Abstract The topography of the Milešov part of the České středohoří Mts represents a suitable model for study of spatial distribution of diversity and the effects of ecological factors on species diversity and composition. Near-natural forest vegetation was sampled at eleven hills by stratified-randomly sited relevés. Soil samples were collected in relevés at nine hills also. The soil samples were used for maximal capillary capability, pH, carbon and nitrogen volume analyses. These ecological factors, as well as tree cover, altitude and heat load index, were used for examination of the correlation of ecological factors with diversity, species richness and species composition. Positive relationship between species richness and heat load index and soil reaction was identified. Species diversity (Shannon index) positively correlates with soil reaction also. After partialling out geographic components in the samples, a significant correlation between the heat load index, tree cover and altitude and species composition of the herb and shrub layer was found. Values of alpha and beta components were rated using partitioning of diversity to alpha and beta components at four levels (relevé - aspect - hill - landscape). The beta component at the aspect level and the beta component at the hill level were...

The hills of Yazoo Basin have a long history of land use modification and subsequent erosion and flood control issues. In response, federal actions were taken to address these issues beginning after the Mississippi River flood of 1927. Four major flood control reservoirs were built in 1932-1957, and instream low-drop grade control structures (GCS) were installed beginning in the 1980s. The objective of my dissertation was to ascertain the long-term effects of these efforts on stream fish assemblages and channel morphology. To assess whether the reservoirs affected upstream fish assemblages as barriers to recolonization by fluvial fishes or as source population for invasion by lentic generalist fishes (Chapter 1), I used stream data collected 43-61 years after the rivers were impounded to test for differences in fish assemblages between sites upstream and downstream of the reservoirs. Analysis of catch per effort and diversity metrics displayed little influence of the reservoirs, but trait-based analysis revealed marginal increases in planktivores, herbivores, detritivores, and generalists in upstream assemblages. After determining that potential effects of reservoirs would not confound further analysis, I assessed the effects of GCS on channel morphology (Chapter 2) and fish assemblages (Chapter 3) 30 years post-installation. To assess GCS effects on channel morphology, stream cross-sections were used to calculate Bank Height Ratio, Width/Depth Ratio, and Entrenchment Ratio, while point estimates made along the transects were used to calculate the average sediment size distribution. Analyses revealed that the GCS were successful in checking channel incision moving headward in the streams: sites upstream of the GCS were less incised and had greater accumulations of fine substrates compared to downstream sites and sites on streams lacking erosion control structures. The GCS could potentially affect fish assemblages through habitat modification or by selectively filtering the assemblages as a barrier to upstream migration. Analysis of beta diversity revealed that diversity was driven by species replacement rather than nestedness, which indicates GCS were not acting as filters on the assemblages. Analysis of catch per effort data confirmed differences in assemblage structure that echoed the instream habitat differences revealed in Chapter 2.

Amphibians are the most abundant terrestrial vertebrates on Earth. They are crucial in maintaining the transfer of energy and matter from freshwater to terrestrial systems and are also indicators of ecosystem health. Mexico hosts great amphibian diversity with high levels of endemism. Nevertheless, the knowledge of amphibian ecology in the country is at an early stage. This thesis aspires to contribute to the knowledge of Mexican amphibian ecology and to the understanding of the processes underlying amphibian responses to environmental changes. To do so the thesis includes: 1) analyses from fine scales (at landscape level) based on data from two consecutive rainy seasons of fieldwork (nocturnal sampling), in two protected areas in southern Mexico, La Pera and Nahá; 2) at regional scales, analyses based on spatial databases of conservation instruments (i.e. environmental services, governmental, private, and community protected areas, etc.) generated specifically for Mexico; 3) to coarse scales (the whole country), analyses based on ecological niche modelling using the most complete database for Mexican amphibian records and climate layers developed purposely for the country. Thus, the thesis involves different time-scale processes, from ecological to biogeographical. In addition this thesis contains an analysis of the media representation of amphibian biodiversity threats and issues, specifically climate change, based on literature research. I was involved in the process of generating most of the databases used in this thesis. Whilst the main theme of this thesis is amphibian conservation, it also encompasses a wide range of specific subjects. Firstly, foundational knowledge about amphibian conservation is established in Chapter I. Also, the region, Chiapas in southern Mexico, where the fieldwork was carried out for two consecutive years (2009-2010) is described within a historical context and a glossary of terms is presented. In Chapter II, based on one year of fieldwork in two fragmented protected areas (PAs) of different management category, one state and one biosphere reserve, I examine how community structure is related to key features of the environment. The possible effects of governance issues in protected areas and their relationship with the drivers of amphibian metacommunities are also explored. A total of 144 transects were sampled from 33 patches in La Pera and 140 transects from 36 patches in Nahá. In each transect environmental variables were recorded. Partial Canonical Correspondence Analyses (partial CCA) indicated that the drivers of metacommunity patterns vary between the sampled landscapes. Habitat structure explained more of the community variation than either space or weather conditions: > 50% for La Pera and 30% Nahá; but the relationship to geographical space and local climate varied greatly. The differences in relationships among the environmental variables and between them and the amphibian metacommunities finds expression also in the pattern of human exploitation of these areas, which has latterly at least also found expression through differing governance. In Chapter III, the effects of environmental variation on metacommunities structure are explored. Metacommunity theory assumes that emergent properties can be determined that characterise a set of linked communities within a landscape. It follows that change in environmental conditions should generate changes in the metacommunity structure. In La Pera a total of 30 patches were sampled, with a total of 120 transects in 2009, and 133 transects in 2010. In Nahá 31 patches were sampled, with a total of 111 transects in 2009 and 122 transects in 2010. In the analyses of this chapter only transects sampled in both years are included. The total number of individuals increased greatly from 2009 to 2010, but the most abundant species between surveyed years varied slightly, in both areas. In La Pera metacommunity the structure changed from quasi-Clementsian to quasi-Gleasonian, while in Nahá it changed from Clementsian to Gleasonian. CCA show that the variance explained between years was similar. Re-arrangements in the metacommunity structures linked to environmental changes are observed. Results show that amphibian metacommunity structure can change with short environmental changes or disturbances, mainly weather variations from one year to another. This would suggest that metacommunity structures are a dynamic property in fluctuating systems. The aim of Chapter IV is to assess patterns of beta diversity for Mexican terrestrial vertebrates, and explore their relationships with environmental heterogeneity metrics at different spatial scales, identifying the most important surrogates at each spatial scale. The analyses in this chapter are based on the most complete database of Mexican terrestrial vertebrates, comprising distribution maps of 2513 species: 883 resident birds, 344 mammals, 364 amphibians and 811 reptiles. Higher β-diversity values are found along mountain ranges for amphibians, reptiles and mammals, whereas for birds high values are also found on the Mexican Plateau. Results demonstrate that the relationships between β-diversity and the environmental heterogeneity surrogates vary in form and strength across scale and between vertebrate groups. In Chapter V, I set out to characterize at fine scale, alpha and beta diversity patterns for Mexican amphibians and analyze how these patterns might change under a moderate climate-change scenario, and to highlight the overall consequences for amphibian diversity at the country level. The analyses are performed with a climatic envelope modelling approach using MaxEnt and a set of climatic layers developed specifically for Mexico. Models of future scenarios for Mexican amphibian alpha and beta diversity for 2020, 2050, 2080, show that high levels of species extinctions follow if low dispersal capability and high presence thresholds are used, but the overall geographic pattern of beta diversity remains stable. Zones of high beta diversity are associated with topographic formations, whilst the values of beta diversity initially increase, then decline over time under a moderate climate scenario. Extinctions (complete loss of range within country boundaries) are particularly intense during the period 2020–2050. The results imply that heterogeneous zones associated with mountain ranges will remain particularly important for amphibian diversity and thus such areas should be targeted for continued conservation prioritization in the face of climate change scenario. There is an inevitable degree of uncertainty associated with future climate projections and the possible ecological and biogeographical responses. Nevertheless, the climate change projections are typically translated in the media as certain. Chapter VI illustrates the interplay of these competing communication goals, through a review of the representations of the golden toad (Incilius [Bufo] periglenes) in print media and in peer-reviewed literature. The concept of “distanciation”, which means placing a distance between two connected issues (cause and effect), is introduced in this chapter, along with the potential issues that this process may generate in the implementation of conservation strategies. Distanciation is a perception created in the members of the audience of the media, but does not imply a total separation regarding an issue. For example, the audience is interested in the news about climate change effects, but they feel distant because the effects of climate change might be evident within a large time period (i.e. 2050); and although the causes are occurring now, the audience does not see the urgent need to act. Chapter VII represents the first attempt to analyze the status of conservation of some microendemic amphibians in Latin America when some social initiatives (e.g. private and community reserves) are included in the assessment. The efficiency of the existing set of governmental protected areas (PA), and the contribution of social initiatives for land protection of amphibians are evaluated. The chapter shows how the role of land conservation, through social initiatives, is fast becoming a crucial element for the survival of a substantial number of species not protected by state-designated PA. Given the current speed of land use change, we cannot expect to save all species from extinction, and so it must be decided, rather quickly, how to focus the limited resources available to prevent the greatest number of extinctions. In Chapter VIII, a simple conservation triage method is proposed. Using this triage method, the threat status for 145 micro-endemic Mexican amphibian species is evaluated, alongside potential threat abatement responses derived from existing policy instruments and social initiatives. Both indicators are combined to provide broad-scale conservation strategies that would best suit amphibian micro-endemic buffered areas (AMBAs) in Mexico. Results show that almost 25% of the species analysed urgently need field-base verification to confirm their persistence; for the rest, a conservation strategy is developed based on existing conservation instruments. Monitoring populations is essential in order to understand temporal patterns of community change and to better comprehend the underlying processes that shape and maintain biodiversity. These aspects, along with a general discussion focused mainly on the distanciation problem are addressed in Chapter IX.

Submitted by Franciele Moreira (francielemoreyra@gmail.com) on 2018-04-19T15:22:11Z No. of bitstreams: 2 Tese - Danielle Katharine Petsch - 2018.pdf: 6114628 bytes, checksum: f05e8c7a9a2b8dc23bd5a1e1cc003c83 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-04-23T11:41:56Z (GMT) No. of bitstreams: 2 Tese - Danielle Katharine Petsch - 2018.pdf: 6114628 bytes, checksum: f05e8c7a9a2b8dc23bd5a1e1cc003c83 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-04-23T11:41:56Z (GMT). No. of bitstreams: 2 Tese - Danielle Katharine Petsch - 2018.pdf: 6114628 bytes, checksum: f05e8c7a9a2b8dc23bd5a1e1cc003c83 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2018-03-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The increase in similarity among communities is a process known as biotic homogenization. In freshwater ecosystems, biotic homogenization may be promoted by different natural (e.g. flood pulse) and human (e.g. land use) causes. In the first chapter, I reviewed the main causes and consequences of freshwater homogenization. In the second chapter, using an experimental approach, I showed that habitat simplification may cause homogenization of periphytic algae, but the results depended on how dissimilarity was estimated. In the third chapter, using zooplankton and macrophytes data, I showed that floods homogenized individual lakes across time but did not make the lakes spatially more similar. In the fourth chapter, I demonstrated that taxonomic beta diversity of aquatic insects was higher among tropical streams but functional beta diversity was higher among boreal streams. The increase of environmental harshness and decrease of environmental heterogeneity did not cause taxonomic or functional homogenization of aquatic insects among tropical or boreal streams. Finally, in the fifth chapter, I found in a meta-analysis that human modified streams have low species richness and equitability, although a distinct species composition regarding to reference streams. However, land-use changes did not cause biotic homogenization. Although the effects of possible biotic homogenization causes are still controversy, we recommend that biodiversity studies should include beta diversity to better understand mechanisms structuring communities under pressure of human or natural disturbances. / O aumento da similaridade entre comunidades é um processo conhecido como homogeneização biótica. Em ecossistemas aquáticos continentais a homogeneização biótica pode ser promovida por diversas causas naturais (e.g. pulso de inundação) e antrópicas (e.g. modificações do uso do solo). No primeiro capítulo, revisei as principais causas e consequências da homogeneização de biotas aquáticas continentais. No segundo capítulo, por meio de um experimento, demonstrei que a simplificação de habitats pode causar homogeneização de algas perifíticas, embora o resultado dependa da forma como se estima a homogeneização. No terceiro capítulo, usando dados de zooplâncton e macrófitas, mostrei que as cheias homogeneizaram uma mesma lagoa ao longo do tempo, mas não tornam lagoas mais similares espacialmente. No quarto capítulo demonstrei que a diversidade beta taxonômica de insetos aquáticos foi maior entre riachos tropicais enquanto a diversidade beta funcional foi maior entre riachos boreais. O aumento da degradação ambiental e redução na heterogeneidade de habitat relacionados ao uso do solo não causaram homogeneização taxonômica nem funcional dos insetos aquáticos em riachos tropicais ou boreais. Por fim, no quinto capítulo, observei em uma meta-análise que riachos modificados possuem menor riqueza e equitabilidade além de uma diferente composição de espécies em relação aos riachos mais conservados. No entanto, modificações no uso do solo não causaram homogeneização biótica. Embora os efeitos de possíveis causas de homogeneização de biotas aquáticas sejam ainda controversos, recomendamos que estudos sobre biodiversidade incluam a diversidade beta para uma melhor compreensão dos mecanismos que estruturam as comunidades frente a distúrbios antrópicos ou naturais.

Submitted by Celso Magalhaes (celsomagalhaes@ufrrj.br) on 2018-10-02T13:28:26Z No. of bitstreams: 1 2013 - Leonardo Mitrano Neves.pdf: 2710150 bytes, checksum: e76a622435676fcc3b2281358ce93865 (MD5) / Made available in DSpace on 2018-10-02T13:28:27Z (GMT). No. of bitstreams: 1 2013 - Leonardo Mitrano Neves.pdf: 2710150 bytes, checksum: e76a622435676fcc3b2281358ce93865 (MD5) Previous issue date: 2013-04-30 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico - CNPQ / Rocky reef fish assemblages change along extreme environmental conditions gradients; both spatial (across gradients of distance from the river mouths) and short term temporal (diel cycle of light intensity). Moreover, changes in connection to habitat heterogeneity can occur, even for tropical rocky reefs with a more homogenous habitat structure. Knowledge of the way that fish assemblages respond to these changes is fundamental to identify the variables that determine spatial patterns and to predict how impacts in great or low intensity can affect diversity. The main aims of this study were: (1) to determine influence of physical (distance from river mouth and wave exposure), biological (benthic cover) and structural (substratum height and number of shelters) variables in structuring fish assemblages, species richness, abundance, biomass and trophic groups diversity; (2) to assess diel changes in composition and structure of fish assemblages; (3) to relate changes in species composition (beta diversity) with habitat heterogeneity for a small scale (among transects in a given area), and the relationship between beta and alfa diversity (species richness, richness estimation and Shannon diversity). Subaquatic visual census were carried out in Ilha Grande coastal reefs, encompassing (1) islands distributed along a spatial gradient of distance from river mouth; (2) six different time periods, i.e., sunrise (06:00h), morning (08:30h), afternoon (14:00h), sunset (17:30h), early night (19:30h) and night (21:00h) in two shallow coastal reef; and (3) in transect in four areas to assess beta biodiversity. Habitat structure (benthic cover and topographic complexity) assessment was performed (objectives 1 and 3). The distance from river mouth explained from 12.4% to 38.2% of the estimated components of variation (ECV) of PERMANOVA for all analyzed response variables, playing a major role in determining spatial patterns of fish assemblages. Differences between reefs close and far from river mouth reached a maximum of 4.5x for richness, 11x for biomass and 10x for abundance. The substrate height was positively related to fish abundance, species richness and trophic groups diversity (ECV between 7.3 % and 17.4%), whereas the number of shelters was positively associated to small-sized species abundance such as Stegastes fuscus, Emblemariopsis signifer and Scartella cristata. Benthic cover had significant influence to determine spatial pattern in fish assemblage structure and diversity of trophic groups (ECV = 8% and 10%, respectively), but not in species richness, biomass and fish abundance. Wave exposure had significant influence on fish assemblage structure only (ECV = 10%). The fish assemblage changes drastically along diel cycle. Species richness and fish abundance were at the highest during the period of the day with intermediary values at twilight periods, and at the lowest during the night. The highest difference in assemblage structure was found between the periods of the day and the night. The families Sciaenidae, mainly represented by Pareques acuminatus, and Pempheridae represented by Pempheris schomburgkii were more abundant during the night, whereas Haemulidae Haemulon steindachneri, Pomacentridae Abudefduf saxatilis, Chaetodondidae Chaetodon striatus, and Labrisomidae Malacoctenus delalandii were more abundant during the day. The twilight periods were similar in assemblage structure, and had as characteristics species of the day (H. steindachneri, M. acutirostris) and the night (P. acuminatus), reflecting a transitional period. Significant positive relationship was detected between habitat heterogeneity and beta diversity. The area with more ix homogeneous habitat and low variation in fish assemblage was dominated by little threedimensionally complex organisms (zoanthids), while areas that had fleshy algae, turf and zoanthids with a more even percentage cover had higher heterogeneity and beta diversity. For all measures of examined alfa diversity, the area with more heterogeneous habitat and with the highest beta diversity had the highest alfa diversity compared with areas with more homogenous habitat e lowest beta diversity. However, positive relationship between alfa and beta diversity was significant for species richness, but not for estimate of richness and Shannon index. This study demonstrated that changes in assemblages in spatial and short term (from transects to 10 km, and diel cycle) scales may be attributed to changes in local habitat structure, both composition of dominant benthic organisms and habitat heterogeneity and can be associated to behavioral characteristics mainly related to strategies of food acquirement and protection against predation / As assembleias de peixes recifais variam atrav?s de gradientes de mudan?as extremas nas condi??es ambientais, tanto espaciais (ao longo de gradientes de dist?ncia da foz de rios) quanto em escalas temporais curtas (ao longo do ciclo di?rio de intensidade luminosa). Al?m disto, varia??es em resposta ao n?vel de heterogeneidade do habitat tamb?m podem ocorrer, mesmo entre recifes rochosos situados fora de intensos gradientes ambientais. Entender como as assembleias de peixes respondem a tais mudan?as ? fundamental para identificar vari?veis determinantes dos padr?es espaciais e predizer como impactos de grande e pequena intensidade podem afetar os padr?es de diversidade. Os principais objetivos deste estudo foram: (1) determinar a influ?ncia de vari?veis f?sicas (dist?ncia da foz do rio e exposi??o a ondas), biol?gicas (cobertura b?ntica) e estruturais (altura do substrato e n?mero de ref?gios) na estrutura??o das assembleias de peixes, riqueza de esp?cies, abund?ncia, biomassa e diversidade dos grupos tr?ficos; (2) avaliar as mudan?as ao longo do ciclo di?rio na composi??o e estrutura da assembleia de peixes recifais; (3) relacionar a varia??o na composi??o de esp?cies (beta diversidade) com a heterogeneidade do habitat, para uma pequena escala (entre transectos de uma mesma ?rea), e as rela??es entre a beta diversidade e medidas de diversidade alfa (riqueza de esp?cies, estimativa da riqueza e diversidade de Shannon). Para tal, censos visuais subaqu?ticos foram realizados (1) em cost?es rochosos da ba?a da Ilha Grande, em ilhas localizadas atrav?s de um gradiente de dist?ncia da foz de rios; (2) em seis diferentes hor?rios, compreendendo o amanhecer (06:00h), manh? (08:30h), tarde (14:00h), anoitecer (17:30h) e in?cio da noite (19:30h) e noite (21:00h) em dois recifes rochosos rasos; e (3) em transectos de quatro ?reas para avaliar diversidade beta. Avalia??es da estrutura do habitat (cobertura b?ntica e complexidade topogr?fica) foram realizadas (para objetivos 1 e 3). A dist?ncia da foz do rio explicou entre 12,4% a 38,2% da estimativa dos componentes de varia??o (ECV) da PERMANOVA de todas as vari?veis respostas analisadas, desempenhando um papel principal nos padr?es espaciais da assembleia de peixes. Diferen?as entre recifes pr?ximos e distantes da foz atingiram um m?ximo de at? 4,5x para a riqueza, 11x para a biomassa e 10x para a abund?ncia. A altura do substrato foi positivamente relacionada com a abund?ncia de peixes, riqueza de esp?cies e diversidade dos grupos tr?ficos (ECV entre 7,3% a 17,4%), enquanto o n?mero de ref?gios foi associado positivamente com a abund?ncia de esp?cies de pequeno porte, como Stegastes fuscus, Emblemariopsis signifer e Scartella cristata. O efeito da cobertura b?ntica foi significativo em determinar os padr?es espaciais da estrutura da assembleia de peixes e da diversidade dos grupos tr?ficos (ECV = 8% e 10%, respectivamente), por?m n?o foram observadas influ?ncias significativas da cobertura b?ntica na riqueza de esp?cies, biomassa e abund?ncia. A exposi??o ?s ondas teve um efeito significativo apenas para a estrutura da assembleia de peixes (ECV = 10%). As assembleias de peixes variaram drasticamente ao longo do ciclo di?rio. A riqueza de esp?cies e a abund?ncia de peixes foram maiores durante os hor?rios do dia, com valores intermedi?rios nos hor?rios crepusculares e atingiram os menores valores durante a noite. Maiores diferen?as na estrutura da assembleia foram observadas entre o per?odo diurno e noturno. Durante a noite, as fam?lias Sciaenidae, representado por Pareques acuminatus, e Pempheridae vii representado por Pempheris schomburgkii foram mais abundantes, enquanto Haemulidae Haemulon steindachneri, Pomacentridae Abudefduf saxatilis, Chaetodondidae Chaetodon striatus, e Labrisomidae Malacoctenus delalandii foram abundantes durante o dia. Os hor?rios crepusculares foram semelhantes entre si, sendo caracterizados por esp?cies tanto dos hor?rios do dia (H. steindachneri, M. acutirostris) quanto da noite (P. acuminatus), refletindo esse per?odo de transi??o. Rela??es positivas significativas foram detectadas entre a heterogeneidade do habitat e a beta diversidade. A ?rea com habitat mais homog?neo e de menor varia??o na composi??o da assembleia foi dominada por organismos tridimensionalmente pouco complexos (zoant?deos), enquanto a ?reas que apresentaram algas frondosas, matriz de algas epil?ticas (MAE) e zoant?deos com uma percentagem de cobertura mais equitativa, tiveram a maior heterogeneidade do habitat e beta diversidade. Para todas as medidas de diversidade alfa utilizadas, a ?rea com habitat mais heterog?neo e com maior beta diversidade, apresentou uma diversidade alfa maior do que a ?rea com habitat mais homog?neo e de menor beta diversidade. Entretanto, as rela??es positivas entre a beta diversidade e a diversidade alfa foram significativas apenas para a riqueza de esp?cies, e n?o para a estimativa da riqueza e a diversidade de Shannon. Este estudo demonstrou que varia??es nas assembleias em escalas espaciais e temporais curtas (desde entre transectos at? 10 km, e ao longo do ciclo di?rio) podem ser atribu?das a mudan?as na estrutura dos habitats locais, tanto na composi??o dos organismos bent?nicos dominantes quanto na heterogeneidade do habitat e podem ser associadas a caracter?sticas comportamentais principalmente associadas a estrat?gias de obten??o de alimento e prote??o contra preda??o

Les mécanismes à l’origine du maintien de la forte diversité locale des arbres des forêts tropicales humides constituent encore une énigme pour les scientifiques. Cette thèse a pour but d’étudier et de comprendre certains facteurs biotiques et abiotiques qui influencent l’assemblage des communautés des forêts tropicales humides d’Amazonie. A l’aide d’une approche empirique conduite dans les forêts tropicales de Guyane française et du Loreto au Pérou, de nombreuses expériences de terrain ont été mises en place dans le but d’apporter des éléments de réponse sur les mécanismes impliqués dans le maintien de la diversité des communautés d’arbres et d’insectes des forêts amazoniennes. Dans un premier temps, cette thèse permet de souligner l’importance des pressions biotiques exercées sur les communautés d’arbres. En effet, les communautés d’insectes peuvent influencer la composition des communautés d’arbres le long d’un gradient environnemental conduisant à des compromis entre la défense et la croissance. Ces compromis ou tradeoff permettent de maintenir la coexistence des espèces de forêts tropicales humides en favorisant la spécialisation des arbres à leur habitat (Chapitre 1, Annexe 3). Cependant, de nombreux facteurs peuvent engendrer des variations dans les compromis d’allocation exhibés par les plantes, ce qui peut compliquer la validité de ces résultats. Dans ce sens, nous avons souligné l’influence du rôle de la cascade trophique et l’existence chez certaines espèces d’arbres de stratégies d’évitement des insectes (Chapitre 2). Dans un second temps, nous avons montré que les filtres environnementaux et les distances géographiques favorisent un fort turnover de la composition des arthropodes des forêts tropicales (chapitre 3, Annexe 2). Les résultats de cette étude ont des implications fondamentales sur les mécanismes qui expliquent la structuration des communautés d’insectes herbivores. Nous avons souligné l’importance de l’interaction des communautés des insectes herbivores et de leurs plantes associées. De plus, des prédictions sont présentées sur le degré de spécialisation des insectes à leur plante-hôte (Annexe 3), notamment sur les implications possibles dans les compromis d’allocation chez les plantes. Finalement, des perspectives de recherche sont proposées en vue de poursuivre ces travaux de recherche, et notamment des extensions de mes expériences vers d’autres régions tropicales et tempérées et l’intégration de la phylogénie pour comprendre des mécanismes de coévolution entre communautés d’arbres et insectes. Nous proposons également une intégration des résultats de cette thèse dans les stratégies locales et régionales de conservation des forêts tropicales du bassin amazonien. / The mechanisms underlying the maintenance of local diversity of trees in tropical rainforests remain under debate. This dissertation aims to study and understand some biotic and abiotic factors that may influence both tree and insect community assembly in lowland tropical forests of Amazonia. I used an empirical approach to study communities of trees and insects in tropical forests of French Guiana and Peru, to address the extent to which insect herbivores contribute to the turnover of tree species across strong environmental gradients. In Chapter 1, I studied how herbivorous insect communities can influence the composition of tree communities along an environmental gradient by reinforcing tradeoffs between defense and growth that promote habitat specialization (Chapter 1, Appendix 3). The complicated variation in the patterns of growth and defense from this study led me to pursue further observations of an alternative plant defense strategy of time-avoidance of herbivores, which I examined in detail in Chapter 2. I found evidence for coordinated leaf production in some tree species that was consistent with the satiation of herbivores, suggesting that multiple interactions between plants and their herbivores may be responsible for patterns of habitat specialization in trees. In the second part of the dissertation, I examined insect herbivore communities in detail to test for turnover in species composition across geographic and environmental gradients. In Chapter 3, I present evidence for substantial beta-diversity in arthropod communities throughout lowland Amazonian forests. In the discussion I propose research perspectives to complete this research, including the extension of observations to compare tropical and temperate regions and the integration of molecular phylogenetics information to study coevolution of plant lineages and their insect herbivores. I conclude with suggestions for the integration of the results of this thesis in local and regional strategies for the preservation and conservation of tropical forests in the Amazon basin.

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.

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.

Orientador: Mauro Galetti Rodrigues / Resumo: A conversão de paisagens florestais para usos antrópicos é a principal causa do desmatamento das florestas tropicais em todo o mundo. Essas florestas são conhecidas por conter parte significativa da biodiversidade terrestre global, porém pouco se sabe sobre como as modificações na paisagem, como a perda de habitat para produção agropecuária e o principalmente o impacto do gado afetam a diversidade e ocupação de mamíferos resilientes nesses fragmentos. Sendo assim, nós examinamos como a riqueza de espécies e a composição de mamíferos são explicadas pela configuração da paisagem e como a presença do gado afeta a detecção de mamíferos de médio e grande porte. Foram amostradas 20 paisagens dominadas por pastagens ao longo de um gradiente de cobertura florestal (8% a 98%), no sudeste do Brasil. Nós registramos 75% das espécies de mamíferos esperadas para esta região em uma cobertura florestal de média a alta. A cobertura florestal, distância euclidiana do vizinho mais próximo e área estrutural foram as variáveis que melhor explicaram a ocorrência de algumas espécies de mamíferos dependentes de floresta. As comunidades de mamíferos exibiram um alto grau de alternação de espécies entre as paisagens, representando 95% da diversidade beta total. Os impactos da pecuária foram mostrados devido ao seu efeito negativo na detecção de espécies florestais e positivo na detecção de grupos de espécies não florestais. Discutimos a importância de manter fragmentos com alta cobertura vegetal para... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The landscape conversion to anthropic uses is the major cause of deforestation worldwide. Tropical forests are known to contain a significant portion of global terrestrial biodiversity, but little is known about how changes in landscape, such as habitat loss for livestock and its impacts affect the diversity and occupation of resilient mammals in forest fragments immersed in pasture matrices. Here we examine how species richness and mammal composition are explained by landscape configuration and how cattle presence affects the detection of medium and large mammals. We sampled 20 landscapes dominated by pastures along a forest cover gradient (8% to 98%) in southeastern Brazil. We recorded 75% of the mammalian species expected for this region in a medium-to-high forest cover. Landscapes metrics, as forest cover, Euclidean distance from the nearest neighbor and structural area were the variables that best explained the occurrence of some forest mammal species. Mammalian communities exhibited a high degree of species turnover between landscapes, representing 95% of total beta diversity. Livestock impacts were shown due to its negative effect on the detection of forest-dwelling species and positive on the detection of non-forest species groups. We discuss the importance of maintaining forest fragments with high vegetation cover to improve connectivity between disturbed landscapes, favoring mammalian species flow. There is an urgent need for a better understanding of livestock gene... (Complete abstract click electronic access below) / Mestre

Das Miandam-Untersuchungsgebiet (35° 1′- 5′ N, 72° 30′-37′ E) liegt in der Swat-Region der Provinz Khyber Pakhtunkhwa (ehemals North West Frontier Province) im nördlichen Pakistan. Die vorliegende Arbeit berücksichtigt sowohl ethnobotanische und pflanzensoziologische Aspekte als auch die Pflanzenartendiversität innerhalb des Gebietes. Aufgrund der hohen Habitatvielfalt weist das Miandam-Gebiet einen großen Reichtum von Medizinalpflanzen auf. Die im Rahmen der Arbeit durchgeführte ethnobotanische Studie dokumentiert das Vorkommen der Medizinalpflanzen sowie deren Nutzung in der Region. Weiterhin wurden die durch Sammlerpräferierten Lebensräume bestimmt und evaluiert inwiefern die Heilpflanzen durch Sammlung und Habitatzerstörung bedroht werden. Insgesamt wurden 106 traditionelle Heilpflanzen aus 54 Pflanzenfamilien verzeichnet. Zu den am häufigsten gefundenen Wuchsformen zählten mehrjährige (43%) und kurzlebige Kräuter (23%), Sträucher (16%) und Bäume (15%). Ein Großteil der untersuchten Heilpflanzen und ihrer Produkte wird zur Behandlung von Magen-Darm-Erkrankungen eingesetzt. Die Produkte werden vorrangig als Sud oder Pulver zubereitet und oral angewendet. Achtzig der 106 traditionellen Heilpflanzen gehören der Gruppe der einheimischen Arten an. Fast 50% der Pflanzenarten treten dabei in synanthroper Vegetation auf, während der Rest in naturnaher Umgebung (z.B. extensiv beweidete Wald- und Graslandbereiche) vorgefunden werden kann. Wälder sind der Ursprung der meisten nicht synanthropen einheimischen Medizinalpflanzen. Drei Arten (Aconitum violaceum, Colchicum luteum, Jasminum humile) können als Folge intensiven Sammelns als bedroht eingestuft werden. Um die pflanzensoziologischen und phytogeografischen Aspekte des Projektes abzudecken wurde die Vegetation des Miandam-Gebietes mit einem Fokus auf Wäldern, Gebüschen und anderen Formationen untersucht. Die Ergebnisse der Vegetationserhebungen wurden mit denen anderer Studien in der weiteren Umgebung des Hindukush-Himalayas verglichen. Weiterhin wurde untersucht inwiefern die Waldökosysteme durch anthropogene Aktivitäten im Untersuchungsgebiet bedroht sind. Die im Gebiet verzeichneten Gefäßpflanzenarten umfassen insgesamt 33 Bäume, 52 Sträucher, 305 Kräuter und 11 Lianen. Basierend auf einer multivariaten Analyse konnten 12 Pflanzengesellschaften identifiziert werden. Die Spanne dieser Gesellschaften reichte von subtropischen semiariden Wäldern mit Ailanthus altissima im Tiefland zu alpinen Rasen von Sibbaldia cuneata durchsetzt mit Juniperus. Die dominierende Vegetation des Untersuchungsgebietes besteht aus von Abies pindrow und Viburnum grandiflorum Wäldern. Eine georeferenzierte Karte der Vegetation erleichtert die Lokalisierung der ökologisch interessanten Vegetation. Artenreichtum und –diversität wurden entlang eines Höhengradienten untersucht. Dazu wurde die Alpha- sowie Beta-Diversität verschiedener Wuchsformtypen bestimmt. Der Artenreichtum aller Gefäßpflanzenarten erreichte sein Maximum zwischen 2200-2500 m. Dagegen zeigte der Artenreichtum der Sträucher einen glockenkurvenartigen Verlauf mit einem Maximum zwischen 2000 und 2200 m. Die höchste Alpha-Diversität der Gefäßpflanzenarten wurde in den tieferen Lagen des Untersuchungsgebietes verzeichnet. Die Beta-Diversität aller Wuchsformtypen zeigte entlang des gesamten Höhengradienten hohe Werte und somit einen starken Artenwechsel. Die Beta-Diversität der Straucharten fluktuiert entlang des Höhengradienten und zeigt damit ein einzigartiges Muster.