>Magister Scientiae - MSc / The collection of biological information has a long history, motivated by a variety of reasons and in more recent years is largely being driven for research and academic purposes. As a result biological information is often linked to a specific species or ecosystem management and is discipline specific, not relating to general management actions at a specific conservation site. The biological data that exists is often not consolidated in a central place to allow for effective management of conservation sites. Different databases and formats are often used to cover biological, infrastructural, heritage and management information. Biological information has traditionally not influenced real-time site-specific conservation management, with long term data sets being used to draw conclusions before they can influence management actions. In order to overcome this problem of scattered and unfocused data a biodiversity database related to specific site management was developed. This study focuses on the development of this database and its links to the management of spatially defined sites. Included in the solution of scattered data are the applications of information management tools which interpret data and convert it into management actions, both in terms of long term trends and immediate real- time management actions as the information is received and processed. Information systems are always difficult to describe in words as much of the layout and information is visual and hence difficult to convey I just the text of this document. A breakdown of the resultant information system is outlined in detail in the conclusion section. During the development of a Biodiversity Database it was found that management tools had to be developed to integrated data with management. Furthermore it was found that human error was a significant factor in poor data quality; as a result an observer training programme was developed.

One goal central to ecology is to understand how species interactions and biophysical processes interact over vastly different scales to govern past, current, and future patterns of diversity. Today, this goal is particularly critical given the degree to which rapid environmental change is affecting species distributions and community composition. Natural environmental gradients provide excellent opportunities to uncover possible mechanistic links between species distributions and environmental conditions links that are invaluable for understanding how species may respond to environmental change. This dissertation builds on recent approaches that combine information on species' functional traits and evolutionary histories to refine our view of how contemporary and historical processes jointly govern the distribution of biodiversity. In the context of tropical tree communities of Puerto Rico, the following four chapters evaluate hypotheses about the distribution of different dimensions of diversity (i.e., species, functional, and phylogenetic) across regional abiotic gradients. In chapter 1, I develop an island-wide molecular phylogeny for the native and naturalized trees of Puerto Rico, and show preliminary evidence that dry forests comprise an evolutionarily clustered subset of the total island tree flora. In chapter 2, I examine functional and phylogenetic diversity across spatial resource gradients, and use these patterns to infer variation in community assembly processes along a gradient of water availability. In chapter 3, I use temporal shifts of functional and phylogenetic diversity during secondary succession to infer the shifts in the processes underlying successional change in wet forests of Puerto Rico. Finally, in chapter 4, I evaluate the linkages between species functional traits and their geographic distributions, and test the hypothesis that community-weighted mean trait values reflect the `optimal' strategy for a given set of abiotic conditions. A theme common to all chapters is the idea that functional and phylogenetic dimensions of diversity can shed light on the processes underlying patterns of diversity better than more traditional metrics of species diversity. I provide recommendations for future research directions at the end of each chapter and in the final conclusions.

Much of modern population genetics revolves around neutral genetic differences among individuals, populations, and species. In this dissertation, I study how sex-specific life history traits affects neutral diversity levels within populations (polymorphism) and between species (divergence) on autosomes and sex chromosomes. In chapter 1, I consider the effects of sex specific life histories, and particularly generation times, on substitution rates along the great ape phylogeny. Using a model that approximates features of the mutational process in most mammals, and fitting the model on data from pedigree-studies in humans, I predict the effects of life history traits on specific great ape lineages. As I show, my model can account for a number of seemingly disparate observations: notably, the puzzlingly low X-to-autosome ratios of substitution rates in humans and chimpanzees and differences in rates of autosomal substitutions among great ape lineages. The model further suggests how to translate pedigree-based estimates of human mutation rates into split times among extant apes, given sex-specific life histories. In so doing, it largely bridges the gap reported traditional fossil-based estimates of mutation rates, and recent pedigree-based estimates. In chapter 2, I consider the effects of sex- and age- dependent mortalities, fecundities, reproductive variances and mutation rates on polymorphism levels in humans. Using a coalescence framework, I provide closed formulas for the expected polymorphism rate, accounting for life history effects. These formulas generalize and simplify previous models. Applying the model to humans, my results suggest that the effects of life history – and of sex differences in generation times in particular – attenuate how changes in historical population sizes affect X to autosome polymorphism ratios. Applying these results to observations across human populations, I find that life history effects and demographic histories can largely explain the reduction in X to autosome polymorphism ratios outside Africa. More generally, my work elucidates the major role of sex-specific life history traits – and male and female generation times in particular – in shaping patterns of neutral genetic diversity within and between species.

The spotted turtle (<i>Clemmys guttata</i>) and Blanding’s turtle (<i>Emydoidea blandingii</i>) are two state-endangered species in Indiana whose populations are in decline. Historically, both species were found across the northern portion of Indiana in various wetland habitats. There are multiple causes of population decline for both species, including habitat fragmentation, habitat loss and degradation, urban development and encroachment, poaching, and road mortality. Despite efforts to record these species across the state, there has been no intensive population assessments. Based on this need, I conducted both visual encounter surveys across the state and used Maximum Entropy (MaxEnt) modeling to facilitate understanding the current distribution of both species in Indiana. Twenty-three locations were visited and surveyed in Indiana, with trapping being conducted at an additional four locations where populations were known to be larger. Surveys aided in delineation of six populations of Blanding’s turtles and five populations of spotted turtles. A total of 69 Blanding’s turtles and 70 spotted turtles were observed between surveying and trapping. Delineated populations were mainly found in the northern third of Indiana. This data and other occurrences were used to predict suitable habitat across Indiana. The Blanding’s turtle models were sufficiently resolved to predict potential localities or potential sites for focused management or repatriation. Spotted turtle model performance reflected the need for more samples, but also the likelihood of fewer numbers due to declining habitat availability. Both Blanding’s turtle and spotted turtle models argue for the need of more intense survey efforts based on historical occurrences, as well as restoration efforts across the state. Most models for both species were observed to have a trend towards suitable habitat in the northern third of the state, correlating with the results of the survey efforts. The results of this project indicate that Blanding’s turtle and spotted turtle populations are still in decline likely due to limited habitat availability.

Récemment, Agaricus subrufescens est devenu un champignon d’intérêt de par ses propriétés médicinales. Sa production commerciale s’est développée dans des pays tropicaux à partir de matériaux locaux. Cependant, les données disponibles dans la littérature ne concernent que des cultivars qui sont génétiquement similaires. Notre étude sur un ensemble de cultivars et de souches sauvages a conduit à une meilleure connaissance de la biologie de l’espèce. Contrairement aux cultivars, les souches sauvages présentent un haut niveau de polymorphisme génétique. Une variabilité phénotypique élevée a été mise en évidence pour l’accroissement mycélien, la productivité et la morphologie. Des analyses chimiques par RMN du solide et l’estimation des activités anti-oxydantes ont montré que les souches sauvages comme les cultivars sont une source à exploiter comme aliment fonctionnel pour prévenir les maladies cardio-vasculaire, les cancers et le diabète. L’adaptation des conditions culturales à partir du substrat utilisé pour la culture d’A. bisporus a permis d’obtenir des fructifications d’A. subrufescens, puis d’augmenter le rendement et d’optimiser des caractères agronomiques d’intérêt. Du matériel sauvage avec une activité antioxydante et un rendement élevés a été identifié. L’évaluation d’hybrides intercontinentaux a montré la possibilité de transférer des caractères d’intérêt à une descendance. Agaricus subrufescens pourrait être proposé aux champignonnistes français comme alternative à Agaricus bisporus pendant la saison estivale. / Agaricus subrufescens is becoming a mushroom of interest because of its medicinal properties. Commercial production had developed in tropical countries using local materials. However, data available in the literature referred to cultivars that are genetically similar. Our study of a set of cultivars and wild strains led to a better understanding of the biology of the species. Contrary to cultivars, wild strains exhibited a high level of genetic polymorphism. High phenotypic variability was identified in mycelial growth, productivity and morphology. Chemical analyses by solid-state 13C NMR and antioxidant activities showed that the wild strains as well as the cultivars proved a valuable source of functional food to prevent cardiovascular diseases, cancers and diabetes. Using cultivation substrate produced for A. bisporus and modifying cultivation conditions allowed fruiting of A. subrufescens, then increase in strain yield and optimization of agronomic traits of interest. Wild material with good antioxidant activity and high productivity was identified. The evaluation of intercontinental hybrids showed the possibility to transfer traits of interest to offspring. A. subrufescens could be proposed to French mushroom growers as an alternative to Agaricus bisporus during the summer season.

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Carbon forestry projects have proliferated over last few years on the premise of cost efficient climate mitigation along with co-benefits of biodiversity conservation and livelihood improvement. Multilateral, bilateral, public and private sources have invested billions of dollars in the carbon forestry projects based on these claims. However, there is little empirical evidence to support the enthusiasm. This gap is further accentuated by the insufficient understanding of the governance challenges of these projects. These issues are social, political and ecological in nature and hence require a multidisciplinary political ecology framework for a comprehensive analysis. This thesis explores the multiple benefit claims and governance issues by analysing two forestry-based Clean Development Mechanism projects from India. One, in Haryana state focuses on private lands, the other in Himachal involves three different types of lands viz. community, public and private for plantation activities. This thesis examines the carbon, biodiversity and livelihood benefits of each project, and the governance challenges associated with them. I show that both projects have sequestered substantially less carbon than was originally predicted, which has serious implications for carbon revenues and hence economic viability of these projects. In the case of biodiversity, the results are mixed. In Haryana, the tree and herb biodiversity has improved in the project plots as compared to control plots, whereas shrub biodiversity has marginally declined. In case of Himachal project, biodiversity has declined at tree, shrub and herb levels. I have analysed livelihood impacts in terms of foregone crop, fodder and fuel wood benefits across small, medium and large category of farmers. Both the projects have adverse livelihood impacts on the participants, more so in Haryana because of the plantations on private lands. Although the project has adversely affected the livelihoods of all three categories of farmers, however it has affected small farmers the most due to their low incomes and risk-bearing capacities. Hence, these projects have serious equity implications. This thesis also explores the governance challenges of carbon forestry in terms of their interaction with existing policy mechanisms, especially the Forest Rights Act of 2006, which recognises the ownership and use rights of forest dependent communities comprehensively first time in independent India. The analysis suggests that there are various issues that carbon forestry projects pose for the implementation of the Act due to which civil society groups are opposing these projects. This thesis contributes to our understanding of the multiple benefit claims of carbon forestry projects with empirical evidence and a political ecological analysis. It shows that there is possibility of tradeoffs and many other scenarios in carbon forestry projects rather than just the projected 'win-win-win' outcomes. It contributes to the political economy literature by establishing that changes in global commodity markets can influence land use choices at local level, affecting the sustainability of such efforts. This thesis also advances the literature on governance of carbon forestry projects by reflecting on various policy and implementation level issues related to property rights, community institutions, transparency and accountability.

Les méthodes actuelles utilisées pour définir les enjeux de biodiversité peinent à prendre en compte : les espaces agricoles et les pratiques, à la fois réservoir et pression pour la biodiversité et les dynamiques spatiales et temporelles, modifiant l’occupation du sol et la présence, la qualité et la connectivité des habitats. Ce travail a pour objectif de proposer des solutions pour ces 2 aspects.Nous avons identifié des pratiques agricoles favorables à la biodiversité. Pour comprendre les enjeux liés au développement de ces pratiques, nous avons étudié des leviers pour leur mise en place. Nous avons confirmé la difficulté à mesurer un effet général de certaines pratiques sur la biodiversité. Néanmoins, l’hétérogénéité, dans les pratiques, les types de culture et les éléments semi-naturels environnants est un aspect favorisant la biodiversité. Inciter leur développement nécessite de s’appuyer sur les avantages pour les agriculteurs, au travers des services écosystémiques et d'une multitude de supports de diffusion. Nous avons aussi montré l’importance d'intégrer l’agriculture dans l’identification d’enjeux de conservation.Nous avons présenté les limites des scénarios existants pour l’échelle régionale. Nous proposons une méthode alliant ces deux types de scénarios pour explorer l’impact des changements sur les continuités écologiques. Cette utilisation revêt un intérêt particulier pour les questions d’aménagement, par ex. pour mesurer l’effet, cumulé ou non, de certains projets. Avant le transfert vers des projets appliqués, il convient néanmoins de poursuivre la recherche sur cette méthode, notamment en la complétant avec d’autres mesures de continuités écologiques. / Actual ways to define priorities for biodiversity conservation experience difficulties to take into account: agricultural areas and practices, both reservoir and source of pressure for biodiversity and spatial and temporal dynamics modifying land-cover and land-use and the presence, the quality and the connectivity of habitats. This research work have for objective to propose solutions for these two aspects.We wanted to identify biodiversity-friendly agricultural practices. To understand the issues related to the development of these practices, we also studied the levers to their application. We confirm the difficulty to measure a general effect of some practices on biodiversity. Nevertheless, the heterogeneity, in practices, crops types and semi-natural elements, favor the biodiversity. Encourage their development need to rely on benefits for farmers, through ecosystem services and various substrate for information spread. We show the importance to taking into account agriculture in the identification of conservation priorities.We introduced the limits from existing scenarios to explore changes at regional scale. We proposed a method coupling these two types of scenarios to measure the impact of changes on ecological networks, with an indicator of connectedness, for three species. The application of scenarios to ecological networks’ analyses have a particular interest for land planning questions, for example to measure the, cumulative or not, effect of some projects. Before transfer to applied projects, research on this method have to be continued, in particular completing it with others measures of ecological networks.

O objetivo deste estudo foi coletar e reunir informações sobre a diversidade de anfíbios e répteis nas bacias hidrográficas do Alto e Médio Paranapanema, estado de São Paulo e avaliar os impactos que o pastoreio de gado pode provocar na riqueza e abundância de anuros e lagartos de formações abertas de Cerrado. A riqueza de anuros registrada no Alto Paranapanema é muito superior a encontrada no Médio Paranapanema, existindo um gradiente decrescente na riqueza de espécies partindo da porção sul e sudeste do Alto Paranapanema, onde predominam a floresta ombrófila, em direção ao Médio Paranapanema que apresenta formações de Cerrado e floresta estacional. O pastoreio de gado não causou efeitos negativos na riqueza e abundância total dos anuros e lagartos amostrados. É possível que a intensidade de pastoreio ocorrida nestas formações não foi suficiente para promover modificações consideráveis na estrutura das fitofisionomias, o que pode ter minimizado alterações nos nichos ecológicos das espécies. / The aim of this study is to collect information on the diversity of amphibians and reptiles in the hydrographic basins of the Upper and Middle Paranapanema, São Paulo state and assess the impact that cattle grazing can provoke on the species richness and abundance of anurans and lizards of open Cerrado formations. The species richness of anurans reported in the Upper Paranapanema is far greater to that found in the Middle Paranapanema, with a decreasing gradient in the richness from the southern and southeastern portion of Upper Paranapanema, where the ombrophilous forest predominates, towards the Middle Paranapanema in which Cerrado formations and seasonal forests are dominant. Cattle grazing did not cause negative effects on the species richness and total abundance of the anurans and lizards sampled. It is possible that the intensity of grazing was insufficient to cause significant changes in the structure of the phytophysiognomies, which could have minimized alterations in the ecological niches of the species.