Physical Sciences and Mathematics Commons^™

Using Cuda To Enhance Data Processing Of Variant Call Format Files For Statistical Genetic Analysis, Heather Mckinnon

All Graduate Projects

Utilizing the power of GPU parallel processing with CUDA can speed up the processing of Variant Call Format (VCF) files and statistical analysis of genomic data. A software package designed toward this purpose would be beneficial to genetic researchers by saving them time which they could spend on other aspects of their research. A data set containing genetics from a study of trichome production in Mimulus guttatus, or yellow monkey flower, was used to develop a package to test the effectiveness of GPU parallel processing versus serial executions. After a serial version of the code was generated and benchmarked, OpenACC …

Sampling The Local Fare: Fishes At The Sam Israel House Pit (45gr76), Soap Lake, Washington, Adam Fruge

All Master's Theses

The Sam Israel site is a precontact archaeological complex with numerous fish bones at the north end of Soap Lake, Washington. Excavated in 1976, the fish remains recovered from there were never fully analyzed prior to this research. Since this inland Columbia Plateau site had thousands of fish bones, it contained untapped potential for our understanding of ancient local fish procurement. As such, I conducted a detailed analysis of 2,862 fish bone specimens from the Sam Israel House Pit locus to: study a larger sample of fish bones in greater detail than was done before; compare the distribution of fishes …

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) …

Software Development For Genome Sequence Analysis, David Farr

Symposium Of University Research and Creative Expression (SOURCE)

The cost of genome sequencing has decreased rapidly, expanding availability for many biological applications (Muir 2016). For example, researchers can now obtain genome sequences from multiple populations under different types of selection. Comparison of these sequences allows for identification of chromosome regions and specific genes associated with adaptive evolution (Kelly 2013). As an increasing number of researchers engage in this type of inquiry, many have created in-house computer scripts to analyze the raw sequence data (e.g., Kelly 2013), creating a gap in both continuity and standardization.

Using a test dataset and preliminary results from an ongoing artificial selection experiment in …

Resolving Gnetum Evolutionary History, Angela Mcfadden

All Master's Theses

Gnetum are non-flowering seed plants of the tropics, indigenous to South America, Africa, and Asia. This group of about 40 species is fascinating to botanists because it shares distinctive morphological characteristics with flowering plants, such as broad leaves, woody stems, and flower-like strobili. There are still questions surrounding the relationships within the genus of Gnetum. With that in mind, I focused my work on generating phylogenetic hypotheses, using two molecular data sets: a concatenation of over 60 different chloroplast genes (66,815 base pairs), and the whole chloroplast genome (128,772 base pairs). This allowed me to compare the two phylogenies …

Conservation And Restoration Of Pine Forest Genetic Resources In México, C. Sáenz-Romero, Amy E. Snively, R. Lindig-Cisneros

Student Published Works

Deforestation rates in México are about 670,000 ha/year. This threatens the richness of forest genetic resources in México, causing the disappearance of locally adapted populations and rare and endangered pine species. México is one of the six megadiverse countries in the world, with half of the world’s Pinus species. Pinus is one of the most economically and ecologically important forest genera in México. We suggest that delineation of seed zones and the establishment of a network of Forest Genetic Resource Conservation Units (FGRCUs), linked with forest management and ecological restoration programs will protect this valuable resource. We estimate that FGRCUs …