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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.

Climate change is rapidly altering natural ecosystems. Plastic and adaptive responses to climate change (i.e., range shifts and phenology) have been widely noted across taxa. However, the effects of climate change on evolutionary processes such as interspecific gene flow (hybridization) are less well known. In this study, we quantified hybridization rates in response to experimental manipulations of rainfall, an important dimension of global change. We used rain-out shelters in the field and quantified rates of hybridization between two congeners, Helianthus annuus (common sunflower) and H. petiolaris (prairie sunflower). We found that H. annuus maternal plants produced hybrid progeny more than H. petiolaris maternal plants, with a trend for decreased rates of hybridization with increased soil moisture (when rain-out shelters were absent). The relative number of open inflorescences of each species predicted hybridization rates. Thus, this study demonstrates how changing environmental conditions, specifically precipitation, could influence hybridization rates.

Although the Neophocaena is currently thought to be monotypic (¡§Neophocaena phocaenoides¡¨) with three ¡§subspecies¡¨, the taxonomy of this genus still remains uncertainty. The finless porpoise (¡§Neophocaena phocaenoides¡¨) is one of the small cetacean species under threats from human activities. At present, finless porpoise is listed in Appendix I of Convention on International Trade in Endangered Species of Wild Flora and Fauna (CITES). For conservation issue, it is important to define appropriate and unambiguous ¡§units¡¨. In this study, I intended to settle the taxonomic status of the specimens of finless porpoise from the southern part of the East China Sea (including the Taiwan Strait) in which the status has been under debate. Results from this study, indicated that they should belong to ¡§N. p. sunameri¡¨. Comparing the genotypes of the microsatellite of additional individuals of the ¡§N. p. asiaeorientalis¡¨ belonging to the VN-type group given in Xia and coworkers report with our data, three distinguished genetic groups were revealed: (1) the group occurring in the Taiwan Strait (i.e., the W-type group, currently recognized as ¡§N. p. phocaenoides¡¨); (2) the group occurred in the Yangtze Rive (i.e., the VN-type group, currently recognized as ¡§N. p. asiaeorientalis¡¨); (3) the group occurred in the Yellow Sea and the Taiwan strait (i.e., the IN-type + UN-type group, currently recognized as ¡§N. p. sunameri¡¨). Population differentiation was absent not only within the W-type group but also within the IN-type +UN-type group. I tried to detect the taxonomy of the two parapatric groups in where the W-type and IN-type +UN-type groups are co-exit sympatrically. No specimens with intermediate character state of the width of the dorsal denticles (i. e., hybrids) were presented in Matsu Islands on the Chinese coast where the W-type and UN-type groups were sympatric. Hybrid individual exhibiting the hybrid states of the 11 microsatellite loci between these two groups was also not found. According to E.O. Wiley¡¦s criteria for recognizing species, these two groups are eligible to be considered separate species. Based on Crandall and his coworkers¡¦ criteria of evolutionarily significant unit (ESU), the three groups, the W-type, IN-type +UN-type and VN-type groups, should be treated as three distinct ESUs.

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Horizontal gene transfer (HGT), a mechanism that facilitates exchange of genetic material between organisms from different lineages, has a profound impact on prokaryotic evolution. To infer HGT, we first developed a comparative genomics-based tool, APP, which can perform phyletic pattern analysis using completely sequenced genomes to identify genes are unique to a genome or have sporadic distribution in its close relatives. Performance assessment against currently available tools on a manually created 18-genome dataset and 2 benchmarking datasets revealed the superior accuracy of APP over other methods. We then utilized a parametric method to construct a gene exchange network. The composition-based method, Jenson-Shannon Codon Bias (JS-CB), groups genes into clusters based on similar codon usage bias. These clusters were analyzed using APP and examined for the enrichment HGT associated marker genes, then annotated as of native or alien origin based on these multiple lines of evidence. Intergenome clustering enabled identification of genes mobilized across alien components of the genomes (alien-alien transfer) and from native components of donor genomes to the recipient genomes (native-alien transfer). Functional classification of alien gene clusters revealed that metabolism associated genes are most frequently mobilized, in concurrence with previous reports, and additionally, a large number of genes with yet unknown functions were found to have been horizontally transferred, a important finding that needs to be further investigated.

Refuges of non-Bacillus thuringiensis (Bt) cotton are used to delay Bt resistance in several key insect pests. In 2004, I discovered that Bt cotton plants sometimes enter refuges via the seed bag, and hypothesized that this type of gene flow could have important effects on resistance evolution in insect pests. In the research described herein, I investigated the sources of Bt plants in the non-Bt cotton seed supply and assessed the potential implications of this gene flow on pest resistance evolution. I report results from an empirical study of gene flow in 15 non-Bt cotton seed production fields, as well as results from simulation modeling studies of gene flow from one-toxin and two-toxin Bt cotton. The current policy on gene flow from genetically engineered crops in the United States is also reviewed, including the implications of my research findings for policymakers. Key findings of this study included the prominent role of seed-mediated gene flow in the seed-production setting, and the utility of a geographic information system (GIS) ring analysis approach for describing pollen-mediated gene flow in cotton fields. Modeling results indicated that high rates of gene flow of Bt cotton into refuges could have large effects on pest resistance evolution under certain sets of assumptions, particularly in parts of the world where farm-saved seed is planted year after year in cotton fields. It appears that some of these effects could be mitigated by using non-cotton refuges or by using plants that contain linked transgenes that confer multiple toxins. There are no clear regulations in the United States regarding gene flow of Bt cotton into refuge seed or into seed production fields of non-Bt cotton, as Bt cotton has been deregulated following extensive safety testing. Nevertheless, results from this research suggest that limiting gene flow into refuge seed could be important for sustaining the efficacy of Bt cotton against targeted insect pests in regions where refuges are used.

0009014A Msc thesis Science Animal plant and environmental sciences / Anopheles arabiensis is considered an important vector of human malaria in the southern African region where the disease is the major cause of morbidity and mortality. Gene flow plays an important role in malaria control with the spread of insecticide resistance. The main objectives of this study were to (i) measure the genetic variability within and between five populations (Botswana, Namibia, South Africa, Swaziland and Zimbabwe) of wild An. arabiensis and (ii) estimate the level of gene flow between natural populations across the Southern-limits of An. arabiensis. A total of 1225 An. arabiensis specimens were identified out of 1300 mosquitoes collected from 2000-2003 with the sample sizes ranging from 180-292 per country. Variation at four microsatellite markers was investigated on non-denaturing polyacrylamide gels. The results showed fewer variations between populations (2.96%) than within populations (82.60%) suggesting considerable homogeneity. However, estimates of gene flow (Nm) calculated from mean FST and RST statistics were relatively low, 1.14 and 1.19 respectively, suggesting somewhat restricted gene flow between populations. The occurrence of gene flow within subpopulations of An. arabiensis in Zimbabwe but not in South Africa is interesting with regard to the spread of insecticide resistance in Zimbabwe. The results presented here are obviously subject to the limitations inherent in manual, silver staining method of analysing microsatellite DNA markers. It is possible that a different set of results would be obtained if an Automated Sequencing Analyzer were used. ii

Begonia L. is one of the largest plant genera, comprising over 1500 species. Weak species cohesion, and the rapid evolution of reproductive barriers in allopatry, are two processes that have been postulated to explain the generation of such hyper-diversity of taxa within a single genus of plants. The aim of this thesis is to investigate whether these factors are likely to have been important contributors to the diversity of species found in Central American Begonia. Species cohesion was analysed in the widespread Central American species Begonia heracleifolia and B. nelumbiifolia. Interpopulation seed flow was estimated with seven plastid microsatellites. Breeding system estimates and measures of genetic differentiation at nine nuclear microsatellites were used to infer levels of interpopulation pollen flow. Controlled crosses were employed to assess the strength of reproductive barriers both between populations within species, and between species differing in ecology. The potential for gene flow between species in the wild was assessed in natural hybrid zones using molecular markers. Finally a quantitative trait locus (QTL) approach was employed to investigate the genetic basis of reproductive traits that differ between species. No plastid polymorphisms were found in B. nelumbiifolia, suggesting it has been through a recent population bottleneck. In contrast, B. heracleifolia possessed many plastid haplotypes that were strongly differentiated between populations (G’ST = 0.829). Nuclear microsatellites showed high genetic differentiation within species, and both species were self-compatible and self-fertilize at a moderate rate (B. heracleifolia F’ST = 0.506, FIS = 0.249; B. nelumbiifolia F’ST = 0.439, FIS = 0.380). F1s between ecologically similar B. heracleifolia and B. sericoneura were partly fertile (2-5% seed set), and F1s and early generation backcrosses were found in a hybrid swarm. F1s between B. heracleifolia and the ecologically contrasting B. nelumbiifolia were pollen sterile, and 3 hybrid swarms showed no evidence of hybrids beyond the F1 generation. Seven QTL were found for reproductive traits, including: sex ratio, pollen sterility and stamen number. The population biology of Begonia, with limited seed and pollen dispersal, small population sizes and frequent self-fertilization predisposes them to genetic isolation, increasing the chances that reproductive barriers evolve. These characteristics may underlie the large number of endemics in Begonia.