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...
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...
Uncertainties in the age and phylogenetic position of Pinaceae fossils present significant obstacles to our understanding of the timing of diversification in the family. We demonstrate that simultaneous phylogenetic analyses of chloroplastDNA(matK and rbcL) and nonmolecular characters that include both extant genera and a limited number of fossil taxa provide...
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,...
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...
This study describes a specimen that extends the oldest fossil evidence of Pinus L. to the Early Cretaceous Wealden Formation of Yorkshire, UK (131-129 million years ago), and prompts a critical reevaluation of criteria that are employed to identify crown group genera of Pinaceae from anatomically preserved seed cones. The...
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...
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...
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...