This thesis focuses on the spatial structure and methods to identify spatial structure in plants. Methods that investigate genetic structure can mainly be divided into equilibrium methods that reveal summed dispersal over many generations, and cluster methods, that reveal more recent dispersal events. Depending on the spatial level, local or global, suitable methods are different. The thesis consists of four papers. The first explores the spatial genetic structure in two epiphytic bryophytes that have different dispersal strategies (Orthotrichum speciosum and O. obtusifolium) using three different approaches based on pairwise kinship coefficients assessed from AFLP data. The spatial kinship structure was detected with both autocorrelation analysis and generalized additive models, but linear regression failed to detect any structure in O. speciosum. In the second paper the spatial genetic structure in marginal populations of the forest tree Quercus robur is investigated at both local and regional scales. At the local scale, dispersal kernels as estimated using maximum likelihood parentage methods showed to be comparable to results acquired in central located populations. At the regional scale the degree of isolation at the margin of the distribution is shown. The third paper compares a number of sibship clustering methods. It was found that the performances of the sibship reconstruction algorithms are strongly dependent on fulfilling the assumptions of the model and that using an overly simple model produced very unreliable results. The amount of information included in the model affected the results; models including all the available information outperformed the models using only a subset of the information. In the last paper we show that the number of clusters as estimated by the software Structurama depends on sample size. At high number of subpopulations, the estimated number of clusters tends to be grossly underestimated when the number of sampled individuals per subpopulation is low.

A short sequence of ca. 658-bp of the mitochondrial gene COI was used to investigate its utility as a DNA barcode in the medically important Simuliidae or black flies. Sixty-five species and species complexes were tested. Results indicate that the barcoding gene discriminated among morphologically distinct species with nearly 100% of efficacy and proved useful for revealing cryptic diversity. The DNA barcoding gene was also tested for revealing phylogeographic patterns in the western cordilleran Prosimulium travisi and the Prosimulium neomacropyga species-group. Phylogeographic analyses on these species revealed areas that acted as glacial refugia, postglacial history, cryptic speciation episodes and timing of the events that lead to their present-day distribution. The results obtained concur with other phylogeographic studies on similarly-distributed cordilleran organisms. In conclusion, the barcoding gene not only resulted useful for species discrimination in black flies but also for studies at the population level, providing value-added to this molecular marker.

Karenia brevis is the major harmful bloom forming dinoflagellate in the Gulf of Mexico. The toxin produced by this dinoflagellate can cause large fish kills, marine mammal mortality, respiratory irritation, and neurotoxic shellfish poisoning in humans. Blooms can occur anywhere in the Gulf of Mexico (hereafter Gulf) but are predominantly observed off the west coast of Florida and the coast of Texas. The west coast of Florida has been hypothesized to be the origin for blooms of K. brevis in other regions within the Gulf based upon the frequent formation of blooms in this region. To investigate this possibility, microsatellite markers were used to determine the population-genetic structure of K. brevis in the Gulf of Mexico. The difficulties of culturing K. brevis required development and use of a single-cell PCR amplification protocol for preserved cells. Lugol's iodine-preserved bloom samples of K. brevis were destained with sodium thiosulfate and subjected to two rounds of PCR amplification. The destaining protocol resulted in the successful, simultaneous amplification of five microsatellite markers from single cells of K. brevis. A total of 18, highly polymorphic microsatellite markers are available for K. brevis. Each marker was amplified from 40 cultures of K. brevis isolated from water samples from Florida and Texas. Observed genetic diversity was high but similar to the genetic diversity observed in other phytoplankton species. No genetic divergence was detected between isolates from Florida and isolates from Texas. Single cells from a total of 38 field samples were analyzed at five microsatellite markers to determine if population-genetic structure was present in K. brevis in the Gulf. Significant genetic divergence between several individual samples was detected, reflecting the high genetic diversity present within the species. Observed genetic divergence was low between blooms from the west coast of Florida and the coast of Texas and supports the hypothesis of a common origin for blooms of K. brevis in the Gulf of Mexico.

The transition from cross-fertilization to predominant self-fertilization is considered the most common evolutionary transition in flowering plants. This change in mating system has profound influences on the amounts and patterns of genetic diversity within and among populations, and on key genetic and demographic processes. The main goal of my thesis is to determine the molecular population genetic consequences of this transition in the annual neotropical aquatic plant Eichhornia paniculata (Pontederiaceae) using DNA sequence from individuals sampled from throughout the species’ geographic range. Populations exhibit a wide range of mating patterns associated the evolutionary breakdown of tristyly facilitating specific contrasts between outcrossing and selfing populations. Analysis of molecular variation supported the hypothesis of multiple origins of selfing, including the evolution of two morphologically distinct selfing variants from Central America and the Caribbean. A survey of 10 nuclear loci from 225 individuals sampled from 25 populations demonstrated the joint influence of mating system, population size and demographic bottlenecks in affecting patterns of nucleotide variation. Small selfing populations exhibited significantly lower genetic diversity compared with larger outcrossing and mixed mating populations. There was also evidence for higher population differentiation and a slower decay of linkage disequilibrium in predominately selfing populations from the Caribbean region. Coalescent simulations of the sequence data indicated a bottleneck associated with colonization of the Caribbean from Brazil ∼125,000 years ago. To investigate the consequences of transitions from outcrossing to selfing across the genome, I used high-throughput, short-read sequencing to assemble ~27,000 ESTs representing ∼24Mbp of sequence. Characterization of floral transcriptomes from this dataset identified 269 genes associated with floral development, 22 of which were differentially expressed in three independently derived selfing lineages compared to an outcrossing genotype. Evidence for relaxed selection in selfing lineages was obtained from an analysis of a subset of ~8000 orthologous sequences from each genotype, as predicted by theory. Selfing genomes showed an increase in the proportion of nonsynonymous to synonymous changes and relaxation of selection for codon usage bias. My thesis represents the most detailed investigation to date of the molecular population genetic consequences of intraspecific variation in the mating systems of plants.

A short sequence of ca. 658-bp of the mitochondrial gene COI was used to investigate its utility as a DNA barcode in the medically important Simuliidae or black flies. Sixty-five species and species complexes were tested. Results indicate that the barcoding gene discriminated among morphologically distinct species with nearly 100% of efficacy and proved useful for revealing cryptic diversity. The DNA barcoding gene was also tested for revealing phylogeographic patterns in the western cordilleran Prosimulium travisi and the Prosimulium neomacropyga species-group. Phylogeographic analyses on these species revealed areas that acted as glacial refugia, postglacial history, cryptic speciation episodes and timing of the events that lead to their present-day distribution. The results obtained concur with other phylogeographic studies on similarly-distributed cordilleran organisms. In conclusion, the barcoding gene not only resulted useful for species discrimination in black flies but also for studies at the population level, providing value-added to this molecular marker.

The transition from cross-fertilization to predominant self-fertilization is considered the most common evolutionary transition in flowering plants. This change in mating system has profound influences on the amounts and patterns of genetic diversity within and among populations, and on key genetic and demographic processes. The main goal of my thesis is to determine the molecular population genetic consequences of this transition in the annual neotropical aquatic plant Eichhornia paniculata (Pontederiaceae) using DNA sequence from individuals sampled from throughout the species’ geographic range. Populations exhibit a wide range of mating patterns associated the evolutionary breakdown of tristyly facilitating specific contrasts between outcrossing and selfing populations. Analysis of molecular variation supported the hypothesis of multiple origins of selfing, including the evolution of two morphologically distinct selfing variants from Central America and the Caribbean. A survey of 10 nuclear loci from 225 individuals sampled from 25 populations demonstrated the joint influence of mating system, population size and demographic bottlenecks in affecting patterns of nucleotide variation. Small selfing populations exhibited significantly lower genetic diversity compared with larger outcrossing and mixed mating populations. There was also evidence for higher population differentiation and a slower decay of linkage disequilibrium in predominately selfing populations from the Caribbean region. Coalescent simulations of the sequence data indicated a bottleneck associated with colonization of the Caribbean from Brazil ∼125,000 years ago. To investigate the consequences of transitions from outcrossing to selfing across the genome, I used high-throughput, short-read sequencing to assemble ~27,000 ESTs representing ∼24Mbp of sequence. Characterization of floral transcriptomes from this dataset identified 269 genes associated with floral development, 22 of which were differentially expressed in three independently derived selfing lineages compared to an outcrossing genotype. Evidence for relaxed selection in selfing lineages was obtained from an analysis of a subset of ~8000 orthologous sequences from each genotype, as predicted by theory. Selfing genomes showed an increase in the proportion of nonsynonymous to synonymous changes and relaxation of selection for codon usage bias. My thesis represents the most detailed investigation to date of the molecular population genetic consequences of intraspecific variation in the mating systems of plants.

Thesis (Ph. D.)--University of Chicago, Committee of Genetics, 2002. / Includes bibliographical references. Also available on the Internet.

Thesis (M.S.)--Boise State University, 2009. / Includes abstract. Includes bibliographical references (leaves 31-41).

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (p. 103-118).

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 94-106).