Genetics Commons^™

The Genetic Diversity Of An Endangered Buttercup, Ranunculus Triternatus, Ryan Garcia

All Graduate Projects

Ranunculus triternatus, a rare endemic species of the Columbia River Gorge, faces conservation challenges due to its limited range and fragmented populations. This study assesses the genetic diversity of R. triternatus and compares it with its widespread congener, Ranunculus glaberrimus, using inter-primer binding site (iPBS) markers. Genetic data from 80 individuals across eight populations were analyzed using Nei’s genetic diversity, Shannon’s diversity index, and AMOVA. Results showed R. triternatus had higher genetic diversity than western populations of R. glaberrimus, with eastern populations of R. glaberrimus displaying greater diversity than western ones. PCA, UPGMA, and STRUCTURE analysis revealed …

The Genetic Diversity Of An Endangered Buttercup, Ranunculus Triternatus, Ryan Garcia

All Master's Theses

Ranunculus triternatus, a rare endemic species of the Columbia River Gorge, faces conservation challenges due to its limited range and fragmented populations. This study assesses the genetic diversity of R. triternatus and compares it with its widespread congener, Ranunculus glaberrimus, using inter-primer binding site (iPBS) markers. Genetic data from 80 individuals across eight populations were analyzed using Nei’s genetic diversity, Shannon’s diversity index, and AMOVA. Results showed R. triternatus had higher genetic diversity than western populations of R. glaberrimus, with eastern populations of R. glaberrimus displaying greater diversity than western ones. PCA, UPGMA, and STRUCTURE analysis revealed …

Cross Species Use Of Human Microarray Genotyping Technology For Bornean Orangutan (Pongo Pygmaeus) Snp Discovery, Ruth Ella Linsky, R. Steven Wagner, Reniastoetie Djojoasmoro, Joseph G. Lorenz, Biruté M. F. Galdikas

Student Published Works

Previous genetic studies of orangutans (Pongo spp.) have relied mainly upon mitochondrial DNA or microsatellite short tandem repeats (STR) for genomic genotyping analysis. Scientists have yet to take advantage of the genetic closeness of the great apes to humans for genomic analysis by using advanced techniques available for human genotyping. To genotype orangutans at Tanjung Puting National Park, we developed a novel combination of a methyl-based magnetic enrichment capture of genomic fecal DNA with genotyping on a human targeted single nucleotide polymorphism (SNP) microarray, and compared this to additional microsatellite (STR) micro-capillary genotyping. We successfully isolated 125 known human genomic …

Transcriptional Analysis Of The Response Of C. Elegans To Ethanol Exposure, Mark G. Sterken, Marijke H. Van Wijk, Elizabeth C. Quamme, Joost A. G. Riksen, Lucinda Carnell, Laura D. Mathies, Andrew G. Davies, Jan E. Kammenga, Jill C. Bettinger

Biology Faculty Scholarship

Ethanol-induced transcriptional changes underlie important physiological responses to ethanol that are likely to contribute to the addictive properties of the drug. We examined the transcriptional responses of Caenorhabditis elegans across a timecourse of ethanol exposure, between 30 min and 8 h, to determine what genes and genetic pathways are regulated in response to ethanol in this model. We found that short exposures to ethanol (up to 2 h) induced expression of metabolic enzymes involved in metabolizing ethanol and retinol, while longer exposure (8 h) had much more profound effects on the transcriptome. Several genes that are known to be involved …

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 …

Ecological And Genetic Connectivity Of Shrews (Sorex Spp.) Across Interstate-90 In The Washington Cascade Range, Jordan Ryckman

All Master's Theses

Roads negatively affect wildlife by degrading and fragmenting habitat. The I-90 Snoqualmie Pass East project was established to improve traffic safety for both humans and wildlife. Here, the Washington State Department of Transportation is constructing wildlife crossing structures to increase ecosystem connectivity as part of this project. The goal of my study was to investigate shrews – very small mammals with presumably low mobility and dispersal capacity – at sites on the eastern slopes of the Cascade Range where wildlife crossing structures will be built in the future. My main objectives were to verify shrew species composition, assess population genetic …

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) …

Human Dispersal From Siberia To Beringia: Assessing A Beringian Standstill In Light Of The Archaeological Evidence, Kelly E. Graf, Ian Buvit

All Faculty Scholarship for the College of the Sciences

With genetic studies showing unquestionable Asian origins of the first Americans, the Siberian and Beringian archaeological records are absolutely critical for understanding the initial dispersal of modern humans in the Western Hemisphere. The genetics-based Beringian Standstill Model posits a three-stage dispersal process and necessitates several expectations of the archaeological record of northeastern Asia. Here we present an overview of the Siberian and Beringian Upper Paleolithic records and discuss them in the context of a Beringian Standstill. We report that not every expectation of the model is met with archaeological data at hand.

Transgenerational Plasticity Is Sex-Dependent And Persistent In Yellow Monkeyflower (Mimulus Guttatus), Kayla C. Akkerman, Arash Sattarin, John K. Kelly, Alison G. Scoville

Student Published Works

Transgenerational phenotypic plasticity, whereby environmental cues experienced by parents alter the phenotype of their progeny, has now been documented in diverse organisms. Transmission of environmentally determined responses is known to occur through both maternal and paternal gametes, but the underlying mechanisms have rarely been compared. In addition, the persistence of induction over multiple generations appears to vary widely, but has been characterized for relatively few systems. Yellow monkeyflower (Mimulus guttatus) is known to exhibit transgenerational induction of increased glandular trichome production in response to simulated insect damage. Here, we test for differences between maternal and paternal transmission of …

Analysis Of Fy Promoter And Hepatocystis Load In South African Vervet Monkeys (Chlorocebus Aethiops), Benjamin J. Gombash

All Master's Theses

There are species of Hepatocystis and Plasmodium, related blood parasites, that enter the cell through a chemokine receptor, coded for by the Duffy antigen/receptor for chemokines in humans, and the FY*0 (FY Null) allele in the promoter of this gene results in the absence of this receptor on the exterior of the cell (Miller et al., 1977; Miller et al., 1975; Miller et al., 1976; Barnwell et al., 1989; Perkins and Schall, 2002; Martinsen et al., 2008; Tung et al., 2009). Humans without the receptor show resistance to multiple strains of Plasmodium (Tournamelle, et al., 1995; Zimmerman, et al. …

Influence Of Landscape On Gene Differentiation In The American Pika (Ochotona Princeps) Within The Interstate 90 Snoqualmie Pass Corridor, Craig P. Fergus

All Master's Theses

Understanding the impact of different landscape features on the movement of genes among populations can be helpful in managing wildlife populations. Our study used GIS tools to compare genetic connectivity among 13 American pika (Ochotona princeps) habitat patches across an approximately 77 square km area adjacent to Interstate 90 near Snoqualmie Pass, WA. Tissue samples were collected from 85 individuals and genotyped at six microsatellite loci to determine genetic differentiation among each pair of patches. A variety of models estimating the influence of landscape factors on gene flow were then used to find “resistance scores” between each pair …

The Evolution Of Sex Determination And The Dmrt1 Gene In The Japanese Gecko (Gekko Japonicus), Lisa-Marie Mullen

All Master's Theses

There are different sex-determining mechanisms in our environment, which are separated into two groups known as genotypic sex determination (GSD) and environmental sex determination. The most well-known mechanism in the ESD group is temperature-dependent sex determination (TSD). In this study, the presence of the Doublesex and mab-3-related Transcription Factor (Dmrt1) gene was observed during embryonic development in geckos with a TSD mechanism. To do this, I observed the rate of transcription of the Dmrt1 gene in the Gecko species Gekko japonicus. Pregnant geckos were caught around Nanjing, China. Once the females laid their eggs, the eggs were …

Genetic Diversity Of North American Captive-Born Gorillas (Gorilla Gorilla Gorilla), Noah D. Simmons, Ronald S. Wagner, Joseph G. Lorenz

All Faculty Scholarship for the College of the Sciences

Western lowland gorillas (Gorilla gorilla gorilla) are designated as critically endangered and wild populations are dramatically declining as a result of habitat destruction, fragmentation, diseases (e.g., Ebola) and the illegal bushmeat trade. As wild populations continue to decline, the genetic management of the North American captive western lowland gorilla population will be an important component of the long‐term conservation of the species. We genotyped 26 individuals from the North American captive gorilla collection at 11 autosomal microsatellite loci in order to compare levels of genetic diversity to wild populations, investigate genetic signatures of a population bottleneck and identify …

Genetic Analysis Of Putative Familial Relationships In A Captive Chimpanzee (Pan Troglodytes) Population, Renato Robledo, Joseph G. Lorenz, Jeanne Beck, James Else, Patrick Bender

Anthropology and Museum Studies Faculty Scholarship

Twelve autosomal dinucleotide repeat loci were analyzed in chimpanzees genomes by DNA amplification using primers designed for analysis of human loci. The markers span the entire length of human chromosomes 21 and 22. Nine markers were polymorphic in chimpanzee as well, with a somewhat comparable level of polymorphism and allele size range. Even in the presence of very limited information and in spite of missing samples, it was possible to reconstruct a complex pedigree and to provide molecular data that corroborate family relationships that were deduced from cage history and behavioral data. The conclusions were further supported by mitochondrial DNA …

Genetic Comparison Of Water Molds From Embryos Of Amphibians Rana Cascadae, Bufo Boreas And Pseudacris Regilla, Kori K. Ault, James E. Johnson, Holly C. Pinkart, R. Steven Wagner

All Faculty Scholarship for the College of the Sciences

Water molds that cause the disease saprolegniasis have been implicated in widespread mortality of amphibian embryos. However, because of the limitations of traditional identification methods, water mold species involved in die-offs or utilized in ecological studies often remain unidentified or identified only as Saprolegnia ferax. Furthermore, water mold taxonomy requires revision, so very distinct organisms may all be called S. ferax. Recent DNA-based studies indicate that the diversity of water molds infecting amphibian embryos is significantly higher than what was previously known, but these studies rely on culture methods, which may be biased towards taxa that grow best …

Mendelian Breeding Units Versus Standard Sampling Strategies: Mitochondrial Dna Variation In Southwest Sardinia, Daria Sanna, Joseph G. Lorenz

All Faculty Scholarship for the College of the Sciences

We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and …

Implications Of The Plastid Genome Sequence Of Typha (Typhaceae, Poales) For Understanding Genome Evolution In Poaceae, Mary M. Guisinger, Timothy W. Chumley, Jennifer V. Kuehl, Jeffrey L. Boore, Robert K. Jansen

All Faculty Scholarship for the College of the Sciences

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including …

The Complete Plastid Genome Sequence Of Welwitschia Mirabilis: An Unusually Compact Plastome With Accelerated Divergence Rates, Skip R. Mccoy, Jennifer V. Kuehl, Jeffrey L. Boore, Linda A. Raubeson

All Faculty Scholarship for the College of the Sciences

Background

Welwitschia mirabilis is the only extant member of the family Welwitschiaceae, one of three lineages of gnetophytes, an enigmatic group of gymnosperms variously allied with flowering plants or conifers. Limited sequence data and rapid divergence rates have precluded consensus on the evolutionary placement of gnetophytes based on molecular characters. Here we report on the first complete gnetophyte chloroplast genome sequence, from Welwitschia mirabilis, as well as analyses on divergence rates of protein-coding genes, comparisons of gene content and order, and phylogenetic implications.

Results

The chloroplast genome of Welwitschia mirabilis [GenBank: EU342371] is comprised of 119,726 base pairs and exhibits …

Distance-Based Genome Rearrangement Phylogeny, Li-San Wang, Tandy Warnow, Bernard M.E. Moret, Robert K. Jansen, Linda A. Raubeson

All Faculty Scholarship for the College of the Sciences

Evolution operates on whole genomes through direct rearrangements of genes, such as inversions, transpositions, and inverted transpositions, as well as through operations, such as duplications, losses, and transfers, that also affect the gene content of the genomes. Because these events are rare relative to nucleotide substitutions, gene order data offer the possibility of resolving ancient branches in the tree of life; the combination of gene order data with sequence data also has the potential to provide more robust phylogenetic reconstructions, since each can elucidate evolution at different time scales. Distance corrections greatly improve the accuracy of phylogeny reconstructions from DNA …

Effects Of Ultraviolet-B Radiation On Leaf Morphology Of Arabidopsis Thaliana (L.) Heynh. (Brassicaceae), Maria Regina Torres Boeger, Mary E. Poulson

Biology Faculty Scholarship

Reduction of the ozone layer results in the increase in ultraviolet radiation reaching the earth's surface, especially the ultraviolet-B (UV-B). The increase of radiation may induce structural and physiological changes in plants, influencing their growth and development. This paper evaluates the effects of ambient UV-B radiation upon to the leaf morphology of Arabidopsis thaliana developed under controlled conditions. The seeds of A. thaliana grown in environmental chamber, with 300 µmol m^-2s^-1 de photosynthetically active radiation (PAR) with and without 6 kJ m^-2 s^-1 of radiation UV-B_be (UV-B_be; UV-B biologically effective). After 21 …

Methods For Obtaining And Analyzing Whole Chloroplast Genome Sequences, Robert K. Jansen, Linda A. Raubeson, Jeffrey L. Boore, Claude W. Depamphilis, Timothy W. Chumley, Rosemarie C. Haberle, Stacia K. Wyman, Andrew J. Alverson, Riannon Peery, Sallie J. Herman, H. Matthew Fourcade, Jennifer V. Kuehl, Joel R. Mcneal, James Leebens-Mack, Liying Cui

All Faculty Scholarship for the College of the Sciences

During the past decade there has been a rapid increase in our understanding of plastid genome organization and evolution due to the availability of many new completely sequenced genomes. Currently there are 43 complete genomes published and ongoing projects are likely to increase this sampling to nearly 200 genomes during the next five years. Several groups of researchers including ours have been developing new techniques for gathering and analyzing entire plastid genome sequences and details of these developments are summarized in this chapter. The most important recent developments that enhance our ability to generate whole chloroplast genome sequences involve the …

Chloroplast Dna Rearrangements In Campanulaceae: Phylogenetic Utility Of Highly Rearranged Genomes, Mary E. Cosner, Linda A. Raubeson, Robert K. Jansen

All Faculty Scholarship for the College of the Sciences

Background

The Campanulaceae (the "hare bell" or "bellflower" family) is a derived angiosperm family comprised of about 600 species treated in 35 to 55 genera. Taxonomic treatments vary widely and little phylogenetic work has been done in the family. Gene order in the chloroplast genome usually varies little among vascular plants. However, chloroplast genomes of Campanulaceae represent an exception and phylogenetic analyses solely based on chloroplast rearrangement characters support a reasonably well-resolved tree.

Results

Chloroplast DNA physical maps were constructed for eighteen representatives of the family. So many gene order changes have occurred among the genomes that characterizing individual mutational …

Patterns Of Mtdna Diversity In Northwestern North America, Ripan S. Malhi, Katherine E. Breece, Beth A. Schultz Shook, Frederika A. Kaestle, James C. Chatters, Steven Hackenberger, David Glenn Smith

All Faculty Scholarship for the College of the Sciences

The mitochondrial DNA (mtDNA) haplogroups of 54 full-blooded modern and 64 ancient Native Americans from northwestern North America were determined. The control regions of 10 modern and 30 ancient individuals were sequenced and compared. Within the Northwest, the frequency distribution for haplogroup A is geographically structured, with haplogroup A decreasing with distance from the Pacific Coast. The haplogroup A distribution suggests that a prehistoric population intrusion from the subarctic and coastal region occurred on the Columbia Plateau in prehistoric times. Overall, the mtDNA pattern in the Northwest suggests significant amounts of gene flow among Northwest Coast, Columbia Plateau, and Great …

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 …

The Feasibility Of Avian Karyotypes In Taxonomy, Gerald Francis Shields

All Master's Theses

The purpose of this paper is twofold: first, to evaluate the usefulness of various karyotypic procedures using domesticated and passerine birds and second, to comment on the validity of the application of karyotypic data to taxonomy.

Evaluation Of The Short Sternum As Diagnostic Evidence For Trisomy-E, Frank George Deeter

All Master's Theses

This study has demonstrated that a reliable technique for determining short sternums has been developed. Evidence for its reliability is given by two distinct and highly significant correlations.

How Teachers Of High School Biology May Introduce Heredity And Birds Through The Use Of Doves, Donald Hood Dickinson

Graduate Student Research Papers

It was the purpose of this study (1) to present a method of teaching principles of heredity at a level understandable to students of a high school biology class, (2) to present a list of resource materials for use in a heredity unit, and (3) to show how the use of live animals might intensify student interest in this subject as well as in other phases of bird life such as nest building, incubation of eggs, hatching of eggs, voice and communication, and effects of nutrition on chick development.