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Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1), and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species. Using population-level data from a closely related species (P. tremuloides), we also investigate various approaches for filtering GBS data to retain high-depth, informative SNPs that can be used for population genetic analyses. We find a data filter that includes the designation of ambiguous alleles resulted in metrics of population structure and Hardy-Weinberg equilibrium that were most consistent with previous studies of the same populations based on other genetic markers. Analyses of the filtered data (27,910 SNPs) also resulted in patterns of heterozygosity and population structure similar to a previous study using microsatellites. Our application demonstrates that technically and analytically simple approaches can readily be developed for population genomics of natural populations.

Background Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined aligned nucleotide sequences, indels, gene and nucleotide composition, inversions, and gene order at the boundaries of the inverted repeats. Results We present the plastome sequences of Equisetum arvense , a horsetail, and of Isoetes flaccida , a heterosporous lycophyte. Phylogenetic analysis of aligned nucleotides from 49 plastome genes from 43 taxa supported monophyly for the following clades: embryophytes (land plants), lycophytes, monilophytes (leptosporangiate ferns + Angiopteris evecta + Psilotum nudum + Equisetum arvense ), and seed plants. Resolution among the four monilophyte lineages remained moderate, although nucleotide analyses suggested that P. nudum and E. arvense form a clade sister to A. evecta + leptosporangiate ferns. Results from phylogenetic analyses of nucleotides were consistent with the distribution of plastome gene rearrangements and with analysis of sequence gaps resulting from insertions and deletions (indels). We found one new indel and an inversion of a block of genes that unites the monilophytes. Conclusions Monophyly of monilophytes has been disputed on the basis of morphological and fossil evidence. In the context of a broad sampling of land plant data we find several new pieces of evidence for monilophyte monophyly. Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; we posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the \"true ferns,\" including Marattiaceae.

Background Tortula ruralis , a widely distributed species in the moss family Pottiaceae, is increasingly used as a model organism for the study of desiccation tolerance and mechanisms of cellular repair. In this paper, we present the chloroplast genome sequence of T. ruralis , only the second published chloroplast genome for a moss, and the first for a vegetatively desiccation-tolerant plant. Results The Tortula chloroplast genome is ~123,500 bp, and differs in a number of ways from that of Physcomitrella patens , the first published moss chloroplast genome. For example, Tortula lacks the ~71 kb inversion found in the large single copy region of the Physcomitrella genome and other members of the Funariales . Also, the Tortula chloroplast genome lacks petN , a gene found in all known land plant plastid genomes. In addition, an unusual case of nucleotide polymorphism was discovered. Conclusions Although the chloroplast genome of Tortula ruralis differs from that of the only other sequenced moss, Physcomitrella patens , we have yet to determine the biological significance of the differences. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for mosses) of the generation of DNA markers for fine-level phylogenetic studies, or to investigate individual variation within populations.

The Gesneriaceae is a family known for convergent evolution of complex floral forms. As a result, defining genera and resolving evolutionary relationships among such genera using morphological data alone has been challenging and often does not accurately reflect monophyletic lineages. The tribe Episcieae is the most diverse within Neotropical Gesneriaceae in terms of its number of species and morphological diversity. As a result, defining genera using floral characters has been historically troublesome. Here we investigate relationships among genera of the tribe using an array of chloroplast DNA, nuclear ribosomal genes, and low-copy nuclear genes to provide resolution for the monophyly of the genera and relationships among the monophyletic groups. All known genera in the tribe (with the exception of the monospecificLampadaria) have been sampled, and most have been sampled to provide an assessment to determine their monophyly. Of the 17 genera in the tribe that comprise more than a single species, we have sampled 15 with at least two species. The following six genera are identified as para- or polyphyletic:Neomortonia,Episcia,Paradrymonia,Nautilocalyx,Codonanthe, andNematanthus.Our results strongly support at least three independent origins of fleshy fruits, which are defined here as fleshy display capsules or indehiscent berries.

Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some new plastome sequence data. We review what we know about the evolutionary history of plastome structure across the fern phylogeny and we compare plastome organization and patterns of evolution in ferns to those in seed plants. A large clade of ferns is characterized by a plastome that has been reorganized with respect to the ancestral gene order (a similar order that is ancestral in seed plants). We review the sequence of inversions that gave rise to this organization. We also explore global nucleotide substitution patterns in ferns versus those found in seed plants across plastid genes, and we review the high levels of RNA editing observed in fern plastomes.

Hymenophyllum wrightii is a filmy fern known primarily from Japan and Korea. In North America, it is known as a sporophyte only in Haida Gwaii (Queen Charlotte Islands), British Columbia, Canada. Rare independent, filmy fern gametophytes found from the late 1950s and onward at a handful of locations in British Columbia and southeastern Alaska were presumed to be H. wrightii. Our 2006 surveys in southeastern Alaska determined that these gametophytes are common within specific habitats, and our survey in 2008 found gametophyte populations on the Olympic Peninsula in Washington State—the first report of H. wrightii in the contiguous United States. Samples from gametophyte populations from southeastern Alaska, British Columbia and Washington show no variation in rbcL or rps4-trnS sequence and are similar to sequences from Asian H. wrightii sporophytes, providing corroborating evidence of the identity of these independent gametophyte populations.

Two of the main areas of focus in university academics are research and education. The mission statements of Utah State University and the Department of Biology emphasize both areas, as do the requirements of funding agencies. I attempted to integrate research and education by using tools that I developed to support and inform my biological research projects to teach science. Ferns have a life cycle with alternating haploid and diploid life stages, both of which are free-living and potentially long-lived. The haploid gametophytes of some ferns reproduce asexually and may have different environmental requirements than the diploid sporophytes, so it is possible for populations of gametophytes to exist without sporophytes. This dissertation includes a description of surveys for Hymenophyllum wrightii, a fern with independent gametophytes in the Pacific Northwest, and improves our understanding of the range, distribution, and habitat requirements of these plants which were previously assumed to be rare. It also describes an attempt to explore the population genetics of gametophytes of Crepidomanes intricatum, a widespread fern in the Appalachian Mountains for which no sporophytes have ever been found. To help visualize evolutionary processes in independent gametophyte populations I developed the Virtual Population Genetics Simulator (VPGsim) to simulate populations of ferns in a 3-dimensional environment. This dissertation includes a description of VPGsim, a learning module using it to teach undergraduate genetics, and a study demonstrating its effectiveness at improving students' understanding of science content and confidence in their ability to perform science inquiry. That simulation tool led to a collaboration to find other ways to teach science with simulations, and to the development of a Virtual Plant Community simulator (VPCsim) for teaching middle school students about the effects of the environment and human impacts on living organisms. This dissertation describes VPCsim and a learning module built around it, which is currently being used in two Utah school districts. This dissertation demonstrates one way that research to expand scientific knowledge can lead to the creation of tools to share that knowledge with students.