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Genetic Effects Of Anthropogenic Disturbance On Native Charrs, Brad Erdman
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
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 …
Population Genomics Of Redbreast Sunfish (Lepomis Auritus): Exploring Gene Flow And Local Adaptation In A Widely Distributed Freshwater Fish, Garret J. Strickland
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 …
Florida Sand Skink And Blue-Tailed Mole Skink: Expanding Geographic Coverage Of Genetic Analysis For Conservation, Emma Simpson
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 …
Applying Conservation Genomic Techniques To Guide Management Of The Reticulated Flatwoods Salamander (Ambystoma Bishopi), Miranda Gaupp
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 …
A Method For Identifying Ancient Introgression Between Caballine And Non-Caballine Equids Using Whole Genome High Throughput Data., Kalpani De Silva
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 …
Comparative Conservation Genomics Of A Suite Of Imperiled Freshwater Mussels, Scott C. Meyer
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 …
Population Structure And Reproductive Biology Of Monilinia Vaccinii-Corymbosi (Reade) Honey In Lowbush Blueberry In Maine, Katherine A. Ashley
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 …
Effects Of Impoundments On The Community Assemblage And Gene Flow Of Stream Crayfishes, Zanethia Choice Barnett
Effects Of Impoundments On The Community Assemblage And Gene Flow Of Stream Crayfishes, Zanethia Choice Barnett
Electronic Theses and Dissertations
Dams and their impoundments block movement of stream organism and change stream physiochemical properties, which subsequently changes biological assemblages and creates barriers to gene flow. While changes in species assemblages and gene flow have been assessed for numerous impoundments and stream organisms, no study has assessed the effects of large impoundments on crayfish assemblages and population genetic diversity and connectivity. I examined the physiochemical, biological, and genetic effects of impoundments on crayfishes. Between May 2015 and August 2017, I sampled multiple sites up- and downstream of three impounded streams, and along the lengths of two unimpounded streams, in the Bear …
This Is Just A Phase : The Impact Of Population Structure On Haplotype Phasing And Linkage Disequilibrium Measures At Functional Genetic Sites., Roxanne Kaaren Leiter
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 …
A Population Genetic Investigation Of The Reticulated Flatwoods Salamander (Ambystoma Bishopi) On Eglin Air Force Base, Alexander S. Wendt
A Population Genetic Investigation Of The Reticulated Flatwoods Salamander (Ambystoma Bishopi) On Eglin Air Force Base, Alexander S. Wendt
Electronic Theses and Dissertations
The reticulated flatwoods salamander (RFS) is an endangered salamander with a unique life history. One of the largest known, best studied refuges for RFS is found on Eglin Air Force Base, and these RFS have been sampled and managed extensively since 2010. My thesis seeks to better understand RFS by using genetic techniques to address several unknowns, including: 1) determining the population structuring of RFS and the manageable units for species conservation, 2) estimating the size and status of populations, 3) understanding dispersal of RFS and factors that influence this, 4) exploring the breeding biology and recruitment patterns of RFS …
Evolutionary Linkage Of Mimetic And Non-Mimetic Color Traits In A Coral Snake Mimicry Complex, John D. Curlis Jr
Evolutionary Linkage Of Mimetic And Non-Mimetic Color Traits In A Coral Snake Mimicry Complex, John D. Curlis Jr
Electronic Theses and Dissertations
Color polymorphism in aposematic mimicry systems is a perplexing phenomenon for evolutionary biologists, as theoretically the benefits of converging on a model phenotype should constrain the evolution of phenotypic diversity in these systems (i.e., color polymorphism should not occur). Nevertheless, color polymorphism in mimicry systems is prevalent throughout many taxa. In some of these systems, the evolution of color polymorphism results in the existence of non-mimetic morphs, such as those that are cryptic. The case of ground snakes (Sonora semiannulata) is unique in that color polymorphism encompasses both mimetic and cryptic morphs, as well as individual mimetic and …
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 …
Panmixia Across The Range Of The Assortatively Mating Lesser Snow Goose, Brent B. Horowitz
Panmixia Across The Range Of The Assortatively Mating Lesser Snow Goose, Brent B. Horowitz
Electronic Theses and Dissertations
The Lesser Snow Goose has been shown to exhibit imprinted positive assortative mating on the basis of its color phases, blue and white, and it has been proposed that the geographic cline of the color phases reflects a historic allopatry of the phases. Using ddRAD-seq, thousands of SNPs were analyzed in both phases and in colonies across the range of the species to examine genetic evidence for separation of the color phases or along the two migratory pathways, which have also been hypothesized to be separate. These analyses did not reveal any genetic differentiation between the color phases nor by …
Genetic Structure Of Ixodes Scapularis Say 1821 (Acari: Ixodidae), The Blacklegged Tick, By Microsatellite Analysis, John Ludwig
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 …
Inter-And Intra-Population Variability Across The Transcriptome Of Lake Baikal’S Endemic Copepod With Ramifications For Adapting To Climate Change, Larry L. Bowman Jr
Inter-And Intra-Population Variability Across The Transcriptome Of Lake Baikal’S Endemic Copepod With Ramifications For Adapting To Climate Change, Larry L. Bowman Jr
Electronic Theses and Dissertations
The future of Lake Baikal’s biodiversity is uncertain in response to climate change. Unlike its diverse benthos, Lake Baikal’s zooplankton is species poor, with up to 96% of its biomass being composed of a single Calanoid copepod species, Epischura baikalensis. This study characterizes the genetic differentiation and differential gene expression of E. baikalensis. Using partial-transcriptome sequences obtained by 454 Rosche and Illumina sequencing technologies, the genetic differentiation at inferred single nucleotide polymorphism (SNP) sites and differential gene expression in populations sampled from various parts of the lake were analyzed. The functional genomics of genes showed significant differential …
Conservation And Population Biology: Genetics, Demography And Habitat Requirements Of The Atlantic Coast Beach Mice, Haakon Myklevoll Kalkvik
Conservation And Population Biology: Genetics, Demography And Habitat Requirements Of The Atlantic Coast Beach Mice, Haakon Myklevoll Kalkvik
Electronic Theses and Dissertations
The conservation biology field seeks to preserve biodiversity and the processes shaping that variation. Conservation biology is intimately tied to evolutionary research, in order to identify evolutionary distinct lineages that may be in danger of disappearing. Interestingly, patterns and processes of lineage divergence and persistence change with respect to spatial and temporal scale. I seek to evaluate biodiversity, the factors that have shaped this heterogeneity, and how this variability persists. To accomplish this I used a phylogeographic approach as well as niche and population modeling on the Peromyscus maniculatus species group found widely distributed in North America. My emphasis was …
Using Landscape Genetics To Assess Population Connectivity In A Habitat Generalist, Tyler Duncan Hether
Using Landscape Genetics To Assess Population Connectivity In A Habitat Generalist, Tyler Duncan Hether
Electronic Theses and Dissertations
Understanding the nature of genetic variation in natural populations is an underlying theme of population genetics. In recent years population genetics has benefited from the incorporation of landscape and environmental data into pre-existing models of isolation by distance (IBD) to elucidate features influencing spatial genetic variation. Many of these landscape genetics studies have focused on populations separated by discrete barriers (e.g., mountain ridges) or species with specific habitat requirements (i.e., habitat specialists). One difficulty in using a landscape genetics approach for taxa with less stringent habitat requirements (i.e., generalists) is the lack of obvious barriers to gene flow and preference …