Genetics and Genomics Commons^™

Climate Change, Woodpeckers, And Forests: Current Trends And Future Modeling Needs, Eric S. Walsh, Kerri T. Vierling, Eva Strand, Kristina Bartowitz, Tara W. Hudiburg

Aspen Bibliography

The structure and composition of forest ecosystems are expected to shift with climate‐induced changes in precipitation, temperature, fire, carbon mitigation strategies, and biological disturbance. These factors are likely to have biodiversity implications. However, climate‐driven forest ecosystem models used to predict changes to forest structure and composition are not coupled to models used to predict changes to biodiversity. We proposed integrating woodpecker response (biodiversity indicator) with forest ecosystem models. Woodpeckers are a good indicator species of forest ecosystem dynamics, because they are ecologically constrained by landscape‐scale forest components, such as composition, structure, disturbance regimes, and management activities. In addition, they are …

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.

Distribution And Population Structure Of The Invasive Nitellopsis Obtusa (Desv. In Loisel.) J. Groves And Native Species Of Characeae In The Northeast U.S.A., Robin Sleith

Dissertations, Theses, and Capstone Projects

Freshwater ecosystems are some of the most biologically diverse environments on Earth. Billions of humans rely on functioning freshwater ecosystems for drinking water and many other services. These ecosystems are increasingly threatened by human impacts including nutrient pollution, invasive species, and climate change. Here I contribute four research chapters that investigate freshwater diversity and ecosystem threats using the Characeae, a family of freshwater green macroalgae, as a study system. Characeae are a diverse and ancient group with more than 500 extant species and a fossil history spanning at least 250 million years. These algae are macrophytes in freshwater ecosystems, and …

Activation Of The Bile Acid Pathway And No Observed Antimicrobial Peptide Sequences In The Skin Of A Poison Frog, Megan L. Civitello, Robert Denton, Michael A. Zasloff, John H. Malone

Biology Publications

The skin secretions of many frogs have genetically-encoded, endogenous antimicrobial peptides (AMPs). Other species, especially aposematic poison frogs, secrete exogenously derived alkaloids that serve as potent defense molecules. The origins of these defense systems are not clear, but a novel bileacid derived metabolite, tauromantellic acid, was recently discovered and shown to be endogenous in poison frogs (Mantella, Dendrobates, and Epipedobates). These observations raise questions about the evolutionary history of AMP genetic elements, the mechanism and function of tauromatellic acid production, and links between these systems. To understand the diversity and expression of AMPs among frogs, we assembled skin transcriptomes of …

Predatory Hymenopteran Assemblages In Boreal Alaska: Associations With Forest Composition And Post-Fire Succession, Alexandria Wenninger, Teresa Hollingsworth, Diane Wagner

Aspen Bibliography

Changes to the fire regime in boreal Alaska are shifting the ratio of coniferous to deciduous dominance on the landscape. The increase in aspen and birch may have important effects on predatory hymenopteran assemblages by providing a source of extrafloral nectar and increasing prey availability. Furthermore, fire-induced changes in successional age alter habitat structure and microclimate in ways that may favor ants. This study is the first to characterize the influence of fire-related vegetation changes on boreal predatory hymenopteran assemblages. We compare the abundance, species richness, and composition of predatory hymenopteran assemblages among forests at different stages of succession and …

De Novo Development And Characterization Of Tetranucleotide Microsatellite Loci Markers From A Southeastern Population Of The House Finch (Haemorhous Mexicanus), Edgar E. Sanchez, J Dylan Maddox, Douglas G. Barron

Journal of the Arkansas Academy of Science

Microsatellites are short tandem repeats (e.g. TAGATAGA) of base pairs in a species’ genome. High mutation rates in these regions produce variation in the number of repeats across individuals that can be utilized to study patterns of population- and landscape-level genetics and to determine parentage genetically. In this project our objective was to develop microsatellite markers for the House Finch, Haemorhous mexicanus. This species has become one of the most well-studied species of songbirds due to its unique geographical, evolutionary, and epidemiological history. Using mist-nets we captured birds on the Arkansas Tech University campus and collected blood samples to …

Tiger Monitoring In Bhutan Using Non-Invasive Genetic Tools, Tashi Dhendup

Graduate Student Theses, Dissertations, & Professional Papers

Large carnivores are one of the most threatened group of animals in the world. They suffer from prey depletion, persecution by humans, and habitat loss and fragmentation which are extensively driven by anthropogenic activities. One such species is the tiger Panthera tigris. Tigers are found in thirteen countries in Asia and are protected across the range; however, tiger numbers have declined as an after effect of habitat loss, prey depletion and poaching. Human-induced changes have reduced the tiger's historical range to about 7% in which a little more than 3900 tigers are found. Most of these individuals currently exist …

Insects And The Evolution Of Developmental Pathways: Functional Analysis Of Genetic Sex Determination Mechanisms In Oncopeltus Fasciatus, Josefine Just

Honors Theses

Natural selection alters genetic pathways over evolutionary time. However, different pathways have been shown to maintain mutations at varying rates, leading to different levels of conservation across developmental pathways. Sex determination pathways, in particular, show vast diversity across animals despite the fundamental conservation of biological sex itself. Here, I investigated the sex determination pathway of the hemimetabolous insect, Oncopeltus fasciatus. The large milkweed bug, O. fasciatus, is part of the order Hemiptera, which provides a relevant outgroup study to other insects in which sex determination has been studied to date. I studied three sex determination genes, intersex, fruitless …

Haplotype Diversity And Population Genetic Structure Of Antistrophus Gall Wasps Associated With Two Silphium Species And Implication For Host Mediated Speciation, Jiaxin Deng

Masters Theses

Gall making insects form a special feeding guild of phytophagous animals, and by manipulating host plant tissue differentiation, are able to avoid plant chemical defenses and thus have no need for counter defense mechanisms. Host plant selection is crucial to the evolution of these insects because successful gall formation is largely dependent on host plant ability to respond to stimuli. In Illinois and neighboring states, Antistrophus gall wasps associated with the rosin weed (S. integrifolium) and the cup plant (S. perfoliatum) are morphologically indistinguishable and thus have been treated as belonging to single species. However, the wasps from the host …

Phenotypic And Genetic Variation Of The Brazilian Malaria Vector Nyssorhynchus Darlingi At Regional And Local Scales, Virginia Mildred Chu

Legacy Theses & Dissertations (2009 - 2024)

There have been major successes in the fight to eliminate malaria in the Americas, with 11

Exploration Of Sonic Hedgehog Gene Expression In Fathead Minnows (Pimephales Promelas), Brooke Renee Greiner

Undergraduate Honors Theses

Pollutants, as a result of wastewater treatments, have been shown to have negative impacts on aquatic ecosystems. To better understand the possible consequences caused by effluents on ecosystems, it is important to examine ecotoxicology data. One of the most commonly used species for water quality testing is the fathead minnow, Pimephales promelas. Ecotoxicology can then be taken one step further to understand the effects of pollutants on a molecular level. Previous research had identified effluents as causes for abnormal minnow fin morphology. In order to collect additional data on development, tanks with fathead minnows were placed at the Charleston …

Causes And Possible Consequences Of Hybridisation In Angelfishes At Christmas Island, Federico Vitelli

Theses: Doctorates and Masters

The angelfishes (family Pomacanthidae) have the greatest proportion (~30%) of hybridising species, compared to other families of reef fishes, with 26 species implicated in hybridisation. However, very little is known about hybridisation in angelfish, especially in terms of fitness of the hybrids and possible ecological consequences. Hybrids between three species (C. flavissima, C. eibli and C. vroliki) in the genus Centropyge have previously been reported from Christmas island, where these have been observed in heterospecific harems and interbreeding. This provides the unique opportunity to examine the breakdown in assortative mating in marine fishes. The broad aim of this …

A Novel Snp Genotyping Technique To Determine Orangutan Relatedness And Genetic Diversity At Camp Leakey In Tanjung Puting, Central Kalimantan, Ruth Ella Linsky

All Master's Theses

Genetic studies of dispersal patterns in wild populations of orangutans (Pongo spp.) have sought to confirm behavioral observations that female orangutans tend to stay near their natal range while males disperse. In order to genotype a previously unsampled wild population of endangered orangutans at Tanjung Puting National Park I developed novel application of a methyl based magnetic capture for enrichment of fecal DNA and commercial human targeted single nucleotide polymorphism (SNP) microarray technology. I confirmed results of this new genotyping technique through standard microsatellite short tandem repeat (STR) micro-capillary genotyping. I estimate genetic diversity and relatedness (r) …

Population Structure And Connectivity Of A Groundwater Crustacean Across Northwestern Montana Aquifers, Megan N. Ritter

Master’s Theses

Floodplain aquifer systems are diverse and heterogenous ecosystems that serve many ecological functions, including habitat provision to a range of groundwater species. The Flathead River system of northwestern Montana is home to many floodplain aquifers of great ecological importance to the region. The basic biology, population structure, and dispersal patterns of obligate groundwater organisms that reside within the aquifers of the Flathead are still largely unknown. In this study, we investigate the population structure of one such taxon, an undescribed species of the amphipod genus Stygobromus. For our low-coverage RADseq dataset, we tested the suitability of three different analysis …

Spatial Genetic Structure And Local Adaptation Within And Among Foxtail Pine (Pinus Balfouriana Subsp. Balfouriana) Populations Located In The Klamath Mountains, California, Rebecca D. Piri

Theses and Dissertations

Foxtail pine (Pinus balfouriana) is a subalpine conifer endemic to California, notably separated into two disjunct subspecies. Previous studies have described the northern subspecies,Pinus balfouriana subsp. balfouriana,as having an uncommonly high level of genetic differentiation and no discernible spatial patterns in phenotypic variation. This study seeks to characterize the spatial genetic structure and patterns of selection of the northern subspecies (Pinus balfouriana subsp. balfouriana) using genome-wide data and to identify the influence of ecology and environment on the unique genetic patterns. I show that genetic differentiation among populations is much less than previously estimated …

Intraspecific Variation In Dehydration Tolerance: Insights From The Tropical Plant Marchantia Inflexa, Rose A. Marks

Theses and Dissertations--Biology

Plants are threatened by global change, increasing variability in weather patterns, and associated abiotic stress. Consequently, there is an urgent need to enhance our ability to predict plant community dynamics, shifts in species distributions, and physiological responses to environmental challenges. By building a fundamental understanding of plant stress tolerance, it may be possibly to protect the ecological services, economic industries, and communities that depend on plants. Dehydration tolerance (DhT) is an important mechanism of water stress tolerance with promising translational applications. Here, I take advantage natural variation in DhT to gain a deeper insight into this complex trait. In addition, …

Ecophysiological Determinants Of Sexual Size Dimorphism: Integrating Growth Trajectories, Environmental Conditions, And Metabolic Rates, Marie-Claire Chelini, John P. Delong, Eileen A. Hebets

Eileen Hebets Publications

Sexual size dimorphism (SSD) often results in dramatic differences in body size between females and males. Despite its ecological importance, little is known about the relationship between developmental, physiological, and energetic mechanisms underlying SSD. We take an integrative approach to understand the relationship between developmental trajectories, metabolism, and environmental conditions resulting in extreme female-biased SSD in the crab spider Mecaphesa celer (Thomisidae). We tested for sexual differences in growth trajectories, as well as in the energetics of growth, hypothesizing that female M. celer have lower metabolic rates than males or higher energy assimilation. We also hypothesized that the environment in …

Contemporary Sexual Selection Does Not Explain Variation In Male Display Traits Among Populations, J. Colton Watts, Allissa Flynn, Brigitte Tenhumberg, Eileen Hebets

Brigitte Tenhumberg Papers

Sexual selection is widely hypothesized to facilitate the evolution of reproductive isolation through divergence in sexual traits and sexual trait preferences among populations. However, direct evidence of divergent sexual selection causing intraspecific trait divergence remains limited. Using the wolf spider Schizocosa crassipes, we characterized patterns of female mate choice within and among geographic locations and related those patterns to geographic variation in male display traits to test whether divergent sexual selection caused by mate choice explains intraspecific trait variation. We found evidence of phenotypic selection on male behavior arising from female mate choice, but no evidence that selection varied …

Multi-Locus Phylogenetic Inference Of The Howler Monkey (Alouatta) Radiation In South America., Esmeralda Ferreira

Dissertations and Theses

Abstract

Howler monkeys (Alouatta) are the most widely distributed New World primates, ranging from southern Mexico to northern Argentina. They occur in tropical rain forests, flooded and gallery forests, and deciduous and semi-deciduous environments. Despite their importance as seed dispersers, howlers have also been known to be ecological indicators. Available phylogenetic hypotheses for this genus have used chromosomal characters, morphological characteristics, and a limited number of molecular markers and specimens. In spite of these analyses, branching patterns among howler species lineages conflict between studies or remain unresolved. Using 14 unlinked non-coding intergenic nuclear regions under both a concatenated …

Using Environmental Dna And Occupancy Modeling To Estimate Rangewide Metapopulation Dynamics Of The Endangered Tidewater Goby Eucyclogobius Spp., Chad M. Martel

Cal Poly Humboldt theses and projects

Conservation of species is most effective when metapopulation dynamics are well understood and incorporated into management plans, allowing managers to target conservation efforts where they will be most effective. The development of environmental DNA (eDNA) methods provides an efficient and highly sensitive approach to generate presence and absence data needed to elucidate metapopulation dynamics. Combining sample detection histories from eDNA surveys with occupancy models that account for non-detection can offer unbiased estimates of rangewide metapopulation dynamics. However, traditional occupancy models do not allow direct evaluation of the drivers of site occupancy, extinction, and colonization. Herein, I utilize a novel dynamic …

Testing For Cryptic Diversity And Inference Of Population Structure In The Cosmopolitan Hoplonemertean Emplectonema Gracile (Nemertea), Paul L. Delaney Iv

Theses and Dissertations

Emplectonema gracile (Johnston 1837) is a hoplonemertean of marine intertidal hard-bottom communities and is distributed throughout the Northern Hemisphere. Although possessing a planktonic larval stage in its life history, the range of such cosmopolitan marine invertebrate species is often explained by cryptic speciation and anthropogenic transport. The purpose of this study is to test for possible cryptic species using mtDNA markers (COI and 16S rDNA) and to investigate population structure in E. gracile over a portion of its geographic range using mtDNA markers and ddRADseq nuclear SNP data. The results of both phylogenetic- and tree-based species delimitation revealed that E. …

Impact Of Seasonal And Host-Related Factors On The Intestinal Microbiome And Cestode Community Of Sorex Cinereus And Sorex Monticola, Katelyn D. Cranmer

College of Graduate Studies: Theses & Dissertations

The intestinal microbiome of mammals plays a significant role in host health and response to environmental stimuli and can include both beneficial native bacteria as well as parasitic worms. In this study, I examined the intestinal cestode and bacterial communities of two closely related species of shrew, Sorex monticola and Sorex cinereus, over a six month period in 2016. Specimens were collected approximately every three weeks from May to October from the Sangre de Cristo Mountains in Cowles, New Mexico. A total of 79 shrews were prepared with the gastrointestinal tracts removed and flash-frozen in liquid nitrogen. An additional …

Population Health Of Spotted Salamanders (Ambystoma Maculatum) In Created Vernal Pools: An Integrative Approach, Alice R. Millikin

Graduate Theses, Dissertations, and Problem Reports (ETD)

Habitat creation is an important tool for conservation to counteract habitat loss and degradation. Vernal pools are susceptible to destruction due to limited detection, protection, and regulation. These wetlands provide fishless breeding habitat for many amphibian species including spotted salamanders (Ambystoma maculatum) in eastern North America. Determining whether created vernal pool habitat is successful is often determined by demographic data of colonizing populations. I suggest that hormone levels, population genetics, and disease prevalence can improve our understanding of population health in created habitat. The goal of this dissertation was to assess the health of spotted salamander larvae in …

Harnessing Population Genetics For Pest Management: Theory And Application For Urban Rats, Matthew Combs, Kaylee Byers, Chelsea Himsworth, Jason Munshi-South

Human–Wildlife Interactions

Effective management of rodent pests requires an ecological understanding of how they move through their environment and how those movements influence the invasion, persistence, or reinvasion of problematic colonies. Traditional methodologies used to describe rodent movement patterns, such as mark-recapture, are hindered by their time-consuming nature and limited geographic scope. As such, our understanding of how rodents interact with urban environments remains limited. Population genetic principles and tools have the capacity to greatly increase our understanding of rodent population dynamics, ecological relationships, and movements across space, but this field is often unapproachable to non-scientist pest management professionals (PMPs). In this …

The New Natural Distribution Area Of Aspen (Populus Tremula L.) Marginal Populations In Pasinler In The Erzurum Province, Turkey, And Its Stand Characteristics, Halil Bariş Özel, Sezgin Ayan, Serdar Erpay, Bojan Simovski

Aspen Bibliography

Background and Purpose: Genetic diversity is the basis for adaptation and survival of tree species under changing environmental conditions, representing the key issue of stability and productivity of forest ecosystems. This paper studies the marginal population characteristics and stand dynamics of aspen tree (Populus tremula L.) in natural, pure and mixed forest stands with Scots pine (Pinus sylvestris L.). These populations were observed on founding sites between Timarli Valley and Timan Plateau located in Pasinler in the Erzurum Province in Turkey.
Materials and Methods: Three replicated sample sites were established according to a randomised block design …

Understanding The Impacts Of Current And Future Environmental Variation On Central African Amphibian Biodiversity, Courtney A. Miller

LSU New Orleans Theses and Dissertations

Global climate change is projected to impact multiple levels of biodiversity by imposing strong selection pressures on existing populations, triggering shifts in species distributions, and reorganizing entire communities. The Lower Guineo-Congolian region in central Africa, a reservoir for amphibian diversity, is predicted to be severely affected by future climate change through rising temperatures and greater variability in rainfall. Geospatial modelling can be used to assess how environmental variation shapes patterns of biological variation – from the genomic to the community level – and use these associations to predict patterns of biological change across space and time. The overall goal of …

Dependence Of Aspen Stands On A Subsurface Water Subsidy: Implications For Climate Change Impacts, D. M. Love, M. D. Venturas, J. S. Sperry, P. D. Brooks, J. L. Pettit, Y. Wang, W. R. L. Anderegg, X. Tai, D. S. Mackay

Aspen Bibliography

The reliance of 10 Utah (USA) aspen forests on direct infiltration of growing season rain versus an additional subsurface water subsidy was determined from a trait- and process-based model of stomatal control. The model simulated the relationship between water supply to the root zone versus canopy transpiration and assimilation over a growing season. Canopy flux thresholds were identified that distinguished nonstressed, stressed, and dying stands. We found growing season rain and local soil moisture were insufficient for the survival of 5 of 10 stands. Six stands required a substantial subsidy (31–80% of potential seasonal transpiration) to avoid water stress and …

Miniscule Differences Between Sex Chromosomes In The Giant Genome Of A Salamander, Melissa C. Keinath, Nataliya Y. Timoshevskaya, Vladimir A. Timoshevskiy, S. Randal Voss, Jeramiah J. Smith

Biology Faculty Publications

In the Mexican axolotl (Ambystoma mexicanum), sex is determined by a single Mendelian factor, yet its sex chromosomes do not exhibit morphological differentiation typical of many vertebrate taxa that possess a single sex-determining locus. As sex chromosomes are theorized to differentiate rapidly, species with undifferentiated sex chromosomes provide the opportunity to reconstruct early events in sex chromosome evolution. Whole genome sequencing of 48 salamanders, targeted chromosome sequencing and in situ hybridization were used to identify the homomorphic sex chromosome that carries an A. mexicanum sex-determining factor and sequences that are present only on the W chromosome. Altogether, …

Phylogeographic Analyses Of A Widely Distributed Populus Davidiana: Further Evidence For The Existence Of Glacial Refugia Of Cool‐Temperate Deciduous Trees In Northern East Asia, Zhe Hou, Zhaoshan Wang, Zhanyang Ye, Shuhui Du, Shuya Liu, Jianguo Zhang

Aspen Bibliography

Despite several phylogeographic studies had provided evidence to support the existence of glacial refugia of cool‐temperate deciduous trees in northeast China, the species used in these studies were limited by the species ranges, which could not exclude the possibility that northern populations were the colonists from southern refugial populations during the last glacial maximum (LGM). Here, we estimated the nucleotide variation in Populus davidiana, a widespread species distributed in Eurasia. Three groups in northeast, central, and southwest China were constructed according to the simulation results from SAMOVA, composition of chloroplast haplotypes and structure results. We revealed that the northeast …

Accumulation And Transmission Dynamics Of A Naturally-Occurring Mtdna Deletion In Caenorhabditis Briggsae, Jennifer Anne Sullins

Dissertations and Theses

Maintaining mitochondrial genome sequence integrity is essential for preserving normal mitochondrial function. Several human diseases have been associated with heteroplasmic mitochondrial genome mutations, but few genetic systems can simultaneously represent pathogenic mitochondrial genome evolution and inheritance. The nematode Caenorhabditis briggsae is one such model. Natural C. briggsae isolates are globally-distributed and phylogenetically grouped into three distinct clades, with isolates exhibiting varying levels of a large-scale mtDNA deletion, nad5∆. Furthermore, a small subset of clade II isolates exhibits putative compensatory mutations that may reduce the risk of deletion formation and accumulation in those populations. In this thesis, the author characterizes the …