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Annotation Of Non-Model Species’ Genomes, Taiya Jarva
Annotation Of Non-Model Species’ Genomes, Taiya Jarva
Master's Theses
The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …
Genetic Population Structure And Effective Number Of Breeders In Systems Across The Range Of The Gulf Sturgeon, Jacob Zona
Master's Theses
Gulf sturgeon (Acipenser oxyicnhus desotoi) are a large, anadromous fish belonging to an ancient lineage that diverged as early as 400 MYA. Overfishing for meat and caviar during the early 1900’s reduced their range and abundance and continued habitat destruction and mortality have limited their ability to recover, leading to their listing under the Endangered Species Act. This study uses genetic techniques to determine the effective number of breeders for multiple spawning groups of Gulf sturgeon in river systems across their range to set a baseline for tracking reproductive success of the species. Accompanying genetic information relevant to …
Incorporating Sex Chromosomes In Transcriptome Prediction Models And Improving Cross-Population Prediction Performance, Daniel S. Araujo
Incorporating Sex Chromosomes In Transcriptome Prediction Models And Improving Cross-Population Prediction Performance, Daniel S. Araujo
Master's Theses
Transcriptome prediction models built with data from European-descent individuals are less accurate when applied to different populations because of differences in linkage disequilibrium patterns and allele frequencies. We hypothesized multivariate adaptive shrinkage may improve cross-population transcriptome prediction, as it leverages effect size estimates across different conditions - in this case, different populations. To test this hypothesis, we made transcriptome prediction models for use in transcriptome-wide association studies (TWAS) using different methods (Elastic Net, Matrix eQTL and Multivariate Adaptive Shrinkage in R (MASHR)) and tested their out-of-sample transcriptome prediction accuracy in population-matched and cross-population scenarios. Additionally, to evaluate model applicability in …
Conservation Genomics: Utilizing Genetic And Transcriptomic Sequencing For Effective Conservation Management Of Astragalus Osterhoutii, Christine Mowad
Conservation Genomics: Utilizing Genetic And Transcriptomic Sequencing For Effective Conservation Management Of Astragalus Osterhoutii, Christine Mowad
Master's Theses
Astragalus osterhoutii M.E. Jones (Fabaceae) is a federally listed, rare, endemic species restricted to seleniferous soils in Grand County, CO (Anderson, 1989). This research utilized both RADseq and RNAseq to generate neutral and adaptive genomic datasets. Neutral data analysis aimed to determine i) the genetic diversity of A. osterhoutii and each of its populations level, ii) how genetic structure is partitioned across the species range, and iii) the closest relative to A. osterhoutii. Analysis of adaptive, RNAseq data aimed to identify i) differentially expressed genes, ii) if patterns of expression are similar to neutral data, and iii) differences in Se …
Understanding Species Boundaries Between Penstemon Acaulis And Penstemon Yampaensis: Implications For Conservation And Management, Juliet Simpson
Understanding Species Boundaries Between Penstemon Acaulis And Penstemon Yampaensis: Implications For Conservation And Management, Juliet Simpson
Master's Theses
Effective conservation management relies upon accurate taxonomic information and an understanding of the genetic health and population structure for each species. Penstemon acaulis and P. yampaensis are endemic species to Colorado, Utah, and Wyoming, and have been considered for listing under the Endangered Species Act (ESA). There is little biological data published about either and there remains taxonomic uncertainty surrounding the two. Phylogenetic analyses showed P. acaulis and P. yampaensis to be distinct, monophyletic lineages and morphological data further supported taxonomic recognition of both species, however these results did not support the previous species boundaries. Eastern populations of P. acaulis …
Population-Matched Transcriptome Prediction Increases Discovery And Replication Rate In Twas, Elyse Geoffroy
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 …
Using Crispr-Cas9 As A Restriction Enzyme, Zack Crawley
Using Crispr-Cas9 As A Restriction Enzyme, Zack Crawley
Master's Theses
Restriction digests are a commonly utilized process for cleaving DNA at specific, but relatively common sites. Restriction enzymes have widespread use in DNA manipulation. CRISPR/Cas9 is a recently identified endonuclease which utilizes a customizable guide sequence to recognize and cut specific ~20 bp sites located in a DNA sequence. This preliminary research aimed to exploit the potential benefit of DNA restriction using the CRISPR/Cas9 procedure through alterations of different components involved in that system. We sought to refine existing CRISPR/Cas9 protocols and make a budget friendly, user-selectable CRISPR/Cas9 restriction digest protocol. The motivation for this research was to simplify and …
Geographic Patterns Of Genetic Distribution Within Calochortus Gunnisonii In The Central And Southern Rocky Mountains, Ryan Scott Fuller
Geographic Patterns Of Genetic Distribution Within Calochortus Gunnisonii In The Central And Southern Rocky Mountains, Ryan Scott Fuller
Master's Theses
Organismal population ranges and genetic architecture have largely been shaped by climatic events. The Quaternary Period (2.6 million years to present) has been characterized by a series of climatic events manifested as Ice Ages. During glacial periods, plants and animals in temperate and arctic regions were restricted to small patches of suitable habitat less affected by expanding glaciers and extreme cooling. These refugia held importance for the persistence of organisms through glacier interphases. Mountain system vegetation in temperate latitudes was affected by patchy glacier patterns that separated some species into multiple refugia. The isolation of such populations has had a …
The Role Of Carotenoid Cleavage Dioxygenase 4 In Flower Color Of The Allopolyploid Brassica Napus, Leanne Denice Fogg
The Role Of Carotenoid Cleavage Dioxygenase 4 In Flower Color Of The Allopolyploid Brassica Napus, Leanne Denice Fogg
Master's Theses
Allopolyploids are formed by interspecific hybridization and whole genome duplication, with the resulting organism contains multiple distinct subgenomes in one nucleus. Subgenomic interactions result in massive genetic and epigenetic reconstruction, contributing to variable phenotypic traits noted in newly formed allopolyploids. To better understand these mechanisms in the context of molecular biology, evolution, and plant breeding, plant biologists study the model organism Brassica napus (farmed as canola or oilseed rape). With white-flowering and yellow-flowering progenitors, flower color phenotype of B. napus presents an opportunity to examine subgenomic interactions. CAROTENOID CLEAVAGE DIOXYGENASE 4 (CCD4) is known to play a major …
Genetic Determinants Of Habitual Physical Activity And Overweight And Obesity, Harold Lee
Genetic Determinants Of Habitual Physical Activity And Overweight And Obesity, Harold Lee
Master's Theses
We tested 6 single nucleotide polymorphisms (SNPs) associated with obesity from genome wide association studies for their association with physical activity (PA). Healthy European-American women (n=265) and men (n=230) (23.5±0.3yr, 24.6±0.2kg•m-2) were genotyped for MC4R (rs17782313), FTO (rs9939609), TMEM18 (rs6548238), NEGR1 (rs2815752), SH2B1 (rs7498665), and KCTD15 (rs11084753), and completed the Paffenbarger PA Questionnaire. We examined gene interactions by summing the number of obesity effect alleles. RESULTS: Normal weight subjects with MC4R T expended 1981.2±741.7kcal∙wk-1 less than non-carriers in total PA (p=0.008), 1825.9±650.2 kcal∙wk-1 less in sports/recreation (p=0.027), and 1231.3±552.7 kcal∙wk-1 less …
A Study Of Genetic Variability In Larval And Adult Populations Of Dungeness Crab (Cancer Magister), Cairbre Fanslow
A Study Of Genetic Variability In Larval And Adult Populations Of Dungeness Crab (Cancer Magister), Cairbre Fanslow
Master's Theses
Spatial and temporal genetic variation was assessed using mitochondrial DNA from adult and megalopae of Dungeness crabs, Cancer magister, from Fraser Delta in British Columbia, Washington, Oregon, and California. Megalopae were continuously sampled using light traps in one location, Coos Bay, Oregon, and compared with adults sampled across the species' range. While small-scale spatial and temporal variation were evident, there was no significant fit to the Isolation-by-Distance model when considering adult and larvae populations sampled over a coastal length of ~1700 km (Mantel r = 0.059, p = 0.289). Smaller bays showed higher genetic diversity than larger bays, contrary to …
Analysis Of Microsatellites From Sclerocactus Glaucus And Sclerocactus Parviflorus To Assess Hybridization Levels And Genetic Diversity, Anna Louise Schwabe
Analysis Of Microsatellites From Sclerocactus Glaucus And Sclerocactus Parviflorus To Assess Hybridization Levels And Genetic Diversity, Anna Louise Schwabe
Master's Theses
Sclerocactus glaucus is an endemic Colorado species that is federally threatened under the Endangered Species Act. Sclerocactus glaucus is losing habitat due to disturbance by oil and gas exploration, urbanization, open range cattle grazing and recreational land use. Due to the low number of wild populations, conservationists question the genetic integrity of the species. Field biologists have observed S. glaucus populations with individuals possessing morphological characteristics of the closely related and widely distributed Sclerocactus parviflorus. Individuals from 28 populations of S. glaucus, 9 populations of S. parviflorus, and 1 population of S. cloveriae were sampled. Microsatellite analysis using 13 variable …
Genetic Population Structure And Cryptic Speciation Of Ghost Shrimp (Neotrypaea Californiensis) In North American West Coast Estuaries, Daphne Anne Gille
Genetic Population Structure And Cryptic Speciation Of Ghost Shrimp (Neotrypaea Californiensis) In North American West Coast Estuaries, Daphne Anne Gille
Master's Theses
Many marine species produce larvae that disperse and develop into post-larvae in the open ocean over a period of weeks to months. However, the patterns and potential of larvae to disperse across long geographic distances are poorly understood. Here genetic variation found at the mitochondrial locus, cytochrome C oxidase subunit I, in adult ghost shrimp, Neotrypaea californiensis, was used as a proxy to infer dispersal potential of ghost shrimp larvae found in estuaries along the west coast of the United States. Multiple haplotypes were shared among 346 adult ghost shrimp specimens collected from estuaries in Washington, Oregon, and California indicated …