Electronic Theses and Dissertations

The neotropics are characterized as the most species rich region in the world. Unfortunately, the region's unparalleled biodiversity has not protected it from ongoing threats such as agriculture, mining, logging, oil extraction, and climate change. I studied the biodiversity and evolution of the herpetofauna of South America in order to investigate the influence of historical geological and climatological events in shaping extant neotropical diversity, particularly the Guiana shield. For my research, I set out to explore the processes involved in shaping the remarkable extant diversity using anuran amphibians as models. With my dissertation, I provide a comprehensive review of the …

Parasitaemia Data And Molecular Characterization Of Haemoproteus Catharti From New World Vultures (Cathartidae) Reveals A Novel Clade Of Haemosporida, Michael J. Yabsley, Ralph E.T. Vanstreels, Ellen S. Martinsen, Alexandra G. Wickson, Amanda E. Holland, Sonia M. Hernandez, Alec T. Thompson, Susan L. Perkins, Christopher A. Lawrence Bryan, Christopher A. Cleveland, Emily Jolly, Justin D. Brown, Dave Mcruer, Shannon Behmke, James C. Beasley

Faculty & Staff Scholarship

Background: New World vultures (Cathartiformes: Cathartidae) are obligate scavengers comprised of seven species in five genera throughout the Americas. Of these, turkey vultures (Cathartes aura) and black vultures (Coragyps atratus) are the most widespread and, although ecologically similar, have evolved differences in morphology, physiology, and behaviour. Three species of haemosporidians have been reported in New World vultures to date: Haemoproteus catharti, Leucocytozoon toddi and Plasmodium elongatum, although few studies have investigated haemosporidian parasites in this important group of species. In this study, morphological and molecular methods were used to investi- gate the epidemiology and molecular biology of haemosporidian parasites of …

Natural And Anthropogenic Drivers Of Tree Evolutionary Dynamics, Brandon M. Lind

Theses and Dissertations

Species of trees inhabit diverse and heterogeneous environments, and often play important ecological roles in such communities. As a result of their vast ecological breadth, trees have become adapted to various environmental pressures. In this dissertation I examine various environmental factors that drive evolutionary dynamics in threePinusspecies in California and Nevada, USA. In chapter two, I assess the role of management influence of thinning, fire, and their interaction on fine-scale gene flow within fire-suppressed populations of Pinus lambertiana, a historically dominant and ecologically important member of mixed-conifer forests of the Sierra Nevada, California. Here, I find evidence …

Functional Variation In The Mitochondrial Genome Of The Yeast Saccharomyces Cerevisiae, John F. Wolters

Graduate Dissertations and Theses

Mitochondrial haplotypes contribute to functional diversity in natural populations. Uniparental inheritance makes it difficult to characterize the genetic architecture of mitochondrially driven phenotypes. In this work I explored the natural diversity of mitochondrial genomes in the yeast Saccharomyces cerevisiae. Few complete mitochondrial genomes were available for S. cerevisiae owing to challenges in high-throughput sequencing. I developed sequencing strategies using new technologies to generate complete high quality yeast mitochondrial genomes. Comparisons of 100 complete yeast mitochondrial genomes demonstrated extensive variation between populations in coding sequences and variable introns.

I demonstrated that these mitochondrial variants directly caused growth differences in strains with …

From Ground Pools To Treeholes: Convergent Evolution Of Habitat And Phenotype In Aedes Mosquitoes, John Soghigian, Theodore G. Andreadis, Todd P. Livdahl

Biology

Background: Invasive mosquito species are responsible for millions of vector-borne disease cases annually. The global invasive success of Aedes mosquitoes such as Aedes aegypti and Aedes albopictus has relied on the human transport of immature stages in container habitats. However, despite the importance of these mosquitoes and this ecological specialization to their widespread dispersal, evolution of habitat specialization in this group has remained largely unstudied. We use comparative methods to evaluate the evolution of habitat specialization and its potential influence on larval morphology, and evaluate whether container dwelling and invasiveness are monophyletic in Aedes. Results: We show that habitat specialization …

Developmental Nonlinearity Drives Phenotypic Robustness, Rebecca M. Green, Jennifer L. Fish, Nathan M. Young, Francis J. Smith, Benjamin Roberts, Katie Dolan, Irene Choi, Courtney L. Leach, Paul Gordon, James M. Cheverud, Charles C. Roseman, Trevor J. Williams, Ralph S. Marcucio, Benedikt Hallgrímsson

Biology: Faculty Publications and Other Works

Robustness to perturbation is a fundamental feature of complex organisms. Mutations are the raw material for evolution, yet robustness to their effects is required for species survival. The mechanisms that produce robustness are poorly understood. Nonlinearities are a ubiquitous feature of development that may link variation in development to phenotypic robustness. Here, we manipulate the gene dosage of a signaling molecule, Fgf8, a critical regulator of vertebrate development. We demonstrate that variation in Fgf8 expression has a nonlinear relationship to phenotypic variation, predicting levels of robustness among genotypes. Differences in robustness are not due to gene expression variance or …

Why Does It Take Two To Tango? Lifetime Fitness Consequences Of Parental Care In A Burying Beetle, Ashlee N. Smith, J. Curtis Creighton, Mark C. Belk

Faculty Publications

In species that require parental care, each parent can either care for their offspring or leave them in the care of the other parent. For each parent this creates three possible parental care strategies: biparental care, uniparental (male or female) care, and uniparental desertion by either the male or female. The burying beetle, Nicrophorus orbicollis, typically exhibits biparental care of offspring, and thus provides a unique system that allows us to compare the fitness benefits of these parental care strategies in an unconfounded way. In this study, we assess the lifetime fitness of biparental care, uniparental care, and uniparental …

Deep Ancestry Of Programmed Genome Rearrangement In Lampreys, Vladimir A. Timoshevskiy, Ralph T. Lampman, Jon E. Hess, Laurie L. Porter, Jeramiah J. Smith

Biology Faculty Publications

In most multicellular organisms, the structure and content of the genome is rigorously maintained over the course of development. However some species have evolved genome biologies that permit, or require, developmentally regulated changes in the physical structure and content of the genome (programmed genome rearrangement: PGR). Relatively few vertebrates are known to undergo PGR, although all agnathans surveyed to date (several hagfish and one lamprey: Petromyzon marinus) show evidence of large scale PGR. To further resolve the ancestry of PGR within vertebrates, we developed probes that allow simultaneous tracking of nearly all sequences eliminated by PGR in P. marinus and …

T6ss Intraspecific Competition Orchestrates Vibrio Cholerae Genotypic Diversity, Benjamin Kostiuk, Daniel Unterweger, Daniele Provenzano, Stefan Pukatzki

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Vibrio cholerae is a diverse species that inhabits a wide range of environments from copepods in brackish water to the intestines of humans. In order to remain competitive, V. cholerae uses the versatile type-VI secretion system (T6SS) to secrete anti-prokaryotic and anti-eukaryotic effectors. In addition to competing with other bacterial species, V. cholerae strains also compete with one another. Some strains are able to coexist, and are referred to as belonging to the same compatibility group. Challenged by diverse competitors in various environments, different V. choleare strains secrete different combination of effectors - presumably to best suit their niche. Interestingly, …

Robust Algorithms For Detecting Hidden Structure In Biological Data, Roman Sloutsky

Arts & Sciences Graduate Student Theses and Dissertations

Biological data, such as molecular abundance measurements and proteinsequences, harbor complex hidden structure that reflects its underlyingbiological mechanisms. For example, high-throughput abundance measurementsprovide a snapshot the global state of a living cell, while homologousprotein sequences encode the residue-level logic of the proteins' functionand provide a snapshot of the evolutionary trajectory of the protein family.In this work I describe algorithmic approaches and analysis software Ideveloped for uncovering hidden structure in both kinds of data.Clustering is an unsurpervised machine learning technique commonly usedto map the structure of data collected in high-throughput experiments,such as quantification of gene expression by DNA microarrays orshort-read sequencing. …

The Discovery Of Xy Sex Chromosomes In A Boa And Python, Tony Gamble, Todd A. Castoe, Stuart V. Nielsen, Jason L. Banks, Daren C. Card, Drew R. Schield, Gordon W. Schuett, Warren Booth

Biological Sciences Faculty Research and Publications

For over 50 years, biologists have accepted that all extant snakes share the same ZW sex chromosomes derived from a common ancestor [1, 2, 3], with different species exhibiting sex chromosomes at varying stages of differentiation. Accordingly, snakes have been a well-studied model for sex chromosome evolution in animals [1, 4]. A review of the literature, however, reveals no compelling support that boas and pythons possess ZW sex chromosomes [2, 5]. Furthermore, phylogenetic patterns of facultative parthenogenesis in snakes and a sex-linked color mutation in the ball python (Python regius) are best explained by boas and pythons possessing …

Review Of The Sub-Saharan Africa Species Of Dignomus And Phylogenetic Analysis Of The Bostrichoids (Coleoptera: Bostrichoidea: Ptinidae), Amelia Lesbeth Smith

Masters Theses & Specialist Projects

Sub-Saharan Africa is home to nine described species of Dignomus Wollaston, 1862. Study and dissection of specimens has led me to the hypothesis that there are nine undocumented species in this region. Descriptions and images of the new species are presented and discussed, along with a compiled list of all described species from the Sub- Saharan region. The probable biology as geographic distributions for members of the genus are also given.

Additionally, a phylogenetic analysis of 95 species of bostrichoids using CO1 molecular data was done with a focus on the origins of Dignomus and Pseudomezium. parsimony and bayesian analyses …

A Linkage Map For The Newt Notophthalmus Viridescens: Insights In Vertebrate Genome And Chromosome Evolution, Melissa C. Keinath, S. Randal Voss, Panagiotis A. Tsonis, Jeramiah J. Smith

Biology Faculty Publications

Genetic linkage maps are fundamental resources that enable diverse genetic and genomic approaches, including quantitative trait locus (QTL) analyses and comparative studies of genome evolution. It is straightforward to build linkage maps for species that are amenable to laboratory culture and genetic crossing designs, and that have relatively small genomes and few chromosomes. It is more difficult to generate linkage maps for species that do not meet these criteria. Here, we introduce a method to rapidly build linkage maps for salamanders, which are known for their enormous genome sizes. As proof of principle, we developed a linkage map with thousands …

The Santa Ana Speckled Dace (Rhinichthys Osculus): Phylogeography And Molecular Evolution Of The Mitochondrial Dna Control Region, James Jay Vanmeter

Electronic Theses, Projects, and Dissertations

The purpose of this genetic study of the Santa Ana Speckled Dace Rhinichthys osculus was three-fold. The first goal was to characterize the molecular structure of the mtDNA control region of R. osculus. An 1143 base-pair region of the mitochondrial DNA genome, which included the complete control region was sequenced for all individuals. Analysis of the sequence data revealed that the molecular structure of the speckled dace control region was similar to the molecular structure described for other vertebrate taxa. The speckled dace control region contains three major domains, which vary in base frequency as well as in the frequency …

Interaction Between Predation Environment And Diet Constrains Body Shape In Utah Chub, Gila Atraria (Cypriniformes: Cyprinidae), Trevor J. Williams, Jerald B. Johnson, Mark C. Belk

Faculty Publications

Evolution typically occurs in response to a suite of selective pressures. Yet, many studies of natural selection in the wild only investigate a single selective agent at a time. This can be problematic when selective agents act in non-additive ways. Here we evaluate the interactive effects of diet and predation on the evolution of body shape in the cyprinid fish Utah chub (Gila atraria). We found that both factors and the interaction between them are significant predictors of body shape. This interaction is likely a result of different forms of selective pressures, where predation is a stabilizing selective …

Oldest Skeleton Of A Plesiadapiform Provides Additional Evidence For An Exclusively Arboreal Radiation Of Stem Primates In The Palaeocene, Stephen B. Chester, Thomas E. Williamson, Jonathan I. Bloch, Mary T. Silcox, Eric J. Sargis

Publications and Research

Palaechthonid plesiadapiforms from the Palaeocene of western North America have long been recognized as among the oldest and most primitive euarchontan mammals, a group that includes extant primates, colugos and treeshrews. Despite their relatively sparse fossil record, palaechthonids have played an important role in discussions surrounding adaptive scenarios for primate origins for nearly a half-century. Likewise, palaechthonids have been considered important for understanding relationships among plesiadapiforms, with members of the group proposed as plausible ancestors of Paromomyidae and Microsyopidae. Here, we describe a dentally associated partial skeleton of Torrejonia wilsoni from the early Palaeocene (approx. 62Ma) of New Mexico, which …

Human Evolution And Divine Agency, Alexandra Rakestraw

Dialogue & Nexus

Modern Christians often find themselves at a crossroads when confronted with the two predominant understandings of human and universal origins. Plain sense readings of Genesis lead many to believe in a historical six-day creation that occurred in the past ten thousand years while proponents on the other side of the spectrum use current scientific understanding to support a creation that occurs through evolutionary means. How one views human origins has a profound impact on one’s concept of how God works in the cosmos. In this paper, I will lay out a background to better understand the characters of Adam and …

Moral Awareness, Original Sin And The Atonement, Tanner Gregory

Dialogue & Nexus

I will explore how evolution impacts the Christian notion of The Fall of man, and, ultimately, the atonement. Various theories of atonement in the Christian tradition generally assume universal and individual sinfulness in humanity. In some cases, this sinfulness is thought to be the result of a distinct moment of rebellion against God, and is transmitted to all of the descendants of Adam. Here, atonement involves Christ’s sacrifice as the means liberate humanity from the bondage of our sinful nature. Evolution collides with these traditional models. Instead of a creation originally void of death and later corrupted by sin, evolution …

Immunology Of The Gray Short-Tailed Opossum During Pregnancy And Prenatal Development, Victoria L. Hansen

Biology ETDs

Vertebrate species that bear live young have overcome the evolutionary challenge of maintaining both a functional adaptive immune system and viviparous life cycle. In normal pregnancy, viviparous mothers are able sustain and nourish a fetus that is genetically half non-self without mounting an immunological attack. In 1953 Sir Peter Medawar brought attention to the “enigma of the fetal graft” and immunologists have been puzzling out the intricacies of fetal tolerance ever since. Although viviparity has evolved in all jawed vertebrate lineages aside from Aves, the vast majority of reproductive immunology research has been limited to eutherian mammals. There are insights …

Novel Approaches To Exploring Silk Use Evolution In Spiders, Rachael Elaina Alfaro

Biology ETDs

Spider silk is enigmatic, and web structure, design, and adult morphology of the spinning apparatus of spiders once informed how systematists approached the spider phylogeny. The orb-web and adaptation of viscous silk was considered a key innovation leading to rapid diversification of spiders. However, the advent of molecular techniques including recent phylogenomics studies, overturned this major paradigm in spider evolution. Clades once considered monophyletic are no more. The orb-web is not a pinnacle of evolution, and the former sister group, using cribellate silk (loops of fibrils combed from a specialized silk plate on the abdomen), is now sister to the …

Evolution And The Fall, Andrew Tate

Dialogue & Nexus

Within Christianity, there are a spectrum of beliefs regarding the function and mode of baptism, what constitutes original sin (or in what form it exists), modes of worship, gender roles (or if they even exist). I will argue here that despite varying dogmas and ideologies one consistent position over two millennia is that Jesus, as the Son of God, came to the earth, died on a cross, and was raised from the grave. Following this is the belief that in some way through these actions, either natural or supernatural, he has given humanity the opportunity to be redeemed. Through this …

Divine Action And Teleology In An Evolutionary World, Emily Sparks

Dialogue & Nexus

In this paper I explore three possibilities: 1) whether or not there is room for divine action in a dynamic, undetermined, evolutionary world; 2) if divine action is necessary to explain the outcome of creation; and 3) if there is purpose (e.g. teleology) in such a world. I will address the implications of indeterminacy, parts-and-whole behavior (or emergence), and directionality for divine agency. Models of God’s action informed by these trends will be provided. Finally, I will explain the teleological implications of these discoveries and God’s action and conclude with implications to the Christian faith.

Phylogenetics, Biogeography, And Patterns Of Diversification Of Geckosacross The Sunda Shelf With An Emphasis On The Genuscnemaspis (Strauch, 1887), Perry Lee Wood

Theses and Dissertations

In my dissertation I investigate two genera of geckos (Cyrtodactylus and Cnemaspis) that are distributed across Southeast Asia with an emphasis on Cnemaspis. In Chapter 1 I use a multilocus dataset, ancestral area analyses, and molecular clock dating to generate a species level time calibrated phylogeny to test the monophyly of Cyrtodactylus and to identify major biogeographical patterns. I identified that Cyrtodactylus is monophyletic only if the the Sri Lankan genus often recognized as Geckoella is included. The results of the Biogeographical analyses reveal a west to east pattern of diversification. Chapter 2 I use a traditional morphological dataset to …

Crassulacean Acid Metabolism As A Continuous Trait: Variability In The Contribution Of Crassulacean Acid Metabolism (Cam) In Populations Of Portulacaria Afra, Lonnie J. Guralnick, Kate Gladsky

Arts & Sciences Faculty Publications

Portulacaria afra L. is a dominant facultative CAM species growing in the Southeastern Cape of South Africa. P. afra is well adapted to regions of the Spekboom thicket in areas of limited and sporadic rainfall. P. afra populations occur in isolated drainages. We hypothesized the utilization of CAM would vary in the different populations in response to rainfall and temperature gradients. Carbon isotope composition can be used to determine the contribution of CAM in leaf tissue. P. afra leaves of populations were analyzed in transects running south to north and east to west in locations from the coast to elevations …