京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第19547号 / 理博第4207号 / 新制||理||1603(附属図書館) / 32583 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 幸島 司郎, 教授 伊谷 原一, 教授 村山 美穂 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(地域研究) / 甲第20734号 / 地博第225号 / 新制||地||83(附属図書館) / 京都大学大学院アジア・アフリカ地域研究研究科アフリカ地域研究専攻 / (主査)教授 木村 大治, 准教授 安岡 宏和, 助教 佐藤 宏樹, 教授 市川 光雄 / 学位規則第4条第1項該当 / Doctor of Area Studies / Kyoto University / DGAM

Whole genome sequencing (WGS) projects for model mammalian organisms exposed the magnitude to which transposable elements (TEs) have contributed to DNA content, but led to inferences on repeat composition and activity patterns which do not capture the true diversity within Mammalia. Understanding of the evolutionary importance of TEs and the development of TEs for biological applications are hindered when considering only the data gathered from a limited sampling of model organisms. The research presented here begins with analysis of a mouse lemur WGS dataset, revealing an exception in the primate lineage to the generalizations garnered from model organisms. A recently active TE was uncovered with evidence of horizontal transfer involving a primate and another mammal; this discovery may lead to a useful transfection vector with known efficacy in mammalian cells. Furthermore, an opportunity to observe atypical patterns of TE diversification within a mammalian family was achieved through survey sequencing and comparative analyses of five vespertilionid taxa and a phyllostomid outgroup. A potential inverse relationship between the two classes of TEs was tentatively described, and further explored by an in-depth analysis of the dominant TE family from each class in a species with WGS data available. The interplay of the two classes could not previously be investigated in mammals, due to ~40 million years of Class II TE inactivity in model organisms. Through exploration of activity patterns of both classes, this study provides insight on the relationship between TEs and their host.

Heterogeneous landscapes made up of variegated patches are common among managed ecosystems, and often provide diverse structural and compositional habitat characteristics. Landscape heterogeneity can affect distribution of resources, competition, and dispersal of organisms over space and time. Therefore, understanding how species respond to dynamic landscapes is necessary when implementing management decisions that foster biodiversity within managed ecosystems. My study uses hierarchical models in a Bayesian framework to quantify effects of landscape context on meso-mammal predators and northern bobwhite (Colinus virginianus) occupancy in an intensively managed loblolly pine forest. Results indicate that edge density can positively influence occupancy of meso-mammal predators, while age of stand, or years since disturbance, can negatively influence occupancy of northern bobwhite. These results further illustrate the importance of considering biodiversity implications when making management decisions.

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Understanding marine mammal populations and how they are affected by human activity and ocean conditions is vital, especially in tracking population declines and monitoring endangered species. However, tracking marine mammal populations and their distribution is challenging due to difficulties in observation and costs. Using surrounding plankton environmental DNA (eDNA) has the potential to provide an indirect measure of monitoring cetacean abundances based on ecological associations. This project aims to apply statistical methods to assess the relationship of visual abundances of common species of baleen whales with amplicon sequence variants (ASV) of plankton eDNA samples from the NOAA-CalCOFI Ocean Genomics (NCOG) project. Modeling this relationship of eDNA with marine mammal sightings may greatly aid the ability to predict the abundance of whales in the ocean. There are several key challenges associated with the analysis of this NCOG data. Plankton eDNA samples are an example of compositional data, where the proportions of each ASV must sum to one; this provides a challenging constraint for statistical analysis and interpretation. High dimensionality (the number of parameters exceeds the observations) and sparsity (many observed zeros) of the genetic sequencing data also pose challenges in estimating parameters. Finally, the model associations should be adjusted for related factors, including seasonality and oceanographic factors, the latter of which goes beyond this project's scope. This thesis develops and fits models to estimate cetacean abundance from plankton eDNA by leveraging methods of compositional data analysis and high-dimensional regression. This project applies log-ratio data transformations and corresponding log-contrast models to address the compositional aspect of eDNA reads. Regression methods involving high-dimensional data typically rely on dimensionality reduction or regularization. This project implements both reduction and regularization through sparse partial least squares (sPLS) regression. In addition to the data modeling objective of using plankton eDNA to predict baleen whale abundances, this project also identifies ecological correlations between whale abundance and plankton eDNA.

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Thesis (M.S.)--Oregon State University, 2007. / Printout. Includes bibliographical references. Also available on the World Wide Web.

Thesis (M.S.) -- University of Tennessee, Knoxville, 2006. / Title from title page screen (viewed on Jan. 31, 2007). Thesis advisor: Lisa I. Muller. Vita. Includes bibliographical references.