Ecology and Evolutionary Biology Commons^™

Past And Present Patterns Of Neutral And Adaptive Genetic Diversity In Wild Mandrills (Mandrillus Sphinx), Anna Weber

University of New Orleans Theses and Dissertations

Although primates have fascinated researchers and the public alike for generations, one species that has remained enigmatic is the mandrill (Mandrillus sphinx), a large Cercopithecine monkey endemic to Central Africa. Mandrills are currently in decline due to bushmeat hunting, urbanization, and habitat loss. Neutral and adaptive genetic diversity are important tools for understanding evolutionary history and future viability, since diversity influences a species’ ability to adapt to a changing environment. However, thus far, minimal genetic information has been available for wild mandrills. Because of the dense vegetation in their tropical forest habitat, studying wild mandrills has proven to …

Pillars Of Biology: 'The Genetical Evolution Of Social Behaviour, I And Ii'., Geoff Wild

Applied Mathematics Publications

None.

Evaluating Population Genetic Structure And Potential Genomic Signals Of Natural Selection In A Migratory Songbird (Protonotaria Citrea), Tyler A. Hohenstein

Theses and Dissertations

In this study I attempted to further resolve the population genetic structure in the Prothonotary Warbler (Protonotaria citrea), and conducted an outlier SNP analysis and exploratory gene ontology analysis to investigate potential ongoing natural selection in the species. This analysis of population structure confirms previous work by DeSaix et al. (2019), where weak population structure was observed between eastern sites along the Atlantic Coastal Plain, and western sites in the Mississippi Alluvial Valley, possibly due to a genetic discontinuity across the Appalachian Mountains. I conducted two forms of outlier SNP analyses, a principal component analysis (PCA)-based approach to identify SNPs …

A Cophylogenetic Analysis Of Fungus Gardening Ants And Their Symbiotic Fungi, Katherine Beigel

Biology Theses

Fungus-growing ants (Tribe Attini) and their fungal cultivars share a 50-million-year coevolutionary history. Large scale phylogenetic analyses depict a strong co-phyletic signal among ants and their farmed fungi yet fungus sharing among unrelated ant lineages is somewhat widespread. An overview of sharing has been hampered by a lack of genetic markers that exhibit intraspecific variation and surveys across geographic regions. For example, previous studies have shown similar sequences of the internal transcribed spacer (ITS) region of fungus in different species of Trachymyrmex, suggesting that these ant species are farming the same fungal clone. To examine whether this was a …

The Evolution Of Bivalve Shell Matrix Proteins, Mark Ira Duhon Ii

LSU Doctoral Dissertations

This dissertation focuses on the molecular underpinnings surrounding the evolution of the biomineralized shells of marine bivalves. Bivalve molluscs synthesize remarkably complex shells from calcium carbonate and an organic matrix of proteins secreted from the dorsal edge of the mantle. Molecular analyses of shell matrix proteins (SMPs) have suggested high rates of gene turnover despite the conserved nature of the shell itself. Here, I used proteomic and transcriptomic data to identify the SMPs and other biomineralization proteins from seven bivalve species that diverged 3-513 Mya. Contrary to previous studies that identified only a few shared biomineralization transcripts across the Bivalvia, …

Genetic Analysis Of Flower Color Differences Between A Hummingbird-Pollinated And A Self-Pollinated Monkeyflower (Mimulus) Species, Caitlin Foster

University Scholar Projects

Flower color plays an important role in pollinator discrimination and speciation. Understanding the genetic contributions to flower color differences between two closely related species, Mimulus cardinalis and Mimulus parishii, can improve understanding of how they developed different pollination syndromes and diverged from a recent common ancestor. M. cardinalis is hummingbird-pollinated and has large, bright red flowers while M. parishii is self-pollinated and has small, pale pink flowers. An F2 hybrid population between these two species was created to establish a platform for analysis of the genetic architecture controlling the differences in anthocyanin pigmentation. Statistical analysis of anthocyanin concentration distribution …

Molecular Differentiation Of Astragalus Species And Varieties From The Western United States: The Chloroplast Dna Bridge Between Evolution And Molecular Systematics, Marwa Neyaz, Daniel Cook, Rebecca Creamer

Poisonous Plant Research (PPR)

Locoweeds are the most widespread poisonous plant problem in the world and have been reported in the Western United States since the 1800s, causing tremendous losses in livestock. Consumption of locoweeds by grazing animals stimulates the neurological disease, locoism, characterized by weight loss, ataxia, and lack of muscular coordination. The name locoweed is used for Astragalus and Oxytropis species known to contain swainsonine, the toxic principle produced by the plant endophytic fungus Undifilum. Astragalus includes 2,500-3,000 species and many varieties that have almost identical morphological characteristics that overlap among species, leading to improper identification. Therefore, the aim of this study …

The Effects Of Internal Physiology On Polyphenic Horn Development In The Dung Beetle Onthophagus Taurus, Naomi Garrett Williamson

Graduate Theses, Dissertations, and Problem Reports

An organism’s phenotype can be affected in development by alterations to gene expression based on environmental inputs. Nutrition is one such environmental input and the central regulator of development of large horn or small horn phenotypes in the dung beetle species, Onthophagus taurus. However, little is known about the nature of chemical compounds that are critical to this plastic horn development. To better understand these compounds, we are utilizing an untargeted metabolomic approach as well as a targeted gene approach. Through the metabolomic approach, it was uncovered that environmental conditions tend to have a greater impact on metabolomic composition …

Mixing It Up: The Impact Of Episodic Introgression On The Evolution Of High-Latitude Mesocarnivores, Jocelyn P. Colella

Biology ETDs

At high latitudes, climatic oscillations have triggered repeated episodes of organismal divergence by geographically isolating populations. For terrestrial species, extended isolation in glacial refugia – ice-free regions that enable terrestrial species persistence through glacial maxima – is hypothesized to stimulate allopatric divergence. Alternatively, upon glacial recession, divergent populations expanded from independent glacial refugia and often contacted other diverging populations. In the absence of reproductive isolating mechanisms, this biogeographic process may trigger hybridization and ultimately, gene flow between divergent taxa. My dissertation research aims to understand how these episodic periods of isolation and contact have impacted the evolution of high latitude …

Plant Mitochondrial Genome Evolution And Structure Has Been Shaped By Double-Strand Break Repair And Recombination, Emily Wynn

School of Biological Sciences: Dissertations, Theses, and Student Research

Plant mitochondrial genomes are large but contain a small number of genes. These genes have very low mutation rates, but genomes rearrange and expand at significant rates. We propose that much of the apparent complexity of plant mitochondrial genomes can be explained by the interactions of double-strand break repair, recombination, and selection. One possible explanation for the disparity between the low mutation rates of genes and the high divergence of non-genes is that synonymous mutations in genes are not truly neutral. In some species, rps14 has been duplicated in the nucleus, allowing the mitochondrial copy to become a pseudogene. By …

Phylogenetic History Of The Amy Gene Cluster In Catarrhines, Christian M. Gagnon

Theses and Dissertations

This study phylogenetically analyzed 30 AMY-related genes from 11 primates. The results show the gradual expansion of the AMY gene family which could have allowed primates to adapt to various ecological landscapes and maximize energy intake from starch-rich foods in periods of food scarcity.

Impacts Of Genome And Nuclear Architecture On Molecular Evolution In Eukaryotes, Xyrus Maurer-Alcalá

Doctoral Dissertations

The traditional view of genomes suggests that they are static entities changing slowly in sequence and structure through time (e.g. evolving over geological time-scales). This outdated view has been challenged as our understanding of the dynamic nature of genomes has increased. Changes in DNA content (i.e. polyploidy) are common to specific life-cycle stages in a variety of eukaryotes, as are changes in genome content itself. These dramatic genomic changes include chromosomal deletions (i.e. paternal chromosome deletion in insects; Goday and Esteban 2001; Ross, et al. 2010), developmentally regulated genome rearrangements (e.g. the V(D)J system in adaptive immunity in mammals; Schatz …

Advancing Behavioural Genomics By Considering Timescale, Clare C. Rittschof, Kimberly A. Hughes

Entomology Faculty Publications

Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early …

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 …

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 …

Principles Of Biology, Robert Bear, David Rintoul, Bruce Snyder, Martha Smith-Caldas, Christopher Herren, Eva Horne

Open Access Textbooks

This textbook is designed specifically for Kansas State's Biology 198 Class. The course is taught using the studio approach and based on active learning. The studio manual contains all of the learning objectives for each class period and is the record of all student activities. Hence, this textbook is more of a reference tool while the studio manual is the learning tool.

The textbook was originally published and is also available to download at http://cnx.org/contents/db89c8f8-a27c-4685-ad2a-19d11a2a7e2e@24.1.It is licensed under a Creative Commons Attribution License 4.0 license.

Is Your Learning Style Paranoid?, Kirby Farrell

kirby farrell

We learn—and grow—by engaging with anomalies: new things that don't fit our familiar categories. It's a gut process, not just a philosophical choice. Anxiety can make us paranoid about what's new and strange. Knowing that can spur fascination and help us to adapt.

An Exploration Of The Phylogenetic Placement Of Recently Discovered Ultrasmall Archaeal Lineages, Jeffrey M. O'Brien

Honors Scholar Theses

In recent years, several new clades within the domain Achaea have been discovered. This is due in part to microbiological sampling of novel environments, and the increasing ability to detect and sequence uncultivable organisms through metagenomic analysis. These organisms share certain features, such as small cell size and streamlined genomes. Reduction in genome size can present difficulties to phylogenetic reconstruction programs. Since there is less genetic data to work with, these organisms often have missing genes in concatenated multiple sequence alignments. Evolutionary Biologists have not reached a consensus on the placement of these lineages in the archaeal evolutionary tree. There …

Population And Demographic Structure Of Ixodes Scapularis Say In The Eastern United States., Joyce M. Sakamoto, Jerome Goddard, Jason L. Rasgon

College of Agriculture & Life Sciences Publications and Scholarship

INTRODUCTION: The most significant vector of tick-borne pathogens in the United States is Ixodes scapularis Say (the blacklegged tick). Previous studies have identified significant genetic, behavioral and morphological differences between northern vs. southern populations of this tick. Because tick-borne pathogens are dependent on their vectors for transmission, a baseline understanding of the vector population structure is crucial to determining the risks and epidemiology of pathogen transmission. METHODS: We investigated population genetic variation of I. scapularis populations in the eastern United States using a multilocus approach. We sequenced and analyzed the mitochondrial COI and 16S genes and three nuclear genes (serpin2, …

The Roles Of Phenotypic Plasticity And Genotypic Specialization In High Altitude Adaptation, Danielle M. Tufts

School of Biological Sciences: Dissertations, Theses, and Student Research

In vertebrates living at high altitude, arterial hypoxemia may be ameliorated by reversible changes in the oxygen-carrying capacity of the blood (regulated by erythropoiesis) and/or changes in blood–oxygen affinity (regulated by allosteric effectors of hemoglobin function). These hematological traits often differ between taxa that are native to different elevational zones, but it is often unknown whether the observed physiological differences reflect fixed, genetically based differences or environmentally induced acclimatization responses (phenotypic plasticity). Here, we report measurements of hematological traits related to blood–O₂ transport in populations of deer mice (Peromyscus maniculatus) that are native to high- and low-altitude …

A Tale Of Two Haplotypes: The Eda2r/Ar Intergenic Region Is The Most Divergent Genomic Segment Between Africans And East Asians In The Human Genome, Amanda M. Casto, Brenna M. Henn, Jeffery M. Kidd, Carlos D. Bustamante, Marcus W. Feldman

Human Biology Open Access Pre-Prints

Single nucleotide polymorphisms (SNPs) with large allele frequency differences between human populations are relatively rare. The longest run of SNPs with an allele frequency difference of one between the Yoruba of Nigeria and the Han Chinese is found on the long arm of the X chromosome in the intergenic region separating the EDA2R and AR genes. It has been proposed that the unusual allele frequency distributions of these SNPs are the result of a selective sweep affecting African populations that occurred after the Out-of-Africa migration. To investigate the evolutionary history of the EDA2R/AR intergenic region, we characterized the haplotype structure …

Two Boundaries Separate Borrelia Burgdorferi Populations In North America, Gabriele Margos, Jean I. Tsao, Santiago Castillo-Ramirez, Yvette A. Girard, Anne G. Hoen

Dartmouth Scholarship

Understanding the spread of infectious diseases is crucial for implementing effective control measures. For this, it is important to obtain information on the contemporary population structure of a disease agent and to infer the evolutionary processes that may have shaped it. Here, we investigate on a continental scale the population structure of Borrelia burgdorferi, the causative agent of Lyme borreliosis (LB), a tick-borne disease, in North America. We test the hypothesis that the observed d population structure is congruent with recent population expansions and that these were preceded by bottlenecks mostly likely caused by the near extirpation in the 1900s …