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.

Human parainfluenza 3 (HPIV3) is a member of the Paramyxoviridae, a single strain negative-sense non-segmented RNA virus in the order Mononegavirales. It is a respiratory pathogen with a broad spectrum of presentations for which there is currently neither a vaccine nor licensed treatment for HPIV3. To date most research on HPIV3 has been conducted using significantly culture adapted reference strains. Therefore, minimally adapted clinical strains were grown in two cell culture systems: immortalised and primary. Plaque phenotype, growth kinetics and inflammatory response triggered were evaluated and it was found that there is a range of phenotypes exhibited by clinical strains with potential implications in vivo. To examine the genetic diversity of circulating strains of HPIV3 in the UK, a new amplicon based sequencing pipeline for whole genome sequencing of HPIV3 was developed and validated. A short hypervariable region in the HPIV3 genome was identified and evaluated as a potential candidate for subsequent phylogenetic analysis compared to whole genome data. This method was then applied to tracking an HPIV3 outbreak that took place on a paediatric oncology ward. It was found to be a point-source outbreak and the clinical impact in this setting, as well as the infection control procedures involved were evaluated. Finally a robust in vitro model for the evaluation of potential therapeutic candidates for HPIV3, based on a panel of minimally passaged clinical strains as well as a culture-adapted reference strain, was set up. This model was applied to three potential inhibitors of HPIV3: ribavirin, favipiravir and zanamivir. The results showed that clinical strains were at least as susceptible to ribavirin and favipiravir as the laboratory reference strain and significantly more susceptible to zanamivir. This indicates that further work on minimally adapted clinical strains is essential to further the understanding of this important virus.

It is well known that nucleotide diversity varies across the genomes of eukaryotic species in ways consistent with the effects of natural selection. However, the contribution of selection on advantageous and deleterious mutations to the observed variation is not well understood. In this thesis, I aim to disentangle the contribution of background selection and selective sweeps to patterns of genetic diversity in the mouse genome, thus furthering our understanding of natural selection in mammals. In chapter 1, I introduce core concepts in evolutionary genetics and describe how recombination and selection interact to shape patterns of genetic diversity. I will then describe three projects in which I examine aspects of molecular evolution in house mice. In the first of these, I estimate the landscape of recombination rate variation in wild mice using population genomic data. In the second, I estimate the distribution of fitness effects for new mutations, based on the site frequency spectrum, then analyse population genomic simulations parametrized using my estimates. In the third, I use a model of selective sweeps to estimate and compare the strength of selection in protein-coding and regulatory regions of the mouse genome. This thesis demonstrates that selective sweeps are responsible for a large amount of the variation in genetic diversity across the mouse genome.

Thesis (M.Sc. (Crop science)) --University of Limpopo, 2007 / Vernonia (Vernonia galamensis) is a new potential industrial oilseed crop. The seeds of this crop contain unusual naturally epoxidised fatty acids which are used in the production of various industrial products. The objective of this study was to evaluate the genetic diversity of selected vernonia lines in Limpopo Province through morphological, seed oil content and RAPD DNA markers. Significant differences were observed for days to 50 % flowering (93 - 140 days), plant height (141.80 - 166.33 cm), number of productive primary heads (29 - 60 head/plant), number of productive secondary heads (12 - 30 head/plant), thousand seed weight (1.85 - 3.52 g) and seed yield (454.44 - 786.85 kg/ha) between lines. Further results from oil analysis showed differences in the contents of seed oil (22.4 - 29.05%), vernolic acid (73.09 - 76.83%), linoleic acid (13.02 - 14.05%), oleic acid (3.77 - 5.28%), palmitic acid (2.48 - 2.98%) and stearic acid (2.26 - 2.75%). Among 13 RAPD DNA primers screened, primer OPA10 amplified DNA samples and resulted in four distinct groupings among tested lines. Four promising lines were selected viz. Vge-16, Vge-20, Vge-27 and Vge-32 displaying greater seed yield, increased vernolic acid content and reduced number of days to 50 % flowering. / National Research Foundataion

No presente trabalho nós investigamos a história filogeográfica de dois passeriformes: Dendrocincla turdina (Dendrocolaptidae) e Drymophila squamata (Thamnophilidae). As duas espécies são endêmicas de baixadas da Mata Atlântica e boa parte de suas distribuições é coincidente, mas D. turdina chega a altitudes maiores e D. squamata ocorre em uma região disjunta no nordeste onde D. turdina não ocorre. Foram analisadas a estrutura genética das duas espécies e suas histórias demográficas, também foram feitas inferências sobre os processos históricos que poderiam ter contribuído para a diversidade genética que observamos hoje. Para D. turdina foram utilizados sete microssatélites, um marcador mitocondrial e um íntron. Enquanto para D. squamata foram utilizados um marcador mitocondrial e dois íntrons. O primeiro capítulo da Tese aborda os dados de D. turdina, que mostraram ausência de estrutura geográfica e evidências de expansão populacional. A utilização de microssatélites reforçou a possibilidade de ser uma população única, uma vez que, dada a alta taxa de mutação desses marcadores, em geral é possível detectar divergências recentes. A expansão demográfica foi evidenciada e datada a partir do último máximo glacial (UMG) baseado no marcador mitocondrial e no íntron. A computação Bayesiana aproximada (ABC) foi utilizada para testar esse cenário de população única com expansão populacional baseado nos nove marcadores. Os parâmetros estimados foram congruentes com os resultados das outras análises. Parece ter ocorrido um gargalo genético seguido por aumento do tamanho populacional, sendo que no UMG o tamanho efetivo populacional era duas ordens de grandeza menor do que o atual. No segundo capítulo da Tese analisamos a espécie D. squamata, para a qual foram encontradas quatro linhagens mitocondriais separadas geograficamente. Sendo que as linhagens Sul, Centro e Norte parecem ter se divergido durante o Pleistoceno médio, enquanto o grupo Nordeste, composto pela população disjunta, parece ter se diversificado há mais tempo, cerca de 1,1 milhão de anos atrás. Para os clados Sul e Norte foram identificadas expansões demográficas no UMG. Tanto eventos geotectônicos quanto oscilações climáticas do Quaternário podem ter atuado no processo de diversificação; enquanto os rios podem ter contribuído para a manutenção dessas divergências, ao menos entre os clados Norte e Centro. Os grupos genéticos encontrados no presente estudo não condizem com a distribuição geográfica descrita para as subespécies descritas de D. squamata, isso indica a necessidade de uma revisão taxonômica. A divergência do clado Nordeste parece ser bastante antiga e essa linhagem ocorre em uma área reduzida e impactada da mata Atlântica, além de geograficamente isolada das maior área de distribuição do táxon. Isso indica que o clado Nordeste merece atenção quanto à sua conservação. A presente Tese contribuiu com o melhor entendimento da distribuição da diversidade genética das espécies aqui estudadas e da história da biodiversidade da mata Atlântica, trazendo informações sobre dois táxons com histórias filogeográficas diferentes, embora possivelmente moldadas por processos semelhantes. / Here we present the phylogeographic history of two Passerine birds: Dendrocincla turdina (Dendrocolaptidae) and Drymophila squamata (Thamnophilidae). Both are endemic species of the Atlantic Forest lowlands and their occurrence overlaps along most of their geographic distribution, but D. turdina reaches higher altitudes and D. squamata has in a disjunct population in the northeast, where D. turdina does not occur. The genetic structure and the demographic history of both species was studied, and inferences about potential historical processes that could have influenced their genetic diversity pattern were made. For D. turdina we used seven microsatellites and sequences of one mitochondrial (mtDNA) gene and one intron. For D. squamata sequences of one mtDNA gene and two introns were obtained. The first chapter shows that D. turdina does not present population genetic structure but has evidences of population expansion. Microsatellite analyses also show absence of structure and given their high mutation rates, this indicates that there is no evidence of any recent divergences. Results based on mtDNA and intron sequences showed that the demographic expansion started during the last glacial maximum (LGM). Approximate bayesian computation (ABC) was used to test this scenario of a unique population with expansion based on nine molecular markers. The results were congruent with those from other analyses. It seems that a bottleneck was followed by an increase of population size, and at the LGM the population effective size was two orders of magnitude lower than nowadays. The second chapter presents data on D. squamata. Four mitochondrial lineages that are geographically separated were observed. Lineages South, Center, and North seem to have diverged in the middle of the Pleistocene and the Northeast lineage, that grouped the disjunct population, seems to have diverged around 1.1 million years ago. Clades South and North presented evidences of demographic expansions during the LGM. Both geotectonic and climatic oscillations from the Quaternay could have beeen involved in the diversification process; while rivers may helped to maintain the lineages differentiated, at least clades North and Center. The geographic distribution of these lineages did not match the one described for D. squamata subspecies. Thus, indicating that a taxonomic revision is needed. The divergence of the Northeast lineage seems to be old and it occurs in a reduced and deforested area, besides it is geographically isolated from the main distribution of the species. This highlights that the conservation of the Northeast lineage should be granted major attention. This thesis contributed with data on two avian species with distinct phylogeographic histories that could have been shaped by similar processes that occurred in the Atlantic forest.

<i>Festuca hallii</i> [(Vasey) Piper] (plains rough fescue) is a dominant native grass species in the Fescue Prairie region of North America that has undergone dramatic range reduction in the past century. This research is undertaken to address the related issues associated with the effectiveness of sampling in capturing genetic diversity, the influence of habitat fragmentation on genetic variation, the geographic variation of seed germination characteristics, and the comparative genetic variation of differential germination. It was found that the tiller samples revealed slightly larger among-population variation than the seed samples. The fescue plant was genetically diverse, as revealed by the proportion of polymorphic bands, the mean band frequency, and the within-population variation. The genetic variation was not highly differentiated with only 6.5% of the total AFLP variation residing among populations. Mantel test revealed a significant correlation between genetic and geographic distances and a spatial autocorrelation up to 60 km among populations was detected. Base temperatures (<i>T_b</i>, minimal or base temperature permitting germination) of the 15 populations fell into a narrow range within 2.2°C with an average of 1.1°C. High final germination percentage was reached at a wide temperature range from 5 to 20°C with the highest germination percentage at 10°C. Germination rate index increased with increasing temperature from 5 to 20°C. <i>T_b</i> was positively correlated with latitude and negatively with longitude and the thermal time requirement for 50% germination was negatively correlated with latitude. The AFLP variation and germination responses were significantly associated with environmental attributes related to moisture, indicating local adaptation. However, the AFLP variation and germination was not significantly associated with the estimated population size and geographic distance to the nearest neighbor, suggesting that fragmentation has not generated considerable genetic and germination impact on the fescue populations. Marked differences in estimates of mean band frequency were observed for various groups of germinating seeds under different test temperatures. Comparisons of AFLP variation among 27 groups of seeds representing population, germination timing and test temperature indicates seed genotypes respond slightly differently to environmental variation, resulting in significant but small impact of germination timing and temperature on the genetic diversity of populations. These findings are significant not only for understanding and predicting the ecological adaptation of the species, but also for formulating effective restoration strategies for remnant populations.

Genetic diversity has rarely been the focus of study in species at risk in Canada. <i>Tradescantia occidentalis</i> is one of 157 species listed by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC 2005a). This species is nationally threatened due to the limited number of populations, their geographic isolation from each other and from the main distribution in the United States of America, and habitat loss. The National Recovery Team for Plants at Risk in the Prairie Provinces and the Alberta Western Spiderwort Recovery Team have called for research into the habitat requirements, demography, and genetic diversity of <i>T. occidentalis</i> in Canada. As a result, this study was designed to address the following objectives: 1) to conduct an inventory of the Canadian populations, 2) to investigate intra- and interpopulation genetic diversity in <i>Tradescantia occidentalis</i>, and 3) to provide recommendations for the conservation management of this species. <p>Information on demography and plant communities in <i>Tradescantia occidentalis</i> habitats indicated that the numbers of individuals in the Saskatchewan and Manitoba populations were similar to previous surveys; however, the Alberta population was significantly larger in number than prior estimates, indicating population growth. Taxonomic lists were prepared for each province in habitats with and without <i>T. occidentalis</i>. Community types, as separated by RA analysis, differed by province and not by association with <i>T. occidentalis</i>. Euphorbia esula, an invasive species in Canada, was observed in the Saskatchewan and Manitoba populations but was absent in Alberta. <p> Using amplified fragment length polymorphisms (AFLPs), genetic diversity was assessed at the intra- and interpopulation levels. Relatively low levels of intrapopulation variation were observed in Saskatchewan and Alberta, while higher levels were found in Manitoba. Gene flow via pollen or propagule transfer may account for higher genetic diversity among the closely situated Manitoba populations. The lack of correlation between dendrogram topology and geographic distribution suggests panmixia in all populations. Levels of intrapopulation diversity were low to moderate depending on primer combination used, indicating that populations are isolated within each province. <p>Information on population demography and genetic diversity are important within a conservation context. The large number of individuals within each population and the perceived increase in some populations suggest that the existing populations of <i>Tradescantia occidentalis</i> are relatively stable. Although levels of genetic diversity are low in Saskatchewan and Alberta compared to Manitoba, it appears that all populations are adapted to their local environments based on their apparent size and stability. The most viable conservation strategy for this species is in situ protection. This should include controlling invasive plant species, monitoring grazing, and preventing further habitat fragmentation. Ex situ methods must also be explored. Transplantation of individuals from one population to the next may not be a successful conservation strategy due to the moderate level of population differentiation. Alternatively, it is recommended that a seed bank from each population be implemented in case of a drastic population decline.

Genetic diversity has rarely been the focus of study in species at risk in Canada. <i>Tradescantia occidentalis</i> is one of 157 species listed by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC 2005a). This species is nationally threatened due to the limited number of populations, their geographic isolation from each other and from the main distribution in the United States of America, and habitat loss. The National Recovery Team for Plants at Risk in the Prairie Provinces and the Alberta Western Spiderwort Recovery Team have called for research into the habitat requirements, demography, and genetic diversity of <i>T. occidentalis</i> in Canada. As a result, this study was designed to address the following objectives: 1) to conduct an inventory of the Canadian populations, 2) to investigate intra- and interpopulation genetic diversity in <i>Tradescantia occidentalis</i>, and 3) to provide recommendations for the conservation management of this species. <p>Information on demography and plant communities in <i>Tradescantia occidentalis</i> habitats indicated that the numbers of individuals in the Saskatchewan and Manitoba populations were similar to previous surveys; however, the Alberta population was significantly larger in number than prior estimates, indicating population growth. Taxonomic lists were prepared for each province in habitats with and without <i>T. occidentalis</i>. Community types, as separated by RA analysis, differed by province and not by association with <i>T. occidentalis</i>. Euphorbia esula, an invasive species in Canada, was observed in the Saskatchewan and Manitoba populations but was absent in Alberta. <p> Using amplified fragment length polymorphisms (AFLPs), genetic diversity was assessed at the intra- and interpopulation levels. Relatively low levels of intrapopulation variation were observed in Saskatchewan and Alberta, while higher levels were found in Manitoba. Gene flow via pollen or propagule transfer may account for higher genetic diversity among the closely situated Manitoba populations. The lack of correlation between dendrogram topology and geographic distribution suggests panmixia in all populations. Levels of intrapopulation diversity were low to moderate depending on primer combination used, indicating that populations are isolated within each province. <p>Information on population demography and genetic diversity are important within a conservation context. The large number of individuals within each population and the perceived increase in some populations suggest that the existing populations of <i>Tradescantia occidentalis</i> are relatively stable. Although levels of genetic diversity are low in Saskatchewan and Alberta compared to Manitoba, it appears that all populations are adapted to their local environments based on their apparent size and stability. The most viable conservation strategy for this species is in situ protection. This should include controlling invasive plant species, monitoring grazing, and preventing further habitat fragmentation. Ex situ methods must also be explored. Transplantation of individuals from one population to the next may not be a successful conservation strategy due to the moderate level of population differentiation. Alternatively, it is recommended that a seed bank from each population be implemented in case of a drastic population decline.

<i>Festuca hallii</i> [(Vasey) Piper] (plains rough fescue) is a dominant native grass species in the Fescue Prairie region of North America that has undergone dramatic range reduction in the past century. This research is undertaken to address the related issues associated with the effectiveness of sampling in capturing genetic diversity, the influence of habitat fragmentation on genetic variation, the geographic variation of seed germination characteristics, and the comparative genetic variation of differential germination. It was found that the tiller samples revealed slightly larger among-population variation than the seed samples. The fescue plant was genetically diverse, as revealed by the proportion of polymorphic bands, the mean band frequency, and the within-population variation. The genetic variation was not highly differentiated with only 6.5% of the total AFLP variation residing among populations. Mantel test revealed a significant correlation between genetic and geographic distances and a spatial autocorrelation up to 60 km among populations was detected. Base temperatures (<i>T_b</i>, minimal or base temperature permitting germination) of the 15 populations fell into a narrow range within 2.2°C with an average of 1.1°C. High final germination percentage was reached at a wide temperature range from 5 to 20°C with the highest germination percentage at 10°C. Germination rate index increased with increasing temperature from 5 to 20°C. <i>T_b</i> was positively correlated with latitude and negatively with longitude and the thermal time requirement for 50% germination was negatively correlated with latitude. The AFLP variation and germination responses were significantly associated with environmental attributes related to moisture, indicating local adaptation. However, the AFLP variation and germination was not significantly associated with the estimated population size and geographic distance to the nearest neighbor, suggesting that fragmentation has not generated considerable genetic and germination impact on the fescue populations. Marked differences in estimates of mean band frequency were observed for various groups of germinating seeds under different test temperatures. Comparisons of AFLP variation among 27 groups of seeds representing population, germination timing and test temperature indicates seed genotypes respond slightly differently to environmental variation, resulting in significant but small impact of germination timing and temperature on the genetic diversity of populations. These findings are significant not only for understanding and predicting the ecological adaptation of the species, but also for formulating effective restoration strategies for remnant populations.

Honey bees (Apis mellifera) are the most economically important insect pollinator of agricultural crops in the United States. Honey bee colonies are required for pollination of approximately one-third of the nation’s fruit, vegetable, nut, and forage crops, with an estimated annual value in the billions of dollars. The economic value of a honey bee colony comes from its population size, as large colonies provide the necessary foraging force required for large-scale crop pollination services. A major component of colony strength is its genetic diversity, a consequence of the reproductive mating strategy of the queen known as polyandry. Despite some inherent risks of multiple mating, several studies have demonstrated significant advantages of intracolonial genetic diversity for honey bee colony productivity. Colony-level benefits include better disease resistance, more stable brood nest thermoregulation, and greater colony growth. Instrumental insemination of honey bee queens is a technique to precisely control queen mating, and thereby creates the opportunity to investigate the effects of intracolonial genetic diversity on colony performance. In this dissertation, I first consider the effects of intracolonial genetic diversity on pollen foraging using colonies headed by queens which were instrumentally inseminated with either one or twenty drones to generate colonies of very high or very low intracolonial genetic diversity, respectively. I found that colonies with high intracolonial genetic diversity amass significantly more pollen and rear more brood than colonies with low intracolonial genetic diversity. Of particular interest, colonies with low intracolonial genetic diversity collected a significantly greater variety of pollen types. I discuss these results in the context of scouting and recruiting, and suggest a more efficient foraging strategy exists among genetically diverse colonies. While intracolonial genetic diversity is positively correlated with collected pollen, its effect on the colony’s ability to process and distribute inbound protein resources is unknown. Again using colonies headed by queens instrumentally inseminated with either one or twenty drones, I studied the effects of intracolonial genetic diversity on pollen consumption and digestion by nurse bees, as well as protein allocation among nestmates by assessing total soluble protein concentration of late instar larvae, and total soluble hemolymph protein concentration in both nurses and pollen foragers. I found that nurse bees from colonies with high intracolonial genetic diversity consume and process more protein than nurses from colonies with low intracolonial genetic diversity, even when given equal access to protein resources. Further, both forager hemolymph protein concentrations and larval total protein concentrations were higher among the colonies with high intracolonial genetic diversity. My findings suggest that protein processing and distribution within a honey bee colony is affected by the social context of the hive. I discuss “worker policing”, and the role of nurse bees in modulating the foraging effort. Finally, I assess the standing genetic variability among several colonies sourced from different genetic and geographic locations. Using microsatellite DNA from workers sampled from each colony, I determined allelic richness, gene diversity, and effective mating frequency for each genetic line. I found differences in all three metrics between lines, and for one line in particular, there was no correlation with genetic variation and effective mating frequency, suggesting non-random mating. My results showed very different levels of intracolonial genetic diversity among naturally mated queens. Because of its impact on colony performance, the importance of maintaining genetic diversity in breeding populations is discussed.