Biodiversity loss is of global concern, and is due in part to deforestation and high consumer demand for wood and wood products. The neotropical tree species Cedrela odorata (“Spanish cedar” or “cedro”) is economically valuable for its wood and faces threats of overexploitation. Due to strong similarities in wood features...
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,...
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Aaron I. Liston RichardC. Cronn
This thesis summarizes work completed over the
Data from nuclear ribosomal internal transcribed spacer regions (nrITS) and chloroplast DNA (cpDNA) have failed to resolve phylogenetic relationships in Pinus. To provide greater interspecific resolution, five low-copy nuclear genes were developed from mapped conifer anchor loci. Four genes were sequenced from species representing all Pinus subsections. Individual loci do...
A fossil-calibrated phylogenetic framework based on exemplars from each of the four taxonomic sections within Pinus was created using multiple nuclear and chloroplast loci. Calibration at the well-defined subgeneric split within Pinus with either fossil leaves and cones (ca. 45 million years ago) or fossil wood (ca. 85 million years...
The study of the infra-specific ranks (i.e., subspecies and variety) can be considered
the study of the process of speciation. Astragalus lentiginosus Douglas ex Hooker
(Fabaceae) is the most taxon rich species in the U.S. flora currently including 40
taxonomic varieties. These varieties were described using traditional taxonomic
methods primarily...
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Rich Cronn Aaron Liston
The study of the infra-specific ranks (i.e., subspecies and
This manual provides guidance on creating subject heading proposals for Indigenous topics that can be submitted to the Subject Authority Cooperative Program (SACO) for addition to the Library of Congress Subject Headings.
Fungi play critical roles in ecosystem processes and interact with plant communities in mutualistic, pathogenic, and commensal ways. Fungal communities are thought to be influenced by both associated tree communities and soil properties. However, the relative importance of the biotic and abiotic drivers of soil fungal community structure and diversity...
The cultivated strawberry, Fragaria Xananassa, is one of the youngest domesticated plants. Its 18th century origin via hybridization in Europe between the North American F. virginiana and the South American F. chiloensis was documented by the botanist Antoine Nicolas Duchesne. His 1766 “Natural History of Strawberries” is an extraordinary work...
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...
This dataset is available as supplement for a research article submitted in 2018 and accepted in 2019. Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives. By Kristen N. Finch, B.A.; F. Andrew Jones, Ph.D.; Richard Cronn, Ph.D.
Tree species in the genus Cedrela are threatened by...
Rhizopogon is a large genus of ectomycorrhizal (EM) fungi that grows in association with host trees of the family Pinaceae. We have conducted a series of studies investigating the ecology and evolutionary biology of the EM symbiosis shared between R. subgenus Villosuli and trees of the genus Pseudotsuga. Two members...
In recent years, there has been renewed interest in black raspberry (Rubus
occidentalis L.) breeding. This has been spurred, in part, by an increase in black
raspberry consumption due to studies that have shown them to be particularly high in
anthocyanin content indicating high levels of antioxidants. Present cultivars are...
North America, with over 400 species of Astragalus (Fabaceae), is one of three major centers of diversity, all of which comprise the majority of the nearly 1750 species of Astragalus worldwide. One of the most diverse species, Astragalus lentiginosus of Section Diphysi, is a polymorphic complex of over 40 varieties,...
The climate of the Pacific Northwest is in flux, and existing forest ecosystems are stressed and poised to shift in fundamental ways, with or without human intervention. This dissertation probes the nature of forest responses to environmental change through investigations of morphology and genetics of three species of alder co-occurring...
At a time when the biodiversity on Earth is being rapidly lost, new technologies and methods in genomic analysis are fortunately allowing scientists to catalog and explore the diversity that remains more efficiently and precisely. The studies in this dissertation investigate genomic diversity within the milkweed genus, Asclepias, at multiple...
Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common
phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT.
We sequenced the 158 kb plastome and the 690 kb mitochondrial genome...
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consisted of 30 s at 98°C
followed by 25 cycles of 10 s at 98°C, 30 s at a primer set-specific annealing
Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common
phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT.
We sequenced the 158 kb plastome and the 690 kb mitochondrial genome...
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(Apocynaceae)
Shannon C.K. Straub1,*, RichardC. Cronn2, Christopher Edwards1, Mark Fishbein3, and Aaron
Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common
phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT.
We sequenced the 158 kb plastome and the 690 kb mitochondrial genome...
Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common
phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT.
We sequenced the 158 kb plastome and the 690 kb mitochondrial genome...
Sequence data from nrITS and cpDNA have failed to fully resolve phylogenetic relationships among Pinus species. Four low‐copy nuclear genes, developed from the screening of 73 mapped conifer anchor loci, were sequenced from 12 species representing all subsections. Individual loci do not uniformly support either the nrITS or cpDNA hypotheses...
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...
The legality of wood products in trade often depends on their geographic origin, creating a need for forensic tools that can verify claims of provenance for wood and wood products. Cedrela odorata L. or Spanish cedar is a target of illegal logging. We developed a 140 SNP Agena™ MassARRAY® assay...
This dataset contains a draft assembly of the common milkweed (Asclepias syriaca) nuclear genome, linkage group information, and gene family counts for Asclepias and related species. The genome assembly is accompanied by annotation of gene models, repeat models, transfer RNAs, and open reading frames, and mapping information of Asclepias transcripts,...
PREMISE OF THE STUDY: Hyb-Seq, the combination of target enrichment and genome skimming
allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets
for plant systematics and evolution studies.
METHODS AND RESULTS: Genome and transcriptome assemblies for milkweed (Asclepias syriaca)
were utilized to design enrichment probes for 3385...
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...
Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale (Physeter macrocephalus) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20 mitogenomes from...
Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our...
Published December 1947. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalog
Thirteen healthy adult males, ages 20-40, consuming self selected
diets, were given instructions to take one 500 mg tablet of ascorbic
acid three times a day with their meals for a period of ten weeks. The
effect of this daily supplementation on copper status was investigated.
An estimation made from...
A high performance liquid chromatography (HPLC)
procedure using a LiChrosorb-NH₂ column and a eluant
buffer of 75:25 (v/v) of acetonitrile:0.05 M KH₂P0₄, pH
5.95, was developed for the successful separation and
determination of ascorbic and erythorbic acids in selected
food samples.
Application of the method, which is sensitive, rapid
and...
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A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation
Author(s): Howe, GT (Howe, Glenn T.)[ 1 ] ; Yu, JB (Yu, Jianbin)[ 1 ] ; Knaus, B (Knaus, Brian)[ 2 ] ; Cronn, R (Cronn, Richard)[ 2 ] ; Kolpak,...
• 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...
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99(2): 383-396. 2012. – Data supplement S1 – Page 1
Cronn, Richard, Brian J. Knaus, Aaron Liston
• 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...
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TARGETED ENRICHMENT STRATEGIES FOR NEXT-GENERATION
PLANT BIOLOGY 1
RICHARDCRONN 2,6 , BRIAN
• 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...
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Cronn, Richard, Brian J
Cronn et al. – American Journal of
To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of...
Whitebark pine (Pinus albicaulis) inhabits an expansive range in western North America, and it is a keystone species of subalpine environments. Whitebark is susceptible to multiple threats – climate change, white pine blister rust, mountain pine beetle, and fire exclusion – and it is suffering significant mortality range-wide, prompting the...
BACKGROUND: As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets
of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for
performing this inference has remained largely unexplored. Some methods have been proven to be consistent given...
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, M., Syring, J., Eckert, A. J., Liston, A., Cronn, R., Neale, D. B., &
Rosenberg, N. A. (2014). An
This thesis examines a range of generic influences in William Shakespeare's Richard II. By exploring the play's references to conflicting interpretations of history from different generic perspectives, I hope to advance a more nuanced reading of the play's dynamic staging of history. In Chapter One, I suggest that Richard II...
Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low‐copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to...
The Whale Cove Site, 35LNC60, is a shell midden, showing
occupations from 3010 B.P. to 330 B.P., spanning the Early and Late
Littoral Periods. Analysis of mammalian faunal remains, bone and
antler tools, lithics and discriptions of recovered shellfish
artifacts allows for chronological refinement of the previously
mentioned archeologically defined...
Object oriented programming features information hiding and encapsulation, meaning that 1) each object hides the the implementation details tram access from outside and only a set of methods (interface routines) are visible outside of the object, and 2) changes to the implementation of the object do not require changes to...
Commercially bottled, vitamin C-fortified, cranberry
juice cocktail and cranberry-apple (cranapple) juice
drinks were stored at 5°C under simulated home-use
conditions. Ascorbic acid (AA) and dehydroascorbic acid
(DHA) levels were evaluated over a period of seven days by
high performance liquid chromatography (HPLC). Total
vitamin C content was also determined by...
The purpose of this study of the life and career of Dr. Carl
Leonard Anderson was to recount his professional contributions to
the field of health and relate these to public health and health education. The major emphasis of this study concerned Dr. Anderson's
professional life.
The accomplishment of the...
This dataset contains the taxonomic classifications of environmental DNA (eDNA) sequences obtained from Fall Creek, Oregon, via microfluidic multiplex PCR (Fluidigm Access Array) and high-throughput sequencing. It is accompanied by electrofishing counts taken at the same time as the eDNA samples. Metadata and R scripts are provided to analyze the...
Delta-sigma modulators are currently a very popular technique for making high-resolution
analog-to-digital converters (ADCs) and digital-to-analog converters (DACs).
These oversampled data converters have several advantages over conventional Nyquist-rate
converters, including an insensitivity to many analog component imperfections, a
simpler antialiasing filter and reduced accuracy requirements in the sample and hold....
Delta-sigma modulators are currently a very popular technique for making high-resolution
analog-to-digital and digital-to-analog converters (ADCs and DACs). Most
delta-sigma modulators in production today employ single-bit quantization because a 1-bit DAC is inherently linear, whereas a multi-bit DAC is not. Were it not for this drawback,
the use of multi-bit...
The purpose of this experiment was to investigate the interactive effects of locus of control and instructional method on perceived self-efficacy with computers. The two instructional methods in this
experiment were intended to represent variations in the amount of control over the lesson that students
would have, the amount of...