Yes / Traditional public health methods for detecting infectious disease transmission, such as contact tracing and molecular epidemiology, are time-consuming and costly. Information and communication technologies, such as global positioning systems, smartphones, and mobile phones, offer opportunities for novel approaches to identifying transmission hotspots. However, mapping the movements of potentially infected persons comes with ethical challenges. During an interdisciplinary meeting of researchers, ethicists, data security specialists, information and communication technology experts, epidemiologists, microbiologists, and others, we arrived at suggestions to mitigate the ethical concerns of movement mapping. These suggestions include a template Data Protection Impact Assessment that follows European Union General Data Protection Regulations. / European Research Council Proof of Concept “Enhanced Place Finding” (grant no. 727695).

Mantle plumes are anomalously hot, narrow upwellings of mantle material that originate at the core-mantle boundary. As plumes rise they may form volumetrically large "heads" (~1000 km in diameter) with narrower (~100 km) "tails." Plume head melting is thought to form Large Igneous Provinces (LIPs), vast outpourings of basaltic lava (~106 km3), while plume tail melting forms linear chains of ocean island basalts (OIBs) similar the Emperor-Hawaii Seamount chain. Mantle plume derived melts indicate that these structures sample deep Earth geochemical and lithological heterogeneities. Studying plume-derived lavas can clarify important planetary-scale questions relating to the accretion of the Earth, primordial geochemical reservoirs, the fate of subducted materials, planetary differentiation, and convective mixing. / Ph. D. / Mantle plumes are hot, narrow upwellings of plastically flowing mantle material. These structures are thought to originate at the core-mantle boundary. Because mantle plumes originate in the deep interior of the planet, they are though to sample both primitive materials that are remnants of Earth’s formation as well as recycled crustal materials that have been subducted from the surface into the deep interior of the planet. When mantle plumes near the surface of the planet they begin to partially melt during a process known as adiabatic decompression melting. When these melts cool, they crystallize to form basalts. These rocks and their associated minerals can be studied to determine lava temperatures and pressures of formation. The geologic record suggests that relatively recently mantle plumes cool and eventually become magmatically inactive. In this project, we used the Galapagos plume as a case study to investigate why it has systematically cooled over the last 90 Ma. The Galapagos mantle plume is possibly the oldest active plume and records a 90 Ma volcanic evolution. We studied Galapagos-related lavas and olivine crystals across the entire 90 Ma evolution of the plume to better understand the life-death cycle of mantle plumes. Our data suggest that the plume may be cooling due to an increase in the amount of recycled oceanic crust. Alternatively, a recycled oceanic crust component could have always been present in the source of the plume, though was diluted during high degrees of partial melting when it was hottest at 90 Ma.

Syfte – Startpunkten för den här studien var att identifiera effektiva och ineffektiva delar av en kodbas som kan leda till förbättringar av koden. Detta utfördes på förfrågan av ett företag. För att stödja begärandet utnyttjades en bok av författaren Adam Tornhill. Han diskuterar flera metoder (också kallade analysmetoder) som används för att lokalisera och analysera platser i kod där effektivitet och ineffektivitet föreligger. De använder alla diverse variabler för det här syftet. En webbapplikation utvecklades för att upptäcka den här varianten av kod med hjälp av dessa variabler. Det spekulerades att det kan saknas samband mellan variablerna som kan upptäckas. Detta skulle ge mer insikt i hur verksam och overksam kod kan urskiljas och evalueras, utöver den insikt Adam Tornhills metoder understöder. Det vetenskapliga syftet och bidraget var därför att särskilja potentiella korrelationer mellan analysmetoderna. En frågeställning härleddes från detta syfte: ● Finns det korrelation hos variabler bland befintliga analysmetoder och i sådant fall, vilka är det? Metod – För att svara på frågeställningen var en noggrannare granskning av variablerna nödvändig för att utvärdera vilka som hade potentiella relationer. Efter det hämtades kvantitativa data av de valda variablerna från 7 open source projekter. Data erhölls från git commit historik från 2 år tillbaka. Informationen presenteras i form av grafer som examinerades för mönster och kontext bland de analysmetoder som var i fokus. Statistiska formler (som Pearsons korrelationskoefficient) utnyttjades i syfte att beräkna exakt korrelation för variablerna. Signifikansnivå sattes på 0,001 och ett p-värde kalkylerades. För de projekt med p-värde mindre än signifikansnivå beräknades även ett median och medelvärde med  deras olika korrelationskoefficienten. Resultat – I slutet påträffades två stycken variabler som undersöktes genom grafer för samband. Utredningen visade ett tydligt mönster som indikerar att när fler personer arbetar på en fil kommer också antalet logiska kopplingar att öka för korresponderande fil. För de olika korrelationsvärden visade det sig att 6 av de 7 projekten hade ett p-värde mindre än den satta signifikansnivån 0,001 som innebär att 6 koefficienter är mycket statistiskt signifikanta. Det var bara för 5 av de 6 projekten med godkänd signifikans som positiv korrelation uppmättes. Medelvärdet för de 6 projekten med p-värde mindre än signifikansnivån var 0.41 och medianvärdet 0.63 vilket indikerar en positiv korrelation mellan antal författare och logiska kopplingar Implikationer – I projekt där många personer jobbar på en fil borde försiktighetsåtgärder erfordras med avseende till logiska kopplingar. Vissa förhindrande medel kanske kan etableras för att vägleda andra att minska, eller i alla fall inte onödigt ackumulera, logiska kopplingar när åtskilliga personer inträder på en fil. Begränsningar – Bara två analysmetoder och deras två variabler undersöktes för korrelation och det kan finnas fler variabler som kan ha korrelation. De 7 projekten som det utvanns data från var alla från open source och därför kanske inte resultatet stämmer för closed source projekt. / Purpose – The starting point of this study was to locate efficient and inefficient code in a codebase to improve upon it, as a request from a company. To help with their request a book was used by author Adam Tornhill who has made several methods (also called analysis methods) for this purpose. They all use different variables that locate problems in the code. A web application was developed to use these variables. It was speculated that relationships between the variables may be missing which could improve the analysis methods and in turn uncover efficient and inefficient code better. The main scientific purpose and contribution was therefore to discover associations between the specific variables presented by Adam Tornhill. A question derived from this purpose:   ● Are there correlations with variables among existing analysis methods and in that case, what are they? Method – To answer the question posed, a closer look on the variables was needed to see which ones had a potential connection. After that empirical data of the chosen variables was gathered in the form of quantitative data from 7 open source projects from two years back. This was done by fetching commits from git, called commit history, and presenting the data in a suitable way in form of graphs. In the end the graphs were reviewed to detect possible patterns and then statistical formulas (Pearson's correlation coefficient) were used to calculate the exact correlation between the variables. A significance level was set at 0,001 and then p-value calculated. Median and mean value of the correlation coefficients of projects with p-value less than the significance level were also calculated. Findings – Two variables were inspected in the end, number of authors and number of logical couplings for the same file, and were made into a new analysis method with a graph. Through the graph analysis the methods seem to vary together. The graph shows a clear pattern that as more people work a module the more logical couplings will increase. For 6 out of 7 of the projects analyzed, the p-value was less than the significance level set from the beginning, meaning 6 coefficients were highly statistically significant. It was only for five out of these 6 that a positive coefficient was calculated. For the 6 projects with p-value less than significance the mean correlation coefficient was 0.41 and median 0.63, which both indicate a positive correlation between number of authors and number of logical couplings. Implications – Projects that have several people working on a module should watch out for logical couplings on that same module. Perhaps preventative measures can be made to ensure that people watch out for these logical couplings as more people start working on a module. Limitations – Only two analysis methods and their variables were inspected for further determination of a correlation, and there could be more correlations that are missing. Furthermore, the 7 projects that were used as data were open source and therefore the result from this study may not be the same as for closed source projects.

Les patterns de biodiversité et les mécanismes qui les maintiennent ont toujours intéressé les biologistes et ont été abordés en considérant des facteurs géologiques, évolutifs et écologiques. Les processus écologiques qui déterminent la co-occurrence des espèces diffèrent en fonction de l'environnement physique de l'écosystème. De nombreuses théories ont proposé des relations entre les tendances observées dans la diversité des espèces et les caractéristiques physiques de l’environnement à grande échelle. Dans les milieux terrestres et aquatiques, l’impact de la température sur la distribution de la biodiversité compte parmi les facteurs les plus influentes et étudiés. Toutefois, de nombreux taxa marins représentent des exceptions à cette influence primaire de la température, alors qu'une fraction dominante des espèces marines est planctonique ou à larves dispersibles. La dispersion par le transport physique a certainement un impact majeur sur les patterns d'abondance des espèces dans l’environnement marin. Certains courants océaniques peuvent en effet contraindre la distribution des stades planctoniques de certaines espèces, même lorsque les paramètres démographiques et physiologiques des espèces sont insensibles aux propriétés de l'eau. Les mécanismes de transport peuvent donc influencer la distribution de la diversité à toutes les échelles, de l’individu aux populations jusqu’aux espèces. Contrairement aux écosystèmes terrestres, les écosystèmes en milieu marin sont sujets à une variabilité dont les échelles spatiales et temporelles sont dictées par les processus du transport physique turbulent. Cet aspect complique l’obtention d’informations synoptiques sur la distribution des espèces marines au niveau global et à haute résolution, alors que cette vision globale est essentielle pour pouvoir comprendre les patterns de biodiversité et les mécanismes impliqués dans leurs variations. En outre, les hotspots de biodiversité sont d’importance primaire pour les efforts de conservation. Les objectifs de cet étude sont les suivants: identifier les hotspots de biodiversité pélagique des producteurs primaires à l'échelle globale et à haute résolution; déterminer les processus physiques de l'océan qui contrôlent la dynamique spatio-temporelle des hotspots, en se focalisant sur les mécanismes de transport, de dispersion, advection et mélange; étudier l'influence de ces mécanismes de structuration de la biodiversité sur les niveaux trophiques supérieurs.Pour obtenir ces résultats, les informations sur les parcelles d’eaux aux caractéristiques biophysiques cohérentes (‘niches fluido-dynamiques’) obtenues par satellite sont utilisées pour identifier les hotspots de biodiversité microbienne comme région de forte variabilité spatiale de ces niches. Ces hotspots et le rôle du transport dans leur structuration sont étudiés par l'analyse des modèles écologiques et biophysiques de circulation globale (Modèle ECCO2-Darwin) et par l’examen de données moléculaires et morphologiques sur la structure de la communauté in-situ collectées par l'expédition Tara Oceans et Atlantic Meridional Transect. Les possibles effets ‘bottom-up’ de la diversité des producteurs primaires sur les niveaux supérieurs de la chaine trophique sont évalués par comparaison avec des modèles globaux qui intègrent des bases de données in situ. / Patterns of biodiversity and the mechanisms that maintain them have always interested biologists and have been addressed considering geological, evolutionary and ecological factors. Ecological processes that determine the co-occurrence of species differ according to the physical environment of the ecosystem. Many theories have proposed relationships between patterns in species diversity and large-scale physical features. In terrestrial and aquatic environments, the impact of temperature on the distribution of biodiversity is among the most influent and studied factors. However, many marine taxa are exceptions in the primary influence of temperature, since a large fraction of marine species is planktonic or with dispersible larvae. In the marine environment, dispersal through physical transport has a major impact on patterns of species abundance. Some ocean currents can indeed determine the distribution of planktonic stages of some species, even when demographic and physiological features of the species are unaffected by water properties. Transport mechanisms may therefore influence the distribution of diversity at all scales, from the individual to populations and species. Contrarily to the terrestrial environment, marine ecosystems are characterized by a variability that has spatial and temporal scales defined by specific biophysical processes of turbulent transport. This aspect makes it challenging to provide synoptic information on the distribution of marine species at the global level and at high resolution, features that are essential to understand patterns of biodiversity and the mechanisms involved in their changes. Moreover, hotspots of biodiversity are of primary concerns for conservation efforts. The objectives of this study are therefore: to identify biodiversity hotspots of pelagic primary producers on a global scale and at high resolution; to determine the physical ocean processes that control the spatial and temporal dynamics of such hotspots, focusing on transport-driven mechanisms like dispersion, advection and mixing; study the role of these mechanisms in the structuring of biodiversity at higher trophic levels.To obtain these results, information on water masses with coherent biophysical characteristics ('fluid-dynamical niches') obtained by remote sensing are used to identify hotspots of microbial biodiversity as regions of strong spatial patchiness. These hotspots and the role of transport in shaping their structure are studied by analysing ecological and biophysical global circulation models (Model-ECCO2 Darwin), together with molecular and morphological data on the structure of the community, obtained using in-situ data collected during the Tara-Oceans expedition and Atlantic Meridional Transect. The possible bottom-up effects of the diversity of primary producers on the upper levels of the food chain are evaluated by comparing them with global models integrated with data collected in situ.The ecological models coupled with ocean circulation, identified as biodiversity hotspots of primary producers the most dynamic areas of the global ocean characterized by increased turbulence, mixing and the presence of vortices. These oceanographic features can improve local productivity by transporting nutrients in the photic zone and increase biodiversity by the mixing of species typical of different water masses. In addition, maps of microbial biodiversity suggest a bottom up propagation of biodiversity across the ecosystem, hotspots for primary producers being positively correlated with regions where highest number of top predator species are observed.

Understanding relationships between large herbivores and plant species diversity in dynamic riparian zones, and more specifically sodic zones, is critical to biodiversity conservation. Sodic patches form an integral part of savanna ecosystems because of the ecosystem services and functions they provide, i.e. accumulation of nutrients, provision of open spaces for predator vigilance and formation of wet season wallowing points. Furthermore, these key resource areas sustain body condition for dry season survival and support reproduction through nutritional benefits, making them „nutrient hotspots.‟ The Nkuhlu research exclosures in the Kruger National Park (KNP) provide a unique opportunity to investigate spatial and temporal heterogeneity patterns within riparian zones, and how these patterns are affected by fire and herbivory. A monitoring project was initiated to answer questions pertaining to the dynamics of the herbaceous layer and was aimed at determining (a) whether there exists meaningful variance in herbaceous plant species richness and diversity across different treatments of fire and herbivory in the ecologically sensitive sodic zone, (b) if temporal shifts in plant species composition and diversity occurs, (c) whether an increase in herbaceous biomass, an artifact of herbivory and fire exclusion, suppresses herbaceous plant species diversity and richness, and (d) whether there exists a significant relationship between herbaceous biomass and species richness/diversity. The Nkuhlu exclosures consist of three herbivory treatments, each divided into a fire and no-fire treatment, hence six treatment combinations overall. Herbivory treatments consisted of, (1) a partially fenced area designed to specifically exclude elephants (giraffes are also excluded due to body size), (2) an open, unfenced area and (3) a fully fenced area, designed to exclude all herbivores larger than a hare. Herbaceous vegetation was sampled in two 1 m2 circular sub-plots in the eastern and western corners of each of the 82 fixed plots. Biomass of each plot was estimated with a Disc Pasture Meter (DPM) by sampling ten points diagonally within each plot. DPM-readings were converted to kg/ha according to latest conversions for the Lowveld Savanna. Species richness and biomass showed significant variance across treatments for the 2010 dataset, whereas no significant variation in herbaceous species diversity was perceived. Combined treatment of fire absence and herbivore presence contributed to higher forb species richness in the sodic zone. Biomass was significantly higher in fully fenced areas where herbivores were excluded, opposed to the open and partially fenced areas. Although no significant variation was recorded for diversity across treatments, lowest diversity was recorded in the absence of all herbivores, especially in combination with fire treatment. After nine years of herbivory exclusion, diversity of herbaceous species varied significantly. Herbaceous species composition changed over time in areas exposed to herbivory, while composition of fully fenced treatments did not reveal change. A hump-shaped relationship exists between herbaceous species richness/diversity and field biomass, at least for areas with biomass levels not exceeding 2500 kg/ha. Herbivores are therefore considered essential in sustaining herbaceous plant species richness and system heterogeneity in the sodic zone, since herbaceous species richness/diversity was higher in herbivore presence and herbaceous species composition changed over time in areas exposed to herbivory. Although statistically non-significant, fire seems to suppress species richness. Conservation implications: This study could be used as framework to advance and develop sciencebased management strategies for, at least, the sodic zones of the KNP. Research in these exclosures contributes to our understanding of these landscapes and benefit ecosystem conservation planning. It also provides valuable long-term data for key ecological processes. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2014

Understanding relationships between large herbivores and plant species diversity in dynamic riparian zones, and more specifically sodic zones, is critical to biodiversity conservation. Sodic patches form an integral part of savanna ecosystems because of the ecosystem services and functions they provide, i.e. accumulation of nutrients, provision of open spaces for predator vigilance and formation of wet season wallowing points. Furthermore, these key resource areas sustain body condition for dry season survival and support reproduction through nutritional benefits, making them „nutrient hotspots.‟ The Nkuhlu research exclosures in the Kruger National Park (KNP) provide a unique opportunity to investigate spatial and temporal heterogeneity patterns within riparian zones, and how these patterns are affected by fire and herbivory. A monitoring project was initiated to answer questions pertaining to the dynamics of the herbaceous layer and was aimed at determining (a) whether there exists meaningful variance in herbaceous plant species richness and diversity across different treatments of fire and herbivory in the ecologically sensitive sodic zone, (b) if temporal shifts in plant species composition and diversity occurs, (c) whether an increase in herbaceous biomass, an artifact of herbivory and fire exclusion, suppresses herbaceous plant species diversity and richness, and (d) whether there exists a significant relationship between herbaceous biomass and species richness/diversity. The Nkuhlu exclosures consist of three herbivory treatments, each divided into a fire and no-fire treatment, hence six treatment combinations overall. Herbivory treatments consisted of, (1) a partially fenced area designed to specifically exclude elephants (giraffes are also excluded due to body size), (2) an open, unfenced area and (3) a fully fenced area, designed to exclude all herbivores larger than a hare. Herbaceous vegetation was sampled in two 1 m2 circular sub-plots in the eastern and western corners of each of the 82 fixed plots. Biomass of each plot was estimated with a Disc Pasture Meter (DPM) by sampling ten points diagonally within each plot. DPM-readings were converted to kg/ha according to latest conversions for the Lowveld Savanna. Species richness and biomass showed significant variance across treatments for the 2010 dataset, whereas no significant variation in herbaceous species diversity was perceived. Combined treatment of fire absence and herbivore presence contributed to higher forb species richness in the sodic zone. Biomass was significantly higher in fully fenced areas where herbivores were excluded, opposed to the open and partially fenced areas. Although no significant variation was recorded for diversity across treatments, lowest diversity was recorded in the absence of all herbivores, especially in combination with fire treatment. After nine years of herbivory exclusion, diversity of herbaceous species varied significantly. Herbaceous species composition changed over time in areas exposed to herbivory, while composition of fully fenced treatments did not reveal change. A hump-shaped relationship exists between herbaceous species richness/diversity and field biomass, at least for areas with biomass levels not exceeding 2500 kg/ha. Herbivores are therefore considered essential in sustaining herbaceous plant species richness and system heterogeneity in the sodic zone, since herbaceous species richness/diversity was higher in herbivore presence and herbaceous species composition changed over time in areas exposed to herbivory. Although statistically non-significant, fire seems to suppress species richness. Conservation implications: This study could be used as framework to advance and develop sciencebased management strategies for, at least, the sodic zones of the KNP. Research in these exclosures contributes to our understanding of these landscapes and benefit ecosystem conservation planning. It also provides valuable long-term data for key ecological processes. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2014

Les positions des évènements de recombinaison s’agrègent ensemble, formant des hotspots déterminés en partie par la protéine à évolution rapide PRDM9. En particulier, ces positions de hotspots sont déterminées par le domaine de doigts de zinc (ZnF) de PRDM9 qui reconnait certains motifs d’ADN. Les allèles de PRDM9 contenant le ZnF de type k ont été préalablement associés avec une cohorte de patients affectés par la leucémie aigüe lymphoblastique. Les allèles de PRDM9 sont difficiles à identifier à partir de données de séquençage de nouvelle génération (NGS), en raison de leur nature répétitive. Dans ce projet, nous proposons une méthode permettant la caractérisation d’allèles de PRDM9 à partir de données de NGS, qui identifie le nombre d’allèles contenant un type spécifique de ZnF. Cette méthode est basée sur la corrélation entre les profils représentant le nombre de séquences nucléotidiques uniques à chaque ZnF retrouvés chez les lectures de NGS simulées sans erreur d’une paire d’allèles et chez les lectures d’un échantillon. La validité des prédictions obtenues par notre méthode est confirmée grâce à analyse basée sur les simulations. Nous confirmons également que la méthode peut correctement identifier le génotype d’allèles de PRDM9 qui n’ont pas encore été identifiés. Nous conduisons une analyse préliminaire identifiant le génotype des allèles de PRDM9 contenant un certain type de ZnF dans une cohorte de patients atteints de glioblastomes multiforme pédiatrique, un cancer du cerveau caractérisé par les mutations récurrentes dans le gène codant pour l’histone H3, la cible de l’activité épigénétique de PRDM9. Cette méthode ouvre la possibilité d’identifier des associations entre certains allèles de PRDM9 et d’autres types de cancers pédiatriques, via l’utilisation de bases de données de NGS de cellules tumorales. / The positions of recombination events cluster tightly together in recombination hotspots, which are determined in part by the rapidly evolving protein PRDM9 via its tri- methyltransferase activity. The locations of hotspots are determined by the repetitive ZnF array of PRDM9, which binds to DNA. Alleles of PRDM9 containing the k-ZnF have previously been associated with patients affected with childhood acute lymphoblastic leukaemia. PRDM9 alleles are notoriously difficult to type due to the repetitive nature of the ZnF arrays. Here, we propose a method to characterize the alleles of PRDM9 from next- generation sequencing samples, by identifying the number of alleles containing a specific ZnF type. Our method is based on the correlation between profiles from the sample, representing the counts of nucleotide sequences unique to each ZnF, and from ideal sets of short reads representing an allele pair. We conduct a simulation analysis to examine the validity of the predictions obtained by our method with all pairs of known alleles. We confirm that the method can accurately genotype previously unobserved PRDM9 alleles. We also conducted a preliminary analysis to identify the PRDM9 k-ZnF genotype in a cohort of paediatric glioblastoma (pGBM), a childhood cancer characterized by the recurrent mutations in the coding sequence of the histone H3, the target of the enzymatic activity of PRDM9. Although no associations of k-ZnF containing PRDM9 alleles is found in our pGBM cohort, this method opens the possibility of identifying associations between certain PRDM9 alleles with other types of early onset childhood cancers, through a data-mining effort in public cancer databases.

Nous traversons actuellement une crise de perte de la biodiversité sans précédant. La dégradation des sols et la perte d’habitat, la pollution, la surexploitation et les invasions biologiques contribuent à cette perte mondiale de biodiversité. Par ailleurs, le changement climatique et ses interactions avec les autres menaces, sont probablement l’un des défis majeurs des prochaines décennies pour la biodiversité. À l’heure actuelle, en raison de la multiplication des études et des approches employées, il est difficile d’avoir une vision synthétique des conséquences potentielles de ces changements sur la biodiversité. L’objectif principal de ce travail de thèse a été d’améliorer la caractérisation et la quantification des différents impacts des changements climatiques sur la biodiversité, à l’échelle mondiale par des approches de modélisations et de méta-analyses. Une première partie de mes travaux a ainsi porté sur les conséquences potentielles de la hausse du niveau des mers sur les hotspots insulaires, au cours de laquelle j’ai mis en évidence les conséquences majeures d’une telle hausse pour certains de ces hotspots. Je me suis ensuite intéressée à l’étude des effets conjugués des changements climatiques et des changements d’utilisation des sols sur les invasions biologiques à l’échelle mondiale. Cette partie a permis de mettre en évidence que les conséquences des changements climatiques et des changements d’utilisation des sols sur les espèces invasives dépendent de la région, du taxon et de l’espèce considérée. Ainsi, j’ai mis en évidence que certaines régions pourraient être moins favorables à la présence d’espèce invasives dans le futur. En outre, cette partie a également mis en évidence que les hotspots majoritairement composés d’îles étaient particulièrement favorables à la présence de ces espèces invasives. Finalement, dans une dernière partie, j’ai étudié les conséquences des menaces futures pour les hotspots de biodiversité dans une perspective de conservation. Cette partie a notamment permis d’établir des priorités de recherche et de conservation entre les hotspots de biodiversité en tenant compte des futures menaces qui pèsent sur la biodiversité à l’échelle des hotspots, mais également au sein même des hotspots de biodiversité. Cependant, la mise en œuvre de plans de gestion de sauvegarde d’habitats ou d’espèces ne pourra se faire qu’en intensifiant les collaborations avec l’ensemble des acteurs impliqués. Plus généralement, la mise en œuvre de stratégies d’atténuation et d’adaptation efficaces aux changements climatiques ne pourra pas avoir lieu sans un soutien du grand public. / Global biodiversity is changing at an unprecedented rate due to loss of habitat, biological invasions, pollution, overexploitation. Furthermore, climate changes and their synergies with other threats will probably become the main drivers of biodiversity loss in the next century. Nowadays, the multiplicity of approaches and the resulting variability in projections make it difficult to get a clear picture of the future of biodiversity due to climate change. Yet, the majority of models indicate alarming consequences for biodiversity, with the worst- case scenarios leading to an increase of extinction rates. The aim of this thesis was to improve the knowledge about of the different consequences of climate change on biodiversity worldwide. To do that I mainly used modelisation and meta-analyses approaches. The first part of my work was to investigate the consequences of sea level rise for the ten insular biodiversity hotspot and their endemic species, during which I highlighted that between 6 and 19% of the islands would be entirely submerged. Then I studied the effects of climate and land use changes on biological invasions worldwide. The results showed that invasives species response to climate and land use changes depend on region, taxa and species considered. We also emphasized that some regions could lose a significant number of invasive alien species. Besides, we also found that hotspot that are mainly islands or group of islands are highly suitable for invasive species. Finally, in the last part, I quantified the exposure of biodiversity hotspots to the combined effects of climate change, land use change and biological invasions. This work highlighted the pressing need to consider different drivers of global change in conservation planning. In addition, we established some prioritization framework among the hotspot. Finally, conservation strategies to protect habitat and species under global changes, can only be achieved through closed collaboration with park managers. Overall, implementation of effective adaptation strategies to climate change can only succeed with public support.

Submitted by Erika Demachki (erikademachki@gmail.com) on 2014-09-23T21:19:16Z No. of bitstreams: 2 Peixoto, Franciele Parreira-Dissertação-2013.pdf: 995120 bytes, checksum: 365969ffce47a58af2a011eb0370ed04 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2014-09-23T21:58:54Z (GMT) No. of bitstreams: 2 Peixoto, Franciele Parreira-Dissertação-2013.pdf: 995120 bytes, checksum: 365969ffce47a58af2a011eb0370ed04 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-09-23T21:58:54Z (GMT). No. of bitstreams: 2 Peixoto, Franciele Parreira-Dissertação-2013.pdf: 995120 bytes, checksum: 365969ffce47a58af2a011eb0370ed04 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2013-03-18 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Aim: To investigate global patterns of phylobetadiversity (PBD) in bats, with the purpose to better understand the mechanisms underlying current biodiversity patterns. We also aimed to use a metric that allows partitioning PBD into two components to distinguish the relative roles of local (e.g. lineage filtering) and regional processes (e.g. speciation) in shaping broad-scale patterns of PBD. Furthermore, we analyzed the distance-decay relationship of phylogenetic beta diversity to provide more information about factors that act in the PBD patterns. Location: global, delimited by biogeographic regions. Methods: Using the global distribution of bats and a supertree available for most species, we calculated PBD using the complement of phylosor index. We used a null model to test if two assemblages were more or less phylogenetically dissimilar than expected by chance. In addition, we decoupled PBD into turnover and nestednessresultant components, providing information about two factors that produce differences in assemblage phylogenetic composition. We also performed a Mantel analysis to analyze the distance-decay patterns of PBD and its two components. Results: The most striking difference in PBD was found between the Old and New World “phylogenetic composition”. We found the lowest values of PBD between adjacent regions (i.e., Neotropical/Neartic; Indo-Malay/Paleartic), revealing a strong geographical structure in PBD. These values were even lower when the turnover component was analyzed, demonstrating the differences in the role of regional processes in shaping regional diversity. On the other hand, we found out that for some adjacent regions (e.g., Afrotropical/Paleartic), the observed PBD was higher than expected by chance and comparatively different from expected by the distance decay relationship. This value remained high, even when we analyzed just the PBD turnover component. This demonstrates that although these regions are relatively close in space, there are other factors driving phylogenetic differences between them (e.g. an environmental barrier). Main conclusions: Our analyses revealed differences in the expected patterns of bat PBD among regions, suggesting that at broad scales, besides the effects of distance and geographic barriers, we also have to consider the importance of environmental gradients when studying the phylogenetic origin of bat assemblages. / A abordagem mais comum no uso de PD (diversidade filogenética) para conservação é selecionar locais com maior diversidade evolutiva. Essa estratégia parte do pressuposto de que locais com maior quantidade de PD indicam maior potencial para respostas evolutivas a mudanças ambientais futuras. No entanto, há um crescente debate sobre se as prioridades de conservação deveriam também ser voltadas para locais com baixo valor de PD, que podem representar centros de diversificação de espécies ou “berçários de diversidade”. Alguns trabalhos têm testado se os hotspots globais de biodiversidade, baseados em riqueza, também representam locais de desproporcional concentração de história evolutiva. Nós testamos aqui se os hotspots contêm mais, menos ou igual diversidade filogenética (PD) que o esperado por uma amostragem ao acaso de espécies em qualquer posição na filogenia, para a ordem Chiroptera. Buscamos responder qual a real contribuição de cada hotspot para a conservação de padrões e processos relacionados à diversidade filogenética. Nós utilizamos uma supertree disponível para a maioria das espécies da ordem, e dados de distribuição das espécies. Nós calculamos o PD para cada hotspot separadamente e utilizamos um modelo nulo para obter os valores esperados dado a riqueza. De 34 hotspots, apenas um apresentou maior PD do que o esperado, treze apresentaram valores menores e o restante valores iguais ao esperado. Nós demonstramos que a relação entre PD e riqueza varia entre regiões biogeográficas, de modo que não há como fazer generalizações acerca da contribuição dos hotspots para a conservação de diversidade evolutiva. De modo geral nossos resultados demonstram que devido ao fato da história evolutiva variar regionalmente, também devem ser estabelecidas as prioridades de conservação nessa escala.

Die übergreifende Zielsetzung meiner Studie ist eine Ausarbeitung quantitativer Methoden zur nationalen nationale Schutzplanung in Übereinstimmung mit dem internationalen Ansatz. Diese Zielsetzung erfordert eine Lösung der folgenden Probleme:<br><br> 1) Wie lässt sich Vegetationsvielfalt in grober Auflösung auf Basis abiotischen Faktoren einschätzen?<br> 2) Wie ist der Ansatz 'globaler Hotspots' für die Eingrenzung nationaler Biodiversitäts-Hotspots zu übernehmen?<br> 3) Wie erfolgt die Auswahl von quantitativen Schutzzielen unter Einbezug der Unterschiede nationaler Hotspots bei Umweltbedingungen und durch den Menschen Bedrohung?<br> 4) Wie sieht der Entwurf eines großflächigen nationalen Naturschutzkonzepts aus, das die hierarchische Natur der Artenvielfalt reflektiert? Die Fallstudie für nationale Naturschutzplanung ist Russland. <br><br> Die nachfolgenden theoretischen Schlüsse wurden gezogen:<br> · Großräumige Vegetationsdiversität ist weitgehend vorhersagbar durch klimabedingte latente Wärme für Verdunstung und topographische Landschaftsstruktur, beschrieben als Höhendifferenz. Das klimabasierte Modell reproduziert die beobachtete Artenanzahl von Gefäßpflanzen für verschiedene Gebiete auf der Welt mit einem durchschnittlichen Fehler von 15% <br> · Nationale Biodiversitäts-Hotspots können auf Grundlage biotischer oder abiotischer Daten kartographiert werden, indem als Korrektur für ein Land die quantitativen Kriterien für Planzenendemismus und Landnutzung des Ansatzes der 'globalen Hotspots' genutzt wird <br> · Quantitative Naturschutzziele, die die Unterschiede zwischen nationalen Biodiversitäts-Hotspots in Bezug auf Umweltbedingungen und der Bedrohung durch den Menschen miteinbeziehen, können mit nationalen Daten über Arten auf der Roten Liste gesetzt werden <br> · Ein großräumiger nationaler Naturschutzplan, der die hierarchische Natur der Artenvielfalt berücksichtigt, kann durch eine Kombination von abiotischer Methode im nationalen Bereich (Identifikation großräumiger Hotspots) und biotischer Methode im regionalen Bereich (Datenanalyse der Arten auf der Roten Liste) entworfen werden / The overall objective of the study is an elaboration of quantitative methods for national conservation planning, coincident with the international approach ('hotspots' approach). This objective requires a solution of following problems: <br><br> 1) How to estimate large scale vegetation diversity from abiotic factors only?<br> 2) How to adopt 'global hotspots' approach for bordering of national biodiversity hotspots?<br> 3) How to set conservation targets, accounting for difference in environmental conditions and human threats between national biodiversity hotspots?<br> 4) How to design large scale national conservation plan reflecting hierarchical nature of biodiversity?<br> The case study for national conservation planning is Russia. <br><br> Conclusions:<br> · Large scale vegetation diversity can be predicted to a major extent by climatically determined latent heat for evaporation and geometrical structure of landscape, described as an altitudinal difference. The climate based model reproduces observed species number of vascular plant for different areas of the world with an average error 15%<br> · National biodiversity hotspots can be mapped from biotic or abiotic data using corrected for a country the quantitative criteria for plant endemism and land use from the 'global hotspots' approach<br> · Quantitative conservation targets, accounting for difference in environmental conditions and human threats between national biodiversity hotspots can be set using national data for Red Data book species <br> · Large scale national conservation plan reflecting hierarchical nature of biodiversity can be designed by combination of abiotic method at national scale (identification of large scale hotspots) and biotic method at regional scale (analysis of species data from Red Data book)