Orientador: Maria do Carmo Estanislau do Amaral / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-21T15:01:25Z (GMT). No. of bitstreams: 1 Costa_SuzanaMariadosSantos_M.pdf: 5413800 bytes, checksum: 0fbb691374cc80432664625fb24982bc (MD5) Previous issue date: 2012 / Resumo: O resumo poderá ser visualizado no texto completo da tese digital / Abstract: The abstract is available with the full electronic document / Mestrado / Biologia Vegetal / Mestre em Biologia Vegetal

The Guiana Shield is a sub-region of Amazonia, one of the richest areas on earth in terms of species number. It is also one of the most pristine areas and is still largely unexplored. Species number, distribution, boundaries and their evolutionary histories remain at least unclear but most of the time largely unknown. This is the case for most Anurans, a group which is recognized as threatened globally and is disappearing even from pristine tropical forests. Given the pace of forest destruction and the growing concerns about climate change it is urgently necessary to obtain a better estimate of regional biodiversity in Amazonian frogs as well as a better understanding of the origin and distribution of Anuran diversity. Furthermore, given their sensitivity to climatic conditions, amphibians are a good model to investigate the influence of paleoclimatic events on Neotropical diversification which was supposedly the driving force on biotic evolution during Pleistocene in the Guiana Shield. I first test species boundaries in two species Scinax ruber and Rhinella margaritifera. These species are widely distributed, abundant and largely recognized as species complexes. I used an original species delineation method based on the combined use of mitochondrial and nuclear DNA in phylogenetic and phylogeographic analyses. Phylogenetic analyses demonstrated the polyphyly of Scinax ruber and Rhinella margaritifera. These species consist of multiple lineages that may all merit species status. Conflicting signals of mitochondrial and nuclear markers indicated the possibility of ongoing hybridization processes. Phylogeographic analyses added further information in support of the specific status of these lineages. Our results highlight the utility of combining phylogenetic and phylogeographic methods, as well as the use of both mitochondrial and nuclear markers within one study. This approach helped to better understand the evolutionary history of taxonomically complex groups of species. The assessment of the geographic distribution of genetic diversity in tropical amphibian communities can lead to conclusions that differ strongly from prior analyses based on the occurrence of currently recognized species alone. Such studies, therefore, hold the potential to contribute to a more objective assessment of amphibian conservation priorities in tropical areas. Subsequently, I tested if these first results on cryptic species are generalisable, questioning what would potentially be a minimum estimate of the number of cryptic frog species in Amazonia and the Guiana Shield, using mtDNA with multiple complementary approaches. I also combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs. In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contra to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher genetic distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species. Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia-Guianas. As a consequence the global amphibian decline detected especially in the Neotropics may be worse than realised. The Rhinella margaritifera complex is characterisized by the presence of many cryptic species throughout its wide distribution, ranging from Panama to Bolivia and almost entire Amazonia. French Guiana has long been thought to harbor two species of this group, though molecular data analysed in previous chapters indicated as many as five lineages. I tested whether morphological measurements are correlated or not with genetic data using discriminant analysis and if diagnostic characteristics among the previously determined lineages can be used to describe these new species. This is a novel integrative method which can lead to a facilitation of the description of cryptic species that have been detected by phylogenetic and/or phylogeographic studies. These analyses, combined with published data of other Rhinella species, indicated that two of these lineages represent previously unnamed species. Two of the remaining are allocable to R. margaritifera while the status of the fifth is still unclear because so far it is morphologically indistinguishable from R. castaneotica. Determining if codistributed species responded to climate change in an independent or concerted manner is a basic objective of comparative phylogeography. Species boundaries, histories, ecologies and their geographical ranges are still to be explored in the Guiana Shield. According to the refugia hypothesis this region was supposed to host a forest refugium during climatic oscillations of the Pleistocene but the causes and timing for this have been criticized. We investigated patterns of genetic structure within 18 frog species in the eastern Guiana Shield to explore species boundaries and their evolutionary history. We used mtDNA and nuclear DNA and complementary methods to compare the genetic diversity spatially and temporally. With one exception all the species studied diversified repeatedly within the eastern Guiana Shield during the last 4 million years. Instead of one Pleistocene forest refugium the Guiana Shield has probably hosted multiple refugia during late Pliocene and Pleistocene. Most of these Pleistocene refugia were probably situated on the coast of French Guiana, Amapà, Suriname and Guyana. This diversification likely resulted from forest fragmentation. Many species deserve taxonomic revisions and their ranges to be reconsidered. The local endemism of the Anuran fauna of the Guiana Shield is likely to be much higher and some areas consequently deserve more conservation efforts. Specifically I questioned whether major intraspecific diversification started before the Pleistocene and occurred within the Guiana Shield or ex situ. According to ecological characteristics of the species involved I will test different diversification hypotheses. The consequences on the diversity and the endemism of the Guiana Shield will be explored. My results demonstrate that we have been grossly underestimating local biological diversity in the Guiana Shield but also in Amazonia in general. The order of magnitude for potential species richness means that the eastern Guiana Shield hosts one of the richest frog fauna on earth. In most of the species studied high levels of mtDNA differentiation between populations call for a reassessment of the taxonomic status of what is being recognised as single species. Most species display deep divergence between eastern Guiana Shield populations and Amazonian ones. This emphasizes that the local endemism in the Guiana Shield of these zones is higher than previously recognized and must be prioritised elements taken into account in conservation planning. Nevertheless, a few other species appear widely distributed showing that widespread species do exist. This underlines the fact that some species have efficient dispersal abilities and that the frog fauna of the eastern Guiana Shield is a mixture of old Guianan endemic lineages that diversified in situ mostly during late Pliocene and Pleistocene and more recently exchanged lineages with the rest of Amazonia. Recognizing this strong historical component is necessary and timely for local conservation as these zones are likely to be irremediably modified in the near future.

The Guiana Shield is a sub-region of Amazonia, one of the richest areas on earth in terms of species number. It is also one of the most pristine areas and is still largely unexplored. Species number, distribution, boundaries and their evolutionary histories remain at least unclear but most of the time largely unknown. This is the case for most Anurans, a group which is recognized as threatened globally and is disappearing even from pristine tropical forests. Given the pace of forest destruction and the growing concerns about climate change it is urgently necessary to obtain a better estimate of regional biodiversity in Amazonian frogs as well as a better understanding of the origin and distribution of Anuran diversity. Furthermore, given their sensitivity to climatic conditions, amphibians are a good model to investigate the influence of paleoclimatic events on Neotropical diversification which was supposedly the driving force on biotic evolution during Pleistocene in the Guiana Shield. I first test species boundaries in two species Scinax ruber and Rhinella margaritifera. These species are widely distributed, abundant and largely recognized as species complexes. I used an original species delineation method based on the combined use of mitochondrial and nuclear DNA in phylogenetic and phylogeographic analyses. Phylogenetic analyses demonstrated the polyphyly of Scinax ruber and Rhinella margaritifera. These species consist of multiple lineages that may all merit species status. Conflicting signals of mitochondrial and nuclear markers indicated the possibility of ongoing hybridization processes. Phylogeographic analyses added further information in support of the specific status of these lineages. Our results highlight the utility of combining phylogenetic and phylogeographic methods, as well as the use of both mitochondrial and nuclear markers within one study. This approach helped to better understand the evolutionary history of taxonomically complex groups of species. The assessment of the geographic distribution of genetic diversity in tropical amphibian communities can lead to conclusions that differ strongly from prior analyses based on the occurrence of currently recognized species alone. Such studies, therefore, hold the potential to contribute to a more objective assessment of amphibian conservation priorities in tropical areas. Subsequently, I tested if these first results on cryptic species are generalisable, questioning what would potentially be a minimum estimate of the number of cryptic frog species in Amazonia and the Guiana Shield, using mtDNA with multiple complementary approaches. I also combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs. In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contra to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher genetic distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species. Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia-Guianas. As a consequence the global amphibian decline detected especially in the Neotropics may be worse than realised. The Rhinella margaritifera complex is characterisized by the presence of many cryptic species throughout its wide distribution, ranging from Panama to Bolivia and almost entire Amazonia. French Guiana has long been thought to harbor two species of this group, though molecular data analysed in previous chapters indicated as many as five lineages. I tested whether morphological measurements are correlated or not with genetic data using discriminant analysis and if diagnostic characteristics among the previously determined lineages can be used to describe these new species. This is a novel integrative method which can lead to a facilitation of the description of cryptic species that have been detected by phylogenetic and/or phylogeographic studies. These analyses, combined with published data of other Rhinella species, indicated that two of these lineages represent previously unnamed species. Two of the remaining are allocable to R. margaritifera while the status of the fifth is still unclear because so far it is morphologically indistinguishable from R. castaneotica. Determining if codistributed species responded to climate change in an independent or concerted manner is a basic objective of comparative phylogeography. Species boundaries, histories, ecologies and their geographical ranges are still to be explored in the Guiana Shield. According to the refugia hypothesis this region was supposed to host a forest refugium during climatic oscillations of the Pleistocene but the causes and timing for this have been criticized. We investigated patterns of genetic structure within 18 frog species in the eastern Guiana Shield to explore species boundaries and their evolutionary history. We used mtDNA and nuclear DNA and complementary methods to compare the genetic diversity spatially and temporally. With one exception all the species studied diversified repeatedly within the eastern Guiana Shield during the last 4 million years. Instead of one Pleistocene forest refugium the Guiana Shield has probably hosted multiple refugia during late Pliocene and Pleistocene. Most of these Pleistocene refugia were probably situated on the coast of French Guiana, Amapà, Suriname and Guyana. This diversification likely resulted from forest fragmentation. Many species deserve taxonomic revisions and their ranges to be reconsidered. The local endemism of the Anuran fauna of the Guiana Shield is likely to be much higher and some areas consequently deserve more conservation efforts. Specifically I questioned whether major intraspecific diversification started before the Pleistocene and occurred within the Guiana Shield or ex situ. According to ecological characteristics of the species involved I will test different diversification hypotheses. The consequences on the diversity and the endemism of the Guiana Shield will be explored. My results demonstrate that we have been grossly underestimating local biological diversity in the Guiana Shield but also in Amazonia in general. The order of magnitude for potential species richness means that the eastern Guiana Shield hosts one of the richest frog fauna on earth. In most of the species studied high levels of mtDNA differentiation between populations call for a reassessment of the taxonomic status of what is being recognised as single species. Most species display deep divergence between eastern Guiana Shield populations and Amazonian ones. This emphasizes that the local endemism in the Guiana Shield of these zones is higher than previously recognized and must be prioritised elements taken into account in conservation planning. Nevertheless, a few other species appear widely distributed showing that widespread species do exist. This underlines the fact that some species have efficient dispersal abilities and that the frog fauna of the eastern Guiana Shield is a mixture of old Guianan endemic lineages that diversified in situ mostly during late Pliocene and Pleistocene and more recently exchanged lineages with the rest of Amazonia. Recognizing this strong historical component is necessary and timely for local conservation as these zones are likely to be irremediably modified in the near future.

La connaissance du rayonnement solaire, ou irradiation solaire, à la surface de la Terre est d’un grand intérêt dans de nombreux domaines. Cependant le développement de systèmes utilisant l’énergie solaire nécessitent des données sur le rayonnement solaire denses (spatialement et temporellement) et suffisamment précises pour simuler, concevoir, gérer et optimiser le fonctionnement de ces systèmes. L’objectif principal de cette thèse est de concevoir et développer une méthode d'estimation de l'irradiation solaire applicable à la zone intertropicale. Les travaux de la première partie se concentrent sur la recherche d’une solution méthodologique pour estimer le l’irradiation solaire sur la partie Nord du continent Sud-Américain (Plateau des Guyanes) avec une haute résolution spatiale et temporelle et une précision similaire à celle des aux autres méthodes opérationnelles sous d’autres climats. Dans la deuxième partie, nous proposons d’améliorer les estimations d’irradiation solaire obtenues dans la première partie, notamment celles faites en ciel couvert. Le Plateau des Guyanes étant une zone fortement affectée par la ZIC et avec des passages nuageux très fréquents, il nous est apparu nécessaire de compléter les modifications apportées à la méthode originelle en introduisant une modélisation du ciel couvert. Dans la troisième partie, nous proposons de réaliser des cartographies d’indicateurs en utilisant les estimations d’irradiation obtenues avec la méthode Heliosat-2 modifiée. Enfin, nous concluons sur les avancées obtenues en termes de connaissance sur l’irradiation solaire et sur son exploitabilité sur le Plateau des Guyanes / Knowledge of solar radiation, or solar irradiation, at Earth’s surface is of great interest in many fields. However, the development of systems using solar energy need spatially and temporally dense data on solar radiation, sufficiently accurate to simulate, design, generate and optimize the operation of these systems.The main objective of this thesis is to design and develop a method to assess solar irradiation applicable on intertropical regions. The works of the first part focus on the search of a methodological solution to assess solar irradiation on the northern part of the South American continent (Guiana Shield) with a high temporal and spatial resolution and accuracy on the same level of other operational methods under other climates. In the second part, we propose to improve the solar irradiation assessments obtained in the first part, notably those done in cloudy sky. The Guiana Shield being a zone strongly affected by the ITCZ and with recurrent cloudy periods, it appeared necessary to us to complete the changes brought to the original method by introducing a modeling of the cloudy sky. In the third part, we propose to produce maps of indicators by using the assessments of solar irradiation obtained with the modified Heliosat-2 method. Finally, we conclude on the advances obtained in terms of knowledge on solar irradiation and its exploitability on the Guiana Shield.

Depuis ses balbutiements au début des années 2000, la Réduction des Emissions liées à la Déforestation et la Dégradation forestière, plus connue sous le sigle REDD+, a peu à peu été admise comme un moyen indispensable des politiques globales de lutte contre le changement climatique. Reposant sur le concept de « déforestation évitée », elle nécessite la formulation d’un scénario de référence servant à évaluer les efforts des pays dans la maîtrise de leur niveau de déforestation. Ces scénarios sont au cœur de nombreux débats politiques et scientifiques. Cette thèse constitue une mise en perspective des principes de REDD+ avec, comme cas d’étude, le Plateau des Guyanes. Dans un premier temps, on présentera l’établissement d’un modèle spatialisé de déforestation pour la Guyane française, insistant sur la nécessité de se focaliser sur les moteurs socio-économiques de la déforestation. Ce constat sera renforcé, dans un second temps, par l’étude de la déforestation liée à l’orpaillage à l’échelle de l’ensemble du Plateau des Guyanes, montrant un impact très fort du cours de l’or et des contextes politiques sur le niveau déforestation. Ces résultats alimenteront une discussion critique du mécanisme REDD+, basé sur la formulation de scénarios de référence potentiellement très variables et fondés sur des déterminants davantage politiques que scientifiques, ouvrant ainsi la porte à un potentiel chantage environnemental. / Since its appearance at the beginning of the 2000’s, the Reduction of Emissions from Deforestation and forest Degradation, known as REDD+, has gradually been admitted as an indispensable option for global policies aiming at tackling climate change. Relying on the concept of « avoided deforestation », it requires the formulation of a reference scenario aiming at evaluating efforts made by the countries involved in controlling their level of deforestation. Those scenarios are facing numerous political and scientific debates. This thesis aims at putting into perspective the principles of REDD+, based on a study site covering the Guiana Shield. In a first step, the formulation of a spatialiazed deforestation model over French Guiana will be presented, insisting on the necessity to focus on socio-economic drivers of deforestation. This statement will be reinforced, in a second step, by the the study of deforestation due to gold mining in the Guiana Shield, showing a very strong effect of gold prices and national political contexts on deforestation. These results finally contribute to a critical discussion on REDD+ mechanism, based on the formulation of very variable reference scenarios, relying more on political than on scientific determinants, and potentially enabling the emergence of environmental blackmailing.

Le plateau des Guyanes est une région qui est caractérisée à 90% d’une forêt tropicale primaire et compte pour environ 20% des réserves mondiales d’eau douce. Ce territoire naturel, au vaste réseau hydrographique, montre des intensités pluviométriques annuelles atteignant 4000 mm/an ; ce qui fait de ce plateau une des régions les plus arrosées du monde. De plus les précipitations tropicales sont caractérisées par une variabilité spatiale et temporelle importante. Outre les aspects liés au climat, l’impact des précipitations dans cette région du globe est important en termes d’alimentation énergétique (barrages hydroélectriques). Il est donc important de développer des outils permettant d’estimer quantitativement et qualitativement et à haute résolution spatiale et temporelle les précipitations dans cette zone. Cependant ce vaste espace géographique est caractérisé par un réseau de stations pluviométriques peu développé et hétérogène, ce qui a pour conséquence une méconnaissance de la répartition spatio-temporelle précise des précipitations et de leurs dynamiques.Les travaux réalisées dans cette thèse visent à améliorer la connaissance des précipitations sur le plateau des Guyanes grâce à l’utilisation des données de précipitations satellites (Satellite Precipitation Product : SPP) qui offrent dans cette zone une meilleure résolution spatiale et temporelle que les mesures in situ, au prix d’une qualité moindre en terme de précision.Cette thèse se divise en 3 parties. La première partie compare les performances de quatre produits d’estimations satellitaires sur la zone d’étude et tente de répondre à la question : quelle est la qualité de ces produits au Nord de l’Amazone et sur la Guyane française dans les dimensions spatiales et temporelles ? La seconde partie propose une nouvelle technique de correction de biais des SPP qui procède en trois étapes : i) utiliser les mesures in situ de précipitations pour décomposer la zone étudiée en aires hydro-climatiques ii) paramétrer une méthode de correction de biais appelée quantile mapping sur chacune de ces aires iii) appliquer la méthode de correction aux données satellitaires relatives à chaque aire hydro-climatique. On cherche alors à répondre à la question suivante : est-ce que le paramétrage de la méthode quantile mapping sur différentes aires hydro-climatiques permet de corriger les données satellitaires de précipitations sur la zone d’étude ? Après avoir montré l’intérêt de prendre en compte les différents régimes pluviométriques pour mettre en œuvre la méthode de correction QM sur des données SPP, la troisième partie analyse l’impact de la résolution temporelle des données de précipitations utilisées sur la qualité de la correction et sur l’étendue spatiale des données SPP potentiellement corrigeables (données SPP sur lesquelles la méthode de correction peut s’appliquer avec efficacité). Concrètement l’objectif de cette partie est d’évaluer la capacité de notre méthode à corriger sur une large échelle spatiale le biais des données TRMM-TMPA 3B42V7 en vue de rendre pertinente l’exploitation de ce produit pour différentes applications hydrologiques.Ce travail a permis de corriger les séries satellites journalières à haute résolution spatiale et temporelle sur le plateau des Guyanes selon une approche nouvelle qui utilise la définition de zones hydro-climatiques. Les résultats positifs en terme de réduction du biais et du RMSE obtenus grâce à cette nouvelle approche, rendent possible la généralisation de cette nouvelle méthode dans des zones peu équipées en pluviomètres. / The Guiana Shield is a region that is characterized by 90% of a primary rainforest and about 20% of the world’s freshwater reserves. This natural territory, with its vast hydrographic network, shows annual rainfall intensities up to 4000 mm/year; making this plateau one of the most watered regions in the world. In addition, tropical rainfall is characterized by significant spatial and temporal variability. In addition to climate-related aspects, the impact of rainfall in this region of the world is significant in terms of energy supply (hydroelectric dams). It is therefore important to develop tools to estimate quantitatively and qualitatively and at high spatial and temporal resolution the precipitation in this area. However, this vast geographical area is characterized by a network of poorly developed and heterogeneous rain gauges, which results in a lack of knowledge of the precise spatio-temporal distribution of precipitation and their dynamics.The work carried out in this thesis aims to improve the knowledge of precipitation on the Guiana Shield by using Satellite Precipitation Product (SPP) data that offer better spatial and temporal resolution in this area than the in situ measurements, at the cost of poor quality in terms of precision.This thesis is divided into 3 parts. The first part compares the performance of four products of satellite estimates on the study area and attempts to answer the question : what is the quality of these products in the Northern Amazon and French Guiana in spatial and time dimensions ? The second part proposes a new SPP bias correction technique that proceeds in three steps: i) using rain gauges measurements to decompose the studied area into hydro climatic areas ii) parameterizing a bias correction method called quantile mapping on each of these areas iii) apply the correction method to the satellite data for each hydro-climatic area. We then try to answer the following question : does the parameterization of the quantile mapping method on different hydro-climatic areas make it possible to correct the precipitation satellite data on the study area ? After showing the interest of taking into account the different rainfall regimes to implement the QM correction method on SPP data, the third part analyzes the impact of the temporal resolution of the precipitation data used on the quality of the correction and the spatial extent of potentially correctable SPP data (SPP data on which the correction method can be applied effectively). In summary, the objective of this section is to evaluate the ability of our method to correct on a large spatial scale the bias of the TRMM-TMPA 3B42V7 data in order to make the exploitation of this product relevant for different hydrological applications.This work made it possible to correct the daily satellite series with high spatial and temporal resolution on the Guiana Shield using a new approach that uses the definition of hydro-climatic areas. The positive results in terms of reduction of the bias and the RMSE obtained, thanks to this new approach, makes possible the generalization of this new method in sparselygauged areas.