Entender padrões de diversidade e composição de espécies ao longo de múltiplas escalas espaciais constitui um dos principais objetivos em ecologia e biogeografia. A relativa importância dos mecanismos responsáveis por estruturar as comunidades de plantas e como eles interagem para influenciar estes padrões têm sido foco de intensos debates. No presente estudo, foram utilizados dados do Inventário Florístico Florestal de Santa Catarina a fim de investigar os padrões de diversidade de espécies de árvores e suas relações com a heterogeneidade ambiental sob uma das perspectivas oriundas da teoria de metacomunidades, conhecida como “sorteio de espécies”. A predição chave deste ponto de vista é a de que a composição de espécies varia em resposta a diferenças nas condições ambientais entre manchas de hábitat. O presente estudo é focado nessa predição e objetivou entender como processos relacionados a filtros ambientais interagem direta e indiretamente sobre os padrões de diversidade em uma área de 95000 km 2 (dados de 432 unidades amostrais). Foi utilizada modelagem de equações estruturais (PLS Path Modeling), a fim de investigar os efeitos interativos da topografia, clima, balanço de água e energia e geometria das manchas de floresta sobre os padrões de alfa (α) e beta (β) diversidade de uma metacomunidade de floresta atlântica no sul do Brasil. Fatores relacionados a filtros ambientais mostraram substanciais efeitos sobre a diversidade alfa e beta. A quantidade total da variação na beta diversidade explicada pela filtragem de hábitat foi alta (64%), corroborando a predição testada no nível de metacomunidades. Os fatores mais importantes para explicar a diversidade beta foram: extremos climáticos, balanço de água e energia e alfa diversidade, enquanto tamanho da mancha e balanço de água e energia foram os fatores chaves para a alfa diversidade. O teste de Mantel parcial mostrou que os efeitos ambientais ocorrem amplamente independente de efeitos espaciais, reforçando a predição testada. O estudo provê forte suporte empírico para a predição de que a beta diversidade reflete primariamente processos determinísticos associados com o nicho das espécies e suas respostas às condições ambientais na escala espacial considerada. / Understanding patterns of species diversity and composition across multiple scales is one of the main purpose in ecology and biogeography. The relative importance of the mechanisms that structure plant communities and how they interact to influence these patterns remains a topic of hot debate. In the present study, we use data from the Forest Inventory of Santa Catarina to investigate the patterns of species diversity of subtropical Atlantic forests and its relationships with environmental heterogeneity on a metacommunity perspective (species-sorting). The key prediction of this viewpoint is that community composition varies in response to differences in environmental conditions among habitat patches. Our study focused on this perspective, aiming to understand how environmental filtering processes interact directly and indirectly on diversity patterns in an area of 95000 km 2 (data from 432 forest plots). We employed structural equation modeling (PLS Path Modeling) to disentangle the interactive effects of topography, climate, water-energy balance, and geometry of forest patches upon the alpha and beta diversity of a subtropical forest metacommunity in southern Brazil. Factors related to environmental filtering showed substantial effects upon tree alpha and beta diversity. The total amount of variation in beta diversity explained by environmental filtering was high (64%) and was even more when together with alpha diversity (73%), corroborating the prediction of species-sorting model at the metacommunity level. Climatic extremes, water-energy balance and alpha diversity were the key determinants of beta diversity and patch size and water- energy balance the key determinants of alpha diversity in the South Brazilian Atlantic forests. Partial mantel test showed that environmental effects occurred largely independent of spatial effects, reinforcing the tested prediction. Our study provides strong empirical support for the prediction that beta diversity primarily reflects deterministic factors associated with species niches and their responses to environmental conditions in the studied spatial scale.

Savanna woodlands are vitally important in providing ecological services (e.g. erosion protection, micro-climate) and economic services (e.g. timber, food, fodder non-wood products, and wild-life habitats) that sustain local livelihoods and national economies. Increasing demands and the need for sustainable savanna woodland resource management requires that the ecological, economic, social and cultural values of these resources be explored and brought to the attention of decision makers and the general public. The identification and better understanding of the structure and dynamics of woodland community types, patterns of species distribution and quantitative properties of their diversity is important to the conservation and sustainable management of these woodlands. This study seeks to contribute to a better understanding of Nakasongola woodland community types, species diversity patterns and environment correlates, natural regeneration processes (i.e. sprouting and seedling establishment) and identifying livelihood strategies adopted by households, woody species utilised, and the contribution of charcoal production to household livelihoods. Data on vegetation and environmental variables were collected using 75 rectangular 20 x 50 m (0.1 ha) plots. Data on land use and land cover changes, and relevant associated socio-economic parameters were collected through the analysis of multi-temporal satellite imagery and field observations, as well as interviews of local households and key informants. The basic major livelihood activities for the rural households in this savanna dryland are charcoal production, subsistence crop cultivation and livestock grazing. However, it, sometimes, includes various combinations of activities, i.e. charcoal production and subsistence crop cultivation for both food and cash, and livestock keeping for income generation through selling the livestock products such as milk and, sometimes, the whole animal. At least 24 woody species, including fruit trees (Mangifera indica and Artocarpus heterophyllus), are frequently harvested, including 16 species that are considered the most utilized for charcoal production. Charcoal production, being the major source of income to the rural households, contributes on average US$ 259 ± 46 (S.E.) per household annually. There were significant differences in charcoal production (Kruskal-Wallis; H = 31.42, p < 0.0001), producer sale prices per bag of charcoal (H = 35.62, p < 0.0001), and annual incomes from charcoal production (H = 32.44, p < 0.0001) per households across the 8 sub-counties. Most of the youth (≤ 20 years old) derive their livelihoods from charcoal production, a small amount of trade, offering labour services, livestock keeping, fishing, bee keeping and earth brick making. Charcoal production, livestock keeping and hunting are carried out particularly by men, whereas, crop cultivation, and collection of fire wood, medicinal plants and fruits are carried out, mainly, by women. However, men are also engaged in cultivation only during the rainy seasons. There have been significant land cover changes in the area during the period 1984 to 2001, resulting in a 64% decrease in dense woodland cover, and an 80% increase in areas under cultivation/settlements. These changes are attributed to significant spatial expansion in agriculture increased commercialisation of charcoal production, grazing and human population growth. A total of 44,195 (5,893 plants/ha) woody plants representing 99 species in 67 genera and 31 families were recorded. The most species rich families were Mimosaceae (13), Rubiaceae (9), Moraceae (7), Euphorbiaceae (7), Anacardiaceae (6), Combretaceae (5) and Verbenaceae (5). Density of woody species differed significantly (F2, 72 = 6.3, P < 0.003) among land uses, being higher under charcoal production (7,131 ± 755 plants/ha) and cultivation (6,612 ± 665) areas and significantly lower under grazing lands (4,152 ± 525). Community species composition differed significantly (Global RANOSIM = 0.14, p = 0.001) among land use types. All measures of beta-diversity (spatial “turnover” in species composition) showed consistently higher beta-diversity in the grazing land use (βW = 3.1; βT = 3.1), followed by cultivation (βW = 2.8; βT = 3.0) and charcoal production (βW = 2.7; βT = 2.8), suggesting a more heterogeneous spatial distribution of species in the grazing lands. This suggests that variations in the composition and diversity of woody species are to a great extent influenced by land use type and anthropogenic disturbances in this region. Basal area of woody species differed significantly (F2, 72 = 12.0, P < 0.0001) among land uses, being highest under cultivation and charcoal production and significantly lower under grazing. Woody plant density differed (F2,72 = 6.3, P = 0.003) across landuses, being highest under charcoal production and cultivation and significantly lower under grazing. The species that contributed most to both basal area and density across all the land uses were Combretum collinum and Combretum molle. However, different species contributed the next most i.e. Piliostigma thonningii for grazing; Albizia zygia and Harrisonia abyssinica for cultivation and Vepris nobilis for charcoal production areas. For both basal area and abundance of all woody species, the total variance in species-environmental factor relations (for the combined first four canonical axes) was higher than 50%, suggesting a relatively strong influence of the measured environment variables on species composition and distributions. The CCA points to a significant influence of soil Ca2+ and Mg2+ in association with grazing on gradients in the composition and structure of woody species in the savanna woodland of Nakasongola. Resprouting was generally common among the woody species. A total of 2,595 stumps, representing 74 species in 31 families were recorded from all plots. Of these, 98.3% resprouted and were identified to species level. Density of both stumps and total resprout differed significantly (p < 0.05) among the land uses, being higher in charcoal production areas than in grazing and cultivation land uses. For the overall pooled data, resprouts per stump differed significantly among land uses (F2, 456 = 7.75, p = 0.0005), being highest in charcoal production (mean ± S.E.; 14 ± 1) and cultivation (13 ± 1) land uses and lowest under grazing areas (10 ± 1). Generally, the mean number of resprouts per stump increased with increasing stump basal diameter (BD), being highest for BD size class > 41 cm. In relation to stump height, the highest mean resprouts/stump was found on stumps with heights ranging from 0.31- 0.40 m. Based on pooled species data, regression analyses showed weakly significant negative relationships between BD of leading resprouts and number of resprouts/stump (r2 = 0.123, p < 0.0001) and between height of leading resprouts and number of resprouts/stump (r2 = 0.068, p < 0.0001). Density of seedlings of woody species differed significantly among land use types (ANOVA; F2, 72 =5.9, p = 0.004), being highest for cultivation (3,162 ± 440 individuals ha-1), followed by charcoal production (2,416 ± 295 ha-1) and lowest for grazing (1,629 ± 205 ha-1). Composition of seedlings differed significantly among land use types (Global RANOSIM = 0.119, p = 0.001). The distributions and densities of some seedlings were explained by gradients in environmental variables, with edaphic factors (i.e. Ca2+, Mg2+, K+ and organic matter) and charcoal production being the most important. The first two axes of the Canonical Correspondence Analysis (CCA) explained 41.9% of the variance in species – environmental relations and were a reflection of edaphic and charcoal production land use gradients. All of the 16 highly utilized species were well represented in both the juvenile and adult classes, with gradually declining number of individuals with increasing stem size-class. This indicates that most of these species have high regeneration potential. Juvenile:adult tree ratios >1 and negative DSCD slopes indicate good recruitment and probably successful regeneration for these species. The study revealed land cover changes mainly in the dense and medium dense woodlands, reflected by the increase in open woodland, grasslands and cultivation/settlements. These trends threaten the livelihoods of local communities who are entirely dependent on these natural resources. Sustainable management will require the establishment of suitable integrated community-based institutions and management practices, with support from all key stakeholders (i.e. National Forest Authority (NFA)) and local communities. Maintenance of savanna woodland resources and other ecosystem services essential for human well-being will require an effective legal framework to prevent over-exploitation and give incentives for the protection of the fragile savanna woodland vegetation. An appropriate savanna woodland management policy will be required to guide changes in land use that accommodate the requirements of land users, aided by targeted conservation efforts to all woody plants and particularly for the highly utilized species for charcoal production as well as the multipurpose species. In addition, there is urgent need to build local capacity for improved harvesting and utilization of these tree species. This can be achieved through equipping local users with up to date information as well as observing the existing skills.

Submitted by Erika Demachki (erikademachki@gmail.com) on 2016-01-07T15:35:40Z No. of bitstreams: 2 Dissertação - Fábio Martins Labecca - 2015.pdf: 2107333 bytes, checksum: cf5e7e0ac514e7f834e6ed7aab735b5d (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Erika Demachki (erikademachki@gmail.com) on 2016-01-07T15:37:02Z (GMT) No. of bitstreams: 2 Dissertação - Fábio Martins Labecca - 2015.pdf: 2107333 bytes, checksum: cf5e7e0ac514e7f834e6ed7aab735b5d (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2016-01-07T15:37:02Z (GMT). No. of bitstreams: 2 Dissertação - Fábio Martins Labecca - 2015.pdf: 2107333 bytes, checksum: cf5e7e0ac514e7f834e6ed7aab735b5d (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2015-04-29 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The increasing demand for timber and pulpwood has triggered an increase in areas of tree monocultures. The effects of native vegetation conversion in such monocultures have been extensively debated, but the consequences of this land use change to functionality and evolutionary history conservation have been little studied. Here, we evaluated how the avifauna responds to nature ecosystem conversion in tree monocultures by quantifying changes in local diversity (alpha diversity) and in assemblage composition (beta diversity), in their functional and phylogenetic components. We compiled forty paired bird lists in native vegetation areas and in comparable tree monoculture areas. Changes in alpha diversity were quantified by paired tests of observed values in native vegetation and in tree monocultures, and changes in assemblages composition through additive partitioning of beta diversity in nestedness and turnover components. We observed that tree monocultures are impoverished in number of species, supporting lower functional richness and less functionally similar assemblages. This demonstrates that environmental filter selecting and limiting similarity processes concurrently modify functional structure of bird assemblages, resulting in loss of functional complementarity and redundancy. Species in tree monocultures are also evolutionary younger and less related to each other. We showed that bird assemblages in tree monoculture are composed largely by functionally and phylogenetic different species from that assemblages in native vegetation. Body size, diet and foraging traits were the major functional traits in predicting the absence of the species in tree monocultures. Alson, we show that annual average temperature, annual average pluviosity and stage of understory development in tree monocultures are important predictors of diversity loss in these type of monoculture. / A crescente demanda por madeira e celulose tem desencadeado um aumento das áreas de monocultura florestal. Os efeitos da conversão de áreas de vegetação nativa nesse tipo de monocultura, por sua vez, vêm sendo extensamente debatidos. As consequências dessa mudança no uso do solo para a funcionalidade e conservação da história evolutiva foram até agora pouco estudadas. Neste estudo, nós avaliamos como a avifauna responde a conversão de ecossistemas naturais em monoculturas florestais, quantificando mudanças na diversidade local (diversidade alfa) e na composição dessas assembleias (diversidade beta) em seus componentes funcional e filogenético. Para isto, compilamos quarenta listas pareadas de aves em áreas de vegetação nativa e em áreas comparáveis de monocultura florestal. As mudanças na diversidade alfa foram testadas por testes pareados dos valores observados em vegetação nativa e em monoculturas florestais, e as mudanças na composição das assembleias através da partição aditiva da diversidade beta nos componentes de aninhamento e substituição. Observamos que as áreas de monocultura florestal são empobrecidas no número de espécies, suportam menor riqueza funcional e são menos similares funcionalmente. Isto demonstra que os processos de filtro ambiental e de similaridade limitante modificam a estrutura funcional das assembleias de aves de forma concomitante, resultando em perda de complementaridade e também de redundância funcional. As espécies presentes em áreas de monocultura são também evolutivamente mais jovens e menos aparentadas entre si. Mostramos que as assembleias de monoculturas florestais são compostas em grande parte por espécies funcionalmente e filogeneticamente diferentes daquela avifauna em vegetação nativa. Tamanho corpóreo, dieta e estratégias de forrageamento se mostraram as características funcionais importantes na predição da ausência das espécies em monoculturas florestais. Ainda, mostramos que temperatura e pluviosidade média anual, e o estádio de desenvolvimento do sub-bosque são importantes preditores da perda de diversidade nesse tipo de monocultura.

The microbiome (microbial community) of individuals is crucial when characterizing and understanding processes that are required for organism function and survival. Microbial organisms, which make up an individual’s microbiome, can be linked to disease or function of the host organism. In humans, individuals differ substantially in their microbiome compositions in various areas of the body. The cause of much of the composition diversity is yet unexplained, however, it is speculated that habitat, diet, and early exposure to microbes could be altering the microbiomes of individuals (Human Microbiome Project Consortium, 2012b, 2012a). To date, only one study has reported on microbiome characterization in a shark (Doane et al., 2017; skin microbiome of the common thresher shark). A comparative characterization of microbiomes sampled from different shark species and anatomical locations will allow an understanding of the differences in microbiomes that may be explained by variance in shark habitat and diet. Florida leads as shark bite capitol of the world, with 778 unprovoked bites recorded since 1837, or 4-5 average bites per year. With only a few bites a year, there is not a lot of opportunities to study these bites. What can be studied, however, is how the microbial environment in shark’s teeth is composed. To understand overall microbiome composition, and if microbiomes are distinct from the environment, or specific by species or anatomical location (henceforth location), we characterized microbiomes from the teeth, gill, skin, and cloacal microbiomes of 8 shark species in south Florida (nurse, lemon, sandbar, Caribbean reef, Atlantic sharpnose, blacktip, bull, and tiger) using high throughput DNA sequencing of the 16S rRNA gene V4 region. There was a significant difference in microbial community richness among species, sample location, but not the interaction between species and location. Microbial diversity by location was significantly different for both the Shannon index and Inverse Simpson index. Samples examined by species had no significant difference in microbial community diversity overall for both Shannon and Inverse Simpson indexes. Microbial community diversity of samples by location and species combined significantly differed when submitted to an analysis of variance with the Shannon index, but not the Inverse Simpson index. Teeth microbial communities showed the most diversity based on both Shannon and Inverse Simpson indices. Teeth microbiomes are distinct but also share taxa with the water they inhabit, including potentially pathogenic genera such as Streptococcus (8.0% ± 9.0%) and Haemophilus (2.9% ± 3.3%) in the Caribbean reef shark. The lemon shark teeth hosted Vibrio (10.8% ± 26.0%) and the Corynebacterium genus (1.6%±5.1%). The Vibrio genus (2.8% ± 6.34%), Salmonella enterica (2.6% ± 6.4%), and the genus Kordia (3.1% ± 6.0%) are found in the nurse shark teeth microbial community. Strikingly, the Vibrio genus was represented in the sandbar shark (54.0% ± 46.0%) and tiger shark (5.8% ±12.3%) teeth microbiomes. One OTU related to traditionally non-pathogenic family Phyllobacteriaceae appear to be driving up to 32% of variance in teeth microbiome diversity. We conclude that south Florida sharks host distinct microbiomes from the surrounding environment and vary among species due to differences in microbial community richness. Future work should focus on bacteria found in shark teeth to determine if those present are pathogenic and could provide insights to bite treatment.

No description available.

Contexte: L’importance écologique des fourmis dans les écosystèmes terrestres justifie qu’elles soient considérées comme groupe cible pour des actions de conservation. De plus, de par leur abondance, leur facilité de récolte et leur réponse à des perturbations, elles présentent un potentiel intéressant comme groupe indicateur précoce de l’état de santé des écosystèmes. Par contre, pour le choix d’aires à protéger, leur utilité comme intégrateur des conditions de milieu par rapport à des indicateurs classiques tels que les assemblages de plantes n’est pas clairement établie. En d’autres termes, répondent-elles plus finement que les plantes à différentes conditions de milieu et dans ce cas doit-on s’attendre à trouver au sein de formations végétales comparables plusieurs types d’assemblages de foumis? Si tel est le cas, la méthode utilisant les assemblages de végétaux pour sélectionner les sites à protéger peut ne pas permettre une conservation efficace de la diversité des fourmis. Ce type de problématique s’aborde bien le long de gradients environnementaux. Pour faciliter l’interprétation des résultats en terme de réponse aux facteurs abiotiques il est préférable de limiter le nombre de facteurs qui varient en même temps. Dans ce sens, le Chaco sec paraguayen représente un système très favorable: faible déclivité, faibles variations de températures moyennes mais gamme très étendue de conditions de pluviométrie (350mm à 1000mm de précipitations moyennes annuelles) et des sols variables (texture limoneuse à sableuse). L’aridité est l’un des principaux facteurs pouvant limiter la diversité des fourmis soit directement en exerçant un stress physiologique sur les espèces, soit indirectement en limitant la productivité primaire de l’habitat. Les conditions édaphiques peuvent également avoir une influence en affectant par exemple la survie des colonies qui nidifient dans le sol. Objectifs: Les principaux buts de la thèse sont (1) de déterminer l’influence de l’aridité et des conditions édaphiques sur la distribution et la structure des assemblages de fourmis terricoles du sol en forêts tropicales sèches, (2) mettre en évidence les mécanismes qui facilitent la coexistence des espèces de fourmis à l’échelle locale, (3) déterminer si à l’échelle régionale les fourmis et les plantes répondent de façon similaire aux conditions du milieu. Méthode: Onze localités ont été échantillonnées le long d’un transect régional long de 400km. Au niveau de chaque localité, trois transects élémentaires longs de 200m et séparés les uns des autres par 200m ont été effectués. La myrmécofaune a été échantillonnée à l’aide de 20 pièges à fosse et de 20 Winkler par transect élémentaire. La végétation de chaque site a été caractérisée sur base de l’abondance de 45 espèces d’arbres ou d’arbustes caractéristiques de la flore chaquéenne. Les propriétés physico-chimiques du sol ont également été mesurées. A fine échelle, l’organisation spatio-temporelle d’un assemblage a été étudié dans une localité de référence. Résultats: Au total, plus de 50.000 spécimens correspondant à 206 espèces de fourmis ont été collectés avec en moyenne (± SD) 62 ± 10 espèces par localité. Pour un même effort d’échantillonnage, le nombre d’espèces de fourmis récoltées à l’aide des pièges à fosse augmente avec l’aridité et une tendance inverse est observée pour les Winkler. Puisque les Winkler peuvent entraîner une sévère sous-estimation de la diversité des fourmis d’un habitat, seules les données des pièges à fosse sont utilisées pour la suite des analyses. La diversité locale  des assemblages de fourmis n’apparaît corrélée ni à l’aridité, ni aux conditions édaphiques. En revanche, ces facteurs, et spécialement la texture du sol, influencent la composition des assemblages. Trois complexes myrmécofauniques sont mis en évidence: le premier dans la localité la plus sèche (350mm) et la plus sableuse (>90% de sable dans la fraction minérale du sol), le second dans la localité la plus humide (1000mm, sol argilo-limoneux) et le dernier dans des localités présentant de larges conditions de pluviométrie (350-850mm) et de sol (limoneux à sablo-limoneux). Les plantes répondent encore plus finement à ces facteurs abiotiques. A l’échelle locale, l’établissement d’une ségrégation spatio-temporelle fine des espèces de fourmis lors de l’exploitation des ressources alimentaires facilite la coexistence interspécifique. Cette ségrégation est engendrée par l’existence de deux compromis: l’un entre les capacités des espèces à dominer et à découvrir les ressources et l’autre entre la capacité de dominance et la tolérance aux températures élevées. Conclusions: Nos résultats contredisent l’hypothèse selon laquelle les fourmis répondent plus finement que les plantes aux conditions du milieu. A l’échelle du gradient étudié, une augmentation de l’aridité n’affecte pas la diversité des fourmis. La productivité de l’habitat ne semble pas déterminer la richesse des assemblages et la tolérance à l’aridité semble répandue au sein des Formicidae. La texture du sol apparaît être le facteur le plus déterminant des distributions spatiales observées. Dans le Chaco sec paraguayen, une sélection des sites à protéger sur base des assemblages végétaux est susceptible de maximiser la conservation de la diversité biologique des fourmis. Notre étude de la distribution de la myrmécofaune, basée sur la plus large gamme de pluviométrie envisagée à ce jour, pourra constituer le point de départ d'un suivi des assemblages de fourmis dominantes du Chaco sec paraguayen dans le but d'investiguer l'impact des changements climatiques globaux sur ces organismes.

Budongo Forest Reserve (BFR) is a flagship reserve for primate conservation due to its abundant chimpanzee (Pan troglodytes) population, and its current management policy for multiple economic, conservation and environmental benefits. The identification and better understanding of the structure and dynamics of the forest/plant community types, patterns of species distribution and quantitative properties of their diversity is important to the conservation and sustainable management of tropical rainforests. This study seeks to contribute to a better understanding of the BFR forest community types, species diversity patterns and environmental correlates, as well as natural regeneration processes (i.e. seedling establishment and sprouting). Data on vegetation and environmental variables were collected using rectangular 50 x 100m (0.5 ha) plots, sub-divided into five equal contiguous (20 x 50 m) 0.1 ha sub-plots. Data on land-use/cover changes, and relevant associated socio-economic parameters were collected through the analysis of multi-temporal satellite imagery and field observations, as well as interviews of local households and key informants. The study revealed significant land-use/cover changes, with the area under sugarcane cultivation increasing over 17-fold, from 690 ha in 1988 to 12729 ha in 2002, with a concomitant loss of about 4680 ha (8.2% loss) of forest/woodland, mainly in the southern part of BFR. These changes are attributed to agricultural expansion, a rapidly increasing human population, exacerbated by large influxes of refugees, lack of alternative sources of income, conflicts of interest and political interference in the management of BFR, and an unclear land tenure system. The need for more land for agricultural expansion and the loss of woodlands (a source of building materials and fuelwood for the local communities) is leading to the invasion of and encroachment on BFR, which threatens plant and wild animal conservation. The study revealed that the vegetation of BFR is formed by a mosaic of plant communities, with the major forest types being; Pseudospondias microcarpa Swamp Forest, Funtumia elastica - Pouteria altissima, Lasiodiscus mildbraedi - Khaya anthotheca and Cynometra alexandri - Rinorea ilicifolia forest communities. Canonical correspondence analysis (CCA) indicated that soil nutrients (Si, Ca, N, Fe and Li) and anthropogenic disturbances are the main factors controlling forest community patterns. The variances explained as a proportion of total inertia were relatively high (0.53 and 0.56 for basal area and abundance, respectively), showing how well the measured variables explained species composition. These plant communities differed significantly in terms of woody species diversity and richness; being highest in the Pseudospondias microcarpa swamp and lowest in the Cynometra alexandri-Rinorea ilicifolia forest. However, about 48 species were shared between the forest community types. A total of 269 species representing 171 genera and 51 families was recorded. Fisher’s alpha-diversity ranged 4.45-30.59 and 3.07-29.7 for stem diameters ≥2.0 cm and ≥10 cm, respectively, being significantly higher for stem diameters ≥2.0 cm. The use of stem diameters ≥2.0 cm unveiled 53 more species (19.7%), with only 216 species recorded for the standard ≥10 cm dbh minimum size usually applied in tropical forests. A SHE analysis also showed greater richness (ln(S)) and H diversity for the >2.0 cm than the ≥10cm stem diameters. Hence, the study reaffirmed that the use of 10 cm as a minimum dbh in woody plant diversity studies in forests, where many tree species rarely exceed 10 cm stem diameter, is highly likely to underestimate diversity and richness, potentially biasing the understanding of diversity patterns. The most speciose families were Euphorbiaceae, Fabaceae, Rubiaceae, Moraceae, Meliaceae, Rutaceae, Annonaceae, and Flacourtiaceae, accounting for 147 species. Families with the highest Familial Importance values (FIV) were; Fabaceae (17.5), followed by Euphorbiaceae (16.3), and Ulmaceae (8.35). The BFR exhibits characteristics intermediate between log-normal and log-series species-abundance distributions, indicating a community with a small number of abundant species and a relatively large proportion of rare species. Both Whittaker’s (βw) and the Morisita-Horn Index measures of β-diversity consistently showed higher β-diversity for logged and arboricide treated areas, followed by logged only, and then nature reserve historical management practice types. β-diversity was relatively high at the total forest community scale, but lower for stem diameter ≥2.0 cm than ≥10.0 cm data. Environmental variables significantly explained 66.5% and 61.9% of the variance in species composition for stem diameter ≥2.0 cm and ≥10.0 cm data, respectively. Hence, the variation in species composition of BFR is characterised by significant spatial patterns, and the patterns in β-diversity are to a great extent associated with environmental heterogeneity (i.e. soil nutrients, topographic and light gradients) and anthropogenic disturbances. Investigation of natural regeneration showed that sprouting is generally common among the woody species, with both canopy and sub-canopy trees sprouting prolifically. Of the 122 species affected by ii harvesting, and tree and branch fall disturbances, 199 (97.5%) from 31 families sprouted from the cut stumps, with only Caloncoba crepiniana (De Wild. & Th.Dur.) Gilg exhibiting both stem and root sprouting. Stump basal diameter, height, bark-thickness, and height of stump above the ground at which the first sprout emerged, were significant predictors of sprouting ability among individuals. Number of sprouts/stump differed significantly among families, species, and stump size-classes. Of the 241 seedling species, representing 46 families, about 30.3% were rare (only 2-10 individuals); while 12% were very rare (only 1 individual each). Cynometra alexandri C.H. Wright and Lasiodiscus mildbraedii Engl. were the most abundant seedlings and also among the most widely distributed species in the forest. Analysis of similarity (ANOSIM) revealed significant differences in seedling composition between transects, but not between topographic positions or historical management practice types. Canonical Correspondence Analysis (CCA) showed that the measured environmental variables significantly explained 59.4% of the variance in seedling species distributions, with the three most important variables being organic matter, titanium and leaf area index (LAI; an indicator of light availability below the canopy). Hence, the important mechanisms influencing regeneration via seedlings in BFR operate through the soil system, and the ground and canopy vegetation characteristics. Nine of the 15 intensively studied multiple-use species, namely L. mildbraedii, Celtis Mildbraedii Engl., Pouteria altissima (A. Chiev.) Aubrev. & Pellegr., Chrysophyllum albidum G. Don., C. alexandri, Diospyros abyssinica (Hiern) F. White, Funtumia elastica (Preuss) Stapf., Chrysophyllum perpulchrum Hutch. & Dalz, and Antiaris toxicaria (Pers.) Lesch. had highly negative size-class distribution (SCD) slopes and substantial seedling regeneration. While Alstonia boonei De Wild. and Cordia millenii Bak. had weakly negative SCD slopes and pulsed or sporadic regeneration patterns. The wide distribution of seedlings for a variety of species, and with most of the intensively studied species having population structures showing healthy regeneration patterns, suggests that BFR is currently experiencing a continuous regeneration phase. In conclusion, the gradients in the vegetation of BFR are a reflection not only of site conditions as shown by the edaphic and abiotic factors, but also the history of human interventions.

The savanna woodlands of Southern Africa, colloquially termed the miombo, are poorly described in terms of biodiversity compared to other biomes. They have therefore been underrepresented in the wider understanding of how land use intensification is shaping global biodiversity. Land use change is known to reduce biodiversity and disrupt intactness of ecological communities with consequences for ecosystem functioning, resilience, and services. Miombo woodlands are described as biodiversity hotspots due to a high endemism of species and the presence of megafauna. At the same time, they are also considered dynamic socio-ecological systems shaped by disturbances and the land use activities of people. The patterns of biodiversity change in these tropical ecosystems may, therefore, have their own unique contexts, understanding of which will be essential for biodiversity and land use management in these ecosystems. In this thesis, I identified the patterns of biodiversity change in response to the two major land use practices in the two dominant woodland types in southern African woodlands: the selective logging due to charcoal production in the mopane woodlands, and agricultural expansion in the miombo. I also examined the impact of two main disturbance agents, humans and elephants, on habitat structure and biodiversity in mopane woodlands. Across all chapters in this thesis, I investigated the effects of land use change and habitat modification on biodiversity empirically using chronosequences. To understand biodiversity change, I employed a hierarchical multilevel modelling approach making inferences at the three levels of ecological communities: species, community, and meta-community (set of ecological communities at different sites). I selected six villages in the charcoal production hotspot of southern Mozambique and carried out field surveys for three taxonomic groups: trees, mammals and ground beetles. I modelled the counts of trees and beetles and incidence of mammals using meta-community occurrence models in a Bayesian framework with the intensity class of the villages, above-ground biomass and land cover type as predictors. The results suggested that the species richness of trees and mammals declined by 12 and 8.5 % respectively while that of beetles increased by 3.5%, albeit non-significantly. In addition, the beta diversity of trees decreased while that of mammals increased. The results show that while both trees and mammals reduced in richness, they responded differently to charcoal production in terms of community organisation. The trees underwent subtractive homogenisation (decrease in alpha and beta diversities) primarily because of deterministic processes induced by selective harvesting of tree stems for charcoal. Mammal communities, on the other hand, showed subtractive heterogenization (decrease in alpha, but increase in beta diversity) mainly due to random extinctions. In the agriculture frontier of miombo-dominated northern Mozambique, I investigated the effects of fragmentation and habitat loss caused by agricultural expansion on diversity and composition of trees and mammals. I modelled the occurrences of trees and mammals using occupancy models with the fragmentation and quantity of woodland cover as predictors. The model showed that most tree species (n=10), mainly the timber and firewood species, linearly declined in population size as fragmentation increased. Mammals, on the other hand, showed a nonlinear response. Seven mammal species increased at the lower levels of fragmentation. However, at the higher levels, none of the mammal species increased while two declined. Similarly, the species richness of trees linearly declined, while that of mammals increased up to a fragmentation level of 55-65% and declined above this limit. The beta diversity of trees increased with fragmentation while that of mammals decreased. The results suggest that, although fragmentation reduces species richness of both trees and mammals, it affects their species compositions in different ways. Trees undergo subtractive heterogenization due to random species losses while mammals experience subtractive homogenisation mainly due to the combined effects of fragmentation-led habitat loss and intensified hunting. Finally, this study concludes that, above 75% fragmentation or below 26% habitat quantity, both taxonomic groups endure biodiversity loss. The threshold results here corroborate similar habitat quantity thresholds (20-30%) observed elsewhere in different ecosystems. However, they differ with the widespread notion that above 30% habitat quantity, the effect of fragmentation is non-existent. The results here emphasize that taxonomic groups respond differently, the diversity and population size of mammals reduced only after the habitat threshold, whereas, those of trees showed linear decrease with fragmentation most likely due to fragmentation-led habitat loss. Lastly, I examined the effects of disturbance by humans and elephants on habitat structure and bird diversity by conducting a space for time substitution comparison in the mopane woodlands of Zambia. To examine the woodland structure, I modelled the structural attributes of habitat (stem diameter, stand density, and basal area) using mixed models with the proportion of affected stems by humans and elephants as explanatory variables. I found that elephant disturbance was associated with higher stem diameters, low stand densities, but no change in basal area. Human disturbance, on the other hand, was related to reductions in stand density and basal area, but no change in the stem diameter. Further, I tested species and functional diversity of birds against the covariates of habitat structure and disturbance. I found that bird communities reduced in species richness in both, human as well as elephant disturbed areas. However, the functional diversity did not change with elephant disturbance. I concluded that human disturbance reduces woody biomass (basal area is correlated with woody biomass) of mopane woodlands and functional diversity of birds whilst elephants do not. In this thesis, I conclude that human driven land use change in the miombo woodlands erodes alpha diversity of all taxonomic groups. However, increases in beta diversity of mammals with charcoal land use and trees in agricultural land use may maintain their diversities at the meta-community level.

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La hausse de l’urbanisation et la hausse d’introduction des espèces exotiques qui l’accompagne sont parmi les plus grands risques pour la biodiversité. Les espèces exotiques peuvent non seulement affecter la diversité alpha et réduire les populations d’espèces indigènes, mais également entrainer des changements de la biodiversité bêta. Toutefois, ces phénomènes sont complexes et la littérature sur le sujet présente des résultats variés. C’est pourquoi le but de cette recherche est d’étudier l’influence des espèces exotiques et envahissantes sur la diversité alpha et bêta de 61 boisés urbains de la grande région de Montréal. Nos résultats ont montré que les espèces envahissantes ont un effet plus grand que les espèces non envahissantes sur la diversité alpha. Elles sont toutes deux associées à une hausse de la richesse totale et de la diversité alpha. Toutefois, une hausse du couvert des espèces envahissantes est associée à une diminution de la richesse et du couvert des espèces indigènes. Nos résultats ont également montré qu’un grand couvert en espèces envahissantes provoque des changements significatifs de la diversité bêta en réduisant la différence entre les sites. À l’opposé, lorsque la richesse en espèces exotiques est grande, nous avons observé une différenciation en espèces indigènes qui serait expliquée par la diminution de leur richesse. Pour finir, nous avons constaté que les espèces exotiques et envahissantes sont associées à un changement significatif de la composition en espèces. Nos résultats suggèrent que les espèces exotiques, tout particulièrement les espèces envahissantes, sont associées à des changements importants de la diversité des boisés urbains. Toutefois, des études supplémentaires sont nécessaires pour confirmer si elles sont responsables de ces changements ou simplement le symptôme de perturbations sous-jacentes. / Urbanization and exotic species introduction associated with it are among the most important causes of the current biodiversity crisis. These disturbances are associated with a decrease in native species alpha diversity and with changes in beta diversity worldwide. However, those changes are complex, and studies on this subject show mixed results. Consequently, the impact of exotic species on native flora is still up for debate. In this context, we aimed to study the relationship between exotic and invasive species on the diversity of 61 forest patches in the Metropolitan region of Montreal. Our analysis showed that invasive species had slightly more impact on native diversity than non-invasive ones. However, the effects of invasive and non-invasive species were similar. They both added to the total richness, and their richness was associated with an increase of alpha diversity. They were also associated with a decrease in native species cover and the invasive species with a reduction of native richness. We also found that a high cover in exotic species, especially invasive ones induced homogenization in urban forest patches. However, at high richness, they tend to induce differentiation in native species beta diversity, caused by a decrease in native species richness. Finally, we found that exotic species induce significant changes to the species composition of the forest patches. Our results suggest that exotic species, especially invasive ones, are associated with significant changes in urban forest diversity. However, further research is needed to verify if they are direct actors in those changes or symptoms of underlying disturbances.