As many as 70% of angiosperm species are known to contain polyploids, but many aspects of polyploid evolution are unclear in woody plants. Crataegus is a woody genus of Rosaceae comprising 140-200 species that are widely distributed in the Northern Hemisphere. Several species, particularly those in North America, are shown to contain polyploids. The overall goal of the thesis is to provide a better understanding of polyploid evolution by resolving problems from intergeneric to intraspecific levels in Crataegus using phylogenetic and population genetic approaches. Three major aspects were investigated: (1) Phylogeography of the Old and New World Crataegus; (2) Reproductive system and distribution of cytotypes of the black-fruited series Douglasianae in Pacific Northwest and; (3) Origins, population structure, and genetic diversity of diploid and polyploid species. Phylogenetic analyses of molecular data provide evidences of historical events such as trans-Beringian migrations and North Atlantic vicariance that contributed to modern distribution of Crataegus. Poor resolution and short internal branches in eastern North American species suggest genetic bottlenecks and/or rapid divergence following glaciations. In the Pacific Northwest, polyploids of series Douglasianae show a wider distribution and ecological amplitude than diploids. Parsimony tree and network analyses indicate that autotriploids and allotriploids occur in C. suksdorfii, while tetraploid C. suksdorfii are formed via the triploid bridge followed by introgression of sympatric C. douglasii. At the regional level, microsatellite data indicate a separation of the Pacific coastal diploids and triploids from the Columbia Plateau and Rocky Mountain triploids and tetraploids. High genetic differentiation among C. suksdorfii populations suggests that gene flow is limited by ploidy level differences as well as geographical distance. Within-population multilocus genotypic variation is greatest in sexual diploids, and least in apomictic triploids. Frequent gene flow via seed dispersal contributes to an appreciable level of intrapopulation diversity in apomictic tetraploids, and counterbalances the effects of apomixis and/or self-fertilization, which diminish genetic variation within and between seed families. These findings collectively clarify taxonomy and historical biogeography, provide an explicit reticulation model for polyploid formation, and shed light on evolution of natural populations in woody plants that show heterogeneous ploidy levels and reproductive systems.

The FRIABLE1 (FRB1) gene is identified to be a novel glycosyltransferase involved in cell adhesion, based on reverse genetics and immunocytochemistry studies. A total of 31 FRB1 paralogues were found in Arabidopsis thaliana using a bioinformatics approach. The following expression analysis has revealed 6 FRB1 paralogues to be pollen-specific. One pollen-specific FRB1 paralogue, At1g14970, exhibits longer silique lengths when exposed to higher than normal temperature at 28oC in its T-DNA insertional knockout when compared to Columbia wildtype plants. This may be due to the loss of temperature sensing and the continuous stimulated pollen tube cell wall growth or the up-regulation of genes that encode other glycosyltransferases. Thus, the identification of FRB1 paralogues and homologues in both rice and poplar may have tremendous potential to increase their yield in global warming for agricultural and industrial benefits.

The brevipedicellus (bp) mutant, caused by a loss-of-function mutation in the KNAT1 homeobox gene, is known to affect the stem morphogenesis. BP and ERECTA (ER) genes are required to promote internode and pedicel development and delineate nodal boundaries to maintain the radial symmetry of stems and pedicels. My research aims to identify genes acting on the BP pathway by utilizing a forward genetics approach. The suppressor4 mutant, identified from the bp er mutant screen, exhibits moderate length and perpendicularly-oriented pedicels with partially formed distal pedicel bulges, absent in the bp mutant. The kinky mutant, identified from the bp mutant screen, develops severe bends at the floral nodes and enhanced achlorophyllous stripes. These results suggest the SUPPRESSOR4 gene contribution in inhibiting the development of distal pedicel bulge and influencing both pedicel angle and length whereas the KINKY gene might act with BP in regulating proper inflorescence development.

Master of Science / Department of Biology / Carolyn J. Ferguson / The genus Phlox L. presents intriguing opportunities for systematics research, and P. nana is of particular interest. Phlox nana occurs chiefly in mountains of the Chihuahuan desert to northern New Mexico, and it exhibits much morphological variation across its range. Historically, this taxon has been recognized as a single species (sometimes with infraspecific taxa), or as several species. Perhaps most interesting, variation in ploidy level (cytotypic variation) has been evidenced for P. nana. This research employed flow cytometry methods in conjunction with chromosome counts to document patterns of cytotypic variation. Intensive fieldwork in Arizona, New Mexico and Texas enabled excellent sampling, and evaluation of ploidy level for 76 populations was achieved. Diploid and tetraploid chromosome counts were made (four diploid counts; five tetraploid counts), and flow cytometry was conducted on all populations, providing evidence for diploid, tetraploid and hexaploid populations. Polyploids were found to occur in many geographical areas, and in some regions, diploids and polyploids occur in close geographical proximity (e.g., within both the Davis Mountains and the Chisos Mountains of west Texas). Genome size data are presented (with discussion of unusual populations), and geographic patterns of cytotypic variation are presented and discussed. Patterns are also briefly considered with respect to morphology and taxonomy: cytotypic variation does not readily align with historical recognition of taxonomic variation, and this work sets the stage for ongoing, detailed morphometric study. Research on particular species of Phlox benefits from an understanding of a broad phylogenetic context, and low copy nuclear DNA regions are an important resource for phylogeny development. This research further evaluated part of the NADP-dependent isocitrate dehydrogenase gene (idhB) for its usefulness in inferring relationships in Phlox. Samples were PCR amplified for idhB and cloned, and resulting sequences were added to a larger set of idhB sequence data previously developed in the lab. A total of 163 samples were included, and Bayesian Inference and Maximum Parsimony analyses were conducted for complete data sets. Phylogenetic findings are discussed in light of previous work based on chloroplast and high copy nuclear DNA regions, and challenges and utility of using idhB are discussed.

Master of Science / Department of Biology / David C. Hartnett / The effects of bison activities on forb diversity and cover have been well-established, but less is known about how forb life history is altered by bison-mediated habitat changes. This study had three main objectives: 1) to evaluate the hypothesis that release from aboveground competition with grasses may contribute to the increased cover and diversity of forbs in prairie grazed by bison relative to ungrazed prairie, 2) to determine whether differences in forb reproductive effort between grazed and ungrazed habitats were size-dependent, and 3) to look for evidence of a trade-off between allocation to vegetative and sexual reproduction. The growth, biomass allocation, and sexual reproduction of six common unpalatable perennial species were measured and compared between bison-grazed and ungrazed tallgrass prairie burned at 2-year intervals: Ambrosia psilostachya, Artemisia ludoviciana, Baptisia australis, Psoralidium tenuiflorum, Solidago canadensis, and Vernonia baldwinii. Vegetative reproduction was also measured for B. australis¸ S. canadensis, and V. baldwinii. Light availability, canopy density and height, and percent cover of neighboring plants were measured in each studied individual’s immediate neighborhood and compared between habitats to establish the possibility of differing aboveground competition. Aboveground competition may be lower in bison-grazed habitats, as evidenced by differences in habitat characteristics and plant performance found in this study. In bison-present habitats, sexual reproduction was elevated for all six species and average plant size was greater for all species except A. psilostachya. Vegetative reproduction was not clearly different between habitats for all three species examined. Sexual reproduction increased with size for all species, and the relationship differed significantly between habitats for all species except A. psilostachya. Allocation to vegetative reproduction was not generally related to aboveground biomass, nor was there a clear trade-off between allocation to vegetative and sexual reproduction. The results of this study provide evidence that release from aboveground competition with grasses promotes the growth and sexual reproduction of the studied species of forb, and that differences in sexual reproduction are not entirely size-dependent. Patterns in allocation to vegetative reproduction were less clear and were not clearly tied to sexual reproductive allocation.

Doctor of Philosophy / Department of Biology / Carolyn J. Ferguson / Morus L. (Moraceae) is a temperate and subtropical genus of ten to 15 species distributed in Asia, Africa, Europe, North, Central and South America. Despite its broad distribution and economic importance, it has received little attention from systematic botanists. Two species of this genus, the native M. rubra and the exotic M. alba, co-occur in eastern North America including the Flint Hills region of the Central Plains. In my dissertation research, I have conducted both species level and population level studies to obtain insights into the diversification of Morus. At the species level, my objectives were to re-evaluate the taxonomy and reconstruct the phylogeny of Morus. Based on herbarium and literature study as well as some field study, I recognize 13 species: eight species occurring in Asia, one in Africa and four in the New World. I used sequence data from the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA and the trnL-trnF region of the chloroplast DNA to reconstruct the evolutionary history of Morus. The phylogenies were congruent and indicate a) a monophyletic core group of Morus with two well-supported geographical clades (one containing Asian taxa and one of New World taxa); and b) that Morus, as currently circumscribed, is non-monophyletic. At the population level, I studied sex expression pattern variation between the Morus native-exotic pair in the Flint Hills region, and assessed hybridization between these species at Konza Prairie Biological Station (KPBS). Both species are subdioecious, and Flint Hills populations exhibit significantly male-biased sex ratios, with sex expression being size independent. Approximately 10% of individuals of each species changed sex annually. In the population study at KPBS, I applied randomly amplified polymorphic DNA (RAPD) markers and microsatellites. The Morus species were moderately ([Theta]II = 0.079; RAPD data) to highly differentiated genetically (F[subscript]ST = 0.233; microsatellite data). Analysis of genetic structure suggested interspecific gene flow and indicated the presence of later generation hybrids. The presence of the exotic congener may affect the existence and genetic integrity of the native species. Overall, these studies contribute to our understanding of diversity in this interesting plant study system.

Doctor of Philosophy / Department of Biology / David C. Hartnett / Grazing and drought are instrumental in the development and maintenance of perennial grasslands. In this research I tested the belowground bud bank contribution to tallgrass prairie resistance and resilience when perturbed by grazing and drought. First, I tested the bud bank role in vegetation response to and recovery from severe drought (Chapter 2). I compared above- and belowground responses of experimentally droughted plots to ambient controls and irrigated plots during two years of severe drought and two years of recovery. I found that although aboveground net primary productivity declined 30-60% during drought, bud bank density and demography were insensitive to drought. These results suggest that grassland resistance and resilience when perturbed by drought may be mediated by stability of belowground bud banks. Second, I investigated vegetation and soil nutrient legacies following release from long-term grazing (Chapter 3). I documented a relatively rapid shift in aboveground vegetation within four years of grazer exclusion, with productivity, stem density, and diversity becoming relatively more similar to ungrazed than grazed prairie. The density and composition of the belowground bud bank and soil seed bank shifted more slowly, remaining more similar to grazed than ungrazed prairie. Responses of soil nutrients to removal of grazers varied, and in some cases was affected by recent fire history. These results demonstrate the contribution of belowground propagules to the maintenance of a diverse plant community both during grazing and after grazers are removed. Finally, I examined short-term vegetation responses to both drought and grazing (Chapter 4). Despite extreme drought and simulated grazing that reduced productivity and increased mortality of individual stems, the dominant C4 grasses maintained a stable bud bank. Aboveground net primary productivity and bud bank density of sedges and forbs, however, were reduced by both drought and grazing. This differential response of species to extreme drought and grazing led to shifts in community composition and species diversity over one growing season. Across drought and grazing treatments, live rhizome biomass was highly correlated with bud bank density and may be a useful, more easily measured index of bud bank density.

Biological invasions provide opportunities to study evolutionary processes occurring during contemporary time scales. Here, I combine a literature review of common garden studies of invasive plant species, with field and glasshouse experiments on populations of the outcrossing, perennial, wetland invader Lythrum salicaria (purple loosestrife - Lythraceae), to investigate the evolutionary genetics of local adaptation in reproductive and life-history traits. A review of 32 common garden studies of 28 introduced species identified previously unrecognized latitudinal clines in phenotypic traits in both native and introduced populations. To obtain direct evidence for clinal variation and local adaptation, I investigated populations of L. salicaria sampled along a latitudinal gradient of growing season length in eastern North America. Controlled pollinations of plants from 12 populations provided no evidence for the breakdown of self-incompatibility to self-compatibility towards the northern range limit. However, a quantitative genetic experiment involving 20 populations revealed latitudinal clines in population mean, variance and skew for days to flower and vegetative size. Broad-sense estimates of genetic variance were significant for most traits; however, strong inter-correlations among traits suggested that fitness trade-offs have constrained population divergence. The observed clines supported a model of selection for early flowering in northern populations constrained by a trade-off between age and size at flowering. A comparison of variance-covariance matrices of family and population means (G and D, respectively) of life-history traits demonstrated that populations have evolved in response to selection under genetic constraints, rather than through neutral processes. A reciprocal transplant experiment involving six populations and three common gardens spanning the latitudinal range provided direct evidence for local adaptation in flowering phenology. Populations maintained the same rank-order for time to flowering and vegetative size at each site, and southern populations had the highest fecundity at the southern site but the lowest at the northern site. Finally, a phenotypic selection analysis in each common garden involving 61 F2 families of crosses between a northern × southern populations confirmed that selection favours earlier flowering in northern populations. These results demonstrate that natural selection on reproductive phenology has accompanied the invasive spread of L. salicaria in eastern N. America.

The relationship between an organism’s genome, developmental stage, and environment is complex. The aim of the research presented herein was to provide experimental evidence to contribute to the annotation of the P. trichocarpa genome and to test two major hypotheses addressing the interaction between drought and time of day in A. thaliana and in two hybrid Populus clones. In order to generate data to address these aims, three separate experiments were undertaken. First, all members of the R2R3-MYB family of transcription factors in the P. trichocarpa genome were characterised by phylogenetic analysis and their transcript accumulation patterns across a range of tissues and organs were assessed using whole genome poplar microarrays. Results of this analysis indicated that expansion and diversification of the R2R3-MYB family may have contributed to phenotypic innovation in the Populus lineage. Second, drought-responsive transcriptome adjustments of two hybrid poplar clones, DN34 (P. deltoides X P. nigra) and NM6 (P. nigra X P. maxiomowiczii) were assessed for time-of-day and genotype dependent patterns. For each genotype, each of four time points was characterised by discrete sets of drought-responsive genes. Furthermore, while a number of genes were identified that were responsive to drought in both genotypes, a much larger number of genotype-dependent, drought-responsive transcriptome changes were detected. Finally, the drought-responsive transcriptome adjustments A. thaliana plants were assessed for time-of-day dependent accumulation patterns. Results of this analysis indicate that time-of-day-dependent differences in the drought response were manifest as changes of different magnitudes for a conserved set of genes across the four time points measured. These results emphasise the complex interplay of a plant’s genome, developmental stage, and environment in shaping the observed transcriptome.

Flowering plants possess striking variation in reproductive traits and mating patterns, even among closely related species. In this thesis, I investigate morphological variation, mating and genetic diversity of five taxa of bird-pollinated Babiana (Iridaceae), including two species with specialized bird perches. Field observations in 12 populations demonstrated that sunbirds were the primary pollinators. Babiana ringens exhibited correlated geographic variation in flower and perch size. Controlled field pollinations revealed self-compatibility and low pollen limitation in B. ringens subspecies, and self-incompatibility and chronic pollen limitation in B. hirsuta. Allozyme markers demonstrated moderate to high selfing rates among populations and considerable variation in levels of genetic diversity. In B. ringens there was a positive relation between the geographic and genetic distance of populations. The results of a manipulative field experiment indicated position-dependent herbivory on inflorescences of B. hirsuta and this could play a role in the evolution of specialized bird perches in Babiana.