Life Sciences Commons^™

Range-Wide Analysis Of The Genetic Diversity And Genetic Structure Of The Spotted Turtle (Clemmys Guttata), Madison S. Whitehurst

Theses and Dissertations

Understanding the spatial distribution of genetic diversity and structure in endangered species is vital for effective conservation management. This research discusses the results of an initial analysis of the genetic structure and variation of the spotted turtle (Clemmys guttata), a species of conservation interest. The study sampled 913 individuals from 78 unique locales across 16 states in the eastern portion of the species' range. Utilizing ddRADSeq, a de novo genome assembly was developed to identify nearly 20,000 potential loci. A total of 926 were selected for this analysis. Results revealed no spatial clustering of genetic diversity or structure, …

Evolution Of Forest Bitis (Macrocerastes) In Africa: Phylogeography, Population Genetics, And Potential As A Model For Batesian Mimicry, Eugene Richard Vaughan

Open Access Theses & Dissertations

The major biogeographical patterns characterizing the diversification of widely distributed species in the African rainforest remain poorly understood because of the low number of well-sampled studies that are focused on this region. I examine the phylogeography and population genetics of two broadly sympatric sister lineages of large African forest vipers (genus Bitis, subgenus Macrocerastes), the rhinoceros viper (B. nasicornis) and the Gaboon vipers (B. gabonica and B. rhinoceros). Despite their close relationship, these two lineages have notably different patterns of divergence in time and space. A time-calibrated phylogeny with sequence data from five genes, and population structure and PCA analyses …

Genetic Effects Of Anthropogenic Disturbance On Native Charrs, Brad Erdman

Electronic Theses and Dissertations

Artificial propagation has been utilized for over a century to offset anthropogenic declines of abundance for many fishes. Complex and poorly documented histories of habitat degradation and stockings have resulted in considerable uncertainty regarding whether contemporary populations are of native, hatchery, or mixed origins. This uncertainty is problematic as it precludes prioritizing the conservation of native populations that are postulated to possess local adaptations and greater evolutionary potential. Population genetics can assess the relative reproductive contributions of previous stocking events and in this dissertation I apply these methods to four empirical studies of native charr (genus Salvelinus) that have …

Characterization Of The Immunoglobulin Lambda Chain Across Diverse Human Populations., William Gibson

Electronic Theses and Dissertations

The adaptive immune system relies on a diverse set of over one hundred immunoglobulin (IG) genes across three genomic loci that are variably combined to form antibodies (Ab). The IG Lambda locus is one of two loci which encodes the IG light chain. The complexity of the IGL locus severely limits the effective use of standard short-read sequencing, limiting our knowledge of population diversity in these loci. We leveraged single molecule real-time (SMRT) long-read sequencing in conjunction with IGL-targeted DNA capture to develop the method IG-Cap for accurate and high-throughput sequencing of the IGL locus. We benchmarked this method using …

Landscape Genetics Of The Gulf Coast Tick, Amblyomma Maculatum, Sara Simmons Benham

Biological Sciences Theses & Dissertations

Connectivity among populations helps to maintain genetic diversity, population stability, and resilience. The Gulf Coast tick, Amblyomma maculatum, is a vector of the pathogen Rickettsia parkeri. Persistence of tick populations with high rates of R. parkeri infection poses health risks to humans and animals. Mitochondrial haplotypes were characterized by sequencing a fragment of the mitochondrial 16S rRNA gene. A comparative study of A. maculatum and Amblyomma americanum was conducted to identify similar and unique patterns between the species within the same region. Next, I compared A. maculatum sites across three different regions of the United States. This work …

The Effects Of Habitat Isolation On Fine-Scale Genetic And Geographic Structure Of Populations Of Two Threatened Endemic Insects In Southern Nevada, Pseudocotalpa Giulianii And Icaricia Shasta Charlestonensis, Kristen Tovar

UNLV Theses, Dissertations, Professional Papers, and Capstones

Assessing the role geographic isolation and ecological specialization have on phylogeographic patterns contributes to our understanding of the evolutionary history of a species and the processes that erode genetic diversity. I used mitochondrial and nuclear genomic sequences to assess whether habitat isolation has shaped the fine-scale patterns of present-day genetic structure and diversity in two threatened insect species endemic to southern Nevada. Pseudocotalpa giulianii (Coleoptera; Scarabaeidae) is a dune obligate scarab beetle endemic to only two small, isolated sand dunes in Nye County, Nevada, with a usable habitat of less than 4.2 km sq that is impacted by on-going degradation. …

Population Genetics Of Populus Trichocarpa For Targeted Breeding As A Biofuel Crop, Cai John

Doctoral Dissertations

Populus trichocarpa (poplar) is a woody species native to the western U.S. and Canada. As a fast-growing crop, it has been under investigation by the Department of Energy as a resource for liquid biofuel production. Having recently expanded the collection of poplar whole-genome sequences so that it spans the entire natural species range, we have the novel opportunity to study adaptive responses across this range. This work starts with an initial proof of concept study in a well-studied portion of the species range that has complete whole-genome sequences and RNA expression. The completeness of these data allow robust validation of …

Invasion Of The Northeastern United States By The Southern Pine Beetle, Dendroctonus Frontalis, And The Impacts On Signatures Of Isolation By Distance Assessed Using Mitochondrial Dna, Lora Grace Holman

Honors Theses

The southern pine beetle (SPB) is a small, black beetle that parasitizes pine trees across the United States and Central America. Recently it has been recognized that the range of SPB is not limited to the southern United States, but rather extends northward across the eastern United States, which raises concerns for pine trees that have never encountered the pest before. Using mitochondrial DNA sequences from a section of the cytochrome oxidase I gene and four different measures of genetic distance compared to geographic distance, we tested for evidence of isolation by distance (IBD) among sampled SPB to see whether …

Molecular Evolution And Biogeography Of The New World Eptesicus Bats, Xueling Yi

Theses and Dissertations

Molecular evolution refers to a broad field of studies ranging from microevolution (e.g., population genetics) to macroevolution (e.g., phylogeny), including the bridging field of phylogeography. In natural populations, molecular studies are also combined with biogeography that links biological diversity with geographic distributions to provide a comprehensive understanding of evolutionary processes. The field of molecular evolution has been largely advanced from early exploratory descriptions to statistical tests on biological hypotheses and integrative analyses using sophisticated modeling. However, studies of molecular evolution still face some unresolved questions and challenges, especially in non-model systems. For example, the application of new technology has largely …

An Analysis Of The Spatial Genetic Structure Of A Hybrid Zone Between Two Species Of Killifish, Fundulus Heteroclitus And F. Grandis, Andrew Lee Hardy

UNF Graduate Theses and Dissertations

Hybridization offers unique insight into the evolutionary process of speciation and the forces that maintain barriers to reproduction. In northeast Florida, a hybrid zone between two species of killifish, Fundulus heteroclitus and F. grandis, has been identified near Flagler Beach, FL, although the exact boundaries of the hybrid zone remain unknown (Gonzalez et al. 2009). This study aims to determine the fine-scale spatial genetic patterns of the hybrid zone and test the hypothesis that species ranges are influenced by changes in dominant vegetation. Results from an ADMIXTURE analysis and F_ST data indicated the boundary of the area of …

Implications Of Population Genetics And Physiological Responses On The Conservation Of Moose (Alces Alces Americana), Elias Rosenblatt

Graduate College Dissertations and Theses

Wildlife populations around the globe are facing numerous, complex challengesto their persistence, yet conservation efforts are hindered by limited information about these populations and the anthropogenic pressures they face. North American moose (Alces alces americana), despite being of ecological, cultural, and economical importance, inhabit remote landscapes, making population monitoring difficult. At the same time, many moose populations, including in Vermont and eastern North America, have experienced recent declines mainly due to winter tick (Dermacentor albipictus) epizootics. Anthropogenic landscape change and climate-mediated pressures pose future challenges for moose across the southern extent of their distribution. Though impacts of winter tick infestation …

Elements Of Biocontrol Strategies For Pheretimoid Earthworms, Maryam Nouri-Aiin

Graduate College Dissertations and Theses

Jumping worms (Megascolecidae) in the pheretimoid complex, have raisedconsiderable environmental concerns with conservationists, ecologists, policy makers, and the public. Their impacts on North American forests and high density is distinct from earthworms in other families. Most of the infested forests are near horticultural settings. Practicable options to manage their dispersal into forests do not exist. This dissertation examines the potential of an entomopathogenic fungus to control them in horticulture. It also investigates major barriers to managing their spread and studying their ecology including species identification, phenology, and genetic diversity. First, to discover the best time to apply biocontrol agents, I …

Investigating The Genetic Diversity Of Immune Genes In Non-Native Populations Of American Bullfrogs (Rana Catesbeiana), Luisa Nereyda Segovia

Cal Poly Humboldt theses and projects

The American Bullfrog (Rana catesbeiana) is a highly invasive species that has successfully colonized habitats around the world. The genetic variability of immune genes within invasive populations, like that of bullfrogs, may contribute to how resistant a population is to pathogens. The objective of this project was to characterize the genetic diversity of an immune gene in invasive bullfrog populations in California to better understand how persistent these populations might be over time. To characterize immune gene variability, I isolated exon 2 of the Major Histocompatibility Complex (MHC) Class II Beta chain gene and a neutral mitochondrial marker, …

Population Genomics Of Redbreast Sunfish (Lepomis Auritus): Exploring Gene Flow And Local Adaptation In A Widely Distributed Freshwater Fish, Garret J. Strickland

Electronic Theses and Dissertations

Little information is available concerning the distribution of genetic diversity in non-salmonid, non-imperiled, freshwater fish. In order to fill in this knowledge gap, I conducted a population genomics survey in Redbreast Sunfish (Lepomis auritus; RBS), a widespread, generalist species distributed along the Atlantic slope rivers of eastern North America. I sampled four basins (ACF, Savannah, Roanoke, and James) at eight sites each with a factorial experimental design. Sites were distributed among coastal plain, Piedmont, or mountain ecoregions in order to capture the greatest range of environmental states experienced by RBS, with the intention of finding evidence for local adaptation to …

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 …

Applying Conservation Genomic Techniques To Guide Management Of The Reticulated Flatwoods Salamander (Ambystoma Bishopi), Miranda Gaupp

Electronic Theses and Dissertations

The Reticulated flatwoods salamander (Ambystoma bishopi) is a federally endangered amphibian endemic to the longleaf-pine ecosystem of the southeastern U.S. This study used analyses of single-nucleotide polymorphism (SNP) data, collected from 2,255 unique individuals across 5 breeding seasons, spread across the known extant range of A. bishopi, to characterize the genetic diversity and demographics of populations, genetic relationships among populations, and patterns and spatial extents of gene flow, and to evaluate potential effects of management on A. bishopi’s resiliency. Population structure was strongly hierarchical, with individual breeding ponds (n = 38) acting as semi-connected subpopulations …

Florida Sand Skink And Blue-Tailed Mole Skink: Expanding Geographic Coverage Of Genetic Analysis For Conservation, Emma Simpson

Electronic Theses and Dissertations

The Lake Wales Ridge is important scrub habitat that has been increasingly altered since the post-Columbian settlement in Florida. This loss of habitat has caused extreme anthropogenic fragmentation within the Lake Wales Ridge resulting in isolation among extant scrub patches. To expand the geographic scope of previous studies and answer questions concerning population connectivity, we characterized genetic diversity and differentiation using cytochrome-b and microsatellite genetic markers for two endemic skink species: the Florida Sand Skink (Plestiodon reynoldsi) and Blue-tailed Mole Skink (Plestiodon egregius lividus). Both species display historical isolation between central and southern Lake Wales Ridge …

Effects Of Habitat Disturbances On Reptiles In Sagebrush Steppe, Kristina Joan Parker

Boise State University Theses and Dissertations

Reptiles inhabiting shrub-steppe ecosystems of the Intermountain West have adapted to harsh, unpredictable desert conditions, yet recent changes in disturbance regimes may put species at risk. In southwest Idaho, cheatgrass (Bromus tectorum) has altered the fire regime resulting in a vast conversion of shrub-steppe to mostly annual grasslands that burn too frequently to allow shrublands to recover. Southwest Idaho has the highest reptile diversity in the Pacific Northwest, yet we know little about reptile community dynamics in response to the cheatgrass-fire cycle. We hypothesized that wildfires and cheatgrass negatively affect reptile communities directly (i.e., mortality during fires) and …

A Method For Identifying Ancient Introgression Between Caballine And Non-Caballine Equids Using Whole Genome High Throughput Data., Kalpani De Silva

Electronic Theses and Dissertations

Introgression is one of the main mechanisms that transfer adapted alleles between species. The advantageous variants will get positively selected and retained in the recipient population while rest of the variants undergo negative selection. When analyzing horse genome, two alleles were found in CXCL16 gene, one associated with susceptibility and one with resistance to developing persistent shedding of the Equine Arteritis Virus. The two alleles differ by 4 non-synonymous variants in exon 1 of the gene. Comparison with 3 non-caballine equids (zebras, asses and hemiones) revealed that one haplotype was almost identical to the haplotype found in non-caballines while the …

The Evolutionary History Of Camelina Crantz (Brassicaceae) And Domestication Of The Biofuel Crop, C. Sativa (L.) Crantz, Jordan Brock

Arts & Sciences Electronic Theses and Dissertations

The mustard family, Brassicaceae, is a large and economically important group of plants comprising ~350 genera and ~4060 species. Within the family, one genus, Camelina, has been neglected and nearly forgotten until recent decades. This genus comprises between 7 – 9 species, and includes Camelina sativa, an ancient oilseed crop cultivated for thousands of years in Europe. An allohexaploid, C. sativa contains high levels of omega-3 fatty acids and a seed oil composition amenable for production of aviation jet fuel. With a short generation time and ability to be cultivated on marginal soils with few inputs, C. sativa is set …

Synthesizing Phylogeography And Community Ecology To Understand Patterns Of Community Diversity, Trevor J. Williams

Theses and Dissertations

Community ecology is the study of the patterns and processes governing species abundance, distribution, and diversity within and between communities. Likewise, phylogeography is the study of the historic processes controlling genetic diversity across space. Both fields investigate diversity, albeit at different temporal, spatial and taxonomic scales and therefore have varying assumptions. Community ecology typically focuses on contemporary mechanisms whereas phylogeography studies historic ones. However, new research has discovered that both genetic and community diversity can be influenced by contemporary and historic processes in tandem. As such, a growing number of researchers have called for greater integration of phylogeography and ecology …

Microbial-Host Dynamics And The Evolution Of Nearshore Diversity In Hippocampus Abdominalis, Jimiane L. Ashe

Dissertations, Theses, and Capstone Projects

Local adaptation is a fundamental concept at the core of evolutionary process. Devising means to break down larger concepts and systematically test internal mechanisms are key to understanding the driving forces behind the influence of environmental differences on biological systems. To understand dynamic processes in the natural world, we must strip away layers and confounding variables that may mask the signal we hope to understand. In this case seahorse species, Hippocampus abdominalis, or the pot-bellied seahorse, made an unlikely but ideal study system. The first layer to strip away was neutral genetic variation within the population. A multilocus genetic …

The Genetic Basis Of Adaptation To Environmental Stress In Two Grass Genomic Model Systems, David Mitchell Goad

Arts & Sciences Electronic Theses and Dissertations

Plants are exposed to a wide variety of environmental stress in the wild and have developed an equally diverse set of adaptations to tolerate them. The evolutionary processes that have led to this functional diversification, and the specific genes and physiological mechanisms involved, are of immense interest to both evolutionary biologists and crop breeders. In this dissertation I investigate adaptation to different types of environmental stress in two economically important grass species, seashore paspalum (Paspalum vaginatum Sw.) and rice (Oryza sativa L.).

Seashore paspalum is a halophytic turfgrass that occupies habitats which can dramatically differ in salt concentration. Populations may …

Evolution And Resurrection Ecology Of A Foundational Coastal Marsh Plant, Jennifer L. Summers

Doctoral Dissertations

Stratified storage of dormant seeds in soil can result in natural archives useful for studying evolutionary responses to environmental change. However, few studies leverage soil-stored seed banks as natural archives, in part because of concerns over attrition, bias, and sediment mixing. Here, I examine the persistent seed bank of Schoenoplectus americanus, a foundational brackish marsh sedge, to a) determine whether it can serve as a resource for reconstructing demographic and population genetic/genomic variation, b) whether and how evolution may be occurring across a century. After extracting seeds from radionuclide-dated soil cores taken across the Chesapeake Bay, I “resurrected” age …

The Utilization And Optimization Of Omics Trait Prediction Models Within And Across Diverse Populations, Ashley Mulford

Master's Theses

Most cancer chemotherapeutic agents are ineffective in a subset of patients; thus, it is important to consider the role of genetic variation in drug response. Lymphoblastoid cell lines (LCLs) derived from 1000 Genomes Project populations of diverse ancestries are a useful model for determining how genetic factors impact variation in cytotoxicity. In our study, LCLs from three 1000 Genomes Project populations of diverse ancestries were previously treated with increasing concentrations of eight chemotherapeutic drugs and cell growth inhibition was measured at each dose with half-maximal inhibitory concentration (IC50) or area under the dose-response curve (AUC) as our phenotype for each …

Population-Matched Transcriptome Prediction Increases Discovery And Replication Rate In Twas, Elyse Geoffroy

Master's Theses

Most genome-wide and transcriptome-wide association studies (GWAS, TWAS) focus on European populations; however, these results cannot always be accurately applied to non-European populations due to differences in genetic architecture. Using summary statistics from GWAS in the Population Architecture using Genomics and Epidemiology (PAGE) study, which comprises ~50,000 Hispanic/Latinos, African Americans, Asians, Native Hawaiians, and Native Americans, we perform transcriptome-wide association studies to determine gene-trait associations. Initially, we compared results using two transcriptome prediction models derived from the Multi-Ethnic Study of Atherosclerosis (MESA) populations: the African American (AFA) model and the Hispanic/Latino (HIS) model. We identified 141 unique genome-wide significant trait-associated …

Population Genetics Of A Reintroduced Fisher (Pekania Pennanti) Population In West Virginia, Caroline E. Harms

Graduate Theses, Dissertations, and Problem Reports

Fishers (Pekania pennanti) were reintroduced in West Virginia in 1969 with no population wide genetic analysis ever having been conducted. Genetic analysis of reintroduced populations is vital to assess genetic diversity as an indicative of population viability. My objective was to collect fisher samples throughout West Virginia, nearby states where fisher may be migrating (PA and NY), and the New Hampshire source population to provide a full genetic interpretation of the reintroduced West Virginia population. Genetic analysis was used to measure genetic diversity, admixture or delineation of subpopulations, and effective population size. Sample location and genetic data were …

Comparative Conservation Genomics Of A Suite Of Imperiled Freshwater Mussels, Scott C. Meyer

Electronic Theses and Dissertations

Maintenance of genetic diversity is a critical component to the management and recovery of imperiled species. By ensuring that a species’ genetic diversity is maintained, issues like inbreeding depression and loss of local adaptation can be prevented. However, the genetic diversity of many species are not well-characterized, and the factors that influence a species’ genetic diversity are often not well understood. In the case of imperiled unionid freshwater mussels, it is important to conduct conservation genetic assessments to aid in their management and preserve genetic diversity. This is the first study to conduct a comparative conservation genomic assessment for eight …

The Virome Of Peony And The Population Structure Of Its Most Prominent Viruses, Cullen Shaffer

Graduate Theses and Dissertations

Peony (Peonia lactiflora, Pall.) is a popular ornamental that has been cultivated for millennia. Due to its popularity, plant material is frequently moved across international borders allowing for the spread of viruses. The virome of several peony plants was investigated and four viruses; namely Amazon lily mild mottle virus (ALiMMV), Cycas necrotic stunt virus (CNSV), Gentian Kobu-sho associated virus (GKaV) and Lychnis mottle virus (LycMoV) were detected for the first time in the Western Hemisphere. Incidence ranged from a few plants for ALiMMV to near universal infection for CNSV. GKaV was found in individuals that were infected with Lemoine’s disease …

Population Structure Of A Federally Endangered Plant (Astragalus Jaegerianus Munz, Fabaceae) With Limited Range Using Microsatellites, Sueann Neal

Electronic Theses, Projects, and Dissertations

Studies on population genetics examine the relationship and effects of population structure, migration, gene flow and demographic history, and are therefore important in the conservation of endangered species. Astragalus jaegerianus, a critically federally endangered species found in a geographically restricted range is investigated to determine population structure and genetic variation. Previous research on A. jaegerianus focused on DNA sequence data for cpDNA and nrDNA showed no variation. Further research on A. jaegerianus utilizing AFLP’s on the whole genome indicated substantial gene diversity and population structure consistent with geographically widespread species. AFLP research is a cost-effective process to identify levels …