Fire ecology encompasses the study of the factors, biotic and abiotic, that influence the occurrence of fire in an area, as well as the effects fire has on the flora and fauna native and non-native to the region (Whelan 1995). Fire has had a major influence on shaping biomes as we see them today. Fire has had an effect on vegetation much before the evolution of Homo on Earth (Keeley and Rundel 2005, Pausas and Keeley 2009, Midgley and Bond 2011). With the evolution and expansion of Homo across Earth, fire has been tamed, and then generated and used over time to yield landscapes that were suitable for their existence (Pyne 1991, Bowman et al. 2009, Archibald et al. 2012). Thus, fire, vegetation and humans were, and still are, inextricably linked in certain biomes on Earth. The best examples are observed in tropical savannas and grasslands, biomes that experience distinct seasonality in climate and are thus prone to frequent fires caused either by lightning or by humans (Keeley and Rundel 2005, Archibald et al. 2012). At the other end of the spectrum of tropical vegetation types are rainforests where the occurrence of fires is constrained by a perpetually moist environment (Meyn et al. 2007, van der Werf et al. 2008), in the absence of manipulation of the forest landscape by humans. Frequent fires have been documented to alter structure and cause a decline in forest diversity in rainforests (Cochrane and Schulze 1999, Cochrane 2003), whereas fire exclusion in mesic savannas leads to increases in biomass and transition to forest ecosystems (Bond et al. 2003, Bond et al. 2005 and references therein). A tropical biome that lies between these two extremes of vegetation types is the Seasonally Dry Tropical Forest (SDTF) where the occurrence of fire is common, but for which there are contrasting views on the effect of fire on this system (Saha and Howe 2003, Otterstrom et al. 2006 as examples). Current forest management policies in SDTF areas, especially in India, actively aim to exclude fire from these forests mostly because of the perception held by forest managers and the general public that fire has negative effects on forests. However, very few scientific studies have explored the ecology of fire in SDTFs. In order to formulate fire management policies, it is necessary to have a more comprehensive understanding of the ecology of fire in this tropical forest type. This thesis addresses two components of fire ecology as applied to SDTFs. The first is how fire is influenced by the environment, and the second, how fires influence the biotic community particular to SDTFs. The study was carried out in an SDTF in southern India where fire is a common occurrence -the forests of Mudumalai – a protected area that exhibits a range of SDTF vegetation types, from moist deciduous to dry thorn forest, corresponding to a rainfall gradient. Fire influenced by the environment: For this section, the influence of fuel load, fuel moisture and ambient weather on area burnt, fire occurrence and fire temperatures were studied in the SDTF vegetation types of Mudumalai. The extent of fire (area burnt) in an ecosystem differs according to the relative contribution of fuel load and fuel moisture available (Meyn et al. 2007). At a global scale, these factors vary along a spatial gradient of climatic conditions and are thus “varying constraints” (Krawchuk and Moritz 2011) on fire activity in natural ecosystems (Meyn et al. 2007, Krawchuk and Moritz 2011). Moist ecosystems such as tropical rainforests are at one end of the spectrum where fire activity is constrained by fuel moisture. At the other end are arid ecosystems, such as deserts, where fire activity is limited by the presence of fuels. The potential for the globally widespread seasonally dry tropical forests (SDTFs) to be placed as a single entity in this framework was examined by analyzing the interacting effects of fuel load and fuel moisture on the extent of fire in Mudumalai. Logistic regression was used to model proportion area burnt in a given year with factors that would influence fuel load and fuel moisture – these were proportion area burnt the previous year, wet season rainfall the previous year and early dry season rainfall. Modelling was conducted at two levels – the overall landscape and within four defined moisture regimes (between 700 and 1700 mm yr-1) – using a dataset of area burnt and seasonal rainfall from 1990 to 2010. The landscape scale model showed that the extent of fire in a given year within this SDTF is dependent on the combined interaction of seasonal rainfall and extent burnt the previous year. However, within individual moisture regimes the relative contribution of these factors to the annual extent burnt varied – early dry season rainfall (i.e. a moderator of fuel moisture) was the predominant factor in the wettest regime, while the previous year’s wet season rainfall (i.e. a proxy for fuel load) had a large influence on fire extent in the driest regime. Thus, the diverse structural vegetation types associated with SDTFs across a wide range of rainfall regimes would have to be examined at finer regional or local scales to understand the specific environmental drivers of fire. While the extent burnt in SDTFs is largely dependent on climatic influences, the probability of ignition has not been characterized for SDTFs. Anthropogenic fires are a regular occurrence during the dry season in SDTFs (Stott et al. 1990). We investigated if the occurrences of anthropogenic fire in Mudumalai were associated with any particular weather conditions during the dry season. Logistic regression between probability of a fire day and weather variables -seasonal rainfall, ambient relative humidity and temperature -was examined during the dry seasons of 20042010 in Mudumalai. Fire incidence data was obtained from the Fire Information for Resource Management System (FIRMS; NASA 2002) and weather data from two automatic weather stations within Mudumalai. The analysis showed that days with high probabilities of fire occurrence were associated with low levels of early dry season rainfall, low daily average relative humidity, and high daily average temperatures. These weather conditions are known to influence moisture levels of fine fuels (Viney 1991, Archibald et al. 2009). In Mudumalai as well as other SDTFs the primary fuels for fires are fine fuels such as litter and dried grass that accumulate on the forest floor during the dry season. Our results suggest that the occurrence of fire is moderated by environmental conditions that reduce or enhance the flammability of fine fuels in the dry tropics. A quantitative framework for assessing risk of a fire day has been proposed as an outcome of this analysis to assist forest managers in anticipating fire occurrences in this SDTF, and possibly for those across south Asia. Of the various components of a fire regime, fire intensity is an important aspect. High fire temperatures (one measure of fire intensity, Keeley 2009) and resulting soil temperatures would have an effect on soil properties as well as plant species demography and community structure (Moreno and Oechel 1991, Neary et al. 1999, Morrison 2002). Fires that occur frequently in a region could vary in their intensity and severity depending upon the amount of fuel available and ambient weather conditions (Stinson and Wright 1969, Stott 1986, Stronach and McNaughton 1989, Ansley et al. 1998, Wotton et al. 2012). However, this relationship has not been examined in a multiple regression framework for SDTFs. Fire temperature was recorded and its relationship with ambient weather and fuel load was studied in two SDTFs of southern India -Mudumalai and Biligiri Rangaswamy Temple (BRT) Wildlife Sanctuary in Karnataka. During “controlled burns” conducted by the forest department staff in these reserves in February and March 2010, temperature indicating lacquers on mica sheets were used to measure fire temperature at several points at ground level and one cm below the ground. Biomass was harvested close to the temperature measurement points to estimate fuel load and fuel moisture. Ambient weather conditions were recorded during the controlled burn when the flame passed over the indicators. Temperatures recorded at ground level ranged from <79oC to 760oC, with the most frequently recorded temperatures between 343-399 oC and 510566 oC. Temperatures measured one cm below the ground ranged from <79oC to 302oC, with a majority of the indicators recording temperatures in the <79oC category. Ground-level temperatures increased with increasing biomass. A linear regression of ground-level temperatures with fuel load and ambient weather conditions of relative humidity and temperature was found to explain most of the variation in the data. Ground-level fire temperatures increased with increasing fuel load, but were also found to be lower at higher relative humidities at a given temperature. In order to reduce the intensity of forest fires that occur accidentally during the dry season, we recommend that fuel loads be reduced in the forest by prescribed burning early in the dry season. This applies especially to areas where there is accumulation of biomass over years, such as that of the tall grass Themeda cymbaria found predominantly in dry deciduous forest types. If prescribed burning is incorporated in fire management policies for these forests, then the season of burning will be important to consider. It is known from ecosystems where prescribed burning is regularly applied that early dry season fires are less intense than late dry season fires (Williams et al. 1998). However, this has not been systematically investigated for SDTFs. Through a burning experiment carried out in private land with vegetation type similar to tropical dry thorn forest, we investigated differences in area burnt, ground-level fire temperatures and soil temperatures one cm below the ground in the early dry season in January, late dry season in April and and early wet season in June. We also examined differences in fuel load, fuel moisture, soil moisture and weather conditions of ambient relative humidity (RH), temperature and wind speed in these phases; these factors could be responsible for observed differences in fire and soil temperatures or area burnt. Although area burnt was not significantly different between the early and late phases of the dry season, fire and soil temperatures were significantly lower in the former. The late dry season was characterized by distinctly higher fuel loads, lower fuel moisture, lower relative humidity, higher ambient temperatures and higher wind speeds compared that measured in the early dry season. Differences in soil temperature between these months may be attributed to the increase in fuel load since there were no significant differences in soil moisture. Fire spread was limited in the experimental plots in the early wet season in June, probably due to significantly higher levels of fuel moisture in this month; the resultant fire and soil temperatures recorded were low. Forest management should, therefore, consider early dry season burns in the month of January for prescribed burns in the sanctuary, although this would have to be tested in other SDTF vegetation types with more variable fuel load, fuel moisture and weather conditions. Fire’s influence on the biotic community: Concerns regarding the regeneration capacity of woody species in SDTFs have been voiced with respect to increasing frequencies of fire (Saha and Howe 2006, Kodandapani et al. 2008). Fire is known to cause high mortality of individuals of small size (Swaine et al. 1990, Suresh et al. 2010). However, mortality has been examined for large size classes, and not for seedlings. It is essential to understand the dynamics of seedlings and their contribution to the regeneration potential of SDTFs. Woody species in SDTFs are known to have traits that help them recover from recurring disturbances, such as sprouting from underground root stocks (Vieira and Scariot 2006). Another trait may relate to growth rates of seedlings. Growth rates of seedlings (defined in this study as established individuals between 10 and 100cm height) after dry season (February-March) fires were compared between adjacent pairs of burnt and unburnt transects established at eight sites in Mudumalai across vegetation types of moist deciduous, dry deciduous and dry thorn forest. The growth of grasses, a possible competitor for resources, was also monitored at each site. Seedling and grass heights were monitored at 3-month intervals between August 2009 and August 2010. A second fire in March 2010 affected transects at two sites in Mudumalai. Seedling and grass heights were monitored for two enumerations till August 2010 subsequent to the second fire at these two sites. A total of 1032 individuals across 58 woody species were enumerated. High seedling survivorship (>95%) was observed in both burnt and unburnt areas. Although seedling heights were significantly different between burnt and unburnt areas at the start of the enumeration in August 2009, heights were comparable within a year and a half of the fire. Comparable seedling heights in such a short time span were because of distinctly higher growth rates of seedlings in burnt areas compared to unburnt areas after the fire event, particularly during the pre-monsoon season. Grass biomass (volume), on the other hand, was significantly different between burnt and unburnt areas at both the first and last enumerations. Grass growth (change in volume) did not differ between burnt and unburnt areas. Rapid growth by seedlings after a fire implies adaptation through the use of stored resources for growth, possibly aided by lower competition from grasses, in order to attain a certain size before the subsequent return of unfavourable factors such as a recurrent fire event. Conclusions: The results from the study point to climatically driven fire regimes in an SDTF in southern India, with daily influences of weather conditions during the dry season on fire occurrences. Fire intensities increase with increasing fuel loads in these forests, moderated by weather conditions such as RH and temperature. Since fires are an anthropogenic phenomenon in these forests, active management with the use of prescribed fires in the early phase of the dry season is a possible option to control late dry season fires that would be higher in intensity. The current woody tree species assemblage in this southern Indian SDTF is resilient to fires at the seedling stage, with established individuals exhibiting high survivorship and rapid growth after a fire. However, the effects of fires of varying intensities on the regenerative capacity of the seedlings are not known. The effect of fire on habitat utilisation by large herbivores, or the impact of fire on the faunal community in general has not been studied for vegetation types that comprise SDTFs. The effect of fire exclusion on the ecology of SDTFs will provide useful information that can feed into management policies for this ecosystem type. These are potential areas of research for the future. Fire, if managed wisely, can be an effective tool for the conservation of SDTFs across south and southeast Asia.

The relative contributions of biome history and geological setting to historical assembly of species richness in biodiversity hotspots remain poorly understood. The tropical Andes is one of the world’s top biodiversity hotspots, and with its diverse biomes and the relatively recent but dramatic uplift, the Andes provides an ideal study system to address these questions. To gain insights into the historical species assembly of the tropical Andes, this study focuses on investigating patterns of plant species diversification in the Andean seasonally dry tropical forest (SDTF) biome. Three plant genera are used as study groups: Amicia (Leguminosae, Papilionoideae), Tecoma (Bignoniaceae), and Mimosa (Leguminosae, Mimosoideae). Species limits are re-evaluated to enable dense sampling of species and intraspecific diversity for phylogeny reconstruction for each group. Time-calibrated phylogenies for Amicia and Mimosa are presented and used to determine patterns of species diversification in time and space. For Tecoma, incongruence between nuclear and chloroplast gene trees precludes straightforward estimation of a species tree and this incongruence is attributed to possible reticulation caused by hybridization. Divergence time estimates and patterns of diversification for Amicia and Mimosa are compared with other Andean SDTF groups (Cyathostegia, Coursetia, Poissonia; Leguminosae) using isolation by distance and phylogenetic geographic structure analyses. Consistently deep divergences between sister species and high geographic structure across all five groups suggest that Andean SDTF lineages have persisted over the past 10 million years (My) with high endemism driven by dispersal limitation, caused by geographic isolation, following the most recent episode of rapid mountain uplift 5-10 My ago. This prolonged stasis of the Andean SDTF biome is in line with Miocene fossil and paleoclimate evidence. Finally, wider analyses of the contrasting evolutionary timescales of older SDTF and more recent high-altitude grassland diversity suggest that the exceptional plant species diversity in the Andes is the outcome of highly heterogeneous evolutionary histories reflecting the physiographical heterogeneity of the Andean biodiversity hotspot.

Neste estudo analisamos a diversidade e endemismos da flora lenhosa das florestas estacionais decíduas (FEDs) do norte e centro do Perú. Caracterizamos a diversidade das plantas lenhosas ao longo dos vales, para definir os valores de conservação da área a nível nacional. Os resultados indicam que as FEDs do vale do Marañón apresentam valores significativamente altos em endemias em relação às outras FEDs do Perú e FEDs vizinhas e o padrão de endemismos e estrutura populacional das espécies variam no gradiente geográfico e altitudinal. Em constraste, as FEDs do vale do rio Tambo, centro do Perú, são moderadamente ricas em espécies do que a média das FEDs neotropicais e apresentam escassos endemismos. Esta região necessita de mais esforços de pesquisas para conhecer mais profundamente os elementos da biodiversidade. Neste estudo, também realizamos a caracterização dendro-anatômica do lenho das árvores de 87 espécies, sendo o primeiro registro da anatomia da madeira das árvores dos dois vales. Das análises do lenho das 183 espécies registradas nas florestas do norte e centro do Perú, só 157 apresentam anéis de crescimento e precisam ser analisadas em detalhe com outras pesquisas de desenvolvimento cambial e técnicas tradicionais de análises dendrocronológicas. A derivação desta informação pode alcançar alto impacto em estudos de variabilidade climática e aplicações na conservação. Assim mesmo, a análise preliminar dendrocronológica das taxas de crescimento do tronco revelam que as árvores de Cedrela kuelapensis apresentam as taxas de crescimento mais altas e ressaltam como um excelente recurso para programas de reflorestamento nos vales interandinos, além, das populações endêmicas de Cordia iguaguana e Esenbeckia cornuta são principalmente de exemplares jovens. Esperamos que as informações dos cinco capítulos constituam-se uma eficiente e importante ferramenta para melhorar a gestão dos recursos florestais dos vales estudados. / In this study we analyzed the diversity and endemism of the woody flora of Seazonally dry tropical forests (SDTF) in northern and central Peru. We characterized the diversity of woody plants along the valleys to define the conservation values of the area at the national and international levels. The results indicate that the SDTF s of the Marañón Valley show surprisingly high values in endemics in relation to other SDTF s in Peru and neighboring SDTFs, and the pattern of endemism and population structure of the species varies in geographic and altitudinal grades. In contrast, the SDTFs of the Tambo River Valley, central Peru, are moderately rich in species that average the neotropical SDTFs and have scarce endemism. This region needs more efforts to get to know the elements of biodiversity more deeply. In this study, we also performed the dendroanatomic characterization of 87 species and is the first report of the anatomy of the wood for the two valleys. From the analysis of the wood of the 183 species recorded in the forests of northern and central Peru, only 157 have growth rings and need to be analyzed in detail with other studies of exchange rate development and traditional techniques of dendrochronological analysis. The derivation of this information can reach high impact in studies of climatic variability and conservation applications. Likewise, the preliminary dendrochronological analysis of growth rates reveals that Cedrela kuelapensis showed the highest growth rates and stands out as an excellent resource for reforestation programs in the inter-Andean valleys, in addition, Cordia iguaguana and Esenbeckia cornuta endemic populations are mainly from young individuals. We hope that the information in the five chapters constitutes in efficient and important tool to improve the management of forest resources in the valleys studied.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-03-30T13:02:00Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação_Daniela_Reis_FINAL.pdf: 1679628 bytes, checksum: 38cb33a0301c9b8b0b881b5bee95a35c (MD5) / Made available in DSpace on 2017-03-30T13:02:00Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação_Daniela_Reis_FINAL.pdf: 1679628 bytes, checksum: 38cb33a0301c9b8b0b881b5bee95a35c (MD5) Previous issue date: 2016-02-25 / Universidade Federal de Pernambuco / Florestas Secas são ecossistemas expostos às perturbações antrópicas crônicas (PAC) e estão entre os mais ameaçados por mudanças climáticas devido às previsões de aumento de temperatura e redução de precipitação. Apesar de parecerem gradativos, os efeitos podem ser também bastante deletérios para a biota deste ecossistema. Neste estudo, foi investigado se o aumento da PAC e a redução da precipitação afetam a comunidade e populações de plantas com NEFs e os atributos morfo-anatômicos destas glândulas de duas espécies da Caatinga. O estudo foi realizado no Parque Nacional do Catimbau, onde os indivíduos com NEFs presentes em 19 parcelas ao longo de dois gradientes independentes de PAC e de precipitação foram marcados e suas espécies identificadas. Para análise anatômica foram coletadas amostras de glândulas de Poincianella microphylla e Pityrocarpa moniliformis. Foram encontradas 28 espécies pertencentes a 5 famílias. A composição de espécies variou apenas ao longo do gradiente de precipitação. As abundâncias de Senegalia bahiensis e Senna velutina aumentaram com a precipitação enquanto Po. microhylla e Sapium glandulosum diminuíram. Em relação aos atributos morfológicos, apenas a largura do tecido secretor e o comprimento e largura das glândulas de Pi. moniliformis foram relacionados positivamente com a precipitação e não com o gradiente de perturbação. Nossos resultados indicam que a disponibilidade de água é um fator chave para a Caatinga uma vez que o nível de precipitação local tem uma influência mais forte sobre comunidades e populações de plantas com NEF que a PAC. / Dry forests are exposed to chronic anthropogenic disturbances (CAD) and are one of the ecosystems most threatened by climate changes due to future previsions involving increasing in temperature and decreasing in rainfall. Besides the effects seem to be gradual, they can be seriously deleterious for the biota of this ecosystem. In this study was investigated if an increasing in CAD and a reduction in rainfall level affect the community and population of EFN-bearing plants and the morph-anatomical characters of these glands in Caatinga. The study was carried out at the National Park of Catimbau (Pernambuco, Brazil), where individuals with EFNs were found in 19 plots through two independent gradients of CAD and rainfall where species were marked and then identified. For the morph-anatomical analyses were collected glands surveys of Poincianella microphylla and Pityrocarpa moniliformis. It was found 28 species belonging to 5 families. Species composition changed only through the rainfall gradient. The abundances of Senegalia bahiensis and Senna velutina were positively related to the rainfall, as Po. microhylla and Sapium glandulosum were negatively related. In relation to the morphological attributes only the width of secretory tissue and the lenght of glands of Pi. moniliformis were positively related with the rainfall and not with the disturbance gradient. The results indicate that water availability is a key factor for Caatinga once the rainfall level has stronger influence on communities and populations of plants bearing EFNs than PAC do.

Neste estudo analisamos a diversidade e endemismos da flora lenhosa das florestas estacionais decíduas (FEDs) do norte e centro do Perú. Caracterizamos a diversidade das plantas lenhosas ao longo dos vales, para definir os valores de conservação da área a nível nacional. Os resultados indicam que as FEDs do vale do Marañón apresentam valores significativamente altos em endemias em relação às outras FEDs do Perú e FEDs vizinhas e o padrão de endemismos e estrutura populacional das espécies variam no gradiente geográfico e altitudinal. Em constraste, as FEDs do vale do rio Tambo, centro do Perú, são moderadamente ricas em espécies do que a média das FEDs neotropicais e apresentam escassos endemismos. Esta região necessita de mais esforços de pesquisas para conhecer mais profundamente os elementos da biodiversidade. Neste estudo, também realizamos a caracterização dendro-anatômica do lenho das árvores de 87 espécies, sendo o primeiro registro da anatomia da madeira das árvores dos dois vales. Das análises do lenho das 183 espécies registradas nas florestas do norte e centro do Perú, só 157 apresentam anéis de crescimento e precisam ser analisadas em detalhe com outras pesquisas de desenvolvimento cambial e técnicas tradicionais de análises dendrocronológicas. A derivação desta informação pode alcançar alto impacto em estudos de variabilidade climática e aplicações na conservação. Assim mesmo, a análise preliminar dendrocronológica das taxas de crescimento do tronco revelam que as árvores de Cedrela kuelapensis apresentam as taxas de crescimento mais altas e ressaltam como um excelente recurso para programas de reflorestamento nos vales interandinos, além, das populações endêmicas de Cordia iguaguana e Esenbeckia cornuta são principalmente de exemplares jovens. Esperamos que as informações dos cinco capítulos constituam-se uma eficiente e importante ferramenta para melhorar a gestão dos recursos florestais dos vales estudados. / In this study we analyzed the diversity and endemism of the woody flora of Seazonally dry tropical forests (SDTF) in northern and central Peru. We characterized the diversity of woody plants along the valleys to define the conservation values of the area at the national and international levels. The results indicate that the SDTF s of the Marañón Valley show surprisingly high values in endemics in relation to other SDTF s in Peru and neighboring SDTFs, and the pattern of endemism and population structure of the species varies in geographic and altitudinal grades. In contrast, the SDTFs of the Tambo River Valley, central Peru, are moderately rich in species that average the neotropical SDTFs and have scarce endemism. This region needs more efforts to get to know the elements of biodiversity more deeply. In this study, we also performed the dendroanatomic characterization of 87 species and is the first report of the anatomy of the wood for the two valleys. From the analysis of the wood of the 183 species recorded in the forests of northern and central Peru, only 157 have growth rings and need to be analyzed in detail with other studies of exchange rate development and traditional techniques of dendrochronological analysis. The derivation of this information can reach high impact in studies of climatic variability and conservation applications. Likewise, the preliminary dendrochronological analysis of growth rates reveals that Cedrela kuelapensis showed the highest growth rates and stands out as an excellent resource for reforestation programs in the inter-Andean valleys, in addition, Cordia iguaguana and Esenbeckia cornuta endemic populations are mainly from young individuals. We hope that the information in the five chapters constitutes in efficient and important tool to improve the management of forest resources in the valleys studied.

Parmi les lignées des Caesalpinioideae (dans la famille des Leguminosae), l’un des groupes importants au sein duquel les relations phylogénétiques demeurent nébuleuses est le « groupe Caesalpinia », un clade de plus de 205 espèces, réparties présentement entre 14 à 21 genres. La complexité taxonomique du groupe Caesalpinia provient du fait qu’on n’arrive pas à résoudre les questions de délimitations génériques de Caesalpinia sensu lato (s.l.), un regroupement de 150 espèces qui sont provisoirement classées en huit genres. Afin d’arriver à une classification générique stable, des analyses phylogénétiques de cinq loci chloroplastiques et de la région nucléaire ITS ont été effectuées sur une matrice comportant un échantillonnage taxonomique du groupe sans précédent (~84% des espèces du groupe) et couvrant la quasi-totalité de la variation morphologique et géographique du groupe Caesalpinia. Ces analyses ont permis de déterminer que plusieurs genres du groupe Caesalpinia, tels que présentement définis, sont polyphylétiques ou paraphylétiques. Nous considérons que 26 clades bien résolus représentent des genres, et une nouvelle classification générique du groupe Caesalpinia est proposée : elle inclut une clé des genres, une description des 26 genres et des espèces acceptées au sein de ces groupes. Cette nouvelle classification maintient l’inclusion de douze genres (Balsamocarpon, Cordeauxia, Guilandina, Haematoxylum, Hoffmanseggia, Lophocarpinia, Mezoneuron, Pomaria, Pterolobium, Stenodrepanum, Stuhlmannia, Zuccagnia) et en abolit deux (Stahlia et Poincianella). Elle propose aussi de réinstaurer deux genres (Biancaea et Denisophytum), de reconnaître cinq nouveaux genres (Arquita, Gelrebia, Hererolandia, Hultholia et Paubrasilia), et d’amender la description de sept genres (Caesalpinia, Cenostigma, Coulteria, Erythrostemon, Libidibia, Moullava, Tara). Les résultats indiquent qu’il y aurait possiblement aussi une 27e lignée qui correspondrait au genre Ticanto, mais un échantillonage taxonomique plus important serait nécéssaire pour éclaircir ce problème. Les espèces du groupe Caesalpinia ont une répartition pantropicale qui correspond presque parfaitement aux aires du biome succulent, mais se retrouvent aussi dans les déserts, les prairies, les savanes et les forêts tropicales humides. À l’échelle planétaire, le biome succulent consiste en une série d’habitats arides ou semi-arides hautement fragmentés et caractérisés par l’absence de feu, et abrite souvent des espèces végétales grasses, comme les Cactacées dans les néo-tropiques et les Euphorbiacées en Afrique. L’histoire biogéographique du groupe Caesalpinia a été reconstruite afin de mieux comprendre l’évolution de la flore au sein de ce biome succulent. Ce portrait biogéographique a été obtenu grâce à des analyses de datations moléculaires et des changements de taux de diversification, à une reconstruction des aires ancestrales utilisant le modèle de dispersion-extinction-cladogenèse, et à la reconstruction de l’évolution des biomes et du port des plantes sur la phylogénie du groupe Caesalpinia. Ces analyses démontrent que les disjonctions trans-continentales entre espèces sœurs qui appartiennent au même biome sont plus fréquentes que le nombre total de changements de biomes à travers la phylogénie, suggérant qu’il y a une forte conservation de niches, et qu’il est plus facile de bouger que de changer et d’évoluer au sein d’un biome différent. Par ailleurs, contrairement à nos hypothèses initiales, aucun changement de taux de diversification n’est détecté dans la phylogénie, même lorsque les espèces évoluent dans des biomes différents ou qu’il y a changement de port de la plante, et qu’elle se transforme, par exemple, en liane ou herbacée. Nous suggérons que même lorsqu’ils habitent des biomes très différents, tels que les savanes ou les forêts tropicales humides, les membres du groupe Caesalpinia se retrouvent néanmoins dans des conditions écologiques locales qui rappellent celles du biome succulent. Finalement, bien que la diversité des espèces du biome succulent ne se compare pas à celle retrouvée dans les forêts tropicales humides, ce milieu se distingue par un haut taux d’espèces endémiques, réparties dans des aires disjointes. Cette diversité spécifique est probablement sous-estimée et mérite d’être évaluée attentivement, comme en témoigne la découverte de plusieurs nouvelles espèces d’arbres et arbustes de légumineuses dans la dernière décennie. Le dernier objectif de cette thèse consiste à examiner les limites au niveau spécifique du complexe C. trichocarpa, un arbuste des Andes ayant une population disjointe au Pérou qui représente potentiellement une nouvelle espèce. Des analyses morphologiques et moléculaires sur les populations présentes à travers les Andes permettent de conclure que les populations au Pérou représentent une nouvelle espèce, qui est génétiquement distincte et comporte des caractéristiques morphologiques subtiles permettant de la distinguer des populations retrouvées en Argentine et en Bolivie. Nous décrivons cette nouvelle espèce, Arquita grandiflora, dans le cadre d’une révision taxonomique du genre Arquita, un clade de cinq espèces retrouvées exclusivement dans les vallées andines. / Amongst the lineages of the Caesalpinioideae (in the family Leguminosae), one of the largest groups where phylogenetic relationships remains unclear is the Caesalpinia Group, a clade of ca. 200 species, currently considered to comprise between 14 and 21 genera. The taxonomic complexity of the Caesalpinia Group stems from persisting doubts on the generic delimitations within Caesalpinia sensu lato, a group of 150 species that are provisionally classified into eight genera. In order to establish a stable generic classification, phylogenetic analyses of five chloroplastic loci and the nuclear ribosomal ITS locus were carried out on a matrix containing an unprecedented taxonomic sampling of the Caesalpinia Group (~84% of species of this group included), with virtually all of the morphological variation and geographic distribution represented. These analyses allowed us to determine that several genera of the Caesalpinia Group, as currently defined, are polyphyletic or paraphyletic. We consider that there are 26 well-resolved clades that represent distinct genera, and a new generic classification system is proposed, which includes a key to genera, the description of the 26 genera and all species accepted within these groups. A total of twelve previously accepted genera are maintained in this classification (Balsamocarpon, Cordeauxia, Guilandina, Haematoxylum, Hoffmanseggia, Lophocarpinia, Mezoneuron, Pomaria, Pterolobium, Stenodrepanum, Stuhlmannia, and Zuccagnia), whereas two genea are abolished (Stahlia and Poincianella). In addition, two genera are re-instated (Biancaea and Denisophytum), five new genera are described, (Arquita, Gelrebia, Hererolandia, Hultholia and Paubrasilia), and the description of seven genera are emended (Caesalpinia, Cenostigma, Coulteria, Erythrostemon, Libidibia, Moullava, Tara). Our results also indicate that there could possible be a 27th lineage corresponding to the genus Ticanto, but an increased taxonomic sampling is needed to adequately address this issue. The Caesalpinia Group has a pantropical distribution that corresponds almost perfectly to the geographical distribution of the Succulent Biome, but are also found in deserts, grassland prairies, savannahs, and tropical rainforests. On a planetary scale, the Succulent Biome consists of a series of semi-arid to arid habitats that are highly fragmented, and which are characterised by the absence of fire, such as deserts and dry forests. This biome often harbours succulent plant taxa, such as the Cactaceae in the Neotropics and the Euphorbiaceae in Africa. The biogeographical history of the Caesalpinia Group was reconstructed in order to gain insight into the evolution of the flora within this Succulent biome. This biogeographical portrait of this group was reconstructed using molecular dating analysis, diversification rate shifts tests, the reconstruction of ancestral areas using the dispersal-extinction-cladogenesis model (DEC), as well as through ancestral character reconstruction of the biomes and habits. These analyses demonstrate that intercontinental disjunctions between sister species belonging to the same biome are more frequent than the total number of biome shifts across the phylogeny, suggesting that there is a strong conservation of niches, and that it is easier to move than to switch to and evolve in a different biome. Furthermore, contrary to our initial hypothesis, no changes in diversification rates were detected in our phylogenies, even when species switched biomes or evolved a different plant habit, e.g. becoming lianas or herbaceous perennials. We suggest that even when members of the Caesalpinia Group inhabit different biomes, such as savannahs or tropical rainforests, they are still tracking local ecological conditions that are typical of the Succulent biome. Finally, while total plant species diversity in the Succulent Biome does not compare to the diversity found in tropical rainforests, this biome distinguishes itself by a high number of endemic species, distributed in disjunct patches across the world. This species diversity is probably under-estimated and needs to be carefully re-evaluated, as shown in several recent descriptions of new tree and shrub species from the Succulent biome, all published in the last decade. The last objective of this thesis is to examine the species limits in Caesalpinia trichocarpa, a shrub from the Andes that has a disjunct population in Peru, which potentially represents a new species. Morphological and molecular analyses of populations occurring across the Andes, including Bolivia and Argentina, allow us to conclude that the populations in Peru represent a new species, which is genetically distinct and has subtle morphological characteristics that allow it to be distinguished from populations found in Argentina and Bolivia. We describe this news species, Arquita grandiflora, in a taxonomic revision of the genus Arquita, a clade of five species found exclusively in Andean valleys.

Orientador: Célio Fernando Baptista Haddad / Resumo: Nesta tese exploramos a diversificação de espécies de anuros da Tribo Lophyohylini distribuídas na Mata Atlântica (MA) e Caatinga, biomas do Brasil. Para tanto, utilizamos dados genômicos e métodos de filogeografia estatística para analisá-los, uma abordagem robusta e até então ainda escassa na filogeografia dos organismos sul-americanos. Através do sequenciamento Sanger amostramos trechos de DNA mitocondrial (mtDNA) e através do sequenciamento de alto rendimento obtivemos polimorfismos de nucleotídeo único (SNPs) do DNA nuclear (nDNA). No primeiro capítulo, reunimos 82 amostras da espécie Aparasphenodon brunoi que apresenta distribuição nas terras baixas e costeiras do bioma MA, sendo considerada ideal para investigar o papel da instabilidade climática do Pleistoceno em seu processo de diversificação. Ainda no primeiro capítulo, para avaliar a influência do comportamento filopátrico, associado às diferenças no modo reprodutivo, na dispersão e consequentemente, no fluxo gênico entre populações, reunimos 72 amostras de A. arapapa e A. aff. brunoi. Estas tratam-se de espécies simpátricas, de distribuição mais restrita e com modos reprodutivos contrastantes o que as tornam ideais para esse tipo de comparação. De acordo com a inferência baseada em modelos demográficos, por volta do último máximo glacial (UMG) a população norte de A. brunoi se manteve estável enquanto que a do sul experimentou um gargalo seguido de expansão recente. Além disso, a população norte de A. brunoi apres... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: In this dissertation we explored the diversification of anuran species of the Lophyohylini Tribe distributed in the Atlantic Forest (AF) and Caatinga biomes of Brazil. To do so, we used genomic data and methods of statistical phylogeography to analyze them, a robust and until then still scarce approach in the phylogeography of South American organisms. Through the Sanger sequencing we sampled mitochondrial DNA (mtDNA) and through high-throughput sequencing we obtained single nucleotide polymorphisms (SNPs) from nuclear DNA (nDNA). In the first chapter, we collected 82 samples of the species Aparasphenodon brunoi that is distributed in the low and coastal lands of the AF biome, being considered ideal to investigate the role of Pleistocene climatic instability in its diversification process. In the first chapter, to evaluate the influence of philopatric behavior, associated with differences in reproductive mode, dispersion and consequent gene flow among populations, we also collected 72 samples of A. arapapa and A. aff. brunoi species. These are sympatric species with a narrower distribution and with contrasting reproductive modes, making them ideal for this type of comparison. According to the inference based on demographic models, around the last glacial maximum (LGM) the northern population of A. brunoi remained stable while the southern one experienced a bottleneck followed by recent expansion. In addition, the northern population of A. brunoi exhibits greater nuclear diver... (Complete abstract click electronic access below) / Doutor