A dissertation submitted for the degree of Masters of Science, School of Computational and Applied Mathematics, University of Witwatersrand, Johannesburg, 2014. / The magma equation which models the migration of melt upwards through the Earth’s mantle is considered. The magma equation depends on the permeability and viscosity of the solid mantle which are assumed to be a function of the voidage . It is shown using Lie group analysis that the magma equation admits Lie point symmetries provided the permeability and viscosity satisfy either a power law, or an exponential law for the voidage or are constant. The conservation laws for the magma equation for both power law and exponential law permeability and viscosity are derived using the multiplier method. The conserved vectors are then associated with Lie point symmetries of the magma equation. A rarefactive solitary wave solution for the magma equation is derived in the form of a quadrature for exponential law permeability and viscosity. Finally small amplitude and large amplitude approximate solutions are derived for the magma equation when the permeability and viscosity satisfy exponential laws.

This dissertation presents the suspicions and tensions encountered during ethnographic fieldwork with (what I call) the Predator Project Zambezi (PPZ), a WWF-funded research and conservation organization based in Zambia. It extrapolates the broader contexts of this uneasiness and situates it within global conservation discourses. The distrust that manifests between the wildlife authorities in Zambia, the residents of rural areas, and PPZ epitomizes postcolonial contentions over state sovereignty and the continued hegemony of Euro-American environmental ideologies. Moreover, the objective perspective that is claimed by PPZ as a scientific organization is challenged through analysis of its daily epistemic contradictions. In this ethnography, I show how the priorities of conservation institutions as communicated through PPZ ultimately work to arrest the post-colonies in a continuous state of catching up to the eco-modern condition that is ascribed to the global North.

<p> This project aims to develop a panel of sequence capture baits to use for SNP genotyping for pedigree analysis in Wood Ducks (<i>Aix sponsa </i>) as well as for general population genetic analysis within species in the family Anatidae. SbfI RAD libraries were prepared with samples comprising five duck species (N = 96). Sequenced libraries were aligned to the Mallard (<i>Anas platyrhynchos</i>) reference genome and screened for 120bp regions proximal to the SbfI cutsite that contained SNPs conserved collectively in each species. A series of screenings identified regions which were used to produce 2,508 custom sequence capture baits. These baits were tested in novel individuals from the same species used to design the baits as well as novel species representing different taxonomic ingroup and outgroup levels within Aves. These baits delineate species at various taxonomic scales, even above the taxonomic level that was originally targeted and will prove useful for analyses of population and comparative genetics for species of Anatidae and perhaps more broadly.</p><p>

Typescript. / Digitized by Kansas Correctional Industries

Typescript (photocopy). / Digitized by Kansas Correctional Industries

Habitat modification, when it results in population fragmentation, often results in the loss of genetic diversity due to reduced gene flow, inbreeding, and genetic drift. However, the severity of these effects depends on how diminished dispersal and gene flow become between patches of suitable habitat. An empirical understanding of how habitat change affects dispersal and gene flow within and among patches is essential to predict the effects of increased habitat modification and landscape change on population persistence and processes of divergence. Recent studies in landscape ecology suggest that our understanding of dispersal in a heterogeneous landscape will improve by explicitly considering the heterogeneity of matrix habitats, or unsuitable habitats between patches of suitable habitat. In this dissertation, I describe population genetic structure and dispersal patterns in the Central American Squirrel Monkey (Saimiri oerstedii, Primates: Cebidae), a New World primate threatened with extinction and living in a heterogeneous, human-modified landscape, using analyses that explicitly consider matrix heterogeneity. I focus on the more endangered S. o. citrinellus, whose already restricted distribution in the Central Pacific region of Costa Rica has undergone considerable anthropogenic modification since the early 1900s. I collected non-invasive fecal samples from S. o. citrinellus across the Central Pacific region, obtaining full genotypes from 233 individuals. I also obtained 11 samples from S. o. oerstedii in the Southern Pacific region of Costa Rica from a collaborator, as well as fine-scale landscape data for the Central Pacific. I analyzed the data using molecular systematics, population genetics, and landscape genetic techniques. In this dissertation, first I explore whether molecular genetic support exists for the subspecies distinction between S. o. citrinellus and S. o. oerstedii. Second, I describe population genetic structure and recent migration patterns within S. o. citrinellus using traditional population genetic methods and Bayesian models. I also compare population genetic structure among males versus females to test for sex-biased dispersal patterns in S. o. citrinellus. Then, using landscape genetic approaches, I describe the relationship between landscape heterogeneity and genetic structure in S. o. citrinellus, and inferred which matrix habitats are costly to dispersal. Finally, I offer explicit recommendations for the conservation management of S. oerstedii. My results provide genetic support for S. o. citrinellus and S. o. oerstedii as separate taxa referred to as subspecies. Also, I found evidence of population genetic structure in S. o. citrinellus, with two genetically distinct populations and lower genetic diversity in the western population. I did not find genetic evidence for female-biased dispersal in S. o. citrinellus as expected. Instead, my results suggest that both sexes disperse, with males dispersing over longer distances. The landscape genetic analysis suggests that landscape heterogeneity is important in determining local population genetic structure in S. o. citrinellus in the Central Pacific region of Costa Rica. Specifically, oil palm plantations are moderate barriers to gene flow between populations, but not other matrix habitats. However, these inferences are specific to the composition and configuration of the Central Pacific landscape, and should not be generalized to all S. oerstedii populations. This study generated important information for conservation management. Based on my results, I recommend that conservation managers house the two S. oerstedii subspecies separately in captive facilities, and only transfer, reintroduce, or translocate among groups of the same subspecies. However, transfers, reintroductions, or translocations of either males or females are both likely to be successful for S. o. citrinellus in the Central Pacific region, pending further behavioral study. I also recommend that, in order to augment dispersal to the isolated western population of S. o. citrinellus, conservation efforts should focus on building biological corridors through or around adjacent oil palm plantations. Also, managers should prioritize the maintenance of existing forest connectivity in the Central Pacific region. The results also have important implications for future studies of evolutionary and ecological processes in heterogeneous landscapes. This study contributes to a growing body of research that finds differences in dispersal patterns among local primate populations of the same taxon. My results suggest that predictive models for variation in dispersal patterns should consider both variation among the environments of local populations within a species and temporal variation in local environments (e.g. recent habitat disturbance). Finally, this dissertation also supports the idea that matrix heterogeneity should be considered explicitly in studies of dispersal and gene flow, as opposed to assuming that all non-suitable habitats have a uniform effect on these processes. In the future, agent-based simulation approaches combined with ecological niche models and data on adaptive genetic diversity could expand upon this work to inform predictive models for population divergence and speciation under different climate and landscape change scenarios.

Recent research into the ecological origins and social implications of ecosystem services, the benefits ecosystems provide to society, is predicated on the downward trends observed for many services. Current work increasingly emphasizes how interactions among ecosystem services (synergies and trade-offs) affect the delivery of multiple services, from soil fertility at field scales to watershed-scale hydrological function, to global climate regulation. Meanwhile, research on the relationship between biodiversity and ecosystem functioning has identified substantive linkages between the biodiversity of ecosystems and the services they provide, provoking interest in aligning biodiversity conservation with the sustained delivery of ecosystem services. To better understand the delivery of multiple ecosystem services relevant to smallholder farmer livelihoods in the tropics, the production of wood and livestock forage and the structure and fertility of soils were examined in grazed and improved fallows in western Kenya. The objectives were to investigate fine-scale interactions among ecosystem services, and the potential of fallow plant diversity to enhance levels of multiple services simultaneously, i.e., ecosystem service multi-functionality. To examine influences of fallow vegetation and management on soil structure and fertility, the biomass and functional traits (green tissue N, lignins, polyphenols, lignins+polyphenols) of fallow plants and the condition of soils were quantified. Positive associations of tissue content of lignins+polyphenols with soil organic carbon (SOC) and steady infiltration rates indicated a role of recalcitrant carbon compounds in slowing SOC turnover and supporting soil structural development, while grazed fallows had lower infiltration than improved fallows, likely a result of livestock trampling and soil compaction. To investigate whether woody overstory plants and fallow management generate interactions between the production of wood and livestock forage, the relationships of overstory biomass, overstory diversity as a proxy for niche complementarity, grazing intensity, and soil conditions with the biomass and quality (crude protein:lignin) of forage species were studied. Overstory competition in densely planted improved fallows resulted in an apparent trade-off with forage biomass, however in grazed fallows overstory and forage biomass were positively associated, likely due to negative effects of grazing on both; in addition, reduced forage quality and biomass of quality forage species were attributable to selective grazing. Finally, to assess whether plant diversity enhances joint levels of multiple ecosystem services, two indices of ecosystem multi-functionality were designed for four ecosystem functions: wood biomass, forage biomass, soil base cations, and infiltration. Evidence for positive effects of diversity on multi-functionality was clearer in grazed fallows, while in improved fallows environmental favorability appeared more influential. The difference in the diversity-multi-functionality relationship among fallow types appeared related to contrasting management, disturbance, species composition, and the productivity of vegetation and soils. The results suggest that plant diversity and site productivity can enhance multiple ecosystem services in smallholder fallows, yet diversity effects may vary with management, species composition, and site conditions.

A central aim of conservation science is improving our understanding how different human activities influence the persistence of native biota and associated ecological and evolutionary processes. Meeting this applied biodiversity research challenge requires that we understand (i) patterns in biological responses to anthropogenic environmental change, (ii) what biological mechanisms influence that response, (iii) how the loss of biological diversity will impact important ecological processes, and (iv) how this information can be translated into effective and practical information useful for decision makers. Increasingly, this final translational step is met through the use of ecological indicator assemblages - suites of species whose presence and abundance in a given area provide a useful gauge for measuring and interpreting changing environmental conditions. This thesis aims to improve our understanding of the patterns, causes and consequences of community disassembly for tropical forest insect species. To do this, I have combined systematic literature reviews and empirical approaches to understand how two widespread anthropogenic drivers of environmental change in tropical forest (i.e. land-use change and degradation) influence the community disassembly of Scarabaeine dung beetles in tropical forest, at a variety of spatial scales. I outline the potential for tropical forest defaunation to negatively impact dung beetle communities, summarize the contributions of dung beetles to a range of key ecological processes, provide empirical data demonstrating how dung beetles can serve as a model system to understand terrestrial trophic cascades, discuss the ability of species traits to explain population trends in observed dung beetle community disassembly, and conclude by demonstrating how these various lines of evidence linking dung beetle species with environmental condition strengthen their potential utility as ecological indicator taxa in applied conservation science.

Understanding how plants are spatially and genetically distributed in the environment can be a challenging task given the difficulty to characterize ecological processes, such as gene flow, and to disentangle the relative importance of multiple factors underlying the generation of distinct patterns. In this dissertation, I study different populations of the understory plant Heliconia acuminata L.C. Richard (Heliconiaceae) distributed across 1-ha fragments and continuous forest sites in the Biological Dynamics of Forest Fragments Project (BDFFP), an experimentally fragmented landscape in central Amazonia. I characterize a set of ten microsatellite markers developed for Heliconia acuminata to first evaluate gene flow, which is one of the main processes influencing genetic structure and spatial patterns of plants, and second to assess the potential influence of endogenous (e.g., seed dispersal) and environmental factors on spatial patterns of plants and genetic relatedness distribution. I combine genetic and ecological data in a novel and comprehensive Bayesian model to estimate parentage to more fully characterize the contribution of pollen and seed dispersal to H. acuminata gene flow. I then compare metrics of gene flow between fragments and continuous forest, while taking in consideration the variation in abundance of reproductive plants in each population. I tested the conservation genetics prediction that gene flow is interrupted in fragmented landscapes. Contrary to this hypothesis, I found that that both fragmentation and low population densities were associated with greater immigration rates and longer pollination and seed dispersal distances. My results are one example of how fragmentation does not limit gene dispersal. I suggest that conservation genetics predictions are reformulated by taking in consideration the variation in the behavior of pollinators and seed dispersers across heterogeneous landscapes in response to habitat configuration and to the spatial and temporal availability of food resources. To investigate the influence of endogenous factors (plant - plant interactions) and environmental covariates (light, slope and soil characteristics) on spatial patterns of seedlings and adults, I use a new statistical methodology to model marked point patterns. Using this flexible approach, I also evaluate whether local spatial genetic structure is associated to spatial distribution of plants. The results show that H. acuminata seed dispersal is contagious, but not distance - restricted or genetically structured (presence of highly related plants). The absence of an association between spatial pattern and local genetic structure for adults also suggest the absence of genetic structuring in seedlings over time. Light and zinc availability are positively associated with spatial patterns of seedlings and adults, which may indicate carryover effects of seedlings on recruits over time. Carbon is negatively associated with adults, which may be evidence of competition with large dominant trees. I finally propose a new mechanistic framework to the studies of frugivore - mediated seed dispersal. I conduct a qualitative analysis of existent studies explicitly linking frugivores, fruiting plants and seed shadows and propose a frugivore - centered, process-based view of seed dispersal that integrates animal movement and seed dispersal ecology across multiple spatio - temporal scales. This critical analysis provides the empirical foundation over which we can build a more comprehensive, multi-scaled, research approach to the study of seed dispersal, process which is known to play a crucial role in the dynamics and evolution of plant populations.

Advances in technology and molecular methodologies now provide an unprecedented view into the complex realm of natural populations by elucidating the degree and distribution of genetic variation, historical and contemporary processes driving differentiation, and individual behavior patterns. These critical biological parameters create a framework to enhance wildlife management initiatives, as illustrated here through the implementation of a model approach for the systematic genetic assessment of a group of scarlet macaws Ara macao under threat in La Selva Maya, a tri-national system of protected areas in Mexico, Guatemala, and Belize. A total of 2172 base pairs across four mitochondrial data partitions were employed to test the current hypothesis of subspecific diversification. Phylogenetic reconstruction uncovered two phylogeographic units exhibiting distinct and complex evolutionary histories, emphasizing the importance of Central American populations to intraspecific diversity. Focusing on A. m. cyanoptera, mitochondrial control region sequences of 850 base pairs were examined within a hierarchical context to investigate patterns of genetic substructure at varying spatial scales and extent of molecular variation, including potential temporal shifts in response to anthropogenic pressures. Population-level statistical tests detected evidence of recently restricted gene flow among nest sites in La Selva Maya, a stark contrast to the historical state of panmixia across the region; although overall levels of genetic variation remain high, a decrease in diversity was noted among modern samples originating in the Chiquibul Forest Reserve, Belize. Multilocus genotypes based on eight microsatellite markers were combined with haplotypic data to evaluate whether focal nest sites in the Maya Biosphere Reserve, Guatemala represent distinct genetic clusters. Results from population genetic analyses argue against the presence of site fidelity at fine geographic scales. Examination of pairwise relative relatedness indices supports the observation of genetic connectivity across local breeding areas, while also revealing important insights into recent demographic trends, movement patterns, and breeding behaviors. In summary, this work demonstrates the continuity of biological and ecological influences across individual, local, regional, and continental scales, thus creating an empirical framework to refine population management goals and prioritize mitigation strategies in order to maximize conservation outcomes and foster long-term survival of wild scarlet macaws in La Selva Maya.