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,...
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...
This dataset contains DNA sequence data of Oncorhynchus species, isolated from environmental DNA (eDNA) from Pacific Northwest streams via microfluidic eDNA metabarcoding and high-throughput (Ilummina) sequencing (samples collected from 2017-09-22 to 2017-10-10). It is accompanied by scripts and commands for data analyses including: sequence denoising, calculation of entropy values by...
Primula sect. Parryi comprises five species endemic to western North America: P. parryi, P. angustifolia, P. rusbyi, P. capillaris, and P. cusickiana with four varieties. This section, derived from a clade with representatives in Asia and Europe, exemplifies a phytogeographic pattern in which a widespread species is accompanied by multiple...
Despite knowledge that concerted evolution of high-copy loci is often imperfect,
studies that investigate the extent of intragenomic polymorphisms and comparisons
across a large number of species are rarely made. We present a bioinformatic pipeline
for characterizing polymorphisms within an individual among copies of a high-copy
locus. Results are presented...
Despite knowledge that concerted evolution of high-copy loci is often imperfect,
studies that investigate the extent of intragenomic polymorphisms and comparisons
across a large number of species are rarely made. We present a bioinformatic pipeline
for characterizing polymorphisms within an individual among copies of a high-copy
locus. Results are presented...
Despite knowledge that concerted evolution of high-copy loci is often imperfect,
studies that investigate the extent of intragenomic polymorphisms and comparisons
across a large number of species are rarely made. We present a bioinformatic pipeline
for characterizing polymorphisms within an individual among copies of a high-copy
locus. Results are presented...
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...
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...
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...
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 sweet potato is one of the world’s most widely consumed crops, yet its evolutionary history is poorly understood. In this paper, we present a comprehensive phylogenetic study of all species closely related to the sweet potato and address several questions pertaining to the sweet potato that remained unanswered. Our...
Few plant mitochondrial genomes have been published to date
because of their structural complexity and difficulties in their physical
isolation. Plant mitochondrial genomes are known to have a high level
of heteroplasmy and can exist as several different circular or linear
strands. Sequencing additional mitochondrial genomes will help to
understand...
Hybridization, polyploidy, and apomixis have made phylogenetic estimation in Rubus challenging. I used target capture to sequence approximately 1000 low copy nuclear loci and the chloroplast genome for 94 accessions representing the genus Rubus and distributed worldwide. Species phylogenies were estimated using two coalescent based methods, ASTRAL-II and SVDQuartets, and...
Assembly and genotyping of polyploid genomes poses many problems due to the complex nature of polyploid data, including the inability to determine allelic dosage and mixed inheritance patterns. This study was the first application of POLiMAPS genotyping on whole genome sequences without using cross information. In this study, whole genome...
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...
Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order
polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal
reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the
challenge of distinguishing...
Western Oregon is home to native Rhododendron species and is the center for cultivated
Rhododendron production in the United States. These Rhododendron spp. are known to
be infected with fungal endophytes. However, the community structure of these
endophytes in native and cultivated Rhododendron is poorly understood. Our study
targeted the...
Preservation of rare plant species often requires establishment of new populations. Survivorship surveys are the most common method of post-introduction monitoring. However, they provide an incomplete picture of establishment success. This study is an attempt to develop a model for determining establishment success by determining the factors affecting recruitment in...
Mutualistic associations between corals and symbiotic microalgae of the genus Symbiodium power tropical reef ecosystems, hotspots of marine biodiversity that buffer coastlines, support tourism- and fisheries-based economies, and offer untapped potential for discovery of novel pharmaceutical compounds. However, reef ecosystems are declining at an alarming rate, in large part due...
Described as one of the most destructive pathogens of agricultural crops and forest trees, Phytophthora is a genus of microorganisms containing over 100 known species. Phytophthora alni has caused collar and root disease in alders throughout Europe and a form of the species has recently been isolated in North America....
This dissertation uses manipulative experiments to explore amphibian-Bd infection dynamics. Although there has been almost two decades research since the discovery of Bd, many questions still remain regarding what conditions mediate chytridiomycosis virulence. My research shows how certain host and pathogen factors can influence disease virulence. Identifying how host and...
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...
Research on the population genetics of microbial organisms requires the use of specialized analyses designed for clonal organisms to avoid violating the assumptions of traditional population genetic models. The tools necessary for performing these analyses existed as a set of unrelated software with non-overlapping capabilities and did not cover all...
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...
Whitebark pine (Pinus albicaulis) is an iconic North American high-elevation tree species currently threatened by climate change, mountain pine beetle, and white pine blister rust (WPBR), a lethal disease caused by the non-native fungal pathogen Cronartium ribicola. In collaboration with the USDA Forest Service Dorena Genetic Resource Center, germplasm was...
The order Cornales (dogwoods) is the earliest diverging lineage within the most diverse group of flowering plants, the asterids (>80,000 species). Although molecular phylogenetics have significantly improved our understanding of cornalean systematics, early phylogenetic relationships remain uncertain due to an initial rapid radiation. The fossil record of Cornales is extensive...