Plants with similar traits compete for resources. If related taxa share similar traits, phylogenetic relationships may predict competitive outcomes. Although plants compete for pollinators, flowers are rarely considered in community-assembly theory. I tested the hypothesis that plant communities are structured by competition for pollination. I inventoried communities at three spatial scales, measured seven flower traits, and tested the observed patterns against those generated by a null model to judge if community members were more or less similar in floral traits than expected by chance. I also measured the phylogenetic relatedness of community members to gauge trait-conservatism. Clustering of visually attractive traits suggests they promote facilitation of pollinators while over-dispersion of morphological traits suggests they partition pollinators in to avoid competition. Communities were phylogenetically even, but relatedness did not explain floral trait patterns. I suggest that flowers represent an ecological niche through which species can be sorted.

The Myristicaceae, or nutmeg family, consists of 21 genera and about 500 species of dioecious canopy to sub canopy trees that are distributed worldwide in tropical rainforests. The Myristicaceae are of considerable ecological and ethnobotanical significance as they are important food for many animals and are harvested by humans for timber, spices, dart/arrow poison, medicine, and a hallucinogenic snuff employed in medico-religious ceremonies. Despite the importance of the Myristicaceae throughout the wet tropics, our taxonomic knowledge of these trees is primarily based on the last revision of the five neotropical genera completed in 1937. The objective of this thesis was to perform a molecular and morphological study of the neotropical genera Compsoneura and Virola. To this end, I generated phylogenetic hypotheses, surveyed morphological and genetic diversity of focal species, and tested the ability of DNA barcodes to distinguish species of wild nutmegs. Morphological and molecular analyses of Compsoneura. indicate a deep divergence between two monophyletic clades corresponding to informal sections Hadrocarpa and Compsoneura. Although 23 loci were tested for DNA variability, only the trnH-psbA intergenic spacer contained enough variation to delimit 11 of 13 species sequenced. A morphological and molecular investigation of Compsoneura capitellata showed little discrete morphological variation among populations but significant genetic structure among populations. Phylogenetic analysis of Virola also revealed a deep molecular divergence between two clades having numerous contrasting morphologies. In contrast to Compsoneura, the trnH-psbA intergenic spacer failed to differentiate the majority of Virola species tested. An infraspecific morphological and molecular study of V. sebifera and V. loretensis showed that each of these species contains morphologically and ecologically discrete sympatric morphotypes that likely represent new species. In total, this investigation found 5 provisional new species from fewer than 600 collections at biological stations in Ecuador and Peru where these new species were among the most abundant trees in the forest. This suggests that much diversity likely remains to be described in the Myristicaceae and other tropical plant families.

The Nearctic members of the genus Platycheirus Lepeletier and Serville are revised. Five species, Platycheirus alpigenus Nielsen and Barkalov, Platycheirus brunnifrons Nielsen, Platycheirus clausseni Nielsen, Platycheirus speighti Doczkal, Stuke, and Goeldlin, and Platycheirus splendidus Rotheray, are newly recorded for the Nearctic Region, while three species, Platycheirus sp. trichopus, Platycheirus sp. “hyperboreus dark form” and Platycheirus n. sp. “perpallidus1” are new manuscript names. Females of 42 species are described for the first time. The genus Pyrophaena Schiner is resurrected. The genus Tuberculanostoma Fluke is synonymized with Platycheirus. An illustrated key to all 73 males and 52 females of Platycheirus and the males and females of the 3 species of Pyrophaena occurring in the Nearctic region is provided. Morphological and combined morphological/molecular COI phylogenetic analyses of the Platycheirus albimanus group are presented, as well as a molecular analysis of all available Platycheirus COI sequences. The species groups within Platycheirus are redefined based on these analyses. / NSERC-CANPOLIN

Evolutionary history has been recognized as an important factor in studying ecological communities. Lake fish communities have had limited consideration from a community phylogenetics perspective and present the opportunity to include trophic interactions in the analysis. For the species under study, I used known phylogenies from the literature and genetic information to determine relative branch lengths and phylogenetic relationships by Bayesian inference. Using the resultant phylogenetic tree and fish community data, the phylogenetic community structure was determined for the lakes in the Manitoulin Island and LaCloche regions of Ontario, Canada. Evidence of phylogenetic structuring was found, particularly associated with piscivory, winter hypoxia tolerance, and thermal preferences for deep coldwater lakes. Although the majority of the lakes were weakly structured from a phylogenetic perspective, significant trends were nonetheless apparent; especially when further informed by examining species-specific trends, demonstrating that evolutionary history can play a role in structuring freshwater fish communities.

Evolutionary history has been recognized as an important factor in studying ecological communities. Lake fish communities have had limited consideration from a community phylogenetics perspective and present the opportunity to include trophic interactions in the analysis. For the species under study, I used known phylogenies from the literature and genetic information to determine relative branch lengths and phylogenetic relationships by Bayesian inference. Using the resultant phylogenetic tree and fish community data, the phylogenetic community structure was determined for the lakes in the Manitoulin Island and LaCloche regions of Ontario, Canada. Evidence of phylogenetic structuring was found, particularly associated with piscivory, winter hypoxia tolerance, and thermal preferences for deep coldwater lakes. Although the majority of the lakes were weakly structured from a phylogenetic perspective, significant trends were nonetheless apparent; especially when further informed by examining species-specific trends, demonstrating that evolutionary history can play a role in structuring freshwater fish communities.

Abstract Senecio is one of the largest genera in the Asteraceae family with 28 Senecio species in New Zealand and over 1200 species worldwide. Native Senecio in the Canterbury region are typically naturally uncommon and exhibit extreme fluctuations in population size. Contrary to native Senecio, exotic Senecio in the Canterbury region are thriving. Why some exotic species thrive in a novel environment while native species decline has been an area of intense study since the era of Darwin. However, despite extensive study, we are still unsure about the underlying mechanisms of this phenomenon. This thesis looks at several hypotheses that have been proposed to explain differences in success between native and exotic species including four that have been frequently mentioned in the literature: phylogenetics, natural enemy release and biotic resistance, allopolyploidy and habitat modification. In order to determine if phylogenetic relatedness influences the abundance and distribution of Senecio species in Canterbury, DNA phylogenies of New Zealand’s Senecio were constructed using nuclear (ITS, ETS) and plastid (trnL, trnL-F and psbA-trnH) DNA sequences. The resulting cladograms were used to determine the areas of origin of New Zealand’s Senecio lineages, the identity of their closest relatives and lineages and species that are of allopolyploid origin. The data provided by the phylogenetic analyses was to provide context for analyses of ecological data of 86 native and exotic Senecio populations from the Canterbury region. My results indicate that phylogenetic relatedness is a poor predictor of the amount of folivory experienced by Senecio, although some natural enemies of native and exotic Senecio displayed a positive preference for Senecio depending on their clade. The strongest effects on Senecio and the occurrences of their natural enemies came from the surrounding land use which influenced the amount of folivory and the abundances of natural enemies on Senecio. Enemy release and biotic resistance were land use specific within Canterbury and by themselves cannot explain the variance in folivory when applied to a landscape scale. According to my results, the biggest factor influencing Senecio folivory, abundance and distribution in the Canterbury region is change in the surrounding land use.

Phylogenetic diversity (PD) is a measure of species biodiversity quantified by how much of an evolutionary tree is spanned by a subset of species. In this thesis, we study optimization problems that aim to find species sets with maximum PD in different scenarios, and examine random extinction models under various assumptions to predict the PD of species that will still be present in the future. Optimizing PD with Dependencies is a combinatorial optimization problem in which species form an ecological network. Here, we are interested in selecting species sets of a given size that are ecologically viable and that maximize PD. The NP-hardness of this problem is proved and it is established which special cases of the problem are computationally easy and which are computationally hard. It is also shown that it is NP-complete to decide whether the feasible solution obtained by the greedy algorithm is optimal. We formulate the optimization problem as an integer linear program and find exact solutions to the largest food web currently in the empirical literature. In addition, we give a generalization of PD that can be used for example when we do not know the true evolutionary history. Based on this measure, an optimization problem is formulated. We discuss the complexity and the approximability properties of this problem. In the generalized field of bullets model (g-FOB), species are assumed to become extinct with possibly different probabilities, and extinction events are independent. We show that under this model the distribution of future phylogenetic diversity converges to a normal distribution as the number of species grows. When extinction probabilities are influenced by some binary character on the tree, the state-based field of bullets model (s-FOB) represents a more realistic picture. We compare the expected loss of PD under this model to that under the associated g-FOB model and find that the former is always greater than or equal to the latter. It is natural to further generalize the s-FOB model to allow more than one binary character to affect the extinction probabilities. The expected future PD obtained for the resulting trait-dependent field of bullets model (t-FOB) is compared to that for the associated g-FOB model and our previous result is generalized.

In this thesis, I present a model of multidomain evolution with associated algorithms and software for phylogenetic analysis of multidomain families, as well as applications of this novel methodology to case-studies and the human genome. Phylogenetic analysis is of central importance to understanding the origins and evolution of life on earth. In biomedical research, molecular phylogenetics has proved an essential tool for practical applications. Current molecular phylogenetic methods are not equipped, however, to model many of the unique characteristics of multidomain families. Genes that encode this large and important class of proteins are characterized by a mosaic of sequence fragments that encode structural or functional modules, called domains. Multidomain families evolve via domain shuffling, a process that includes insertion, internal duplication, and deletion of domains. This versatile evolutionary mechanism played a transformative role in major evolutionary transitions, including the emergence of multicellular animals and the vertebrate immune system. Multidomain families are ill-suited to current methods for phylogeny reconstruction due to their mosaic composition. Different regions of the same protein may have different evolutionary histories. Moreover, a protein may contain domains that also occur in otherwise unrelated proteins. These attributes pose substantial obstacles for phylogenetic methods that require a multiple sequence alignment as input. In addition, current methods do not incorporate a model of domain shuffling and hence, cannot infer the events that occurred in the history of the family. I address this problem by treating a multidomain family as a set of co-evolving domains, each with its own history. If the family is evolving by vertical descent from a conserved set of ancestral domains, then all constituent domains will have the same phylogenetic history. Disagreement between domain tree topologies is evidence that the family evolved through processes other than speciation and gene duplication. My algorithms exploit this information to reconstruct the history of domain shuffling in the family, as well as the timing of these events and the ancestral domain composition. I have implemented these algorithms in software that outputs the most parsimonious history of events for each domain family. The software also reconstructs a composite family history, including duplications, insertions and losses of all constituent domains and ancestral domain composition. My approach is capable of more detailed and accurate reconstructions than the widely used domain architecture model, which ignores sequence variation between domain instances. In contrast, my approach is based on an explicit model of events and captures sequence variation between domain instances. I demonstrate the utility of this method through case studies of notch-related proteins, protein tyrosine kinases, and membrane-associated guanylate kinases. I further present a largescale analysis of domain shuffling processes through comparison of all pairs of domain families that co-occur in a protein in the human genome. These analyses suggest that (1) a remarkably greater amount of domain shuffling may have occurred than previously thought and (2) that it is not uncommon for the same domain architecture to arise more than once through independent events. This stands in contrast to earlier reports that convergent evolution of domain architecture is rare and suggests that incorporating sequence variation in evolutionary analyses of multidomain families is a crucial requirement for accurate inference.

The mtDNA genetic relatedness between and within 13 Baganda, 14 Lugbara and 13 Acholi individuals from Uganda was investigated in this research program. The complete mtDNA sequences of the 40 Ugandan samples were established and a phylogeographic analysis of these sequences was conducted using both a Neighbour-Joining and a Maximum Parsimony tree together with a global sample of 387 African sequences. Prior to this study, only two complete and six partial mtDNA sequences of Ugandans had been established. A total of 563 polymorphisms were determined of which 276 were synonymous, 75 were nonsynonymous, 26 were novel and 208 occurred in the control region. The Lugbara sequences clustered more closely with the Acholi sequences than the Baganda sequences within the Neighbour-Joining and Maximum Parsimony tree. A phylogeographic analysis of the sequences demonstrated that the Acholi and Lugbara individuals in this investigation originated from Southern Sudan while the Baganda samples had a diversified origin which comprised of the Niger-Congo basin, Ethiopia and Sudan. Furthermore, the clustering of the Ugandan sequences with sequences from African American and Hispanic individuals was evidence of slave trade involving the shipping of people from Uganda to North America. It was intriguing that the deepest branch in the phylogeny was L5 (instead of L0) suggesting that the Khoi-San may not be the ancestral origin of anatomically modern man. There was increased resolution of macrohaplogroup L (especially for the small haplogroups) as new branches and nodes were formed in the tree. The results also demonstrated that East Africa was the origin and source of dispersal of numerous small macrohaplogroup L haplogroups. These mtDNA sequences from Baganda, Acholi and Lugbara individuals have a potential for forensic, nutrigenomic and pharmacogenomic application and will serve as useful references in assessment of mtDNA sequences in other Ugandan and East African populations. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2010

The mtDNA genetic relatedness between and within 13 Baganda, 14 Lugbara and 13 Acholi individuals from Uganda was investigated in this research program. The complete mtDNA sequences of the 40 Ugandan samples were established and a phylogeographic analysis of these sequences was conducted using both a Neighbour-Joining and a Maximum Parsimony tree together with a global sample of 387 African sequences. Prior to this study, only two complete and six partial mtDNA sequences of Ugandans had been established. A total of 563 polymorphisms were determined of which 276 were synonymous, 75 were nonsynonymous, 26 were novel and 208 occurred in the control region. The Lugbara sequences clustered more closely with the Acholi sequences than the Baganda sequences within the Neighbour-Joining and Maximum Parsimony tree. A phylogeographic analysis of the sequences demonstrated that the Acholi and Lugbara individuals in this investigation originated from Southern Sudan while the Baganda samples had a diversified origin which comprised of the Niger-Congo basin, Ethiopia and Sudan. Furthermore, the clustering of the Ugandan sequences with sequences from African American and Hispanic individuals was evidence of slave trade involving the shipping of people from Uganda to North America. It was intriguing that the deepest branch in the phylogeny was L5 (instead of L0) suggesting that the Khoi-San may not be the ancestral origin of anatomically modern man. There was increased resolution of macrohaplogroup L (especially for the small haplogroups) as new branches and nodes were formed in the tree. The results also demonstrated that East Africa was the origin and source of dispersal of numerous small macrohaplogroup L haplogroups. These mtDNA sequences from Baganda, Acholi and Lugbara individuals have a potential for forensic, nutrigenomic and pharmacogenomic application and will serve as useful references in assessment of mtDNA sequences in other Ugandan and East African populations. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2010