Life Sciences Commons^™

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 …

Characterizing Mekk1: Candidate Behavioural Isolation Gene, Caryn Dooner

Electronic Thesis and Dissertation Repository

Behavioural isolation can occur due to divergence in aspects of courtship and mating, and can contribute to reproductive isolation. The purpose of this study is to determine how a gene, Mekk1, contributes to female rejection behaviour between D. melanogaster and D. simulans. Unique polymorphisms were identified within D. simulans Mekk1 that could contribute to behaviour, most of which are non-coding. Both transcripts of Mekk1 appear to be expressed at similar levels in D. simulans and D. melanogaster. These data also indicate that Mekk1 may be expressed in a specific region of the brain called the mushroom body, …

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 …

Characterizing The Evolutionary Path(S) To Early Homo, Lauren Schroeder, Charles C. Roseman, James M. Cheverud, Rebecca R. Ackermann

James Cheverud

Numerous studies suggest that the transition from Australopithecus to Homo was characterized by evolutionary innovation, resulting in the emergence and coexistence of a diversity of forms. However, the evolutionary processes necessary to drive such a transition have not been examined. Here, we apply statistical tests developed from quantitative evolutionary theory to assess whether morphological differences among late australopith and early Homo species in Africa have been shaped by natural selection. Where selection is demonstrated, we identify aspects of morphology that were most likely under selective pressure, and determine the nature (type, rate) of that selection. Results demonstrate that selection must …

Diaspora, A Large Family Of Ty3-Gypsy Retrotransposons In Glycine Max, Is An Envelope-Less Member Of An Endogenous Plant Retrovirus Lineage, Sho T. Yano, Bahman Panbehi, Arpita Das, Howard M. Laten

Howard Laten

Background The chromosomes of higher plants are littered with retrotransposons that, in many cases, constitute as much as 80% of plant genomes. Long terminal repeat retrotransposons have been especially successful colonizers of the chromosomes of higher plants and examinations of their function, evolution, and dispersal are essential to understanding the evolution of eukaryotic genomes. In soybean, several families of retrotransposons have been identified, including at least two that, by virtue of the presence of an envelope-like gene, may constitute endogenous retroviruses. However, most elements are highly degenerate and are often sequestered in regions of the genome that sequencing projects initially …

Adaptive Evolution And Inherent Tolerance To Extreme Thermal Environments, Jennifer Cox, Alyxandria Schubert, Michael Travisano, Catherine Putonti

Catherine Putonti

Background When introduced to novel environments, the ability for a species to survive and rapidly proliferate corresponds with its adaptive potential. Of the many factors that can yield an environment inhospitable to foreign species, phenotypic response to variation in the thermal climate has been observed within a wide variety of species. Experimental evolution studies using bacteriophage model systems have been able to elucidate mutations, which may correspond with the ability of phage to survive modest increases/decreases in the temperature of their environment. Results Phage ΦX174 was subjected to both elevated (50°C) and extreme (70°C+) temperatures for anywhere from a few …

The Genetic And Environmental Basis For Chc Biosynthesis In Drosophila, Heather Ke Ward

Electronic Thesis and Dissertation Repository

Cuticular hydrocarbons (CHCs) are produced by insects and primarily used to prevent desiccation. In Drosophila, certain compounds have secondary roles as infochemicals that may act during courtship to influence mate choice. Certain CHCs may stimulate courtship with heterospecifics or act to repel conspecifics. The CHC profile produced by an individual is the result of the interaction between its genetic background and the environment, though the genes that underlie species differences in CHC production and how the environment can modulate the abundance of individual compounds within a species is not well known. Here, candidate gene CG5946 was found to be …

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

Biology Faculty Publications and Presentations

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 Electronic Theses and Dissertations

Biological data, such as molecular abundance measurements and protein

sequences, harbor complex hidden structure that reflects its underlying

biological mechanisms. For example, high-throughput abundance measurements

provide a snapshot the global state of a living cell, while homologous

protein sequences encode the residue-level logic of the proteins' function

and provide a snapshot of the evolutionary trajectory of the protein family.

In this work I describe algorithmic approaches and analysis software I

developed for uncovering hidden structure in both kinds of data.

Clustering is an unsurpervised machine learning technique commonly used

to map the structure of data collected in high-throughput experiments,

such …

The Solid & The Shifting: Darwinian Time, Evolutionary Form And The Greek Ideal 
In The Early Works Of Virginia Woolf, Joseph Monroe Kreutziger

Arts & Sciences Electronic Theses and Dissertations

ABSTRACT OF THE DISSERTATION

“The Solid & the Shifting”: Evolutionary Form, Darwinian Time, and the Greek Ideal in the Early Works of Virginia Woolf

By

Joseph Kreutziger

Doctor of Philosophy in English and American Literature

Washington University in St. Louis, 2017

Professors Melanie Micir, Robert Milder, Steven Meyer, Vincent Sherry, Zoe Stamatopoulou

_____________________________________________________________________

“Now is life very solid or very shifting?” Virginia Woolf asks in her diary of 1931, a question she claims haunts her in its contradictions. This dynamism between the solid and the shifting aspects of life and temporality is fundamental to an analysis of Woolf’s writing process. …

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 …

Revisiting The Waxy Locus And The Capsicum Annuum L. Complex, Robert L. Jarret, Phat Dang

Georgia Journal of Science

Waxy locus introns from 35 accessions of the species comprising the Cap­sicum annuum complex [C. annuum (7), C. frutescens (10), and C. chinense (11)1, C. baccatum (5), C. chacoense (1) and C. pubescens (1) were cloned and sequenced. These data were combined with existing GenBank waxy intron data on these same species, C. tovarii, C. ciliatum, Lycianthes heteroclita, L. lenta, and L. glandulosa in order to examine the phyloge­netic relationships within this group of plant materials, and to re-examine the strength of the delimitation of the members of the C. annuum complex provided previously by analysis of indel …

Countering Public Misconceptions About The Nature Of Evolutionary Science

Georgia Journal of Science

Challenges to modern evolutionary science are often rooted in fun­damental misconceptions about the nature of science itself. Among the public, there is a widespread perception that the focus of science on natural cause-and-effect explanations is a thinly disguised effort to promote a godless worldview, rather than an inherent methodologi­cal limitation. Furthermore, the general public often view theories as merely unsubstantiated guesses, rather than as the unifying concepts that give our observations coherence and meaning. Theories within the historical sciences, in particular, are seen as being inherently untestable without an objective basis for assigning validity. Science for many is simply an …

A Review Of The Institute Of Medicine’S Analysis Of Using Chimpanzees In Biomedical Research, Robert C. Jones, Ray Greek

Robert C. Jones, PhD

We argue that the recommendations made by the Institute of Medicine’s 2011 report, Chimpanzees in Biomedical and Behavioral Research: Assessing the Necessity, are methodologically and ethically confused. We argue that a proper understanding of evolution and complexity theory in terms of the science and ethics of using chimpanzees in biomedical research would have had led the committee to recommend not merely limiting but eliminating the use of chimpanzees in biomedical research. Specifically, we argue that a proper understanding of the difference between the gross level of examination of species and examinations on finer levels can shed light on important methodological …

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 …

Evolvability: What Is It And How Do We Get It?, Matthew Moreno

Honors Program Theses

Biological organisms exhibit spectacular adaptation to their environments. However, another marvel of biology lurks behind the adaptive traits that organisms exhibit over the course of their lifespans: it is hypothesized that biological organisms also exhibit adaptation to the evolutionary process itself. That is, biological organisms are thought to possess traits that facilitate evolution. The term evolvability was coined to describe this type of adaptation. The question of evolvability has special practical relevance to computer science researchers engaged in longstanding efforts to harness evolution as an algorithm for automated design. It is hoped that a more nuanced understanding of biological evolution …

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 …

Answers To Common Misconceptions About Biological Evolution, Leah M. Abebe, Blake Bartels, Kaitlyn M. Caron, Adam M. Gleeson, Samuel N. Johnson, Tyler J. Kluza, Nicholas W. Knopik, Kristen N. Kramer, Masiel S. Maza, Kaitlyn A. Stava, Kaitlyn Sullivan, Jordan T. Trimble, Robert M. Zink , Editor

Papers in Evolution

“When you have an established scientific emergent truth, it is true whether or not you believe in it.” Neil deGrasse Tyson, Science in America. Very few people outside of a particular scientific discipline can actually say they understand it, because most do not have the training to “speak the language.” They are then not particularly bothered by its tenets and predictions. Of all the major branches of science, however, evolutionary biology is an exception to this generalization because even though people are not versed in the field, they sometimes have a negative, knee-jerk objection. This objection is often because they …

Evolution: A Divine Interaction Between God And Creation, Hanna V. Larracas

Selected Honors Theses

The purpose of this paper is to provide a framework through relational theology for understanding the randomness evident in genetic variation which is an element within evolution. I propose that evolution can be incorporated into a theology of creation by placing evolution in context of the interaction of love between God and creation when interpreted through a framework of relational theology. Relational theology, as engaging God as primarily self-giving and holistically hospitable (towards God’s self in the Trinity and towards creation), provides space for a theological understanding of randomness genetic variation and mutation within the evolutionary process. Chapter 1 discusses …

Novel Approaches To Exploring Silk Use Evolution In Spiders, Rachael 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 …