Dissertations / Theses on the topic 'Biodiversity hotspots'

Det svenska kulturlandskapet har förändrats radikalt under de senaste 200 åren från ett varierat och heterogent landskap till ett mer monotont, homogeniserat landskap som följd av att olika former av mänskligt resursutnyttjande har effektiviserats. Detta har lett till en fragmentering av livsmiljöerna för flera av kulturlandskapets arter. Kraftledningsgator kan tänkas hysa naturtyper som påminner om vissa av de nu försvunna eller fragmenterade livsmiljöerna (t ex betad skogsmark och vissa typer av ängsmarker) och skulle kunna ha en viktig betydelse som reträttplats och/eller spridningskorridor för dessa arter.

I en fallfällsinventering i Köpings och Strängnäs kommun i Mälardalen undersöktes förekomst och abundans av marklevande evertebrater i kraftledningsgator, skog och betesmark. Jämförelser i förekomst och abundans gjordes mellan dessa marktyper (d v s kraftledningsgator, skog och betesmark), samt mellan positioner inom kraftledningsgator (centrala och distala delar) och närliggande skogsmark. Jämförelserna innefattade dels analyser av artantal (eller snarare antal taxa) och flera olika biodiversitetsindex och dels analyser av likhet i artförekomst och individantal med "likhetsindex" (similarity index). Separata analyser gjordes inom olika taxonomiska grupper (t ex alla taxa, endast inom insekter, endast inom spindeldjur). Antalet replikat tillät statistisk testning av eventuella mönster i antal taxa och biodiversitetsindex.

Inga signifikanta skillnader dokumenterades, varken mellan de olika marktyperna eller mellan positioner inom kraftledningsgator och närliggande skog. Vi tolkar dessa resultat som att kraftledningsgator med avseende på antal taxa respektive biodiversitet inte är (signifikant) sämre än skogs- eller betesmark. Det kan betonas att det inte heller fanns något konsekvent (icke-signifikant) mönster som pekade på att så skulle vara fallet. Antal taxa och biodiversitetsindex tar ingen hänsyn till vilka arter eller taxa som ingår i analyserna. En naturtyp som hyser en individ- och artrik fauna bestående av oönskade arter (introducerade arter, "skadedjur" etc.) registrerar t ex ett högre biodiversitetsindex än en naturtyp med fåtaligt förekommande rödlistade, skyddsvärda arter. Likhetsindex belyser bättre vilka arter som är inblandade. Visserligen tas inte heller här hänsyn till exakt vilka arter som ingår (eller deras eventuella önskvärdhet eller skyddsvärde), men ett högt index indikerar att samma arter förekommer i de jämförda naturtyperna. I denna studie indikerar ett högt likhetsindex dessutom att antalet individer av de inblandade arterna är likartat, eftersom ett index som tar hänsyn till abundans användes.

Resultaten visade överlag höga likhetsindex, speciellt verkade kraftledningsgator och skogsmark hysa likartad evertebratfauna medan likheten mellan kraftledningsgator och betesmark var mindre uttalad. Sammanfattningsvis indikerar studien att kraftledningsgator inte verkar vara lågvärdiga livsmiljöer för de marklevande evertebrat-taxa som ingått i studien. Vi föreslår att kraftledningsgator med väl avvägda rutiner för röjning och skötsel skulle kunna spela en viktig roll i skapandet av artrika kantzoner eller marker som liknar ängs- eller betesmarker med svag hävd.

As a consequence of the intensification of various forms of human resource utilization rural Sweden has changed radically over the past 200 years from offering a varied and diverse landscape to a more monotonous, homogenised type of environment. This has led to fragmentation of habitats for many of the species occurring. Power line corridors might harbour habitats that resemble some of the now lost or fragmented habitats (e.g. grazed forest land and certain types of meadow), and could have important functions as refuge habitats and / or distribution corridors for these species.

In a pitfall trap study in Köping and Strängnäs municipalities in Mälardalen, the occurrence and abundance of ground-living invertebrates were investigated in power line corridors, adjoining forest and pastures. Comparisons were made between these habitat types, and between positions within the power line corridor (central and distal parts) and the nearby forested area. The comparisons included analysis of number of species (or rather the number of taxa) and several biodiversity indexes, as well as analysis of the similarity of the occurrence of certain species and individual numbers by use of "similarity index". Separate tests were made in different taxonomic groups (e.g. all taxa, only within insects, only within spiders). The number of replicates allowed statistical testing of patterns in the number of taxa and biodiversity index.

No significant differences were documented, neither between the different habitat types, nor between positions in the power line corridors and nearby forest. There was also no consistent (non-significant) pattern indicating that this would be the case. We suggest these results to indicate that power line corridors at least are not (significantly) poorer quality habitats than are forest or pasture land with regard to number of taxa and biodiversity. Number of taxa and biodiversity indices take no account of the species or taxa included in the analysis. Thus the same weight is assigned to an unwanted species (e.g. an invasive pest species or parasite) as to a red-listed, highly valued species. Similarity index takes more heed to the species involved. Although similarity indices do not consider the exact identity of involved species (or their possible value or desirability), a high index value indicates that the same species occur in the compared habitats. In this study, where an index that takes into account the abundance of species was used, a high similarity index value also indicates that the numbers of individuals are similar.

Overall, the results showed high similarity between habitat types. This would suggest that, to a large extent, power lines, forest and pasture land had the same composition of taxa, and that the taxa had similar abundances. Power lines and forest seemed to exhibit particularly high similarities, whereas the similarity between power lines and pasture land was less pronounced. Thus, this study indicates, in contrast to several previous suggestions, that power line corridors do not seem to be low quality habitats. We also suggest that power line corridors with well designed management routines could play an important role creating edges and habitats resembling meadow or low intensity grazed pasture land.

Thesis (Honors)--Ohio State University, 2006.
Title from first page of PDF file. Document formattted into pages: contains 32 p.; also includes graphics. Includes bibliographical references (p. 17-19). Available online via Ohio State University's Knowledge Bank.

The south-western tip of Africa holds unique levels of species richness and endemism, and contains two hotspots of biodiversity: the Cape Floristic Region and the Succulent Karoo. Several hypotheses have been proposed to explain the radiation of the region’s diverse flora. However, due to the lack of comprehensive, comparative studies, the major forces that drive plant diversification have remained unclear. My thesis combines near-complete specieslevel molecular phylogenies with detailed biological, ecological and biogeographical information to investigate the evolutionary processes generating southern Africa's exceptional plant diversity. I demonstrate that in the genus Babiana (Iridaceae) climatic niches retain a high degree of phylogenetic conservatism, and show that species of Babiana were only able to successfully extend their range into new biomes with the establishment of more favourable climates. Additionally, results indicate that floral characters in Babiana evolve according to a new 'reversible shift' model, which better explains the evolution of pollination systems through multi-directional transitions in a diverse pollinator environment. These findings challenge the commonly held idea that floral specialisation is an evolutionary dead-end and offer new perspectives towards our understanding of plant-pollinator interactions. Analyses of a comprehensive data set of four large Cape clades show that the temporal dynamics of plant radiations in southern Africa confirm that the flora represents a combination of ancient and young radiations, and that diversification rates have remained constant through time. Finally, I reveal that although several biotic and abiotic factors contribute to the diversity, soil-type shifts is the most important driver of plant diversification in southern Africa. Together with complex geomorphological conditions, this factor, rather than pollinator specialisation or phenological divergence, has given rise to the exceptional diversity found in this region today. Comparisons with other biodiversity hotspots, especially those with Mediterranean climates, will reveal whether this is a global scenario for the evolution of hyper-diverse floras.

Groundwater (GW) -fed streams are a common feature of paraglacial floodplains and are regarded as ‘biodiversity hotspots’, due to their role as valuable aquatic habitats. The hydrological dynamics which support GW-fed streams remain poorly understood. There is a need to improve understanding given paraglacial environments are extremely sensitive to the impacts of climate change. To address this significant knowledge gap site specific research was conducted on GW-fed streams within Denali National Park & Preserve, Alaska, during 2013 and 2014. Hydrometric, hydrochemical, hydrogeomorphic, and geophysical techniques were utilised to improve understanding of the hydrological dynamics and hydrogeomorphic controls that influence GW-fed stream occurrence. Paleochannels across paraglacial floodplains were identified as important preferential flow pathways (PFPs); and a first-order control upon GW-fed streams. In addition hillslope-runoff was established as an important hydrological flux to GW-fed streams. Colluvial deposits (e.g. talus cones) were highlighted as valuable hydrological stores on valleys-sides that made a direct contribution to streamflow. This research has raised concerns about the long-term stability of GW-fed streams in paraglacial environments due to changes in hydrogeomorphic controls (PFPs). It has also raised more immediate concerns about the short- to medium-term implications of shifting hydrologic regimes (e.g. declining winter snowpack) for GW-fed streams.

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

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

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

Myers first identified the world’s 25 biodiversity hotspots and pioneered innovative ideas about the usefulness of biodiversity models for establishing long-term resource conservation strategies at global scales. Since Myers, most of the subsequent studies using hotspot science for biodiversity modeling have used large spatial scales like countries, provinces or states, and other biogeoraphic regions. The California Floristic Province continues to be one of the recognized global biodiversity hotspots. Our study site, San Luis Obispo County is within this hotspot and we created a map of plant biodiversity hotspots at the county scale using GIS technology. We wanted to determine the effectiveness and applicability of biodiversity hotspot mapping at this scale with anticipation that the map will serve as a new tool for establishing long-term resource conservation strategies in the County. Our plant biodiversity hotspot map is based on distribution data collected from herbarium specimens of San Luis Obispo County’s rare flora. These data were extracted from the Hoover Herbarium at Cal Poly and manually digitized into GIS. We built a model with GIS to identify, locate, and quantify the resultant hotspots from the data. The overall approach was successful at identifying and quantifying the attributes and geographic extents of plant biodiversity hotspots at the county scale. Our results are highly applicable for establishing local and regional plant conservation priorities at lower resolutions, which is frequently where land acquisition and reserve establishment occurs. We conclude that biodiversity hotspot modeling with GIS is an effective tool that can be applied to many other finer-scale biological inventories for conservation purposes.

The aims of this study were to develop a detailed record of the tetranychid mites of Kenya and Tanzania, to assess the diversity of tetranychid mites in the east African biodiversity hotspots and to determine female characters that can be used to identify the species of the economically important Tetranychus species found in these countries. The genetic diversity of the most abundant Tetranychus species (Tetranychus evansi Baker & Pritchard) was also assessed. The Tetranychidae (Acari) contain some of the most important pest species of phytophagous mites worldwide. Out of the almost 1,300 species in this family, 256 species are known to occur in Africa. Before this study, ten species had been reported from Kenya and only three in Tanzania. The genus Tetranychus to which most of the pest species belongs to, can only be identified to species level by the use of the male aedeagus that is often difficult to visualize. The natural habitat, the Eastern Arc Mountains and East African Coastal Forests in Kenya and Tanzania is recognized as biodiversity hotspots but prior to his study, information on Tetranychidae in these hotspots was lacking. Thus, no information on the natural mite fauna composition was available. In Kenya, 18 tetranychid mite species from various plant hosts have been recorded. Four of these species belong to the subfamily Bryobiinae and the other 14 to the subfamily Tetranychinae. Eight of the mite species identified belong to the genera Bryobia, Petrobia, Peltanobia, Paraplonobia, Duplanychus, Eutetranychus and Mixonychus and are being reported for the first time in Kenya while the other ten had already been reported before. For Tanzania, six species belonging to the genera Tetranychus, Eutetranychus and Mixonychus are being reported for the first time from Tanzania and other three had been reported before. A list of these species, their brief descriptions as well as a key for identification is provided. A redescription of Peltanobia erasmusi including previously undescribed male characters is given. Schizotetranychus kwalensis sp. nov. from Kenya and Brevinychus meshacki from Tanzania were collected on Omorcarpum kirkii (Fabaceae) from Matuga, Kwale district, Kenya and Philonoptera eriocalyx (Fabaceae) from Sangasanga, Mvomero district, Tanzania respectively and described. Revised keys of Brevinychus and of the African species of Schizotetranychus are also provided. Tetranychus evansi Baker & Pritchard ranked highest in abundance amongst all the tetranychid mites collected. It was found in four out of five fragments of the hotspot, and it survives in a wide range of altitudes from as low as 123 m to 1655 m. Molecular examination of T. evansi collected from Kenya and Tanzania and on different host plants revealed an identical DNA sequence of the mitochondrial COI fragment and 19 identical microsatellite alleles suggesting a single introduction of this species to this part of East Africa. Female characters of four Tetranychus species found in Kenya were explored using the scanning electron microscope. Differences in the distances between the duplex setae of species belonging to the desertorum group (Tetranychus evansi Baker & Pritchard and Tetranychus ludeni Zacher) and those grouped by Flechtmann and Knihinicki (2002) under group 9 (Tetranychus neocaledonicus Andre and Tetranychus urticae Koch) were observed. The dorsal striae of T. evansi, T. neocaledonicus and T. urticae have semicircular lobes whereas those on the dorsal striae of T. ludeni are triangular.
Thesis (PhD (Environmental Sciences))--North-West University, Potchefstroom Campus, 2012.

Les diatomées (Stramenopiles, Bacillariophyceae) jouent un rôle important sur le plan écologique et sont l'un des groupes phytoplanctoniques les plus divers, avec environ 1800 espèces planctoniques estimées. Bien que largement étudiées, leurs modèles de diversité et de distribution biogéographique ne sont pas bien connus. L'avènement du séquençage de l'ADN à haut débit a révolutionné les études de biodiversité moléculaire facilitant la compréhension de la biogéographie, de la structure des communautés et des processus écologiques. Les deux principaux objectifs de cette thèse sont (1) d'enquêter sur les modèles de la biodiversité mondiale et la structure des communautés de diatomées planctoniques à travers les océans du monde, et (2) de comprendre les mécanismes et processus déterminants la structure de la communauté. Cette thèse présente également une première tentative de discerner la répartition des espèces rares dans les communautés de protistes. L'étude a été réalisée en utilisant les données de metabarcoding générées à partir des échantillons biologiques et des données environnementales associées recueillies au cours de la campagne Tara Oceans (2009-2013), une circumnavigation globale couvrant toutes les principales provinces océaniques. Le matériel d’étude pour cette thèse est constitué d’un total de 12 millions de séquences de la sous unité V9 du 18S ribosomal (barcode), récoltées à partir de 46 stations soit 293 échantillons. Basée sur 63371 metabarcodes de diatomées uniques, cette étude présente une évaluation approfondie de la distribution mondiale des diatomées et de leur diversité. Les analyses révèlent des faits marquants liées à la biogéographie des diatomées, par exemple une nouvelle estimation du nombre total d'espèces de diatomées planctoniques, une diversité considérable inconnue, une diversité exceptionnellement élevée en haute mer, et des patrons de diversité complexes entre les provinces océaniques. La thèse examine ensuite les facteurs qui déterminent les modèles de bêta-diversité. Les résultats suggèrent que les diatomées sont des communautés structurées et réglementées par l'hétérogénéité de l'environnement et des processus spatiaux. Néanmoins, la majorité de la variation totale dans la composition de la communauté ne peut être expliquée ni par les facteurs environnementaux, ni par les distances spatiales, ce qui justifie les analyses futures se concentrant sur les interactions biologiques, les événements historiques, et d'autres facteurs qui ne sont pas considérés. La thèse décrit en outre une approche pour caractériser les clusters significativement associés de ribotypes concomitants. Enfin, une étude préliminaire de communautés de protistes fractionnées par taille révèle que la queue (de leurs distributions rang abondance) semble suivre un comportement en loi de puissance dans presque toutes les communautés de protistes. Cette observation peut indiquer un mécanisme universel potentiel qui peut expliquer l'organisation de communautés planctoniques marines. De façon générale, ce travail présent une perspective globale et complète de la distribution et de la diversité des diatomées dans les océans du monde. La thèse propose un cadre global pour l'évaluation de la diversité mondiale basée sur le metabarcoding, qui pourra être utilisé pour étudier la distribution et la diversité des autres lignées taxonomiques. Par conséquent, ce travail fournit un point de référence pour explorer comment les communautés microbiennes feront face à la variation des conditions environnementales
Diatoms (Stramenopiles, Bacillariophyceae) are an ecologically important and one of the most diverse phytoplanktonic groups, with an estimated ~1,800 marine planktonic species. Although widely studied, their diversity and biogeographic distribution patterns are not well known. The advent of high-throughput DNA sequencing has revolutionized molecular biodiversity studies facilitating the understanding of biogeography, community assembly and ecological processes. The two major goals of this thesis are (1) to investigate global biodiversity patterns and structure of marine planktonic diatom communities across the world’s oceans, and (2) to understand the mechanisms and processes determining their community structure and assembly. This thesis also presents an initial attempt to discern the distribution of rare species in protist communities. The study was conducted using the metabarcoding data generated from the biological samples and associated environmental data collected during the Tara Oceans (2009-2013) global circumnavigation covering all major oceanic provinces. A total of ~12 million diatom V9-18S rDNA tags from 46 sampling stations, constituting 293 size fractionated samples represent the study material for the thesis. Using 63,371 unique diatom metabarcodes, this study presents an in-depth evaluation of global diatom distribution and diversity. The analyses study draw a number of revelations related to diatom biogeography, e.g. a new estimate of the total number of planktonic diatom species, a considerable unknown diversity, exceptionally high diversity in the open ocean, complex diversity patterns across oceanic provinces. The thesis then looks into the factors determining the beta-diversity patterns. The results suggest that diatoms represent biogeographically structured ecological communities regulated by both environmental heterogeneity and spatial processes. Nonetheless, the majority of the total variation in community composition remained unexplained by either the examined measured environmental factors or spatial distances, which warrants future analyses focusing on biological interactions, historical events, and other factors that are not considered. The thesis further outlines an approach to characterize significantly associated clusters of co-occurring ribotypes. Finally, a preliminary study of size-fractionated protistan communities reveals that the tail (of their rank-abundance distributions) appears to follow a power-law behavior in almost all protistan communities. This observation may indicate a potential universal mechanism which can explain the organization of marine planktonic communities. In general, this work has presented a global comprehensive perspective on diatom distribution and diversity in the world’s oceans. The thesis offers an overall framework for metabarcoding-based global diversity assessments which in turn can be employed to study distribution and diversity of other taxonomic lineages. Consequently, this work provides a reference point to explore how microbial communities will respond/change in response to environmental conditions

Chi ha la responsabilità di gestire un’area protetta non solo deve essere consapevole dei problemi ambientali dell’area ma dovrebbe anche avere a disposizione dati aggiornati e appropriati strumenti metodologici per esaminare accuratamente ogni singolo problema. In effetti, il decisore ambientale deve organizzare in anticipo le fasi necessarie a fronteggiare le prevedibili variazioni che subirà la pressione antropica sulle aree protette. L’obiettivo principale della Tesi è di natura metodologica e riguarda il confronto tra differenti metodi statistici multivariati utili per l’individuazione di punti critici nello spazio e per l’ordinamento degli “oggetti ambientali” di studio e quindi per l’individuazione delle priorità di intervento ambientale. L’obiettivo ambientale generale è la conservazione del patrimonio di biodiversità. L’individuazione, tramite strumenti statistici multivariati, degli habitat aventi priorità ecologica è solamente il primo fondamentale passo per raggiungere tale obiettivo. L’informazione ecologica, integrata nel contesto antropico, è un successivo essenziale passo per effettuare valutazioni ambientali e per pianificare correttamente le azioni volte alla conservazione. Un’ampia serie di dati ed informazioni è stata necessaria per raggiungere questi obiettivi di gestione ambientale. I dati ecologici sono forniti dal Ministero dell’Ambiente Italiano e provengono al Progetto “Carta della Natura” del Paese. I dati demografici sono invece forniti dall’Istituto Italiano di Statistica (ISTAT). I dati si riferiscono a due aree geografiche italiane: la Val Baganza (Parma) e l’Oltrepò Pavese e Appennino Ligure-Emiliano. L’analisi è stata condotta a due differenti livelli spaziali: ecologico-naturalistico (l’habitat) e amministrativo (il Comune). Corrispondentemente, i risultati più significativi ottenuti sono: 1. Livello habitat: il confronto tra due metodi di ordinamento e determinazione delle priorità, il metodo del Vettore Ideale e quello della Preminenza, tramite l’utilizzo di importanti metriche ecologiche come il Valore Ecologico (E.V.) e la Sensibilità Ecologica (E.S.), fornisce dei risultati non direttamente comparabili. Il Vettore Ideale, non essendo un procedimento basato sulla ranghizzazione dei valori originali, sembra essere preferibile nel caso di paesaggi molto eterogenei in senso spaziale. Invece, il metodo della Preminenza probabilmente è da preferire in paesaggi ecologici aventi un basso grado di eterogeneità intesa nel senso di differenze non troppo grandi nel E.V. ed E.S. degli habitat. 2. Livello comunale: Al fine di prendere delle decisioni gestionali ed essendo gli habitat solo delle suddivisioni naturalistiche di un dato territorio, è necessario spostare l’attenzione sulle corrispondenti unità amministrative territoriali (i Comuni). Da questo punto di vista, l’introduzione della demografia risulta essere un elemento centrale oltre che di novità nelle analisi ecologico-ambientali. In effetti, l’analisi demografica rende il risultato di cui al punto 1 molto più realistico introducendo altre dimensioni (la pressione antropica attuale e le sue tendenze) che permettono l’individuazione di aree ecologicamente fragili. Inoltre, tale approccio individua chiaramente le responsabilità ambientali di ogni singolo ente territoriale nei riguardi della difesa della biodiversità. In effetti un ordinamento dei Comuni sulla base delle caratteristiche ambientali e demografiche, chiarisce le responsabilità gestionali di ognuno di essi. Un’applicazione concreta di questa necessaria quanto utile integrazione di dati ecologici e demografici viene discussa progettando una Rete Ecologica (E.N.). La Rete cosi ottenuta infatti presenta come elemento di novità il fatto di non essere “statica” bensì “dinamica” nel senso che la sua pianificazione tiene in considerazione il trend di pressione antropica al fine di individuare i probabili punti di futura fragilità e quindi di più critica gestione.
Who has the responsibility to manage a conservation zone, not only must be aware of environmental problems but should have at his disposal updated databases and appropriate methodological instruments to examine carefully each individual case. In effect he has to arrange, in advance, the necessary steps to withstand the foreseeable variations in the trends of human pressure on conservation zones. The essential objective of this Thesis is methodological that is to compare different multivariate statistical methods useful for environmental hotspot detection and for environmental prioritization and ranking. The general environmental goal is the conservation of the biodiversity patrimony. The individuation, through multidimensional statistical tools, of habitats having top ecological priority, is only the first basic step to accomplish this aim. Ecological information integrated in the human context is an essential further step to make environmental evaluations and to plan correct conservation actions. A wide series of data and information has been necessary to accomplish environmental management tasks. Ecological data are provided by the Italian Ministry of the Environment and they refer to the Map of Italian Nature Project database. The demographic data derives from the Italian Institute of Statistics (ISTAT). The data utilized regards two Italian areas: Baganza Valley and Oltrepò Pavese and Ligurian-Emilian Apennine. The analysis has been carried out at two different spatial/scale levels: ecological-naturalistic (habitat level) and administrative (Commune level). Correspondingly, the main obtained results are: 1. Habitat level: comparing two ranking and prioritization methods, Ideal Vector and Salience, through important ecological metrics like Ecological Value (E.V.) and Ecological Sensitivity (E.S.), gives results not directly comparable. Being not based on a ranking process, Ideal Vector method seems to be used preferentially in landscapes characterized by high spatial heterogeneity. On the contrary, Salience method is probably to be preferred in ecological landscapes characterized by a low degree of heterogeneity in terms of not large differences concerning habitat E.V. and E.S.. 2. Commune level: Being habitat only a naturalistic partition of a given territory, it is necessary, for management decisions, to move towards the corresponding administrative units (Communes). From this point of view, the introduction of demography is an essential element of novelty in environmental analysis. In effect, demographic analysis makes the goal at point 1 more realistic introducing other dimensions (actual human pressure and its trend) which allows the individuation of environmentally fragile areas. Furthermore this approach individuates clearly the environmental responsibility of each administrative body for what concerns the biodiversity conservation. In effect communes’ ranking, according to environmental/demographic features, clarify the responsibilities of each administrative body. A concrete application of this necessary and useful integration of ecological and demographic data has been developed in designing an Ecological Network (E.N.).The obtained E.N. has the novelty to be not “static” but “dynamic” that is the network planning take into account the demographic pressure trends in the individuation of the probable future fragile points.

Les écosystèmes ultramafiques (serpentiniques) de Nouvelle-Calédonie sont considérés comme des « hotspots » de la biodiversité, notamment en raison des pressions adaptatives exercées par des conditions édaphiques drastiques. En effet, ces sols, résultant de l'altération naturelle du manteau océanique, sont composés de plus de 85% d'oxydes de fer, sont déficients en N, P, K, déséquilibrés en Ca/Mg et riches en métaux lourds (Ni, Cr, Mn, Co). Dans les associations entre végétaux et microorganismes du sol, les deux partenaires jouent un rôle essentiel dans l'adaptation aux conditions édaphiques, essentiellement au niveau de la tolérance aux métaux lourds. Dans notre étude, nous avons choisi des espèces endémiques du genre Tristaniopsis (Myrtaceae) comme plantes modèles pour étudier le rôle des champignons ectomycorhiziens et des bactéries associées à l'adaptation des plantes au nickel. Pour étudier l'effet des sols ultramafiques sur la diversité des ectomycorhizes et des bactéries mycorhizosphériques, ainsi que sur les déterminants génétiques de résistance/adaptation des bactéries associées, environ 150 ectomycorhizes ont été échantillonnées à partir de quatre sites ultramafiques (trois au massif du Koniambo et un dans la forêt de Desmazures) et deux non-ultramafiques reposant sur des sols volcano-sédimentaires (site d'Arama). La caractérisation génotypique et phylogénétique des ectomycorhizes et des bactéries mycorhizosphériques obtenues a révélé la présence d'une grande diversité de champignons (principalement Cortinarius, Pisolithus, Russula, Boletellus) et de bactéries (Pseudomonas, Burkholderia, Bacillus) dans les deux types de sols, avec une richesse spécifique particulièrement élevée dans les sols ultramafiques. De plus, les bactéries mycorhizosphériques provenant des sols ultramafiques avaient des proportions significativement plus élevées d'isolats portant les gènes nreB et cnrT que celles issues des sols volcano-sédimentaires. Une forte corrélation positive a également été observée entre l'occurence de ces gènes, connus pour conférer la tolérance aux métaux lourds chez les bactéries, et la tolérance des isolats au nickel en culture pure. La récente mise en évidence de souches bactériennes mycorhizosphériques Ni-tolérantes et promotrices de la croissance de Pisolithus albus en co-culture doivent permettre d'identifier des bactéries auxiliaires de la mycorhization qui pourront être ensuite exploitées dans le cadre de programmes de revégétalisation de sites ultramafiques miniers en Nouvelle Calédonie
New Caledonian ultramafic (serpentine) ecosystems are considered as hotspots of biodiversity, partly because of the adaptative pressure exerted by drastic edaphic conditions. Indeed these soils resulting from natural weathering of oceanic mantle could be composed of up to 85 % of iron oxides and are deficient in N.P.K., unbalance for the Ca/Mg ratio and rich in heavy metals Ni, Cr, Mn, Co. Both plant and soil microbes play a vital role in the adaptation to soil conditions mainly heavy metal uptake and tolerance. In our study, we choose endemic species of the genus Tristaniopsis (Myrtaceae) as model plant to study the role of ectomycorrhizal fungi and associated bacteria in plant adaptation to nickel. To investigate the effect of ultramafic soils on ectomycorrhiza and mycorrhizosphere bacteria diversities as well as on the genetic determinants of resistance/adaptation of associated mycorrhizosphere bacteria, 200 ectomycorrhizas were sampled from four different ultramafic sites (3 in Koniambo and 1 in Desmazures forest) vs two non-ultramafic ones from volcano-sedimentary soils (Arama). Molecular characterization of ectomycorrhiza (rRNA ITS) and associated mycorrhizosphere bacteria (16S rRNA) from these samples showed the presence of different fungi (Pisolithus albus, Russula spp., Boletellus spp.) and bacteria (Burkholderia spp., Bacillus spp., Pseudomonas spp.) that can be found in both soils. However, bacteria isolated from ultramafic soils could grow in the presence of Ni up to 20 mmol L-1 and contained cnrA and nreB genes, known to confer heavy metal tolerance, contrary to bacteria isolated from non-ultramafic soils. Moreover, we found a strong positive correlation between heavy metal tolerance and P-solubilizing ability. Further knowledge on functional diversity of ectomycorrhiza-mycorrhizosphere bacteria associations and its role in the adaptation of plants to ultramafic soils would help in the understanding of plant functioning on New Caledonian mine sites

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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.

L’Algérie est un cas d’école en matière d’ignorance en biodiversité. A ce jour, on ne dispose d'aucun inventaire complet pour aucun taxon ni aucun atlas à l’échelle du pays ! Pourtant, l’Algérie est d’une grande importance pour la biodiversité mondiale. La façade littorale de l’Algérie fait partie du hostpot de biodiversité mondial qui est le pourtour méditerranéen et compte plusieurs points rouges de biodiversité régionaux. Par ailleurs, la partie saharienne contient une diversité d’organismes endémiques adaptés aux fortes conditions de sécheresse. Les autorités algériennes déploient un projet ambitieux pour la conservation en fixant 50 % de la surface du pays comme objectif pour les aires protégées ! Mais, l’emplacement de ces aires protégées et leur gestion n’obéit pas à des critères basés sur une bonne connaissance de la diversité, mais sont plutôt panifiés à dire d’expert. L’objectif général de cette thèse c’est l’étude de la distribution de l’ignorance en biodiversité en Algérie en se concentrant sur les « Linnean, Wallacean et Darwinian Shortfalls » et de contribuer à les réduire. J’ai consacré un chapitre qui a pour but de réduire le Linnean Shortfall en proposant 1) une première checklist des reptiles et amphibiens d’Algérie qui est le fruit d’un examen précis des publications scientifiques sur ces taxons en Afrique du Nord. 2) une première pré-évaluation des statuts de conservations des reptiles et amphibiens d’Algérie pour la production de la première liste rouge nationale. La deuxième partie de ce manuscrit traite la question de l’ignorance de la distribution géographique des espèces. Le but de cette partie est de cartographier l’ignorance qui est la différence entre la diversité la richesse spécifique attendue et la richesse spécifique observée. La richesse spécifique attendue a été modélisée avec deux approches : 1 l’utilisation des modèles de niches avec la méthode de maximum d’entropie (MaxEnt) pour prédire les habitats favorables pour chaque espèce puis additionner les différentes couches binaires de présence des espèces pour calculer la richesse spécifique. 2) l’addition des couches des aires d’occurrences des espèces construite par la méthode du minimum convex polygon pour produire la carte de distribution de la richesse spécifique. Les deux approches ont montré la même tendance à l’échelle nationale, c’est-à-dire la concentration des zones les plus riches sur le long de l’Atlas Saharien et des hauts plateaux qui sont la zone de transition entre le Sahara et la partie méditerranéenne de l’Algérie. L’opposition de la partie saharienne globalement pauvre en espèce et la moitié nord plus riche. En fin, les massifs sahariens du Hoggar et Tassili forment une zone très distincte avec une richesse nettement supérieure par rapport au reste du Sahara. Pour ce qui est des lacunes, dans la Partie nord, la Kabylie, le parc national d’El Kala et la région d’Oran sont assez bien prospectées. Dans le Sahara, seuls quelques points sont assez bien prospectés comme Biskra, Béchar et quelques zones du Hoggar et Tassili. En fin, la troisième partie porte sur la distribution des lignées génétiques dans le Maghreb. Les objectif de cette partie est localiser les zones de sutures entre les lignées génétiques divergentes des populations de l’est et de l’ouest du Maghreb et d’essayer de comprendre les mécanismes qui ont conduit à ce patron de diversité génétique. Pour répondre à ces questions, j’ai effectué une phylogéographie comparées sur 11 espèces de reptiles et amphibiens à distribution continue et large dans le Maghreb. Deux zones de sutures ont été identifiées : une zone à la frontière de l’Algérie et du Maroc, l’autre EN Kabylie à l’ouest de la vallée de la Soummam. Les divergences entre les clades est et les clades ouest ont eu lieu entre la période pré-messinienne jusqu’au à la limite plio-pleistocène et se seraient maintenues dans des refuges climatiques à l’est et à l’ouest du Maghreb
Algeria is a case study of biodiversity ignorance. To date, there are neither complete inventories for any taxa nor atlas across the country! Yet, Algeria is of great importance for global biodiversity. The coastal area of Algeria is part of the global biodiversity hostpot which is the Mediterranean perimeter and has several regional red spots of biodiversity. Moreover, the Saharan part encompasses a diversity of endemic organisms adapted to the strong conditions of drought. The Algerian authorities are deploying an ambitious project for conservation aiming to reach 50% of the country's surface as protected areas! However, the location of these protected areas and their management don’t obey to a scientific evidence based, but are rather based on experts opinion. The main aim of this thesis is the study of the biodiversity ignorance distribution in Algeria by focusing on the "Linnean, Wallacean, and Darwinian Shortfalls" and to contribute to reduce them. The first chapter aims at reducing the Linnean Shortfall by proposing 1) a first checklist of reptiles and amphibians of Algeria which is the result of an accurate review of scientific publications on these taxa in North Africa. 2) a first pre-assessment of the conservation status of reptiles and amphibians of Algeria for the production of the first national red list. The second part of this manuscript deals with the ignorance of the geographical distribution of species. The purpose of this part is to map the ignorance which is defined as the difference between the expected specific richness diversity and the observed specific richness. The predicted species richness was modelled with two approaches: 1 ecological niche modeling with the maximum entropy method (MaxEnt) to predict the suitable habitats for each species and then add the different binary layers of species presence to calculate the specific richness. 2) Minimum convex polygon method was used to create range maps of each species and were auditioned to obtain predicted species richness. Both approaches have shown the same trend at a national scale: the concentration of the richest areas along the Saharan Atlas and the high plateaux which are the transition zone between the Sahara and the the Mediterranean part of Algeria. The opposition of the Saharan with a low species richness and the northern part with a higher species richness. Finally, the Saharan massifs of the Hoggar and Tassili form a very distinct zone with a much greater wealth compared to the rest of the Sahara. In terms of gaps, in the northern part, Kabylie, El Kala National Park and the Oran region are fairly well surveyed. In the Sahara, only a few points are clearly well prospected as Biskra, Bechar and some areas of the Hoggar and Tassili. The third part deals with the distribution of genetic llineages in the Maghreb. The aim of this section is to locate the phylogeographic breaks between the divergent eastern and western populations of the Maghreb and to try to understand the mechanisms that led to this pattern of genetic diversity. To answer these questions, I carried out a comparative phylogeography on 11 species of reptiles and amphibians with continuous and wide distribution in the Maghreb. Two suture zones have been identified: one zone on the border of Algeria and Morocco, the other in Kabylia west of the Soummam valley. The divergences between the eastern clades and the western clades occurred between the pre-Messinian periods up to the plio-pleistocene boundary and were maintained in climatic refugia in the east and west of the Maghreb

South Africa is a megadiverse country, and its biodiversity is endangered by population pressure and the development needs of a developing country. In order to address the rapid decline in biological diversity, biodiversity planning has become a key focus area that aims at identifying priority areas for species and ecosystem conservation within and outside of formally protected areas. Plant conservation hotspots are identified by the quantification of indicator taxa such as plant taxa richness, rarity and endemism. But the urgent and enormous task of biodiversity assessment for conservation planning requires that we make most of what we know. Therefore, this study seeks to make a contribution by finding new ways of biodiversity pattern estimation from the extrapolation of incomplete sets of plant species distribution data at the Quarter Degree Grid level. Incomplete sampling across the grids of a study area results in false records of species absence and thus a biased biodiversity estimation. As a possible solution, plant distribution data for the western Central Bushveld Bioregion has been standardized using two profiles, namely the ‘Centroid Grid’ and ‘Integrated Grid’ profile. The former involves the strengthening of under-sampled grids by extrapolating species occurrences from three adjacent grids with the most similar vegetation units, whereas the latter integrates phyto-diversity data for the four grids intersecting at each grid reference point. Standardized data has proved to provide a means to counter the bias in plant diversity data linked to Quarter Degree Grids by a) strengthening of under-sampled grids and b) visibly smoothing out the gaps between under- and well-sampled grids, which resulted in improved biodiversity estimation for more representative spatial biodiversity modelling. Interpolation created geo-referenced polygons for more explicit use in the identification of areas of conservation concern at bioregional scale. However, well-sampled grids still dominate the outcomes of the analysis by creating spatial sampling bias. Therefore, this approach to calibrate Quarter Degree Grid resolution of spatial data is an additional attempt to achieve more representative mapping of biodiversity patterns, which is a prerequisite for strategic conservation planning for ‘living landscapes’.
Thesis (MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2012

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:

1) Wie lässt sich Vegetationsvielfalt in grober Auflösung auf Basis abiotischen Faktoren einschätzen?
2) Wie ist der Ansatz 'globaler Hotspots' für die Eingrenzung nationaler Biodiversitäts-Hotspots zu übernehmen?
3) Wie erfolgt die Auswahl von quantitativen Schutzzielen unter Einbezug der Unterschiede nationaler Hotspots bei Umweltbedingungen und durch den Menschen Bedrohung?
4) Wie sieht der Entwurf eines großflächigen nationalen Naturschutzkonzepts aus, das die hierarchische Natur der Artenvielfalt reflektiert? Die Fallstudie für nationale Naturschutzplanung ist Russland.

Die nachfolgenden theoretischen Schlüsse wurden gezogen:
· 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%
· 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
· 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
· 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:

1) How to estimate large scale vegetation diversity from abiotic factors only?
2) How to adopt 'global hotspots' approach for bordering of national biodiversity hotspots?
3) How to set conservation targets, accounting for difference in environmental conditions and human threats between national biodiversity hotspots?
4) How to design large scale national conservation plan reflecting hierarchical nature of biodiversity?
The case study for national conservation planning is Russia.

Conclusions:
· 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%
· 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
· 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
· 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)

Les nombreuses menaces qui pèsent sur le milieu marin et les preuves d’une perte de biodiversité globale au cours des dernières décennies ont rendu indispensable la mise en place de mesures de conservation dans les années à venir. Au sein des Terres Australes et Antarctiques Françaises (TAAFs) en particulier, qui offrent une biodiversité exceptionnelle et sont le cadre d’activités anthropiques intensives à travers les grandes pêcheries industrielles, la délimitation d’Aires Marines Protégées (AMP) serait extrêmement bénéfique pour la conservation du milieu. Pour définir les zones d’importance pour la biodiversité, qui représenteraient de bonnes candidates pour un statut d’AMP, l’utilisation des données de distribution de prédateurs supérieurs apparait idéale. En effet, leur position dans le réseau trophique en fait de bons intégrateurs des niveaux inférieurs, et de plus, ils sont facilement observables lors des campagnes d’observations et offrent des facilités pour l’équipement de dispositifs télémétriques puisqu’ils reviennent régulièrement à terre pendant la période de reproduction. Grâce à l’analyse spatiale des données de distribution obtenues pour un grand nombre de prédateurs supérieurs au sein d’écosystèmes subantarctiques aussi bien qu’en milieu tropical et grâce au développement de modèles d’habitat, nous avons ici déterminé des ‘hotspots’ de biodiversité pour les prédateurs supérieurs des TAAFs. Ces travaux pourraient ainsi servir de base aux propositions de limites pour de potentielles futures AMPs
The numerous threats that marine environment face, coupled with the evidence for a global biodiversity loss during last decades have lead to an increasing need for setting up conservation measures. Particularly, delimiting Marine Protected Areas (MPAs) within the French Southern Territories, which are home to an exceptional biodiversity and extensive human activities through industrial fisheries, would be extremely beneficial for species conservation. In order to identify areas of ecological significance for biodiversity, which could be good MPA candidates, the use of distribution data from top marine predators seems to be ideal. Thanks to their high position in trophic network, they are likely to integrate lowers trophic level species distribution. Moreover, they are easy to observe trough at-sea observation campaigns, and easy to equip with telemetric devices thank to their central place foraging that lead them to return regularly to their colony during breeding season. Here, we analyse distribution data and develop habitat models from several top predators species in both subantarctic and tropical regions to highlight biodiversity hotspots within the French Southern Territories. This work could thus be use as a basis to define potential boundaries for a future MPA

L'archipel des Mascareignes (Réunion, Maurice et Rodrigues) est, avec les Seychelles, les Comores et Madagascar, l'un des 34 « hotspots » de biodiversité reconnus à l'échelle mondiale. Dans un contexte de disparition des habitats par les activités humaines, l'objectif de la thèse a été de comprendre la dynamique évolutive à différentes échelles spatiales et temporelles d'une famille d'espèces indigènes des écosystèmes forestiers, les Sapotacées. Ces espèces arborées présentent une gamme diversifiée de niveaux d’endémisme, d'abondance, de modes de régénération et de caractéristiques biologiques. La famille des Sapotacées comprend 3 genres et 14 espèces indigènes des Mascareignes (Mimusops, Labourdonnaisia et Sideroxylon) dont certaines espèces, rares et protégées, sont endémiques d'une des trois îles de l'archipel des Mascareignes. À l'échelle de la famille, l'analyse des séquences chloroplastiques de la famille des Sapotacées a confirmé la forte différenciation entre genres avec deux clades. Le premier clade est constitué par toutes les espèces de Sideroxylon structurées en trois sous-clades distincts dont deux correspondent aux sections Eusideroxylon et Calvaria, montrant une diversité haplotypique importante. Le deuxième clade est constitué par deux sous-clades formés respectivement par les espèces de Labourdonnaisia et celles de Mimusops. Alors qu'il n'est pas possible de résoudre les relations de parenté des Mimusops, Labourdonnaisia présentent deux lignées évolutives soulevant une incongruence entre les données taxonomiques et phylogénétiques. À l'échelle des deux lignées du genre Sideroxylon (Sections Eusideroxylon et Calvaria), l'analyse des marqueurs microsatellites chloroplastiques a montré une forte diversité haplotypique à la fois chez des espèces communes comme S. borbonicum ou rares comme S. majus associé à différenciation marquée entre l'île Maurice et la Réunion au sein des deux lignées. De plus, il a été mis en évidence des patrons de structure de la diversité génétique différents selon l'île et l'espèce considérée : une structure spécifique dans le genre Sideroxylon de la section Calvaria à Maurice et une structure géographique chez S. cinereum de Maurice et les espèces réunionnaises. À l'échelle de la lignée des Sideroxylon de la section Calvaria, les marqueurs microsatellites nucléaires ont permis d'identifier clairement toutes les espèces avec une forte différenciation entre S. majus de la Réunion et l'ensemble des espèces mauriciennes. À Maurice, la différenciation est plus marquée entre S. grandiflorum et les deux autres espèces S. sessiliflorum et S. boutonianum avec des évènements d'hybridation entre ces deux dernières espèces possibles. À l'échelle de S. majus de la Réunion, une très forte diversité génétique structurée en trois groupes génétiques a été mise en évidence à l'aide de marqueurs microsatellites nucléaires. La comparaison de la diversité génétique des cohortes des adultes et des juvéniles ne présente pas d’érosion génétique. Des méthodes de conservation sont proposées en fonction de ces caractéristiques génétiques pour S. majus, espèce rare en danger. L'ensemble des résultats obtenus chez les Sapotacées endémiques des Mascareignes montre que la diversité génétique est structurée à différentes échelles spatiales, selon les espèces et les lignées évolutives considérées, soulignant la nécessité d'études complémentaires afin de déterminer les processus qui sont à l'origine des patrons détectés
Madagascar is among the top five priorities "hotspots" for global biodiversity conservation. In Madagascar, melliferous flora is diverse and abundant; the endemic honey bee Apis melliferaunicolor inhabits all areas regardless of the climatic conditions and topography. As other islands, Madagascar is fragile and susceptible to invasions of alien species. In 2010, Varroa destructor has been reported parasitizing A. m. unicolor. The ectoparasite is not only a serious threat to beekeeping in Madagascar but it may also alter ecosystems balance.The objectives of this thesis were i) to study the genetic diversity and population structure of both A. m. unicolor and V. destructor in Madagascar, ii) to estimate the impact of V. destructor on honey bee colonies, and iii) to investigate the hygienic behaviour of honey beeOur results confirm that all honey bees collected in Madagascar belonged to the African evolutionary lineage and more than 99% were identified as A. m. unicolor. Despite its lownuclear genetic diversity, two genetic clusters have been detected, corresponding to geographic regions.In Madagascar, only one genetic strain of V. destructor was detected, the Korean haplotype (K1-1) which is the most widespread lineage in the world and the one present in Africa. Genetic studies showed a higher proportion of homozygous genotype (69.5%) and also a high number of MLG (Multi- Locus Genotypes) in the High Lands compared to the East coast. The presence of particular MLG on the High Land reinforces the assumption of its introduction into the capital. The spread of V. destructor in Madagascar is relatively slow in comparison with those observed in African countries. Its presence remains confined to the High Land and the East coast. The impact of the parasite on A. m. unicolor was severe; with about 60% of colony losses in a year reported in 2012. Nevertheless, this is less than observed in Europe, where many more colonies died at the early stage of infestation.Based on the percentage of cleaned cells observed 6 hour after pin killing the brood, the efficiency of A. m. unicolor colonies to detect and uncap cells was comparable to those of Africanised hygienic honey bees and was much higher than those of European honey bees. In Madagascar, the detection of highly hygienic colonies of A. m. unicolor is a great opportunity to develop a programme of selection of tolerant honey bee strains

Natural rubber is in high demand for the manufacture of tyres, and rubber plantations are expanding globally. Southeast Asia is the epicentre of rubber cultivation, where deforestation to make way for rubber has been occurring for decades. This process has caused substantial biodiversity loss and carbon emissions. Expansion has recently shifted northwards into mainland Southeast Asia (the Indo-Burma biodiversity hotspot) due to the development of hardier rubber varieties that can survive longer dry seasons and cooler climates. The northward shift has been exacerbated by replacement of rubber with oil palm further south. Profitability and extent of rubber are comparable to oil palm, but rubber has received far less attention and scrutiny from civil society. Future demand for natural rubber is predicted to require 4.3 – 8.5 million ha of additional plantation area by 2024, relative to a 2010 baseline. Profits accruing from logging and conversion of forest to rubber in Cambodia are shown to be very high. The carbon prices that would be needed for a REDD+ program in Indo- Burma to match costs of forest conservation where rubber is a threat, are $30 – 51 tCO2-1. These prices are far higher than those currently paid on carbon markets or through carbon funds, highlighting the importance of supply-chain initiatives, environmental governance and full valuation of ecosystem services for defending forests from conversion to rubber. Agroforestry methods for cultivating rubber in Thailand were found to produce yields comparable to monocultural methods, while providing modest benefits for bird and butterfly diversity. Agroforests did not support any species of conservation concern, and contiguous forests are irreplaceable for the conservation of forest biodiversity. Functional diversity of birds was found not to differ between rubber agroforests and monocultures, and species that feed primarily on nectar and fruit were extremely scarce in both types of rubber plantation.

Given inadequate budgets with which to stem the rapid destruction of biodiversity, conservationists must set clear priorities for action. Systematic Conservation Planning (SCP) is an approach that uses spatially explicit data to identify areas that meet conservation targets efficiently, usually focusing on species’ representation. Only rarely is the long-term persistence of species taken into account and the costs of conservation are usually ignored. I use the Eastern Arc Mountains of Tanzania as a study area to develop novel methods for creating and integrating the necessary data to fill these gaps in a developing country context. These mountains exhibit exceptional biodiversity but are also highly imperilled. I describe the biological data that I assembled for use in a series of SCP analyses. Fine-scale distribution models for species were mapped for over 500 animal and plant species of conservation concern. I then mapped Ecological and Evolutionary Processes (EEPs), which are crucial to species’ persistence and contribute to healthy ecosystem functioning. My analyses show how the inclusion of biological processes can significantly alter priorities when compared to prioritisation using information on species’ presence alone. Despite their importance, EEPs are often excluded from SCP. This is largely due to the difficulties involved in expressing them quantitatively and in optimising reserve networks to represent them at a minimum cost. This reluctance should be challenged, otherwise reserve networks will, over time, lose those elements of biodiversity that they were established to conserve. I also investigate conservation costs. Despite chronic underfunding for conservation and the recognition that funds must be invested wisely, few data on the costs of conservation are available at the spatial scales needed to inform local site management. I present methods for estimating and mapping protected area management costs, wildlife damage cost and the opportunity costs of conservation. Costs are highest in densely populated and cultivated areas, particularly in the north, whereas large areas of the more remote mountain blocs in the south show lower costs. Integrating these data into SCP demonstrates that using real cost data (rather than assuming that cost per unit area is homogenous) alters priorities and increases the efficiency of conservation within the Eastern Arc. Importantly, the efficiency savings realised through using cost, rather than area, to prioritise conservation efforts were found to be most pronounced when budgets were limited so that not all conservation targets could be met.

The emergence of a multisystemic and invariably fatal syndrome characterised by facial deformity and lethargy in extinct in the wild Christmas Island endemic and invasive reptiles prompted an investigation into its aetiology. Knowledge pertaining to the ecology and impacts of the agent at the time of the outbreak were limited, threatening efforts to conserve the island’s endemic reptiles. The investigations described in this thesis therefore aimed to enrich understanding of the organism’s pathogenesis, pathophysiology, and epizootiology. Investigations into other agents with the potential to jeopardise conservation efforts were also explored. Following morphological characterisation, genomics revealed the agent was a novel species; Enterococcus lacertideformus, within the Enterococcus faecium clade, possessing genes encoding virulence determinants, resistance traits, and genes underpinning its biofilm phenotype and failure to cultivate in-vitro. Efforts to combat E. lacertideformus were also explored. Pharmacokinetics of enrofloxacin in-vitro showed that 10 mg/kg oral enrofloxacin likely achieved sufficient plasma concentrations. An experimental infection model indicated that the clinical course of E. lacertideformus depended on the inoculation route, and transmission likely occurred through direct contact. Following infection, an in-vivo therapeutic trial showed that enrofloxacin and amoxicillin-clavulanic acid were prospective candidates for treatment. Additionally, health surveillance and metagenomics uncovered disease processes and parasites, and two novel papillomaviruses, respectively, in Christmas Island and Cocos Islands reptiles. In summary, this thesis contributes substantial knowledge regarding the bacterium and its host interactions, while also providing foundational health data on reptile populations. Ultimately, this research guides management strategies and conservation opportunities and informs treatment protocols to combat E. lacertideformus.

Increasing human population size is increasing the demand for resources like timber, oil, tea, coffee, and other crops. Plantation crops mimic some aspects of native habitats, and there are studies that report the presence of some native anuran biodiversity in plantations. I focused on tea plantations in the Western Ghats-Sri Lanka Biodiversity Hotspot and studied the diversity and health of anurans in different habitats found within a tea cultivation area, near Munnar region in the Western Ghats, India. The landscape includes tea bushes, native evergreen shola forest patches, and eucalyptus forest stands. I reviewed 40 studies comparing amphibian species richness in plantations and primary forests. The age of the plantation, type of plantation, presence in a biodiversity hotspot, number of species in the dominant plantation type, number of species in the paired forest habitat, and latitudinal zone of the study, did not correlate with species richness, but plantations that had periodic harvesting had higher species richness than plantations that practiced clear-cut harvesting. I tested different methods of standard amphibian sampling in the field season 2012 in Munnar, and found that Visual Encounter Surveys (VES) in the shola habitat and Stream Transects (ST) were the most efficient. Using the VES and ST methods, I sampled amphibians in three upland habitats (tea, shola, and eucalyptus) at four different sites, and 150m of stream transects at each site, for two consecutive monsoon seasons. Fourteen species were encountered in both years and the community structure was similar across the years. The community structure at the four sites that was driven by the presence of exclusive species at each site and species composition in streams was similar across the landscape and was driven by the presence of similar species in streams across the four sites. Two hundred and sixteen anurans of 17 species, were tested for the presence of the lethal fungus Batrachochytrium dendrobatidis. The preliminary results from the Polymerase Chain Reactions were negative. My study provides baseline data for anuran diversity, composition, and health in the Munnar region of India and results of this project can be compared with tea plantations around the world.

Le point chaud de biodiversité de Madagascar et des Iles de l'Océan Indien est réputé pour abriter une grande diversité d'espèces dont une large fraction est endémique. Malgré de nombreuses hypothèses explicatives et une abondante littérature sur le sujet, les connaissances actuelles sur les mécanismes de la diversification des espèces au sein de ce point chaud demeurent limitées. L'importante biodiversité de la région a longtemps été attribué à la fragmentation du Gondwana oriental et de l'isolement qui en a résulté entre Madagascar et le sous-contient Indien (120-160 Ma). Un grand nombre d'études récentes de systématique moléculaire montrent toutefois que l'origine de la plupart des groupes présents aujourd'hui à Madagascar est très largement postérieure à l'isolement de Madagascar. En outre, Madagascar n'est qu'un élément d'un contexte géographique plus vaste constitué d'îles océaniques ou microcontinentales qui varient entre elles du point de vue de l'origine géologique, de l'âge, et de la structure et qui abritent elles-aussi une faune et une flore très diversifiés. La plupart de ces îles sont jeunes (2-10 Ma) et l'important endémisme de leur biodiversité ne peut pas être expliqué par la vicariance gondwanienne, mais résulte plutôt de d'évènements récents de dispersion à longue distance suivis par des processus de diversification in situ. Par ailleurs, certains groupes d'organismes présentent une biodiversité sur les îles volcaniques jeunes plus forte que sur Madagascar, ce qui est contre-intuitif étant donné la plus grande surface et l'importante diversité écologique de Madagascar. Lorsque l'on prend en compte la disparité d'âges géologiques entre Madagascar et les îles environnantes, la théorie prédit que la diversification sur les îles "jeunes" a eu lieu à un rythme élevé après que des changements d'aire de distribution ont pris place dès que de nouvelles régions ou habitats sont devenus accessibles au travers du processus de colonisation. Cette thèse vise à comparer plusieurs lignées de plantes (Asteraceae, Myrsinaceae, Monimiaceae) qui se sont fortement diversfiées dans la région de Madagascar et des Iles de l'Océan Indien. Dans chacune de ces familles, j'ai porté mon attention sur des genres riches en espèces, présentant une forte variabilité phénotypique, contenant de nombreux espèces endémiques à une seule île, et ayant une distribution comprenant Madagascar et des îles avoisinantes. .
The Madagascar and Indian Ocean Islands biodiversity hotspot is renowned for its high levels of species diversity and endemism. Yet despite many hypotheses and a considerable literature, we still know relatively little about the mechanisms of species diversification within the region. Until recently, the major role for high levels of species diversity was attributed solely to breakup of East Gondwana and the isolation of Madagascar and India (120-160Mya). However, an increasing number of studies, employing recent advances in analytical methods, have shown that the origin for many groups post-dates the isolation of Madagascar. Furthermore, Madagascar is embedded in a wider geographical setting of oceanic and microcontinental islands that vary distinctly in origin, age and structure, and that are also home to highly diverse flora and fauna assemblages. Most of these islands are young (2-10My) and the high levels of endemism on these islands therefore can't be explained by Gondwanan vicariance, but only by recent long distance dispersal followed by extensive in-situ diversification processes. In addition, some groups of organisms show higher levels of diversity on young volcanic islands than on Madagascar, which runs counter to expectations given the greater surface area and habitat diversity of Madagascar. Taking into account the disparity in geological ages among the land fragments in the Indian Ocean, theory suggests that diversification on geologically young islands would have proceeded via high levels of diversification rates and rapid shifts over time after new ranges and habitat became available upon colonization. In this thesis we compare major plant lineages (Asteraceae, Myrsinaceae, Monimiaceae) that have undergone extensive diversification in the region. In each of these families we selected highly speciose genera that are characterized by single island endemism, phenotypic diversity and presence on Madagascar and a range of Indian Ocean islands. We found evidence of significant shifts in diversification rates and repeated long distance dispersals to Indian Ocean islands where Madagascar played a central role as a disperser source. .

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Agriculture is the human activity with the greatest impact on the environment. Specifically, it represents the greatest threat to biodiversity. In the future, this activity should expand due to population growth, increased consumption and production of biofuels from food. To understand the possible impacts of this expansion on biodiversity, we used scenarios of land use change between 1970 and 2100 from IMAGE (Integrated Model to Access Global Environment) to test the following hypotheses: (i) areas considered as global priorities for conservation by international NGOs will be preferentially impacted by agricultural expansion in the XXI century, (ii) there is a conflict between the priority areas for carnivores conservation and agricultural expansion, and this conflict can be reduced by incorporating information on agricultural expansion in the prioritization process, (iii) the integration among countries for conservation planning may benefit both biodiversity and agricultural productivity, (iv) Brazilian protected areas will be impacted by agricultural expansion in the future and this impact will differ between protected areas of integral protection and those of sustainable use. We found that: (i) the impact on priority areas for conservation depends on the criteria by which they were set, so that areas defined by its high vulnerability are currently most affected than those of low vulnerability. Throughout the XXI century this impact is expected to increase, although the difference between the two types of priorities remains, except for High Biodiversity Wilderness Areas, defined by their low vulnerability in current time, but for which most pessimistic scenarios forecast an impact similar to priority areas of high vulnerability, (ii) there is a high spatial congruence between areas with high agricultural use in the future and priority areas for conservation of carnivores. This conflict can be reduced if the prioritization process include information on agricultural expansion; this incorporation, however, causes a profound change in the distribution of priority areas and reduces the number of protected carnivore populations, (iii) the integration of countries to create a set of priority areas for conservation that represents 17% of the land surface can protect 19% more mammal populations without reducing food production, compared to a strategy in which each country seeks to protect its territory independently, and (iv) the impact of agriculture in Brazil is expected to increase until the end of the century, threatening even the protected areas and their surroundings. This impact, however, should not be different between areas of sustainable use and those of integral protection. We conclude that agricultural expansion should remain a major threat to biodiversity in the future, even in areas of special interest for conservation. Conservation actions should be planned taking into account this threat in order to reduce their potential impacts. For this, countries like Brazil should strengthen its surveillance on agricultural expansion and on how this activity is developed. Furthermore, the integration of international conservation efforts should be pursued, given its benefits for biodiversity and food production. Finally, humanity must choose methods of agricultural production that reduce its impacts, including avoiding its future expansion, so as to meet the increasing needs of a human population globally.
A agricultura é a atividade humana com maior impacto sobre o ambiente. Particularmente, ela representa a maior ameaça à biodiversidade. No futuro, essa atividade deve expandir-se com o aumento populacional humano, o aumento do consumo e a produção de biocombustíveis a partir dos alimentos. Para entender os possíveis impactos dessa expansão sobre a biodiversidade, nós utilizamos cenários de mudança de uso do solo entre 2000 e 2100 do IMAGE (Integrated Model to Access Global Environment) para testar as seguintes hipóteses: (i) as áreas consideradas como prioridades globais de conservação pelas ONGs internacionais serão preferencialmente impactadas pela expansão agrícola no século XXI; (ii) há um conflito entre áreas prioritárias para a conservação de carnívoros e a expansão agrícola e esse conflito pode ser reduzido com a incorporação da informação sobre expansão agrícola no processo de priorização; (iii) a integração entre os países para o planejamento da conservação pode ser favorável à proteção da biodiversidade e à produção agrícola; (iv) no Brasil, as áreas protegidas serão impactadas pela expansão agrícola no futuro e esse impacto será diferente entre áreas de proteção integral e áreas de uso sustentável. Nós encontramos os seguintes resultados: (i) o impacto sobre as áreas prioritárias para a conservação depende dos critérios pelos quais elas foram definidas, assim, as áreas definidas por sua alta vulnerabilidade estão atualmente mais impactadas do que áreas de baixa vulnerabilidade. Ao longo do século XXI, o impacto geral da agricultura deve aumentar, mas a diferença entre os dois tipos de prioridades se mantém, exceto para as High Biodiversity Wilderness Areas, definidas por sua baixa vulnerabilidade, mas que nos cenários mais pessimistas podem ter um impacto agrícola semelhante ao das áreas de alta vulnerabilidade; (ii) há uma alta congruência espacial entre áreas com elevado uso agrícola no futuro e áreas prioritárias para a conservação de carnívoros; esse conflito pode ser reduzido se o processo de priorização incluir as informações sobre a expansão agrícola; a incorporação dessa informação, entretanto, provoca uma profunda alteração na distribuição das áreas prioritárias e reduz o número de populações de carnívoros protegidas; (iii) a integração entre os países para a criação de um conjunto de áreas prioritárias para conservação que represente 17% da superfície terrestre pode proteger 19% mais populações de mamíferos sem reduzir a produção de alimentos, se comparada a uma estratégia em que cada país busque proteger seu território independentemente; (iv) o impacto da agricultura no Brasil deve aumentar até o fim do século XXI, ameaçando inclusive as áreas protegidas e o seu entorno. Esse impacto, porém, não deve ser diferente entre as áreas de uso sustentável e aquelas de proteção integral. Assim, a expansão agrícola deve continuar a ser uma importante ameaça à biodiversidade no futuro, atingindo inclusive áreas de especial interesse para a conservação. As ações de conservação devem ser planejadas levando em consideração essa ameaça, a fim de reduzir seus impactos potenciais. Para isso, países como o Brasil devem reforçar sua vigilância sobre a expansão agrícola e a maneira como essa atividade é desenvolvida. Além disso, a integração internacional dos esforços de conservação deve ser buscada, dados seus benefícios para a biodiversidade e para a produção de alimentos. E por fim, a humanidade deve optar por formas de produção agrícola que reduzam seus impactos, inclusive evitando sua expansão futura, mas que possam satisfazer as necessidades da população humana globalmente.

In southwest Australia there is a significant need to restore vegetation communities impacted by anthropogenic activities. The series of experiments undertaken over the course of this thesis focus on a notoriously difficult-to-germinate plant family, the Rutaceae. Through the application of field- and lab-based experiments, avenues for seed-based propagation of southwest Australian Rutaceae have been developed, allowing for more effective restoration approaches based upon an improved understanding of seed ecology.

Objectifs généraux: les systèmes fluviaux tropicaux et tempérés d'eau douce sont connus pour soutenir différentes communautés biotiques. Dans cette étude, menée dans une région d'Asie tropicale et dans une région d'Europe tempérée, j'ai étudié la composition et la diversité de la communauté des macro-invertébrés benthiques ainsi que leurs variations spatiales et temporelles. J'ai également examiné les influences des variables physico-chimiques de la qualité de l'eau sur les variations et la diversité de la composition de la communauté et j'ai modélisé l'occurrence d'espèces sélectionnées. Localisation géographique: Asie tropicale: le bassin aval du Mékong (LMB), couvrant une superficie de 609 000 km2; Europe tempérée: Europe occidentale, fleuves flamands (Belgique), couvrant une superficie de 13 787 km2. Matériel et méthodes: Pour le LMB, les données recueillies de 2004 à 2008 ont été utilisées et les valeurs médianes de cette période ont été analysées. Pour les rivières flamandes, les données collectées de 1991 à 2010 ont été utilisées. Les données ont été divisées en 4 périodes: D1: 1991-1995, D2: 1996-2000, D3: 2001-2005 et D4: 2006-2010. Les médianes de chaque période ont été utilisées pour des analyses spatiales détaillées. Des analyses multivariées ont été appliquées pour relier la composition et la diversité de la communauté aux variables physico-chimiques. Cinq techniques de modélisation, à savoir la régression logistique (LR), les Random Forest (RF), le Support Vector Machine (SVM), les réseaux de neurones artificiels (ANN) et les arbres de classification (CT) ont été utilisées pour modéliser l'occurrence desespèces sélectionnées. Principaux résultats: Variations de la composition des communautés, diversité et relation avec les variables environnementales Dans le cours aval du Mékong LMB, 299 taxons de macro-invertébrés distribués dans 196 genres et 90 familles ont été identifiées; dont 131 insectes, 98 mollusques, 38 crustacés et 32 annélides
Overall aims: Freshwater tropical and temperate river systems are known to support different biotic communities. In this study, I investigated benthic macroinvertebrate community composition and diversity and its spatial and temporal variation both in tropical Asian and temperate European regions. I also examined the influences of physical-chemical water quality variables on community composition, variations and diversity, and modelled the occurrence of selected species. Locations: Tropical Asia: the Lower Mekong Basin (LMB), covering an area of 609,000 km2; Temperate Europe: Western Europe, Flemish rivers (Belgium), covering an area of 13,787 km2. Materials and Methods: For the LMB, data collected from 2004 to 2008 were used, and median values of this period were analysed. For Flemish rivers, data collected from 1991 to 2010 were used. The data were divided into 4 periods: D1: 1991-1995, D2: 1996-2000, D3: 2001-2005 and D4: 2006-2010. The medians of each period were used for detailed spatial analyses. Multivariate analyses were applied to relate community composition and diversity to physical-chemical variables. Five modelling techniques namely Logistic Regression (LR), Random Forest (RF), Support Vector Machine (SVM), Artificial Neural Network (ANN) and Classification Tree (CT) were used to model the occurrence of selected species. Main results: Community composition variations, diversity and relationship with environmental variables From the LMB, 299 macroinvertebrate taxa belonging to 196 genera and 90 families were identified: 131 insects, 98 molluscs, 38 crustaceans, and 32 annelids

Sundaland est l'un des points chauds de biodiversité les plus menacés, en raison d’une augmentation rapide des menaces au cours des dernières décennies. Couvrant la péninsule malaise, Sumatra, Java et Bornéo, cette région possède l'une des plus grandes richesses en espèces et endémisme pour les vertébrés, y compris les poissons d'eau douce. Cette biodiversité a longtemps attiré l'attention des biologistes évolutionnistes, notamment en raison de la complexité de l'histoire géologique de Sundaland. Cette question a été abordée en explorant les patrons de fragmentation et dispersion durant la diversification des espèces de poissons d'eau douce de Sundaland. Ainsi, j'ai d'abord cherché à évaluer la correspondance entre la distribution des lignées moléculaires de plusieurs taxons avec les limites des paléorivières en ré-analysant les données moléculaires existantes avec une couverture biologique et spatiale représentative en Asie du Sud-Est (en particulier pour Sundaland). Deuxièmement, je me suis concentré sur l’estimation de l’âge des clades et de la répartition géographique des lignées de Rasborinae, un groupe répandu et extrêmement diversifié de poissons d’eau douce primaires du Sundaland, pour tester l’hypothèse des Paléorivières du Pléistocène en utilisant des données empiriques nouvellement générées. Sur les deux études, je me suis posé les questions suivantes: 1) les paléorivières servaient-elles de corridors de dispersion entre les îles pendant les périodes glaciaires du Pléistocène; 2) les bassins versants des paléorivières ont-ils initié une divergence allopatrique à travers leurs frontières; et 3) les fluctuations climatiques du Pléistocène ont-elles augmenté les taux de speciation. Dans l'ensemble, un niveau élevé de diversité cryptique est observé. Les aires ancestrales inférées révèlent une origine continentale des lignées de poissons d'eau douce de Sundaland, datée à l'Oligocène. Ce résultat valide l'hypothèse d’une installation pré-pléistocène. Ces lignées sont entrées à Sundaland par la paléorivière de la Sonde Nord à Bornéo et se sont dispersées par la suite via une dispersion à longue distance, souvent suivie de diversification in situ. Ces résultats suggèrent que la partie de Bornéo de la paléorivière de la Sonde Nord est le centre d'origine le plus probable des poissons d'eau douce de Sundaland. Contrairement à l'hypothèse initiale que l'abaissement du niveau de la mer en périodes glaciaires reconnecte les bassins versants au sein des paléorivières, cela n'ouvre pas nécessairement de canaux de dispersion inter-îles pour les poissons d'eau douce. Les couloirs de savane et d'écosystèmes forestiers saisonniers à l'intérieur du Sundaland ont servi de barrière à la dispersion. En outre, la perméabilité des limites physiques des bassins versants des paléorivières, ainsi que les variabilités géomorphologique et écologique ont créé temporairement des flux de gènes. Bien qu'une proportion significative des lignées de poissons d'eau douce du Sundaland datent du Pléistocène, nous avons constaté que la dynamique du Pléistocène n'affectait pas le taux de diversification. Les modèles de diversification dépendant du niveau de la mer expliquent mal les schémas de prolifération des espèces pour tous les clades, à l'exception de Channa. En outre, aucun des taxons examinés ne présente de taux de diversification en baisse comme le suggère le modèle de diversification dépendante de la diversité (DDD). Il est suggéré alors que les fluctuations eustatiques du Pléistocène et la dynamique des paléorivières ne sont pas les seuls moteurs de la diversification des poissons d'eau douce du Sundaland, mais seulement une partie des aspects abiotiques qui l'affectent. Les fluctuations climatiques du Pléistocène ont probablement interagi avec d'autres facteurs tels que: la géomorphologie du paysage, la variabilité des écosystèmes et les caractéristiques biologiques des organismes
Sundaland is one of the most threatened biodiversity hotspots, experiencing a fast increase of threat levels during last decades. Covering Malayan Peninsula, Sumatra, Java and Borneo, this hotspot has one of the highest species richness and endemism for vertebrates in SEA, including freshwater fishes. This level of biodiversity has long attracted the attention of evolutionary biologists, particularly by considering effects of Sundaland complex geological history. This study addressed it by exploring time frame of vicariance and dispersal during diversity build-up of freshwater fish species in Sundaland. To support this, we first aimed to assess the match between distribution of molecular lineages from multiple taxa with palaeoriver boundaries using metadata analysis of existing molecular dataset with representative biological and spatial coverage in Southeast Asia (especially in Sundaland). Second, we focussed on estimating clades’ age and geographic distribution of Rasbora lineages in relation to the Pleistocene Palaeoriver Hypothesis by utilising newly generated empirical data for Rasborinae, a widespread and extremely diversified group of primary freshwater fishes in Sundaland. On both steps, we questioned: 1) if palaeorivers served as corridors of dispersal between islands during Pleistocene sea levels low stands; 2) if palaeoriver watersheds initiated allopatric divergence across their boundaries; and 3) if Pleistocene climatic fluctuation increased rates of species diversification. Overall, this study detected high level of cryptic diversity. Ancestral area reconstructions revealed that Sundaland freshwater fish lineages originated from Mainland Asia, and further colonised the region since Oligocene. This result validated the pre-Pleistocene settlement hypothesis. These lineages entered Sundaland mainly through North Sunda palaeoriver in contemporary Borneo and dispersed to other parts of Sundaland via long distance dispersal, often followed by in situ diversification. These results suggest Bornean part of North Sunda palaeoriver is the most likely centre of origin for Sundaland freshwater fishes. Contrary to the initial hypothesis, we found that although lowered sea level during glacial periods reconnected watersheds within palaeorivers, it did not necessarily open up inter-island dispersal channels for freshwater fishes. Corridors of savanna and seasonal forest ecosystems in the interior of Sundaland served as barrier to dispersal. Also, permeability of the physical boundaries of palaeoriver’s watersheds as well as geomorphological and habitat variabilities within palaeoriver created respectively gene flow between palaeorivers and allopatric speciation within palaeoriver. Moreover, although significant proportion of Sundaland freshwater fish lineages originated during Pleistocene, we found that Pleistocene dynamics did not affect diversification rate as sea level-dependent diversification models poorly account for species proliferation patterns for all clades excepting Channa. Besides, none of the taxa examined has declining diversification rates as suggested by diversity-dependent diversification (DDD) model. It is suggested then that global Pleistocene eustatic fluctuation and regional paleoriver dynamics are not sole drivers for Sundaland freshwater fish diversification, but only a part of abiotic aspects affecting it. Pleistocene Climatic Fluctuations likely interacted with other factors such as: landscape geomorphology, local ecosystem/habitat variability and life history traits of organisms

Thesis (MScConsEcol (Conservation Ecology and Entomology))--University of Stellenbosch, 2009.
Habitat loss and fragmentation are two of the most pressing threats to biodiversity. Avifaunal diversity and integrity is under immense pressure from these two processes. We have made major advances in our understanding of avifaunal responses to habitat fragmentation, but mostly focus on either fragment scale and/or landscape scale influences of fragmentation on birds. A more comprehensive approach to assessing the impacts of fragmentation was used in this study. The avifaunas of two different geographical regions and bioregions were surveyed and a multiscale analysis of avifaunal responses to fragmentation was attempted. The study sites include the West Coast and East Coast Renosterveld Bioregions in the Cape Floristic Region, South Africa. Assemblage shifts, feeding guild compositional changes, species abundance variation and species persistence were examined at the three spatial scales. Time- and distance-restricted point counts were used to document birds that were directly dependent on the habitat fragments. Forty fragments were selected in each bioregion and a once-off snapshot of the avifaunal richness and diversity was obtained. Results indicate that the avifauna of the two bioregions responded differently to habitat fragmentation. In the East Coast Renosterveld Bioregion, the assemblages, guild composition and species abundances were most accurately predicted by landscape configuration. An assemblage shift occurred at 20 ha fragment area, compared to the 50 ha fragment area threshold of the West Coast Renosterveld Bioregion’s avifauna composition. In the West Coast Renosterveld Bioregion, fragment area was the better predictor of assemblage, guild composition and species abundances. However in both bioregions, the persistence of common species was equally sensitive to area and landscape scale effects.

Japan is one of the world’s 34 biodiversity hotspots, according to Conservation International (CI). The methods used by various organisations to define priorities differ, however, and all have weaknesses when trying to identify hotspots at finer resolutions. The goal of this thesis is to investigate how biodiversity hotspots in Japan could be revealed and mapped in order to encapsulate conservation elements of biodiversity in practical ways and at various scales. Bioquality is a term that emphasises the concentration within a community of elements of biodiversity with high conservation value. It evaluates the global rarity and taxonomic distinctiveness of plant species or infra-specific taxa using four Star categories. At a plant community level, the Genetic Heat Index (GHI), which is a standardised global range size rarity score, is calculated using weighted Star statuses of species in the community. Bioquality hotspots are assessed here for the first time for the flora and vegetation in Japan – and for temperate Asia – by categorising the Japanese flora into Stars and by applying GHI to survey data and literature-based sources. Keys to Stars are developed for the Japanese flora, with adjustments for variability in species geographic range size information and for taxonomic relatedness. A Flora of Japan (FOJ) database was compiled as a BRAHMS database, containing 8,262 accepted names (30,656 taxon names in total, including synonyms) in 258 families – the first full database of Japanese vascular plants. A total of 7,145 taxa are assigned Stars; from the rarest to the widespread class, there are 884 Black, 756 Gold, 833 Blue, and 4,672 Green Star taxa, confirming that Japan as a whole contains a high proportion of globally rare taxa (23% taxa in Black or Gold). A protocol for calibrating the weight of Stars based on species geographic range is developed based on fine-resolution distribution maps within Japan and coarse–resolution Taxonomic Database Working Group (TDWG) code information. The protocol optimises calculation for temperate regions. The first ever bioquality hotspot maps of Japan are produced using two independent data sources on species distribution at national level: 1) 50 botanical prefectures using 4,830 species from the FOJ database; 2) 1,418 Horikawa ‘geoquadrats’ (0.1° latitude by 0.15° longitude grid) maps covering 829 species. The Ryukyu Islands and Ogasawara Islands are identified as bioquality hotspots, and high mountain ranges in mainland Japan are predicted to contain areas potentially high in GHI; the spatial patterns of GHI are generally concordant between maps of different resolutions. These findings highlight that bioquality assessment can be applied meaningfully at various spatial resolutions. Using field sampling data and existing literature, three study sites are further investigated on a local level: 1) the satochi-satoyama landscape, the current national priority area for biodiversity conservation; 2) various vegetation types of Okinawa-jima Island, the Ryukyu Islands; and 3) the Utaki sacred groves within the predicted hotspot of the Ryukyu Islands. The Ryukyu Islands are confirmed to contain bioquality hotspots within many individual sites, while there was generally low GHI across the satochi-satoyama landscape. The field study outcomes, together with a gap analysis of the existing coverage of protected areas, highlight three important points that are directly relevant to national biodiversity conservation planning: 1) the Ryukyu Islands urgently need newly designated protected areas; 2) the satochi-satoyama landscape conservation should redirect its focus on cultural benefits to the public; 3) the existing protected areas, particularly on mountain areas, need re-evaluation in terms of upgrading their status in light of the bioquality assessment.

Mestrado Erasmus Mundus: Mediterranean Forestry and Natural Resources Management (MEDfOR) - Instituto Superior de Agronomia
Cork oak woodlands or montados are ecosystems of high conservation and socio-economic importance. The present work aimed at 1) identifying and mapping biodiversity and Ecosystem Services in main area of distribution of cork oak montado in Southern Portugal 2) assessing how the distribution of these conservation values relates with the distribution of the network of classified areas and 3) assessing how the distribution of identified conservation values relates with the area of cork oak montado under forest certification. I mapped biodiversity values (presence of species of amphibians, reptiles and threatened birds) and Ecosystem Services (carbon storage and aquifer recharge rates) within the study area. For achieving this I used the open source Q-GIS 2.0.1. software together with the open access online geographic information system WebGIS Hotspot Areas for Biodiversity and Ecosystem Services (HABEaS: www.habeas-med.org). With the exception of Natura 2000 sites the distribution of Biodiversity and Ecosystem Services is largely not coincident with that of classified areas. In relation to forest certified areas, these are presently covering a significant area of cork oak montados where biodiversity values and Ecosystem Services overlap

Includes bibliographical references.
This study reports on an investigation of the phytogeographical patterns retrieved within the exceptionally species rich Cape Floristic Region (CFR), a global biodiversity hotspot in South Africa. Modern Analytical techniques, including a novel approach developed within this study, were used to identify Phytogeographical Centres. Moreover, the efficiency and optimality of these techniques were tested against each other using several different datasets. Endemism and species richness in the core CFR were assessed against contemporary environmental conditions, using a spatially sensitive regression technique. A combined dataset of 4414 taxa was analysed, of which 4000 were recorded in the general CFR area. This represented 44.4% of the 9087 total taxa recorded in the CFR, and the largest dataset examined to date on floristic patterns in the CFR. The combined data (Combined Dataset), a relatively representative sample of the CFR flora, was used to establish overall phytogeographic patterns of endemism. Further, derivative subsets, based predominantly on phylogeny/taxonomy including taxa from eleven plant families, and two ecological guilds, Geophytes and Red Data Listed (RDL) Taxa, were also analysed. Differences between the derivative datasets revealed insights into taxonomically distinct floristic patterns, determined by the dominance of particular floristic/biotic elements within each dataset. This helped explain phytogeographical differences between previous CFR phytogeographical studies, which focused on different floristic/biotic elements. In the Combined Dataset, nearly all Quarter Degree Square (QDS) cells were assigned to PCs in the core CFR, indicating endemism is common throughout the CFR. However, endemic taxa were concentrated in the high winter rainfall west, and southwest areas. The large size of the dataset, and detailed analyses revealed additional finer phytogeographical sub-division, not previously recorded, including six Phytogeographical Provinces, 16 Centres, and 36 Sub-Centres; compared to five equivalent Phytogeographical Provinces and nine equivalent Centres of Weimarck. Hierarchical analyses of the Combined Dataset displayed congruent patterns to the previous two comprehensive phytogeographical studies of Goldblatt and Manning, (2000) and Weimarck (1941). Within the core CFR phytogeographical provinces, common patterns across studies included choria being strongly associated with TMS mountain ranges. This highlighted the importance of substrate and topography explaining floristic patterns, consequent PC formation, and the numeric dominance of montane TMS 'fynbos' taxa. The latter was confirmed through habitat analysis of endemic taxa. However, PC development was also noted on the lower lying areas, notably the Agulhas Plains, and the lowland areas neighbouring the mountains of the Southwest Phytogeographical Province, and to a lesser extent, the Northwest Province. The five analytical methods used to determine candidate PCs were evaluated for performance optimality. Bell Shaped Curve Weighting using UPGMA proved marginally more optimal than the other four methods, but differences between various weighting and clustering algorithms were less than anticipated. However, weighting was seen to be substantially better than not weighting. The novel technique of using a multiple clustering analysis approach was found to highlight areas of conflict, where floristic/biotic elements overlapped, and to supplement occasional poorly resolved trees. In addition, the approach of using GIS interrogation of candidate centres, substantially enhanced the endemic composition and size of PCs, and is strongly recommended. Moreover, post clustering GIS analyses may correct any marginal disadvantages of any single approach. Significant correlations between endemism and PC size, and richness of non-endemics and PC size were found. However, certain PCs still contained more taxa than predicted by area alone, while others contained fewer. In these PCs with over- or under-represented richness, alternative explanations (either historical and/or environmental) were required to explain why these PCs differ from other PCs in the CFR, which was subsequently investigated. Analyses of patterns of endemism and taxon richness against contemporary climatic and environmental variables using a regression technique which accounted for spatial variation in parameter estimates highlighted the importance of both the energy-water hypothesis, and the habitat heterogeneity hypothesis in the CFR. Potential evapo-transpiration and various measures of topographic heterogeneity provided much explanatory power. In addition, length of growing/rain season was particularly important in the western winter rainfall portion of the CFR, and is here retrieved for the first time as a strong predictor variable. Different input units and different floristic components of the dataset required different models for optimisation. The models were adequately able to account for much of the variability in richness (~ = 78.3- 91.2%). The Cape Floristic Region (CFR) -a global hotspot- proved an excellent area to study patterns of endemism, taxon richness, floristic patterns, and how environmental conditions affect richness because of its exceptionally high concentration of both richness because of its exceptionally high concentration of both richness and endemism, and high levels of beta and gamma diversity over relatively short geographic distances.

Habitat loss and fragmentation and human-wildlife conflicts, often resulting in retaliatory killing in response to livestock predation, are one of the main threats to wild felids worldwide, including pumas (Puma concolor). However, mesocarnivores are more abundant than large carnivores, live closer to human settlements, and drive community structure and processes in similar or different ways from large predators. Understanding both large and small carnivores' habitat use is key to their conservation and management. Thus, there is need to explore the ecological roles of predators (including invasive ones like free-ranging dogs [Canis lupus familiaris] and cats [Felis catus]) to examine how ecological context modulates the ecological roles of carnivores . This is especially important in my study area, which was severely burned by a catastrophic mega-wildfire in 2017. I used dynamic occupancy modeling of human-wildlife conflict (HWC) across 52 provinces for 8 years in Chile and found that free-ranging dogs outpace pumas in livestock depredation, killing substantially more livestock than pumas. Occupancy models show that HWC occurrence for both dogs and pumas increased with sheep density. Unexpectedly, dog HWC decreased with anthropogenic habitat degradation indicating that dogs may travel far to prey on livestock. The emergence of puma HWC in a site where it did not occur in the previous year was positively associated with anthropic disturbance. Countrywide, dogs HWC occurrence probability was higher than pumas in 43 out of the 49 provinces where both species occurred. I discuss livestock vulnerability, management strategies, and policy to mitigate HWC, and also highlight threats that free-ranging dogs pose to biodiversity conservation and even human public health. I also used single-species, single-season occupancy models fit to camera-trap data to investigate the patterns of site occupancy and response to mega-wildfires of native mesocarnivores in southern-central Chile: guignas (Leopardus guigna), culpeo foxes (Lycalopex culpaeus) and chilla foxes (Lycalopex griseus). I found that vulnerable guignas avoided burned sites, preferring sites with native, dense vegetation while culpeo foxes were intermediate in being able to use plantations, but avoiding burned sites. Chilla foxes were most tolerant to landscape change with no response to burns and were found closer to human habitation and rivers. Finally, I used two-species, single season occupancy models, and Kernel Density Estimation on circular data, to investigate the spatial and temporal dynamics, and overlap of native and exotic carnivores. I found that feral cats are a potential threat to pumas, guignas, and native foxes given they overlap extensively in time of activity with these species. Also, feral dogs had the widest distribution of all species indicating that their effects could be ubiquitous on the landscape. Thus, exotic species are damaging to wildlife, to livestock industry, and even to public health. I urge dialog between government authorities, wildlife managers, and scientists to generate a legal and public policy framework to properly managing habitat and HWC in southern-central Chile.
Doctor of Philosophy
Landscape transformation and human-wildlife conflict (HWC), which often result in retaliatory killing of wildlife in response to livestock predation, is one of the main global threats to wild cats, including pumas (Puma concolor). Medium-sized carnivores (mesocarnivores or mesopredators) are more abundant than large carnivores, live closer to human settlements and, like large predators, impact ecosystem structure and function significantly. Understanding habitat use of these carnivores is key to their conservation and management and to biodiversity preservation. Thus, there is need to investigate the ecological roles of carnivores (including invasive ones like free-ranging dogs and cats) to determine how interactions with other carnivore species and with the physical environment influence ecological roles of such species. This is especially important in my study area, which was severely burned by a catastrophic mega-wildfire in 2017, and for which there is scant information on wildlife responses to the mega-fire. I determined the distribution and causes of HWC across 52 provinces for 8 years in Chile and found that free-ranging dogs accounted for higher livestock depredation than pumas, killing substantially more livestock. Occurrence of HWC for both dogs and pumas increased with the sheep density of the province. Unexpectedly, dog HWC increased in less degraded habitats, indicating that dogs may travel far to prey on livestock in remote areas. The emergence of puma HWC in a site where it did not occur in the previous year increased with human-caused disturbance. Countrywide, dog HWC was higher than pumas in 43 out of the 49 provinces where both pumas and dogs occurred. I discuss livestock vulnerability, management strategies, and policy changes to address HWC, and discuss the threats that free-ranging dogs pose to biodiversity conservation and even to human public health. I also used remotely-triggered, camera-trap records to explore distribution of three mesocarnivores (guignas, culpeo foxes and chilla foxes across the landscapeand in response to mega-wildfires in southern-central Chile. I found that guignas, a small and vulnerable wild cat, avoided burned sites, preferring sites with native, dense vegetation while culpeo foxes were intermediate in being able to use plantations, but avoiding burned areas. Chilla foxes were most tolerant to landscape change with no response to burns, and they were found closer to human settlements and rivers. Finally, I examined overlap in space and time of day between native species pairs and native and exotic species pairs. I found that dogs were the most widely distributed species across the landscape, but were mostly diurnal while native species were primarily nocturnal. Cats however had high temporal overlap with guinas and chilla foxes, highlighting the potential for competition between them.. Thus, exotic species are damaging to wildlife, livetock and even huan health. I discuss the management implications and urge dialog between government authorities, wildlife managers, and scientists to generate a legal and public policy framework to properly managing habitat and HWC in southern-central Chile.

Seed dispersal mutualisms are important ecological interactions that can shape plant communities by influencing species distributions, community composition, and the regeneration of populations following a disturbance. Considering the fundamental role seed dispersal mutualisms play in many plant communities, it is important to understand, both generally and for individual seed dispersal mutualisms, what determines when animal partners successfully disperse seeds and when they do not. Myrmecochory, the dispersal of seeds by ants, is the most common form of zoochory in Western Australia. Myrmecochore plant diversity is richest in the Kwongan sandplains of the south-west, where ant-dispersed species can make up as much as 36% of the plant community. Here, I studied the determinants of seed dispersal rates to understand local variation in myrmecochorous seed dispersal rates. At a series of 30 sites, we sampled the ant and plant communities, measured aspects of the community structure (vegetation height, openness, topography, soil), measured seed removal rates and observed ant-seed interactions. The most significant factor that governed seed removal rates was the presence of the ant species Rhytidoponera violacea. Additionally, during seed dispersal observation trials, R. violacea removed 95% of all seeds taken. To better understand the fate of Acacia blakelyi seeds dispersed by R. violacea, we simulated variable seed burial depths and elaiosome removal by ants, followed by a bushfire to stimulate germination. Seed burial depth had a significant effect on seedling emergence, with the proportion of emerged seedlings declining with burial depth. The effect of depth was due to the strength of a fire-cue (heat) declining with depth. Seed burial depth also had a fitness cost, with a greater proportion of ârobustâ seedlings emerging from seeds buried closer to the surface. Seeds buried too deep to receive fire-cues remained dormant, adding to a long-lived soil seed bank.

The thesis of Kit Prendergast addressed impacts of urbanisation and introduced honeybees on native bees in southwest Australia. Additionally, efficacy of bee survey methods were evaluated. The study found remnant bushland, with high proportions of native flora, was of greater importance for supporting native bee populations, species, and pollinator networks, compared with residential gardens. Honeybees occupied distinct positions in pollinator networks, and altered network properties, with context-dependent impacts on native bees.

Thesis (MSc)--Stellenbosch University, 2015.
ENGLISH ABSTRACT: The present global biodiversity crisis is characterized mostly by loss of species due to habitat destruction but there other major threats – notably invasive alien species. The term “biodiversity hotspot” has been coined to emphasize areas for conservation prioritization – areas that have high biodiversity under threat from habitat destruction, invasive species, etc. The Cape Floristic Region (CFR) in the Western Cape (WC) Province of South Africa has the highest biodiversity of all Mediterranean-type climate regions globally and is classified among global biodiversity hotspots. The CFR, a Mediterranean-type climate heathland with a naturally high fire frequency, faces threat from transformation by development, disturbed (increased) fire frequencies and intensities, and invasive organisms, most notably invasive trees. Such threats disturb keystone species and keystone processes including insect pollinator assemblages and associated insect flower visitation webs and frequencies. Invasive pines are a serious threat to insect flower visitation as pine trees (Pinus spp.) shade out much indigenous vegetation in the CFR. Little is known of their long-term effects on insect flower visitors and vegetation recovery in post-pine restoration and recovery areas after such trees are removed. I investigated the recovery of vegetation and the most important insect pollinator, bees, after the removal of pines by fire and passive recovery in a CFR valley in the Western Cape. In 1999, a wildfire burned much of the WC Limietberg Nature Reserve along with an adjacent pine tree forestry stand - which was then left to recover, providing an ideal opportunity to investigate the enduring effects of pine afforestation in the CFR. In two data chapters, I compared the post-fire passive recovery of vegetation (Chapter 2) and bee diversity (Chapter 4) in areas which had previously been planted with pines vs. those which had contained natural fynbos. To improve on sampling methodology, I conducted an experiment that demonstrated the Observer Effect in bee sampling with a sweep net (Chapter 3), and I developed a novel sampling device (Chapter 5) for insect flower visitors. Sampling of vegetation and bee diversity was conducted in a paired sampling design, where fynbos (Natural) sub-sites were paired with sub-sites which had previously been afforested with pines (Post-Pine Recovery; PPR) and the two sub-sites were separated by a distinct, linear boundary (Natural/PPR boundary). Sampling was conducted along transects parallel to the boundary and extending in both directions from the boundary into the Natural and in the opposite direction into PPR sub-sites. Five transects were positioned at 3, 10, 20, 30, and 40 m from the boundary (Ecotone) and three were positioned at 60, 80, and 100 m from the boundary (Deep). In Chapter 2, I found that natural sub-sites consistently had higher total plant species abundance and species richness than PPR sub-sites. Approximately two thirds of plant species were more abundant in Natural sub-sites than in PPR sub-sites. There was no significant correlation in species richness or abundance with distance from the Natural/PPR boundary. Some genera are cautiously indicated as having lower success in recovery after pine afforestation: Erica spp., Restio spp., Hypodiscus spp. while Helichrysum spp. is also tentatively indicated to recover well in PPR sub-sites. Soil disturbance and concomitant disruption of normal ecosystem functions, including pollination, is indicated as a probable reason for disruption of plant recovery. In Chapter 3, sweep netting methodology was tested for the Observer Effect. A noticeable increase in bee visitation frequency to a common generalist plant species in bloom, Metalasia densa, was correlated with longer waiting periods after I stopped moving indicating the presence of an Observer Effect. This suggests that sweep netting for bees should only be commenced after a waiting period of five minutes during which the sweep netter is motionless. In Chapter 4, using a flight-intercept modified pan trap, I compared bee species richness and bee species abundance across different seasons and in both mass-flowering and sparser flower patches. There was no significant difference in bee species richness between Natural and PPR sub-sites. All bee species, except one complex, were more abundant in Natural sub-sites. Nearly two thirds of all bee species (n=37 of 56) caught with sweep netting and the modified pan trap are undescribed species. Similar to the vegetation, the effects of soil disturbance as a result of decades of pine forest shading and pine forest litterfall followed by an unusually hot pine forest fire are indicated as the most likely reasons for lower bee abundance in PPR sub-sites. This is due to the difficulty associated with viable nest establishment and suitable pollen and nectar forage availability in disturbed areas. In Chapter 5, the newly developed Pan and Flight Intercept Combination (PAFIC) trap’s design, pilot testing, and comparison with the traditional pan trap is discussed. A preliminary test suggests that the PAFIC trap is more efficient (with higher abundance) than the traditional pan trap. In Chapter 6, I discuss the implications of the disturbance of pine forestry and unusual pine fire to plant species and bee species assemblages. Bee-pollination webs in PPR sub-sites are indicated as being substantially simpler than those in Natural areas as well as compositionally different. The recovery of pollination as a keystone process in post pine-afforestation areas faces a substantial challenge given the disturbance to soil that decades of pine afforestation followed by pine forest fire can cause. Some suggestions are made for the restoration of fynbos areas recovering from pine afforestation including a discussion of augmenting re-vegetation measures (fynbos seed dispersal and seedling planting) with methods of restoring of healthy pedogenesis, epigaeic arthropod communities, and fynbos seedbanks.
AFRIKAANSE OPSOMMING: Die huidige globale biodiversiteit krisis is gekenmerk meestal deur die verlies van spesies as gevolg van die vernietiging van habitat. Maar daar is ook ander groot bedreigings – veral merkbaar indringerspesies. Die term “biodiversiteit brandpunt” is geskep om gebiede vir bewaring prioritisering te beklemtoon - gebiede wat 'n hoë biodiversiteit bevat wat bedreig word deur die vernietiging van habitat, indringerspesies, ens. Die Kaap Floristiese Streek (KFS) in die Wes-Kaap (WK) Provinsie van Suid-Afrika het die hoogste biodiversiteit van alle Mediterreense tipe klimaat streke wêreldwyd, en is onder die globale biodiversiteit brandpunte geklassifiseer. Die KFS, 'n Mediterreense-tipe klimaat heideveld met 'n natuurlike hoë brand frekwensie, word bedreig as gevolg van transformasie deur ontwikkeling, versteurde (verhoogde) vuur regimes, en indringer organismes, veral indringerbome. Sulke bedreigings versteur hoeksteen spesies en die hoeksteen prosesse, insluitende insek bestuiwer samestelling en verwante insek blom besoekings webbe en frekwensies. Indringer dennebome (Pinus spp.) is 'n ernstige bedreiging vir insek blom besoeking want dennebome verskaf skaduwee aan baie inheemse plantegroei in die KFS. Min is bekend oor die langtermyn effekte op insek blom besoekers en plantegroei restorasie na denneboom verwydering en restorasie gebiede na sodanige bome verwyder word. Ek ondersoek die restorasie van plantegroei en die belangrikste insek bestuiwer, bye, na die vernietiging van dennebome deur vuur en passiewe herstel in 'n KFS vallei in die Wes-Kaap. In 1999 het'n veldbrand baie van die WK Limietberg Natuurreservaat saam met 'n aangrensende denneboom bosbouplantasie gebrand - wat toe gelaat is om te herstel via intermediêre suksessie na inheemse fynbos plantegroei. Dit bied 'n ideale geleentheid om die blywende gevolge van denneboom aanplanting in die KFS te ondersoek. In twee data hoofstukke, vergelyk ek die passiewe herstel van plantegroei na ‘n brand (Hoofstuk 2) en by diversiteit (Hoofstuk 4) in gebiede wat voorheen geplant is met dennebome teenoor diegene wat natuurlike fynbos vervat het. Om te verbeter op steekproefmetodiek, het ek 'n eksperiment onderneem wat demonstreer hoe die Waarnemer Effek by monsterneming met 'n vee-net beïnvloed (Hoofstuk 3), en het ek 'n nuwe monsterneming toestel ontwerp (Hoofstuk 5) vir insek blom besoekers. Monsterneming van plantegroei en by diversiteit is uitgevoer in 'n gegroepeerde steekproef ontwerp, waar fynbos (Natuurlik) sub-terreine gegroepeer is met sub-terreine wat voorheen aangeplant was met dennebome (Na Denneboom Verwydering Herstel; NDVH) en die twee sub-terreine is geskei deur 'n duidelike, lineêre grens (Natuurlik / NDVH grens). Steekproefneming is gedoen langs transekte parallel tot die grens en versprei in albei rigtings van die grens tot binne die natuurlike fynbos en in die teenoorgestelde rigting tot binne NDVH sub-terreine. Vyf transekte is geposisioneer binne 50 m van die grens (Oorgang sone) en drie is ver geplaas van die grens (Diep). In Hoofstuk 2 het ek gevind dat natuurlike sub-terreine konsekwent hoër totale getal plant individue en spesierykheid as NDVH sub-terreine gehad het. Ongeveer twee derdes van plantspesies was meer volop in natuurlike sub-terreine as in NDVH sub-terreine. Daar was geen beduidende korrelasie in spesierykheid of totale hoeveelheid plant individue met betrekking tot afstand van die Natuurlike /NDVH grens. Sommige genera word versigtig aangedui as met laer sukses in die restorasie terreine na denneboom aanplanting: Erica spp., Restio spp., Hypodiscus spp. terwyl Helichrysum spp. voorlopig aangedui is as goed herstel in NDVH sub-terreine. Grondversteuring en gepaardgaande ontwrigting van normale funksionering van die ekosisteem, insluitend bestuiwing, word aangedui as 'n waarskynlike rede vir die ontwrigting van die herstel van plantegroei. In Hoofstuk 3 is vee-net metodologie getoets vir die Waarnemer Effek. 'N merkbare toename in by besoeking frekwensie van 'n algemene plantspesie in blomtyd, Metalasia densa, is gekorreleer met langer wagtydperke nadat ek gestop het om te beweeg, en dui dus op die teenwoordigheid van 'n Waarnemer Effek. Dit dui daarop dat die vee-net vir bye eers gebruik moet word na 'n wagtydperk waartydens die waarnemer bewegingloos verkeer. In Hoofstuk 4, met behulp van 'n vlug-onderskep gewysigde pan lokval, het ek by spesierykheid en totale by hoeveelheid vergelyk oor verskillende seisoene en in beide massa-beblomde en yler blom kolle. Daar was geen beduidende verskil in by spesierykheid tussen natuurlike en NDVH sub-terreine. Alle by spesies, behalwe een spesie kompleks, was meer volop in natuurlike sub-terreine. Byna twee derdes van alle by spesies (n = 37 van 56) gevang met vee-nette en die van die gewysigde pan lokvalle is onbeskryfde spesies. Soortgelyk aan die plantegroei, is die gevolge van grondversteuring as gevolg van dekades van denneboom bos skadu en denneboom bos blaar afval gevolg deur 'n buitengewoon warm denneboom bos brand as die mees waarskynlike redes vir laer by hoeveelheid in NDVH sub-terreine aangedui. Dit is as gevolg van die probleme wat verband hou met lewensvatbare nes vestiging en geskikte stuifmeel en nektar voer beskikbaarheid in versteurde gebiede. In Hoofstuk 5 is die nuut ontwikkelde Pan en Vlug Onderskep Kombinasie (PEVOK) lokval ontwerp, aanvanklike toetsing, en vergelyking met die tradisionele pan lokval bespreek. 'N Voorlopige toets dui daarop dat die PEVOK lokval meer doeltreffend (met 'n hoër oorvloed) is as die tradisionele pan lokval. In Hoofstuk 6 bespreek ek die implikasies van die versteuring van denneboom bosbou en ongewone denneboom vuur met betrekking tot plant spesies en by spesies samestelling. By-bestuiwing webbe in NDVH sub-terreine word aangedui as wesenlik eenvoudiger as dié in natuurlike areas asook verskillend in samestelling. Die herstel van bestuiwing as 'n hoeksteen in na denneboom-aangeplante gebiede staar 'n aansienlike uitdaging in die gesig, gegee die versteuring van grond wat dekades van denneboom aanplanting gevolg deur denneboom bos brand kan veroorsaak. Sommige voorstelle is gemaak vir die herstel van fynbos gebiede wat herstel van denneboom aanplanting, insluitend 'n bespreking van die aanvulling van plantegroei hervestiging maatreëls (fynbos saadverspreiding en saailinge plant) met die metodes van die herstel van 'n gesonde pedogenese, bogrondse geleedpotige gemeenskappe, en fynbos saadbanke.

Thesis (PhD)--Stellenbosch University, 2011.
ENGLISH ABSTRACT: Both taxonomic diversity and diversity of species interaction networks are experiencing declines as a result of agricultural intensification at habitat and landscape scales. Reversing this trend is a key conservation issue, particularly for important functional groups such as flower-visiting insects and the networks within which they interact. This is of great concern in regions of high conservation priority such as the Cape Floristic Region (CFR), known for its high level of floral and faunal endemism and exceptional species turnover. Holistic approach to conservation in agricultural landscapes involves both preservation of natural land and wildlife friendly management of the farm land to achieve conservation targets. The value of these extensive management approaches is yet to be fully assessed, especially in perennial systems such as vineyards. I examined here the effects of vineyard management and landscape context on species richness and abundance of flower-visiting insects and their species interaction networks. Possible taxon specific effects were verified. I also investigated whether vineyards under organic and conventional management homogenized insect-flower interaction networks and whether vineyards with different management practices vary in patterns of species turnover. I sampled flower-visiting insects and their interactions in organic and conventional vineyards, and in natural reference sites. Inclusion of natural reference sites enabled me to make management recommendations for patches of natural vegetation in CFR agricultural landscape. Statistical models showed taxon-specific benefit of organic farm management, and of landscape (distance to natural habitat). There was benefit to monkey beetles (Scarabaeidae) but not to bees (Apidae). Organic vineyards had a higher number of insect-flower interactions than conventional ones, but vineyards under the two types of management were similar in terms of other important network indices. However, networks of the vineyards were more nested than the natural sites, indicating that they may be potentially more stable to perturbation and random extinctions. Multivariate dispersion tests revealed insect-flower interaction networks were not homogenized by both organic and conventional vineyards across the landscapes. I also found, through additive partitioning, that organic and conventional vineyards were similar in terms of species turnover of bees and flowering plants. The findings of this study provide heuristic value to current debates on the value of vineyard habitats for insect conservation. Both organic and conventional vineyards that promote sustainable management of the non-crop floral vegetation between vineyard rows are potential solutions for conservation of flower-visiting insects and their interactions. Also, attention has to be paid to the quality and connectivity of the natural habitat patches that are within CFR agricultural landscape. Site specific management and assessment of the value of these landscape elements is important. Management approaches such as carefully controlled burning may be beneficial, as the CFR natural vegetation is a fire-driven community.
AFRIKAANSE OPSOMMING: Taksonomiese diversiteit en diversiteit van spesies-interaksie netwerke ondervind beide afnames as gevolg van landboukundige intensifikasie op habitat en landskap skaal. Om die neiging terug te swaai, is ’n sleutel bewaringsaangeleentheid, veral vir belangrike funksionele groepe soos blom-besoekende insekte en die netwerke waarbinne hulle op mekaar inwerk. Dit is van groot kommer in streke met hoë bewaringsprioriteite soos in die Kaapse Floristiese Streek (KFS), bekend vir sy hoë vlak van plant- en dierendemisme en buitengewone spesies kentering. ’n Holistiese benadering tot bewaring van landboukundige landskappe behels beide die bewaring van natuurlike land en natuurlewe-vriendelike bestuur van die plaasgrond om bewaringsdoelwitte te bereik. Die waarde van hierdie ekstensiewe bestuursbenaderings moet nog volledig bepaal word, veral in meerjarige sisteme soos wingerde. Ek het die uitwerkings van wingerdbestuur en landskapsamehang op spesiesrykheid en volopheid van blombesoekende insekte en hulle spesies interaksie netwerke ondersoek. Moontlike takson-spesifieke uitwerkings is nagegaan. Ek het ook ondersoek ingestel of wingerde onder organiese en gebruiklike bestuur ooreenstemmende insek-blom interaksie netwerke met wingerde met verskillende bestuurspraktyke in patroon van spesies kentering gewissel het. Ek het blom-besoekende insekte en hulle interaksies in organiese en konvensionele wingerde, asook in natuurlike verwysingsgebiede gemonster. Insluiting van natuurlike verwysingsgebiede het my in staat gestel om bestuursvoorstelle vir gebiede van natuurlike plantegroei in KFS landboulandskappe voor te stel. Statistiese modelle toon takson-spesifieke voordeel van organiese plaasbestuur en van die landskap (afstand van natuurlike habitat) self. Daar was voordeel vir bobbejaankewers (Scarabaeidae), maar nie vir bye (Apidae) nie. Organiese wingerde het ’n groter getal insek-blom interaksies as konvensionele wingerde gehad, maar wingerde onder beide tipes van bestuur was soortgelyk in terme van ander belangrike netwerk aanduiders. Netwerke van wingerde was egter meer geklomp dan natuurlike gebiede wat aandui dat hulle potensieel meer stabiel betreffende versteuring en lukrake uitsterwings is. Multivariate verspreidingstoetse het aangetoon dat insek-blom interaksie netwerke by beide organiese en konvensionele wingerde oor landskappe nie eenvormig was nie. Ek het ook bevind deur aanvullende verdeling dat organiese en konvensionele wingerde gelykwaardig was in terme van spesies kentering van bye en blomplante. Die bevindings van hierdie studie verskaf heuristise waarde tot huidige debatte oor die waarde van wingerdhabitatte vir insekbewaring. Beide organies en konvensionele wingerde wat volhoubare bestuur van die nie-gewas plantegroei binne wingerdrye bevorder, is moontlike oplossings vir die bewaring van blom-besoekende insekte en hulle wisselwerkings. Bykomend moet aandag gegee word aan die kwaliteit en verbindings van en tussen natuurlike habitat gebiede binne die KFS landboulandskap. Plekspesifieke (plaaslike) bestuur en bepaling van die waarde van hierdie landskapelemente is belangrik. Bestuursbenaderings, soos noukeurig beheerde brand, mag voordelig wees aangesien die KFS natuurlike plantegroei ’n vuurgedrewe gemeenskap is.

Many regions around the world are renowned as biodiversity hotspots. South Western Australia is one of these. A combination of the recognised high biodiversity and a seemingly unbalanced species distribution of the genus Nunciella across Australia initiated the investigation into the diversity of the south western species of Nunciella. Previous descriptions indicate two of the 11 Nunciella species are found in this region, one of these with a very large recorded distribution in contradiction to the short range distribution of all the other species. Through observations of museum specimens it is hypothesised that there is a much larger species diversity to be found in Western Australia. The aim of this project was to determine if there are more species present than currently described. This was done through sequencing the genes cytochrome c oxidase subunit I (COI) and histone H3 (H3) combined with morphological analysis. The molecular analysis revealed strong COI support for at least seven Nunciella species in the area. As an unexpected result COI also provides support for a new genus with a further six species. H3 results had low support for species level delimitation though strong support for the two genera. The resulting DNA species are further supported by morphological characters suitable for species delimitation, enabling the identification of a further three morphological species. The holotype of Nunciella aspera (Pocock, 1903) was obtained and redescribed including images. Specimens from the type locality of the second species, N. karriensis Kauri, 1954 have been included in this study as well as observations made on the syntype of a synonymised species N. frontalis Roewer, 1931.It is also revealed that Nunciella species may live sympatrically. A secondary aim was to clarify the misconceptions presented in previous descriptions of N. aspera. A number of authors redescribed N. aspera with varying characters from a number of Western Australian locations. This research has identified support for the authors possibly being correct in their examination, though incorrect in their species diagnosis. In summary, this research provides morphological descriptions for ten new Nunciella species, a redescription of the holotype of the type species of Nunciella, brief analysis of the syntype of the synonymised N. frontalis, cautionary predictions on the status of N. karriensis and molecular and morphological support for a new genus with six species.

Em diversos estudos ao redor do globo, a estrutura e heterogeneidade da vegetação têm se mostrado um fator determinante na diversidade de espécies de aves e também de outros grupos de animais. O Cerrado é o segundo mais extenso e mais ameaçado bioma de ocorrência no Brasil. Este bioma também é caracterizado por um evidente gradiente ambiental de estrutura e heterogeneidade de vegetação. Na presente tese analisamos a influência da estrutura e heterogeneidade da vegetação sobre a diversidade em comunidades de aves do Cerrado. Nossa expectativa era corroborar a “Hipótese de Heterogeneidade de Habitats”, que propõe que quanto maior a estrutura e heterogeneidade da vegetação, maior será a diversidade de espécies. No primeiro capítulo, realizamos uma compilação sistemática de estudos publicados sobre a diversidade de aves em áreas ocupadas por algumas fisionomias típicas de Cerrado lato sensu, com o intuito de analisar o conhecimento obtido até então acerca da relação entre diversidade de aves e a estrutura da vegetação no Cerrado. Foram selecionadas 72 amostras de 22 estudos, sendo que estas amostras variaram quanto ao tipo fisionomia amostrada e o método amostral empregado, além de também estarem disponíveis em diferentes artigos e serem realizadas em diferentes regiões geográficas. Para análises destes dados, utilizamos a análise de modelos lineares generalizados de efeitos mistos (modelo com distribuição de erros poisson), que permite analisar os efeitos de variáveis fixas e aleatórias sobre a variável explicativa (riqueza de espécies). As variáveis fixas foram o tipo de vegetação amostrada (vegetação campestre, savânica e florestal) e o método amostral empregado (ponto fixo, transecto e redes de neblina). Já as variáveis de efeito aleatório utilizadas foram o estudo onde os dados foram publicados, o autor de cada estudo e a localidade geográfica. O efeito destas variáveis aleatórias poderiam afetar somente os interceptos das relações entre as variáveis fixas e a variável explicativa ou poderiam alterar a relação entre as variáveis fixas e explicativa. Construímos diversos modelos a partir da combinação de variáveis de efeito fixo e aleatório e a seleção do modelo mais parcimonioso foi feito por meio do critério AICc (critério de informação de Akaike corrigido para pequenas amostras). O modelo que apresentou menor valor de AICc (mais parcimonioso) foi aquele que incluiu os efeitos de ambas variáveis de efeito fixo (fisionomia e método amostral) e também um efeito da interação entre estas duas variáveis. Neste modelo também foram incluídos os efeitos das variáveis aleatórias estudo e localidade geográfica sobre os interceptos das relações entre as variáveis de efeito fixo e a variável explicativa. Estes resultados mostraram que a riqueza de espécies de aves em nosso estudo variou não só em função da fisionomia e do método amostral empregado, mas dependendo do método amostral utilizado a relação entre riqueza e fisionomia também foi alterada. Portanto, esta interação não permitiu que fosse estimada a relação entre fisionomia e riqueza sem considerar o efeito dos métodos. Já os efeitos das variáveis aleatórias mostraram que a variação estimada nos interceptos entre estudos foi duas vezes maior do que a variação estimada entre localidades geográficas. O efeito da interação entre as variáveis fisionomia e método amostral apontou para a existência de heterogeneidade de detecção entre locais com diferentes fisionomias, além também de um efeito das fisionomias na efetividade dos diferentes métodos amostrais. A influência dos métodos amostrais no número de espécies observadas em cada fisonomia pode ser esperada devido às diferenças intrínsecas dos métodos, já que ponto fixo e transecto são baseados em contatos visuais e auditivos com as espécies, enquanto que o método de rede de neblina consiste na captura passiva das espécies que voam na altura das redes. Assim, redes de neblina podem ser mais efetivas em habitats menos estruturados (por ex. campos limpos e sujos), onde a rede alcança quase todo os estratos de vegetação. No entanto, o método de transecto pode ser mais efetivo que o método de ponto fixo em áreas de florestas, pois nestes hábitats as espécies tendem a ter territórios menores e o deslocamento do observador proporciona ao observador cobrir um maior número de terrítórios. Por outro lado, o ponto fixo pode ser mais vantajoso por não produzir ruído e afugentar as espécies, o que pode ser uma desvantagem do método de transecto. Outros fatores, como a experiência e número de observadores, número de pontos amostrais, número de redes utilizadas e comprimento de transectos, podem explicar a grande variação estimada entre os estudos. Uma das maneiras de se contornar estes efeitos metodológicos é utilizar métodos desenvolvidos especialmente para lidar com diferentes probabilidades de detecção entre espécies, entre sítios e até métodos amostrais, o que poderia render dados mais confiáveis para o estudo da ecologia das espécies e para a elaboração de planos de manejo e/ou conservação. No segundo capítulo, a relação entre diversidade de aves e estrutura da vegetação foi analisada a partir de dados coletados em campo e utilizando um protocolo de amostragem específico para se estimar e considerar os efeitos da vegetação sobre a detecção das espécies. As amostragens foram realizadas em um dos maiores e mais preservados remanescentes de Cerrado (Parque Nacional Grande Sertão Veredas-PARNA GSV) e consistiram do registro das espécies de aves em 32 áreas dispostas em um gradiente de vegetação de Cerrado, que variaram desde campos limpos e sujos, campos cerrado a cerrados sensu stricto. O cálculo da riqueza de espécies de aves em cada sítio foi realizado através de modelos de ocupação-detecção, adaptados para estimar a riqueza de espécies em comunidades. A vegetação, por sua vez, foi medida a partir de estimativas de presença da vegetação entre 0 e 4 m de altura (16 intervalos de 22,5 cm cada um) e duas variáveis de estrutura foram obtidas a partir de uma análise de componentes principais, que foi aplicada para resumir a variação da presença de vegetação nos 16 intervalos de altura. Estas variáveis de vegetação foram relacionadas tanto com a ocupação quanto com a detecção das espécies, já que a estrutura da vegetação poderia influenciar não só a ocorrência mas também a detecção das espécies. O dia da amostragem e também a temperatura no momento da amostragem também foram incluídas como covariáveis que poderiam afetar a detecção. Após a estimativa da riqueza de espécies pelo modelo de ocupação-detecção para comunidades, esta riqueza estimada foi relacionada por uma função quadrática com a estrutura da vegetação usando um modelo bayesiano de metanálise, que permitiu incluir a incerteza nas estimativas de riqueza na análise. A título de comparação, também foi ajustado um modelo quadrático GLM (distribuição de erros normal) aos dados de riqueza observada. Os resultados mostraram que a riqueza estimada a partir dos dados das 38 espécies mais detectadas durante as amostragens teve uma fraca relação com as duas covariáveis de estrutura de vegetação, sendo que houve uma maior riqueza de espécies em sítios com vegetação intermediária em altura e uma maior riqueza de espécies de aves em sítios onde houve maior presença de vegetação abaixo de 2 m de altura. No entanto, as relações entre riqueza estimada e estas covariáveis foi menos intensa mas qualitativamente similar às relações entre a riqueza observada e as covariáveis de vegetação. A menor intensidade nas relações da riqueza estimada foi evidenciada principalmente em ambos os extremos do gradiente de estrutura vertical da vegetação e também nas áreas com menor presença de vegetação abaixo de 2 m. Estes resultados mostraram que o efeito da detecção pode alterar o efeito da relação entre riqueza de espécies e estrutura de vegetação. Além disso, ao menos para as 38 espécies mais comumente encontradas na área de estudo, os resultados apontam para a importância de todo o gradiente de estrutura da vegetação para a manutenção da riqueza de espécies de aves no Cerrado. Futuros estudos que visem aprimorar o uso destes modelos de ocupação e detecção para comunidades são fundamentais para permitir o uso dos dados de todas as espécies da comunidade. Além disto, outros estudos que se proponham a analisar a dinâmica e composição das comunidades de aves nestes gradientes de estrutura de vegetação são fundamentais para um maior conhecimento sobre a ecologia e conservação das aves no Cerrado
In several studies around the globe, the structure and diversity of vegetation have been shown to be a determining factor in the diversity of species of birds and also other groups of animals. The Cerrado is the second most extensive and most threatened biome occurrence in Brazil. This biome is also characterized by an obvious environmental gradient of vegetation structure and heterogeneity. In this thesis we analysed the influence of the structure and diversity of the vegetation on the diversity in the Cerrado bird communities. Our expectation was to support the “Habitat Heterogeneity Hypothesis” which suggests that the higher the structure and diversity of vegetation, the greater the diversity of species. In the first chapter, we conducted a systematic compilation of published studies on the diversity of birds in areas occupied by some typical physiognomy of Cerrado textit lato sensu, in order to analyze the knowledge obtained so far about the relationship between diversity of birds and the structure of the vegetation in the Cerrado. We selected 72 samples from 22 studies, and these samples varied as the sampled vegetation physiognomy, the sampling method used, and they also are available in different articles and be carried out in different geographical regions. We performed the analysis of generalized linear mixed effects models (model poisson distribution errors), which allows us to analyse the effects of fixed and random variables on the explanatory variable (species richness). Fixed variables were the type of sampled vegetation (grassland, savanna and forest) and the sample method employed (fixed point, transect and mist nets). The random variables used were the study where the data were published, the author of each study and geographic location. These random variables could only affect the intercepts of the relationship between fixed and variable explanatory variable or could alter the relationship between fixed and explanatory variables. We built several models from the combination of fixed and random effects variables and selection the most parsimonious model was made by the AIC criterion (Akaike information criterion corrected for small samples). The model that showed lower value of AIC (more parsimonious) was the one that included the effects of both fixed effect variables (physiognomy and sampling method) and also an effect of the interaction between these two variables. In this model were also included the effects of random variables study and geographic location of the intercepts of the relationship between the fixed effect variables and the explanatory variable. These results showed that the bird species richness in our study varied not only in terms of physiognomy and sample method, but depending on the sampling method used the relationship between richness and physiognomy has also changed. Therefore, this interaction does not allowed us to estimate the relationship between physiognomy and richness without considering the effect of the methods. Since the effects of random variables showed that the variation in the estimated intercept between studies was twice larger than the estimated variation between geographic locations. The effect of interaction between the vegetation physiognomy and sampling method variables pointed to the existence of heterogeneity detection between locations with different physiognomies, in addition also of an effect of the physiognomies in the effectiveness of different sampling methods. The influence of the sampling method in the number of species observed in each physiognomy may be expected due to intrinsic differences in the methods, since fixed point counts and transect are based on visual and aural contacts with the species, while the mist net method consists in passive capture of species flying at the time of the networks. Thus, mist nets may be more effective in less structured environments (eg. Clean and dirty fields) where the net reaches virtually all vegetation layers. However, transect method can be more effective than the fixed point method in areas of forests since in these habitats species tend to have smaller territory areas, and the observer movement provides the observer cover greater areas. On the other hand, the point counts can be more advantageous not to produce noise and chase species, which may be a disadvantage of transect method. Other factors, such as experience and number of observers, the number of sampling points, the number of nets used and length of transects, may explain the wide variation between studies estimated. One of the ways to overcome these methodological effects is to use methods developed especially to deal with different probabilities of detection of species, between sites and sampling methods, which could yield more reliable data for the ecological study of the species and the development of management plans and/or conservation. In the second chapter, the relationship between diversity of birds and vegetation structure was analysed from data collected in the field and using a specific sampling protocol to estimate and consider the effects of vegetation on the detection of species. The samples were taken in one of the largest and well preserved remnants of Cerrado (Grande Sertão Veredas National Park-PARNA GSV) and consisted of the record of bird speciesin 32 areas arranged in a Cerrado vegetation gradient, ranging from grasslands, open and dense savannas. The calculation of the bird species richness at each site was conducted using occupancy-detection models adapted to estimate the number of species in communities. The vegetation, in turn, was measured from estimates of the presence of vegetation in height intervals between 0 and 4 m (16 intervals of 22.5 cm each) and two structure variables were obtained from a principal component analysis applied to summarize the variation of the vegetation presence in height intervals. These vegetation variables were related to both the occupation and detection of species, since the vegetation structure could influence not only the occurrence but also the detection of species. The day of sampling and also the temperature at the time of sampling were also included as covariates that may a_ect the detection. After the estimation of species richness by model occupancy detection for communities, this estimated richness was related by a quadratic function with the vegetation structure using a Bayesian meta-analysis model, which allowed us include uncertainty in richness estimates. By way of comparison, we also fit a quadratic model GLM (normal distribution errors) to the observed richness data. The results showed that the richness estimated from the data of the 38 most detected species during sampling had a weak relationship with both covariates vegetation structure, and there was a greater number of species at sites with intermediate vegetation height and greater bird species richness in places where there was a greater presence of vegetation below 2 m in height. However, relations between estimated richness and these covariates was less intense but qualitatively similar to the relationship between observed richness and vegetation covariates. The lowest intensity in the estimated richness relationship was observed mainly at both ends of the vertical gradient of vegetation and also in areas with less presence of vegetation below 2 m. These results showed that the effect of detection can change the effect of the relationship between species richness and vegetation structure. Moreover, at least for the 38 species most commonly found in the study area, the results point to the importance of the entire vegetation structure gradient to maintain the bird species richness in Cerrado. Future studies aiming to improve the use of these models of occupation and detection for communities are essential to allow the use of data of all species in the community. In addition, other studies that propose to analyse the dynamics and composition of bird communities in these vegetation structure gradients are fundamental for a better understanding of the ecology and conservation of Cerrado birds

Neste trabalho realizou-se o estudo de distribuição, riqueza e conservação do gênero Davilla Vand. (Dilleniaceae) no Neotrópico. Para tal utilizou-se a modelagem de distribuição de espécies com o algoritmo Maxent. Este produz distribuição das espécies no espaço geográfico a partir de dados ambiental e de ocorrência. Foram estudadas as espécies de acordo com o bioma de ocorrência: Mata Atlântica; Cerrado; e Amazônia. Este grupo está representado no Neotrópico por 25 espécies. Para o Cerrado incluiu-se além das espécies do gênero Davilla as demais espécies da família Dilleniaceae. Os resultados indicaram que no Cerrado o grupo está representado por nove espécies de Davilla, além de Curatella americana L. e três espécies de Doliocarpus Rol., destas cinco são endêmicas (Doliocarpus elegans Eichler e 4 Davilla spp.). Para a Mata Atlântica ocorrem 12 espécies de Davilla, oito delas são endêmicas, incluindo uma espécie ameaçada de extinção. Para a Floresta Amazônica são conhecidas nove espécies, cinco delas endêmicas. Duas outras espécies são Neotropicais, portanto, compartilhadas por todos os biomas citados anteriormente. As demais espécies são de ocorrência em pelo menos dois biomas. Para estes três biomas produziu-se a distribuição e a riqueza de espécies visando comparar os resultados com as unidades de conservação, objetivando discutir questões relativas à conservação deste grupo. Os parâmetros conservacionistas como espécies raras, zonas de endemismo, zonas de alta riqueza, áreas de preservação ambiental, foram confrontados objetivando indicar áreas prioritárias para a conservação do grupo e da biodiversidade. Os resultados indicaram existir três centros de diversidade para este grupo. O principal deles está localizado na Mata Atlântica, principalmente nas florestas litorâneas do estado da Bahia. Outro centro de diversidade localiza-se na região central do Cerrado, especialmente nos estados de Goiás e Bahia. A outra área de diversidade localiza-se próximo à foz do Rio Amazonas e ao longo de seu curso. Devido ao hábito predominante das espécies serem lianas, estas são importantes componentes das florestas, das quais usamos este referencial para discutir questões relativas à conservação destes habitats, de suas espécies e da biodiversidade. As informações completas estão apresentadas nos capítulos de acordo com os respectivos biomas abordados.
In this study was realized to study the distribution, richness and conservation of the Davilla Vand. (Dilleniaceae) in the neotropics. For this purpose was used to distribution model of species with Maxent algorithm. This produces species distribution in geographic in space based on environmental and occurrence data. Species in accordance with biome of occurrence were studied: Atlantic Forest; Cerrado; and the Amazon. This group is represented by 25 species in the neotropics. For the Cerrado was included in addition to the Davilla species all species of Dilleniaceae family. The results indicated that in the Cerrado this group is represented by nine species of Davilla, and Curatella americana L. and three species of Doliocarpus Rol., to these five are endemic (Doliocarpus elegans Eichler and 4 Davilla spp.). For Atlantic Forest occur 12 Davilla species, eight of which are endemic, including an endangered species. For the Amazon are known nine species, five of these endemic. Two other neotropical species are therefore shared by all biomes mentioned above. The other species are occurring in at least two biomes. For these three biomes produced the distribution and species richness in order to compare the results with the protected areas, aiming to discuss issues relating to the conservation of this group. Conservationists parameters as rare species, areas of endemism, areas of high species richness, conservation areas, were confronted aiming indicate priority areas for conservation of biodiversity and too this group. The results indicated three centers of diversity for this group. The main one is located in the Atlantic Forest in coastal forests of Bahia. Another center of diversity is located in central region of Cerrado, especially in the states of Goias and Bahia. The other area of diversity is located near the mouth of the Amazon River and along its course. Due to the prevailing habit of the species are lianas, these are important components of forests, of which we use this framework to discuss issues relating to the conservation of these habitats, their species and biodiversity. Full details are presented in chapters according to their biomes addressed.

A maior parte da biodiversidade global está concentrada nas florestas tropicais. Um dos principais fatores que ocasionam o desaparecimento dessa diversidade é a perda de hábitats pelas ações antrópicas, como o desmatamento e o crescimento urbano desordenado. Fragmentos florestais que possuem elevada biodiversidade, altas taxas de endemismo e fortes pressões antrópicas, são chamados de hotspots. A Floresta Atlântica é um dos hotspots brasileiros mais devastados. Por serem sensíveis as alterações do ambiente, as aves são consideradas importantes bioindicadores da qualidade dos ecossistemas. O presente estudo foi realizado na Reserva Particular do Patrimônio Natural (RPPN) Rio dos Pilões, em uma região antropizada e com remanescentes de Mata Atlântica (Floresta Ombrófila Densa Montana), localizada no município de Santa Isabel, no Estado de São Paulo. A RPPN pertence a um empreendimento imobiliário que visa à integração entre as atividades de proteção dos recursos naturais com as ações humanas. Com o intuito de conhecer e analisar a comunidade de aves da RPPN estudou-se três ambientes principais: um ambiente de campo antrópico (ACA), um ambiente antrópico inundado (AAI) e um ambiente florestal antropizado (AFA). O estudo foi realizado de maio de 2005 a maio de 2006, utilizandose o método de captura e recaptura com redes-neblina e o método de observações em trajetos irregulares, sendo o primeiro aplicado no AFA e o segundo no ACA e no AAI. Foram registradas 141 espécies de aves em um total de 1.824 horas de trabalhos. Estas espécies estão distribuídas em 20 ordens, 46 famílias, 125 gêneros, resultando em 2.243 indivíduos observados, 184 capturados e 17 recapturados. A curva acumulada de espécies não mostrou tendência à estabilização, sugerindo que o esforço de coleta despendido não tenha sido suficiente para amostrar toda a comunidade, indicando assim que novas espécies possam ser registradas. Os Não-Passeriformes somaram 56 espécies, com maior representatividade nas famílias Ardeidae e Trochilidae. Os Passeriformes foram os mais representativos, com 85 espécies, sendo Tyrannidae a de maior número. O ambiente que apresentou maior riqueza foi o AAI com 85 espécies, seguido pelo AFA com 72 e o ACA com 52 espécies. As espécies mais freqüentes (FR) foram Patagioenas picazuro no ACA, Thraupis sayaca no AAI e Chiroxiphia caudata no AFA. A análise da freqüência de ocorrência (FO) mostrou que a maioria das espécies teve FO abaixo de 25%, enquanto que poucas espécies apresentaram FO maior que 75%. As espécies com maiores FO foram Vanellus chilensis, Pitangus sulphuratus, T. sayaca e Basileuterus leucoblepharus. A comunidade foi agrupada em 13 guildas tróficas, sendo a insetívora a de maior predomínio em todos os ambientes. Das espécies registradas, 04 são migrantes e 03 estão ameaçadas de extinção. Embora a RPPN apresente um elevado grau de degradação, possui elevada riqueza e diversidade de espécies de aves, fator este que pode contribuir não somente para aumentar seu valor de conservação, como também auxiliar na implantação de projetos de restauração ecológica dos remanescentes.
The most of global biodiversity is intent in the tropical forests. One of the main factors that they cause the disappearance of this diversity is the loss of habitats for the anthropic actions, as the deforestation and the disordered urban growth. Forest fragments that possess high biodiversity, high taxes of endemism and forts anthropics pressures, are called hotspots. The Atlantic Forest is a Brazilian hotspots more deforested. By being sensible the alterations of the environment, the birds are considered the most important bioindicators of the quality of ecosystems. The present study River of the Piloes was carried through in the Particular Reserve of Patrimony Natural (RPPN), in an anthropic region and with remainders of Atlantic Forest, located in the city of Santa Isabel, State of Sao Paulo. The RPPN belongs to a real estate enterprise that aims at the integration enters the activities of protection of the natural resources with the actions human beings. Whit the intention to know and to analyze the community of birds of the RPPN one studied three main environments: environment of anthropic field (ACA), anthropic environment flooded (AAI) and the anthropic forest environment (AFA). The study has been at the May of 2006 to May of 2005, using the capture method with mist-nets and the method of irregular courses, being the first one applied in the AFA, and as in the ACA and the AAI. They had been registered 141 species of birds in a total of 1.824 working hours. These are distributed in 20 orders, 46 families, 125 genders, resulting in 2.243 observed individuals, 184 captured and 17 recaptured. The accumulated curve of species as soon as did not show to trend to the stabilization, suggesting that the expended effort of collection has not been enough to show to all the community, indicating new species can be registered. The Non- Passeriformes had added 56 species, with bigger representation in the families Ardeidae and Trochilidae. The Passeriformes had been most representative, with 85 species and in Tyrannidae are the bigger. The environment that presented greater wealth was the AAI with 85 species, AFA with the 72 and the ACA with 52 species. The most frequent species (FR) had been Patagioenas picazuro in ACA, Thraupis sayaca in AAI and Chiroxiphia caudata in AFA. The analysis of the occurrence frequency (FO) showed that the majority of the species had FO below of 25%, whereas few species had presented bigger FO that 75%. The bigger with FO had been Vanellus chilensis, Pitangus sulphuratus, T. sayaca and Basileuterus leucoblepharus. The community was grouped in 13 trophic guilds, being the insectivora of the bigger predominance in all environments. Of the registered species, 04 are migrants and 03 are threatened of extinguishing. Although the RPPN presents one high degree of degradation, it possess high wealth and diversity of species of birds, it is the factor that can contribute to not only increase its value of conservation, as well as auxiliary in the implantation of projects of ecological restoration of the remainders.