<p>Members of Zygophylloideae are shrubs, shrublets and herbs of arid and semiarid areas of almost all continents, and many of the species are major components of the vegetation in their areas of distribution. A phylogenetic analysis of Zygophylloideae based on noncoding <i>trnL</i> plastid DNA sequences and morphological data, indicates that the currently recognised genera <i>Augea</i>, <i>Tetraena</i>, and <i>Fagonia</i>, are embedded in <i>Zygophyllum</i>. A new generic classification based on six monophyletic and morphologically distinctive entities is proposed here: <i>Augea</i>, <i>Fagonia</i>, <i>Melocarpum</i>, <i>Roepera</i>, <i>Tetraena</i> and <i>Zygophyllum</i>. </p><p>The taxonomy of the genus <i>Fagonia</i> is revised in detail. A key to the 34 species recognised is presented, as well as descriptions and distribution maps for each species. Five new species are described and illustrated, <i>F. densispina</i>, <i>F. gypsophila</i> and <i>F. latistipulata </i>from Somalia, and <i>F. hadramautica</i> and <i>F. mahrana</i> from the southern part of the Arabian peninsula. Of the accepted species, 26 are restricted to the Old World and eight to the New World. The names of all four species of <i>Fagonia</i> currently on the IUCN Red List of Threatened Plants are put into synonymy. Instead, eight other species are proposed for this list.</p><p>Relationships within <i>Fagonia</i> are inferred from analysis of plastid <i>trnL</i> intron and nuclear ribosomal ITS sequences. The phylogenetic analysis is performed using parsimony and Bayesian model averaging. All species of <i>Fagonia</i> in the Old World, except <i>F. cretica</i>, form a weakly supported clade, and all <i>Fagonia</i> species of the New World, except <i>F. scoparia</i>, form a second, well supported clade, sister to the Old World clade. <i>Fagonia scoparia</i>, endemic to northeastern Mexico,<i> </i>is sister to all other <i>Fagonia</i> species. Vicariance-dispersal analysis indicated that the occurrences of <i>Fagonia</i> in South America and southern Africa are due to dispersals, and that the ancestor of <i>Fagonia</i> had a distribution in agreement with the boreotropics hypothesis.</p>

<p>This thesis concerns the history and the intrafamilial delimitations of the plant family Colchicaceae. A phylogeny of 73 taxa representing all genera of Colchicaceae, except the monotypic <i>Kuntheria</i>, is presented. The molecular analysis based on three plastid regions—the <i>rps16</i> intron, the <i>atpB-rbcL</i> intergenic spacer, and the <i>trnL-F</i> region—reveal the intrafamilial classification to be in need of revision. The two tribes Iphigenieae and Uvularieae are demon-strated to be paraphyletic. The well-known genus <i>Colchicum</i> is shown to be nested within <i>Androcymbium</i>, <i>Onixotis</i> constitutes a grade between <i>Neodregea</i> and <i>Wurmbea</i>, and <i>Gloriosa</i> is intermixed with species of <i>Littonia</i>. Two new tribes are described, Burchardieae and Tripladenieae, and the two tribes Colchiceae and Uvularieae are emended, leaving four tribes in the family. At generic level new combinations are made in <i>Wurmbea</i> and <i>Gloriosa</i> in order to render them monophyletic. The genus <i>Androcymbium</i> is paraphyletic in relation to <i>Colchicum</i> and the latter genus is therefore expanded. An investigation of the distribution of colchicine within the expanded Colchicaceae is conducted to evaluate the potential of colchicine as a synapomorphy of the re-circumscribed family. The results demonstrate presence of colchicine in all genera previously not examined in Colchicaceae and in the genus <i>Burchardia</i>, earlier reported to lack colchicine. Hence, demonstrating colchicine to be a synapomorphy for the family. An attempt to date the phylogeny of the order Liliales together with a dispersal-vicariance (DIVA) analysis indicates that the split between Colchicaceae and Alstromeriaceae-Luzuriagaceae represents a vicariance event following the disintegration of the Australian-Antarctican-South American link, ~34 million years ago. Further, the DIVA analysis indicates that Colchicaceae originated in Australia, first reached Asia and North America, and later Africa, from where they expanded to Europe and also dispersed back to Australia. </p>

Much conservation work focuses on individual species, partly because of the perception that wildlife species are effective symbols for raising funds and drawing awareness to environmental causes. However, for species-based studies to aid conservation efforts, the biological and ecological needs of species need to be addressed in a way that informs decisions and provides concrete recommendations for land managers. This thesis addresses the forest cover needs of Ciconia stormi, a rare and understudied bird species that inhabits the islands of Borneo and Sumatra and parts of peninsular Malaysia. Levels of forest canopy cover associated with areas inhabited by Ciconia stormi are identified at multiple spatial resolutions using a 500m MODIS soft classification product, 30m Landsat data, and hemispherical photographs. Important threshold values of 75 percent tree cover was identified at the regional scale, and 85 percent at foraging sites. There has been severe forest disturbance in regions inhabited by Ciconia stormi between 1993 and 2004, indicating the species may be somewhat tolerant to disturbance. Areas having been logged at least 20 years before present average over 85 percent canopy cover and have few large gaps, indicating that these forests may be suitable habitat for the species.

The overarching objective of this dissertation was to improve our knowledge of the relationship between seascape heterogeneity and diversity of stony coral assemblages across spatial scales. Coral communities on patch reefs in three regions of the Caribbean were used as a model system to investigating this relationship because patch reef heterogeneity could be readily quantified within the seascape using remote sensing and image analysis techniques. I began with a theoretical approach, exploring the origins of observed species diversity among coral communities at increasing spatial scales. Hierarchical sampling and null models revealed that coral diversity was governed by non-random processes at local- (10s of meters) and meso- (100s of m) scales. Spatial autocorrelation and reef heterogeneity were then investigated as potential mechanistic drivers of these non-random diversity patterns. I found limited support for spatial drivers. However, beta diversity was significantly correlated to metrics of reef heterogeneity (measured as reef size, spatial configuration, and complexity), indicating that differences in reef heterogeneity were making a disproportionate contribution to the overall coral community diversity. The relationship between corals and reef heterogeneity was found to be both scale-dependent and region dependent. This theoretical approach was followed by a manipulative approach using an existing artificial patch reef array to experimentally test the influence of reef spatial configuration and topographical complexity on local diversity. Corals were most sensitive to reef size and secondarily reef configuration within the seascape. Unlike reef fishes, reef complexity did not emerge as a strong predictor of the coral community composition in either the observational data or the experimental manipulation. These observational and experimental explorations of the relationship between corals and habitat reveal that intra-habitat variability (i.e. differences between patch reefs) can influence the diversity and abundance of corals. I then focused on applying this improved theoretical understanding towards improving coral management efforts. I present a new methodology to assess the efficacy of marine reserve effects by controlling for natural seascape variation within and beyond the reserve boundary, and I quantified the bias of underestimating coral diversity by using conventional reef monitoring protocols that ignore differences in reef size. In conclusion, I demonstrate empirically that seascape attributes of reef heterogeneity can contribute to coral diversity at relatively small spatial scales (<1km) and can affect corals with different life history traits in different ways. Hence, management and conservation efforts must consider the role of these meso-scale spatial metrics to influence the structure of the coral assemblage at the local scale.

Members of Zygophylloideae are shrubs, shrublets and herbs of arid and semiarid areas of almost all continents, and many of the species are major components of the vegetation in their areas of distribution. A phylogenetic analysis of Zygophylloideae based on noncoding trnL plastid DNA sequences and morphological data, indicates that the currently recognised genera Augea, Tetraena, and Fagonia, are embedded in Zygophyllum. A new generic classification based on six monophyletic and morphologically distinctive entities is proposed here: Augea, Fagonia, Melocarpum, Roepera, Tetraena and Zygophyllum. The taxonomy of the genus Fagonia is revised in detail. A key to the 34 species recognised is presented, as well as descriptions and distribution maps for each species. Five new species are described and illustrated, F. densispina, F. gypsophila and F. latistipulata from Somalia, and F. hadramautica and F. mahrana from the southern part of the Arabian peninsula. Of the accepted species, 26 are restricted to the Old World and eight to the New World. The names of all four species of Fagonia currently on the IUCN Red List of Threatened Plants are put into synonymy. Instead, eight other species are proposed for this list. Relationships within Fagonia are inferred from analysis of plastid trnL intron and nuclear ribosomal ITS sequences. The phylogenetic analysis is performed using parsimony and Bayesian model averaging. All species of Fagonia in the Old World, except F. cretica, form a weakly supported clade, and all Fagonia species of the New World, except F. scoparia, form a second, well supported clade, sister to the Old World clade. Fagonia scoparia, endemic to northeastern Mexico, is sister to all other Fagonia species. Vicariance-dispersal analysis indicated that the occurrences of Fagonia in South America and southern Africa are due to dispersals, and that the ancestor of Fagonia had a distribution in agreement with the boreotropics hypothesis.

This thesis concerns the history and the intrafamilial delimitations of the plant family Colchicaceae. A phylogeny of 73 taxa representing all genera of Colchicaceae, except the monotypic Kuntheria, is presented. The molecular analysis based on three plastid regions—the rps16 intron, the atpB-rbcL intergenic spacer, and the trnL-F region—reveal the intrafamilial classification to be in need of revision. The two tribes Iphigenieae and Uvularieae are demon-strated to be paraphyletic. The well-known genus Colchicum is shown to be nested within Androcymbium, Onixotis constitutes a grade between Neodregea and Wurmbea, and Gloriosa is intermixed with species of Littonia. Two new tribes are described, Burchardieae and Tripladenieae, and the two tribes Colchiceae and Uvularieae are emended, leaving four tribes in the family. At generic level new combinations are made in Wurmbea and Gloriosa in order to render them monophyletic. The genus Androcymbium is paraphyletic in relation to Colchicum and the latter genus is therefore expanded. An investigation of the distribution of colchicine within the expanded Colchicaceae is conducted to evaluate the potential of colchicine as a synapomorphy of the re-circumscribed family. The results demonstrate presence of colchicine in all genera previously not examined in Colchicaceae and in the genus Burchardia, earlier reported to lack colchicine. Hence, demonstrating colchicine to be a synapomorphy for the family. An attempt to date the phylogeny of the order Liliales together with a dispersal-vicariance (DIVA) analysis indicates that the split between Colchicaceae and Alstromeriaceae-Luzuriagaceae represents a vicariance event following the disintegration of the Australian-Antarctican-South American link, ~34 million years ago. Further, the DIVA analysis indicates that Colchicaceae originated in Australia, first reached Asia and North America, and later Africa, from where they expanded to Europe and also dispersed back to Australia.

The purpose of this research project is to identify the species-level diversity and distribution of trees within the urban setting of Peel Region (Ontario, Canada) and to determine how these characteristics change as a function of land use type. To address this, alpha diversity (species richness within a community), evenness, and beta diversity (species richness between communities) were calculated for eight distinct land use types within the study area. As well, the influence that a variety of socioeconomic and urban form variables have in determining urban forest composition was examined using regression techniques. Results indicate that significant relationships exist between land use type, species richness and overall tree abundance. Variables reflecting wealth and urban form are also shown to significantly influence tree abundance. The results of this study address issues pertaining to the adaptation, conservation, and management of the region’s urban tree species.

The purpose of this research project is to identify the species-level diversity and distribution of trees within the urban setting of Peel Region (Ontario, Canada) and to determine how these characteristics change as a function of land use type. To address this, alpha diversity (species richness within a community), evenness, and beta diversity (species richness between communities) were calculated for eight distinct land use types within the study area. As well, the influence that a variety of socioeconomic and urban form variables have in determining urban forest composition was examined using regression techniques. Results indicate that significant relationships exist between land use type, species richness and overall tree abundance. Variables reflecting wealth and urban form are also shown to significantly influence tree abundance. The results of this study address issues pertaining to the adaptation, conservation, and management of the region’s urban tree species.

Geckos of the genus Hemidactylus Oken, 1817 are one of the most widely distributed and species-rich groups of gekkonids. With approximately 90 species, the genus Hemidactylus accounts for 10% of the total number of species in the family Gekkonidae (Carranza and Arnold, 2006). They are found in a range of ecological conditions from wet tropical forest to arid deserts. Their wide distribution is believed to have been facilitated not only naturally, but also through human mediated transport. Indian subcontinent houses 31 species of these geckos, 23 of which are endemic to the subcontinent. The aim of this study was to understand the phylogeny and biogeography of Hemidactylus geckos of the Indian subcontinent. In order to arrive at the conclusions regarding the biogeographic history of this widely distributed taxon on the Indian subcontinent, an integrative approach was followed. First the phylogenetic reconstruction of Indian species was undertaken. The ancestral areas of distribution were reconstructed on the phylogeny and the divergence dates of the species were also estimated. Finally, the biogeographic events were inferred in accordance with the geological events with respect to the divergent times for these radiations. Results indicated that Hemidactylus geckos of the Indian subcontinent belong to three geographical clades: Southeast Asian clade, West-Asian arid clade and a ‘unique Indian radiation’ which consisted majority of the species distributed in India that are largely confined to the Indian subcontinent. Additionally, the three widely distributed, commensal species (H. brookii, H. frenatus and H. flaviviridis) were nested within the Indian radiation suggesting their Indian origin. It was also seen that the endemic Hemidactylus geckos of Sri Lanka have been derived from India through multiple independent dispersal events spread across the Oligocene-Miocene. These dispersals were both geo dispersal as well as transmarine dispersal events. However, the species distributed both in India and Sri Lanka appear to have undergone recent dispersals into Sri Lanka and probably back into India, primarily through human agency. Thus, it was inferred that the Indian subcontinent has served as an important arena for diversification among the Hemidactylus geckos and their spread. In addition, it was discovered that H. anamallensis, a species endemic to Southern Western Ghats of peninsular India was probably genetically distinct from Hemidactylus, indicating that it could not be Hemidactylus at all. Thus, the phylogenetic position of H. anamallensis within the subfamily Gekkoninae was also investigated and its genetic distinctiveness from that of Hemidactylus was also tested. Results showed that H. anamallensis lineage was indeed distinct from Hemidactylus group, as well as from other closely related genera (Cyrtodactylus and Geckoella) in both nuclear and mitochondrial markers. Divergence estimates supported a scenario wherein H. anamallensis dispersed across marine barrier to the drifting peninsular Indian plate in the late Cretaceous, whereas Hemidactylus arrived on the peninsular India after the Indian plate collided with the Eurasian plate. Based on these molecular evidence and biogeographical scenario it was proposed that genus Dravidogecko should be resurrected.

The genus Capricornis Ogilby, 1837, is divided into three species and widely distributed in sourthern China, Tibet, Myanmar, IndoChinese peninsula, Malaysia peninsula, Sumatra, Japanese archipelagos and Taiwan. Using complete cytochrome b sequences (1140 bp) analyzes the genetic variation and phylogeny of genus Capricornis from Taiwan, Japan and Mainland China. Constructed by both distance and maximum parsimony methods, the phyloenetic tree distinguish the Capricornis to three clades: Formosan serow, Japanese serow, and Sumatran serow from mainland China. Formosan serow is more familiar with Sumatran serow than Japanese serow. Local populations of Formosan serow of Taiwan island and Japanese serow of the Japanese archipelagos are already differentiated. Serow and goral are apparently distinguishable. The results of Principal Component Analysis and Discriminant Analysis show that serows from Taiwan, Japan and mainland China and goral are apparently distinguishable at morphological characters. The variation of morphological analysis may be a good tool to identify serow and goral. From the paleogeology and fossil records of serow of Quaternary, we could infer that ancestors of serow from southwestern mountain of mainland China migrated to Taiwan island and Japanese archipelagos through the land bridge of east Asian islands to mainland China in the early Pleistocene caused by the glaciation of Quaternary, then separated from mainland of east Asia and speciation of serow occured in Taiwan island and Japanese archipelagos after the end of the glaciation of Quaternary.