Index Catalog // ScholarsArchive@OSU

Reproductive isolation and interspecific hybridization in the threatened species, Sidalcea nelsoniana

Creator:: Gisler, Steven D.
Abstract:: In addition to its longstanding recognition as an influential evolutionary process, interspecific hybridization is increasingly regarded as a potential threat to the genetic integrity and survival of rare plant species, manifested through gamete wasting, increased pest and disease pressures, outbreeding depression, competitive exclusion, and genetic assimilation. Alternatively, hybridization has also...
Resource Type:: Masters Thesis
Full Text:: throughout my project I give special thanks to lab member and friend, Matthew Carlson, and additional thanks

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

Creator:: Cronn, Richard, Liston, Aaron, Parks, Matthew, Gernandt, David S., Shen, Rongkun, and Mockler, Todd
Abstract:: Organellar DNA sequences are widely used in evolutionary and population genetic studies, however, the conservative nature of chloroplast gene and genome evolution often limits phylogenetic resolution and statistical power. To gain maximal access to the historical record contained within chloroplast genomes, we have adapted multiplex sequencing-by-synthesis (MSBS) to simultaneously sequence...
Resource Type:: Article
Full Text:: First published online 27 Aug 2008; Nucleic Acids Res. Richard Cronn, Aaron Liston, Matthew Parks

Plastome phylogenomics in the genus Pinus using massively parallel sequencing technology

Creator:: Parks, Matthew Benjamin
Abstract:: This thesis summarizes work completed over the previous four years primarily focusing on chloroplast phylogenomic inquiry into the genus Pinus and related Pinaceae outgroups using next-generation sequencing on Illumina platforms. During the time of our work, Illumina sequence read lengths have essentially been limited to 25 to 100 base pairs,...
Resource Type:: Dissertation
Full Text:: ABSTRACT OF THE DISSERTATION OF Matthew Benjamin Parks for the degree of Doctor of Philosophy in

Targeted enrichment strategies for next-generation plant biology

Creator:: Cronn, Richard, Knaus, Brian J., Liston, Aaron, Maughan, Peter J., Parks, Matthew, Syring, John V., and Udall, Joshua
Abstract:: • Premise of the study: The dramatic advances offered by modern DNA sequencers continue to redefine the limits of what can be accomplished in comparative plant biology. Even with recent achievements, however, plant genomes present obstacles that can make it difficult to execute large-scale population and phylogenetic studies on next-generation...
Resource Type:: Article

Canopy epiphyte studies in the central Oregon Cascades : implications for the management of Douglas-fir forests

Creator:: Sillett, Stephen Charles
Abstract:: This thesis includes four separate studies. The first two studies assessed edge effects in a 700-year-old forest. After 20 years of exposure, epiphyte assemblages on the clearcut edge were similar to those of the forest interior, but there were some differences in vertical distribution patterns. Several species restricted to the...
Resource Type:: Dissertation
Full Text:: Acknowledgements I am much indebted to Bruce McCune and Matthew Goslin for their collaboration in Chapters 4

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

Creator:: Parks, Matthew, Cronn, Richard, and Liston, Aaron
Abstract:: Background: Through next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years. Simultaneously, the risk of incorporating ‘noisy’ data with misleading phylogenetic signal has also increased, and may disproportionately influence the topology of weakly supported nodes and lineages featuring rapid radiations and/or...
Resource Type:: Article
Full Text:: the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae) Parks et al. BMC

Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing

Creator:: Njuguna, Wambui, Liston, Aaron, Cronn, Richard, Ashman, Tia-Lynn, and Bassil, Nahla
Abstract:: The cultivated strawberry is one of the youngest domesticated plants, developed in France in the 1700s from chance hybridization between two western hemisphere octoploid species. However, little is known about the evolution of the species that gave rise to this important fruit crop. Phylogenetic analysis of chloroplast genome sequences of...
Resource Type:: Article
Full Text:: genomes (Parks et al., 2009; Straub et al., 2012) can provide unprecedented insights into phylogenetic

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

Creator:: Arighi, Cecilia N., Carterette, Ben, Cohen, K. Bretonnel, Krallinger, Martin, Wilbur, W. John, Fey, Petra, Dodson, Robert, Cooper, Laurel, Van Slyke, Ceri E., Dahdul, Wasila, Mabee, Paula, Li, Donghui, Harris, Bethany, Gillespie, Marc, Jimenez, Silvia, Roberts, Phoebe, Matthews, Lisa, Becker, Kevin, Drabkin, Harold, Bello, Susan, Licata, Luana, Chatr-aryamontri, Andrew, Schaeffer, Mary L., Park, Julie, Haendel, Melissa, Van Auken, Kimberly, Li, Yuling, Chan, Juancarlos, Muller, Hans-Michael, Cui, Hong, Balhoff, James P., Wu, Johnny Chi-Yang, Lu, Zhiyong, Wei, Chih-Hsuan, Tudor, Catalina O., Raja, Kalpana, Subramani, Suresh, Natarajan, Jeyakumar, Cejuela, Juan Miguel, Dubey, Pratibha, and Wu, Cathy
Abstract:: In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have...
Resource Type:: Article

Bioclimatic, ecological, and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries

Creator:: Salamone, Isabella, Govindarajulu, Rajanikanth, Falk, Stacey, Parks, Matthew, Liston, Aaron, and Ashnam, Tia-Lynn
Abstract:: Premise of the Study: Hybrid zones provide "natural laboratories" for understanding the processes of selection, reinforcement, and speciation. We sought to gain insight into the degree of introgression and the extent of ecological-phenotypic intermediacy in the natural hybrid strawberry, Fragaria x ananassa subsp. cuneifolia. Methods: We used whole-plastome sequencing to...
Resource Type:: Article
Full Text:: ISABELLA SALAMONE 2 , RAJANIKANTH GOVINDARAJULU 2 , STACEY FALK 3 , MATTHEW

Detecting continuous lichen abundance for mapping winter caribou forage at landscape spatial scales

Creator:: Nelson, Peter R., Roland, Carl, Macander, Matthew J., and McCune, Bruce
Abstract:: Spatial variation of available food resources can be difficult to accurately quantify for wide ranging organisms at landscape scales. Lichens with usnic acid, a yellowish pigment, constitute a large portion of caribou winter diet across much of their range. We take a new approach of modeling lichen abundances by capitalizing...
Resource Type:: Article
Full Text:: scales Peter R. Nelson a,c,⁎, Carl Roland a, Matthew J. Macander b, Bruce McCune c a Denali National

ScholarsArchive@OSU

Reproductive isolation and interspecific hybridization in the threatened species, Sidalcea nelsoniana

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

Plastome phylogenomics in the genus Pinus using massively parallel sequencing technology

Targeted enrichment strategies for next-generation plant biology

Canopy epiphyte studies in the central Oregon Cascades : implications for the management of Douglas-fir forests

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

Bioclimatic, ecological, and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries

Detecting continuous lichen abundance for mapping winter caribou forage at landscape spatial scales

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