Life Sciences Commons^™

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 …

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 …

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 …

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 …

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 …

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 …

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 …

Population Structure And Reproductive Biology Of Monilinia Vaccinii-Corymbosi (Reade) Honey In Lowbush Blueberry In Maine, Katherine A. Ashley

Electronic Theses and Dissertations

Lowbush blueberry, Vaccinium angustifolium Aiton, is both an economically and culturally important crop in Maine, being one of the few endemic crops to North America. The fungus Monilinia vaccinii-corymbosi (Mvc) causes mummy berry disease and is a significant pathogen of both highbush (Vaccinium corymbosum) and lowbush blueberries. While impacts of this disease are not regularly documented, it is estimated that 30-50% of the yield in an unmanaged field can be lost because of Mvc. This disease is typically managed with fungicides or burning of the field during years when the field is pruned, however, the impacts to the …

Evolutionary Inference From Admixed Genomes: Implications Of Hybridization For Biodiversity Dynamics And Conservation, Tyler Chafin

Graduate Theses and Dissertations

Hybridization as a macroevolutionary mechanism has been historically underappreciated among vertebrate biologists. Yet, the advent and subsequent proliferation of next-generation sequencing methods has increasingly shown hybridization to be a pervasive agent influencing evolution in many branches of the Tree of Life (to include ancestral hominids). Despite this, the dynamics of hybridization with regards to speciation and extinction remain poorly understood. To this end, I here examine the role of hybridization in the context of historical divergence and contemporary decline of several threatened and endangered North American taxa, with the goal to illuminate implications of hybridization for promoting—or impeding—population persistence in …

The Ecology And Evolutionary History Of Two Musk Turtles In The Southeastern United States, Grover Brown

Dissertations

Turtles are among one of the most imperiled vertebrate groups on the planet with more than half of all species worldwide listed as threatened, endangered or extinct by the International Union of the Conservation of Nature. The Southeastern United States is a global biodiversity hotspot for turtles, and it likely represents the last area on the planet of both high diversity and high abundance of turtle species. In the past century, there has been an exponential increase in the number of publications on turtles in the United States and Canada, however a recent review of the literature suggests that this …

A Seascape Genetics Approach To Studying Genetic Differentiation In The Bull Kelp Nereocystis Luetkeana, Lily G. Gierke

Theses and Dissertations

The brown alga Nereocystis luetkeana is a foundation species found from Alaska to California. In the Salish Sea, N. luetkeana is declining, but little is known about its population structure. We explored N. luetkeana 1) allelic dissimilarity and richness using seven microsatellite markers, and 2) tested models of gene flow in the Salish Sea using a hydrodynamic transport model. Our results suggest that the N. luetkeana distribution is comprised of four genetic co-ancestry groups that are geographically coherent, apart from the separation of the Strait of Georgia/Puget Sound by the Strait of Juan de Fuca. Our model supported that environmental …

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 …

Dna Extraction And Microsatellite Amplification Of Daphnia Pulicaria Resting Eggs: Analysis Of Allele Frequencies Through Time, Anna Ries

Departmental Honors Projects

A paleoecological approach allows for the study of genetic change in populations over longer periods of time than would be possible if one were sampling populations from year to year. Daphnia and other cladoceran zooplankton are amenable to this type of study because they produce diapausing embryos (ephippial eggs) when they sexually reproduce, and these resting eggs can remain viable for decades to centuries in lake sediments. This study uses paleoecological methods as well as a new methodology for ephippial DNA extraction and amplification to assay for genetic variation in ephippial eggs obtained from sediments of varying ages from Square …

This Is Just A Phase : The Impact Of Population Structure On Haplotype Phasing And Linkage Disequilibrium Measures At Functional Genetic Sites., Roxanne Kaaren Leiter

Electronic Theses and Dissertations

The block-like structure of the human genome has been the subject of many scientific papers and is of practical significance in large-scale genome-wide association studies. How stringent haplotype block boundaries are within and between populations has been the subject of ongoing debate within human population genetics. This thesis will contribute to the description of universal and population-specific haplotype blocks at functional sites, namely across the IL-10 gene family (including IL-10, IL-19, IL-20 and IL-24), which is involved in a number of immune system processes, and MAPKAP-K2, an adjacent and functionally significant kinase gene. Beyond the description of blocks across these …

Population Structure Of Lethrinus Lentjan (Lethrinidae, Percoidei) Across The South China Sea And The Philippines Is Detected With Lane-Affected Radseq Data, Ellen E. Biesack

Biological Sciences Theses & Dissertations

Southeast Asia includes the Coral Triangle, a marine biodiversity hotspot that supports important fishery resources experiencing varied threats. Patterns of speciation and population structure in the Coral Triangle have been examined to test hypotheses relating to the historical geologic processes that may have influenced this biodiversity phenomenon. This study investigates the genetic population structure of the Pink-ear Emperor Snapper, Lethrinus lentjan (Lacepède, 1802), across the Philippines and the South China Sea. The species is fished throughout the Coral Triangle by subsistence and commercial fishers and their landings have been in decline for several years, which could be indicative of depleted …

Tracing The Genetic Footprints Of The Redbelly Yellowtail Fusilier, Caesio Cuning, Across Multiple Spatial And Evolutionary Scales, Amanda Susanne Ackiss

Biological Sciences Theses & Dissertations

Overfishing is one of the most pervasive threats to coral reef ecosystems, and management of these multi-species resources is hampered by limited species-specific population level information. The reefs in the western tropical Pacific Ocean, including the Coral Triangle, are the most bio-diverse in the world. Home to more than 400 million people, this region contains some of the most threatened coral reef ecosystems. Presented here is the first comprehensive analysis of the genetic structure of Caesio cuning, planktivorous fish inhabiting reefs in the Coral Triangle and western Pacific Ocean. Data from both classical Sanger and next-generation sequencing were analyzed …

Development Of An In Silico Kir Genotyping Algorithm And Its Application To Population And Cancer Immunogenetic Analyses, Howard Rosoff

Dissertations & Theses (Open Access)

Gene content determination and variant calling in the complex KIR genomic region are useful for immune system function analysis, pathogenesis and disease risk factor elucidation, immunotherapy development, evolutionary investigations, and human migration modeling. Sequence-specific oligonucleotide and sequence-specific primer PCR methods are the de facto standards for KIR presence/absence identification, but the current platforms are unsuitable for SNP calling, impractical for KIR typing large cohorts of DNA samples, and inapplicable for typing repositories in which sequence data, but not cells or cell analytes, are available. Alternative typing methods, such as in silico sequence-based typing, can address the problems associated with amplicon-based …

Insights Into The Introduction Histories And Population Genetic Dynamics Of The Nile Monitor (Varanus Niloticus) And Argentine Black And White Tegu (Salvator Merianae) In Florida., Jared Price Wood

Electronic Theses and Dissertations

This dissertation examines the population genetic dynamics of two Florida invasives: the Nile monitor (Varanus niloticus) and Argentine black and white tegu (Salvator merianae). I also provide insights into the introduction histories of both species. This study was developed as part of a collaborative effort with the Florida Wildlife Commission to expand our knowledge of these highly detrimental, invasive lizards. All research activities involving animals and animal tissues were approved by the University of Louisville’s Institutional Animal Care and Use Committee (IACUC Proposal #: 12024). I start with a brief introduction into what makes invasive species …

Global Genetic Connectivity And Diversity In A Shark Of High Conservation Concern, The Oceanic Whitetip, Carcharhinus Longimanus, Cassandra L. Ruck

HCNSO Student Theses and Dissertations

The oceanic whitetip shark, Carcharhinus longimanus, is a circumtropical pelagic shark of high conservation concern (IUCN Red List: “Critically Endangered” in the Western North and Western Central Atlantic and “Vulnerable” globally). I present the first, population genetic assessment of the oceanic whitetip shark on a global scale, based on analysis of two mitochondrial genome regions (entire 1066-1067 bp control region and 784 bp partial ND4 gene), and nine nuclear microsatellite loci. No population structure was detected within the Western Atlantic. However, highly significant population structure was detected between Western Atlantic and Indo-Pacific Ocean sharks across all markers. Additionally, a …

Population Genetic Analysis Of Atlantic Horseshoe Crabs (Limulus Polyphemus) In Coastal Massachusetts., Katherine T. Johnson

Masters Theses

Atlantic horseshoe crabs (Limulus polyphemus) have endured decades of intense harvest pressure. Genetics studies have shown evidence of distinct sub-groups spanning the coast, although few fine-scale studies have been done to delineate these groups on a local level. Massachusetts lies directly between two of these sub-groups. With documented differences in prosomal widths of horseshoe crabs from either side of Cape Cod, it is possible that Cape Cod is a barrier to gene flow and that there are two distinct genetic groups within Massachusetts. Regulations currently consider all horseshoe crabs to be of one stock. I examined 6 microsatellite …

Relative Abundances Of The Recently Introduced Barnacles, Megabalanus Coccopoma And An Unidentified Species Of Megabalanus, In The Southeastern U.S., Jennifer L. Tyson

Honors College Theses

ABSTRACT

Megabalanus coccopoma is a prominent invasive species off the coast of Georgia. Recently, among collected samples thought to be M. coccopoma, several individuals of an unidentified species of barnacle were found. The species has been identified as a Megabalanus species, but is still unidentified to the species level. Species identification is difficult due to morphological variation, inconsistent taxonomic keys, and unknown origin. In this study I developed a method to accurately distinguish M. coccopoma from the unidentified Megabalanus sp. using sequence differences in the mitochondrial Cytochrome Oxidase I (COI) gene. This study will provide an accurate estimate of …

Genetic Structure Of Ixodes Scapularis Say 1821 (Acari: Ixodidae), The Blacklegged Tick, By Microsatellite Analysis, John Ludwig

Electronic Theses and Dissertations

The blacklegged tick, Ixodes scapularis (Acari: Ixodidae) is the subject of intense research due to its economic importance from being a vector of several diseases. Previous studies have examined its taxonomic status and more recently, its genetic structure. This study embarked upon resolving the questions surrounding the genetic structuring of the tick, by using different molecular markers. Molecular data were first phylogenetically analyzed by using four different mitochondrial and nuclear markers (12SrDNA n=483, Dloop n=432, ITS2 n=156, Actin n=117). A Bayesian tree was inferred from the concatenated mitochondrial dataset, whereas nuclear gene markers were found to be uninformative. Nine microsatellites …

Genetic Variation, Local Adaptation And Population Structure In North American Red Oak Species, Quercus Rubra L. And Q. Ellipsoidalis E. J. Hill, Jennifer F. Lind-Riehl

Dissertations, Master's Theses and Master's Reports - Open

Forest trees, like oaks, rely on high levels of genetic variation to adapt to varying environmental conditions. Thus, genetic variation and its distribution are important for the long-term survival and adaptability of oak populations. Climate change is projected to lead to increased drought and fire events as well as a northward migration of tree species, including oaks. Additionally, decline in oak regeneration has become increasingly concerning since it may lead to decreased gene flow and increased inbreeding levels. This will in turn lead to lowered levels of genetic diversity, negatively affecting the growth and survival of populations. At the same …

Population Genetics And Ecology Of Regional Malaria Vectors In Amazonian Brazil, Sascha Naomi Mckeon

Legacy Theses & Dissertations (2009 - 2024)

Species complexes are common among anopheline mosquitoes, but only some members of complexes are disease vectors. Research involving overall patterns of divergence, phylogenetic relationships and population structure is partly driven by the operational need to be able to reliably distinguish component taxa that may be involved in malaria transmission. Anopheles triannulatus, An. nuneztovari and An. albitarsis are broadly distributed species complexes that contain local and regionally important malaria vectors, whose genetic diversity has been largely overshadowed by studies involving An. darlingi, the principal vector of Central and South America. I have analyzed the ecological suitability of habitats and geographical ranges …

Analysis Of The Genetic Structure Of Bithynia Tentaculata Snail Populations In Wisconsin And Minnesota, Sarah J. Whalen

All Graduate Theses, Dissertations, and Other Capstone Projects

In recent years, there have been tens of thousands of waterfowl mortalities in Wisconsin and Minnesota. An invasive species of snail, Bithynia tentaculata, is a host for the trematode parasites (Cyathocotyle bushiensis and Sphaeridiotrema globulus) that have caused these deaths. A microsatellite-enriched genomic library was detected using DNA from a B. tentaculata specimen from Lake Onalaska (Pool 7 of the Upper Mississippi River). Seven polymorphic microsatellite loci were used to genotype snails collected from Lake Butte des Morts, Shawano Lake, and Lake Onalaska in Wisconsin, as well as Lake Winnibigoshish in Minnesota. The genetic diversity of each population was measured …

The Genetics Of Colonization In Two Amphibian Species After The 1980 Eruption Of Mount St. Helens, Kristin Ann Bakkegard

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The genetics of colonization is understudied in salamanders but has large conservation implications as new habitats are formed or restored to their previous condition. The 1980 eruption of Mount St. Helens provided a natural experiment to study the genetic effects of a large infrequent environmental disturbance on two species of salamander, Taricha granulosa (Rough-skinned newt) and Ambystoma gracile (Northwestern salamander). Both these species breed in ponds, and are thought to exhibit high breeding site fidelity and low vagility. I designated three treatments based on the effects of the eruption: new ponds (created by the eruption, immigrants only), recovery lakes (in …