Urbanisation is a key driver in the loss, fragmentation and modification of natural habitats resulting in the global loss of biodiversity. As the human population, and consequently the rate of urbanisation, continues to increase exponentially it is important to understand how to sustain and enhance biodiversity within the built environment. Cities comprise a complex assortment of habitat types yet relatively little is known of how its composition and spatial configuration can influence species presence or foraging activities. It is therefore necessary to examine habitat use and biodiversity patterns at multiple spatial scales to fully understand how species are responding to the urban matrix. There are few other orders of animals that are as strongly associated with people as bats (Chiroptera); for some bat species human habitations provide roosts and adaptations of the environment provide food sources. However bat species richness generally declines with increasing urbanisation indicating that many species are not able to persist in highly urbanised areas. In this thesis, I show that the behaviour, habitat preferences, and distribution of bats are strongly influenced by the built environment at both a local and landscape scale. Although many animal species are known to exhibit sex differences in habitat use, adaptability to the urban landscape is commonly examined at the species level without consideration of potential intraspecific differences. I found that female Pipistrellus pygmaeus show greater selectivity in foraging locations within urban woodland in comparison to males at both a local and landscape scale. There was a lower probability of finding females within woodlands which were poorly connected, highly cluttered, with a high edge: interior ratio and fewer mature trees. The results have important implications for our understanding of how to manage areas for breeding females and highlight the need to supplement acoustic monitoring with trapping data to assess sex differences in habitat use. Determining how morphological or behavioural traits can influence species adaptability to the built environment may enable us to improve the effectiveness of conservation efforts. The morphological similarities between P. pygmaeus and P. pipistrellus suggest that both species should respond similarly to the urban matrix, however I found differential habitat use occurring within a variety of urban habitats (e.g. woodland and waterways) and at a landscape scale. In urban woodland there was a higher probability of P. pygmaeus activity relative to P. pipistrellus in woodlands with low clutter and understory cover which were surrounded by low levels of built environment. Many bat species are strongly associated with aquatic or adjacent riparian habitats yet we know little about the utilisation of urban waterways by bats. After surveying urban waterways throughout the UK, I was able to show that the built environment can negatively affect a variety of bat species from the riparian zone up to 3km from a waterway. This indicates that beneficial urban waterway rehabilitation schemes for bats require management at multiple spatial scales, from retaining a vegetated riparian zone at the local scale to highlighting the necessity for conservation funding to be spent on the implementation of landscape scale environmental improvement schemes that encompass the entire urban matrix. Undertaking surveys to confirm species presence or to estimate population sizes can be difficult, particularly for elusive species such as bats. I was able to demonstrate a variety of ways to increase surveying efficiency (e.g. the use of an acoustic lure to increase bat-capture rate) and a significant relationship between bat activity and the relative abundance of certain species of bat which can maximise the knowledge of diversity in an area whilst minimising wildlife disturbances. Urbanisation has also had strong negative effects on many insect groups, such as moths, which are important components of the diets of many bat species. I found that woodland vegetation characteristics were more important than the surrounding landscapes in determining the abundance, species richness, and species diversity of moth assemblages within urban woodland. This indicates that management at a local scale to ensure provision of good quality habitat may be more beneficial for moth populations than improving habitat connectivity across the urban matrix. The findings presented in this thesis have important implications for our understanding of the adaptability of species to the built environment and for the management and monitoring of bat populations. It also highlights that even common bat species are negatively affected by urbanisation and much greater attention should be paid to securing their future within the urban landscape.

The environmental problems facing the world today are largely attributable to anthropogenic activities and landscape change. Addressing these challenges in an evidence-based way requires an understanding of precisely how species and ecosystems are responding to human impacts. Discerning linkages between stressors and their ecological repercussions, and using this to inform conservation, can be challenging due to the complexity and uncertainty of ecological research. I focused on the responses of five wide-ranging large mammal species – gray wolf (Canis lupus), Canada lynx (Lynx canadensis), coyote (Canis latrans), white-tailed deer (Odocoileus virginianus) and moose (Alces alces) – to human footprint (measure of human infrastructure and landscape change), using 12 years (2001-2013) of snowtrack surveys conducted across the boreal forest of Alberta. I explored three key challenges to discerning the linkages between ecological dynamics and management actions. First, I asked whether the direction and magnitude of species responses vary depending on the spatial extent and grain of the study. Second, I asked whether these species respond more strongly to individual footprint features or to the cumulative effects of footprint (measured as total footprint), and whether responses to footprint are consistent across species. Third, I evaluated the utility of thresholds for large mammal management and asked whether there is evidence for consistent threshold responses to total footprint across scales. In addressing the first two questions, I evaluated a set of generalized linear mixed effects models (GLMM) relating the relative abundance of each species to individual and cumulative effects of human footprint, using an information-theoretic approach. I compared the direction of species responses across our regional study area (approximately 400,000 km2) to those reported in previous smaller-extent studies (median 1,525 km2), and compared responses across three spatial grains (250m, 1500m, and 5000m transect buffers). In addressing the third question, I conducted a review on the utility of ecological thresholds, described as abrupt changes in the response to a continuous driver, for large mammal management. I further tested for thresholds in species responses to total footprint by comparing linear models (logistic regression) to piecewise regression models. I compared threshold values between two grains (approximately 33km2 - 1500m transect buffer, and 5500km2 - grouping transects into clusters), and across four regions (boreal forest extent, three landscape planning units). I found that the direction of species responses varied with spatial extent, but not grain, and that species responded strongly to a broad suite of footprint features, indicating the need to manage for cumulative effects. Despite the appeal of ecological thresholds, using these as targets is challenging and the success of doing so has rarely been evaluated. I found threshold models to be better supported than linear ones across species, but due to variability and uncertainty in threshold values, the results are more suited as guidelines or hypotheses to be further tested, as opposed to specific management targets. Translating research on complex ecological systems into management actions is a continuing challenge, yet, ongoing biodiversity monitoring and adaptive management may refine our existing tools, and ultimately lead to better environmental stewardship. / Graduate / 2017-09-05 / 0329

Grasslands are a significant source of biodiversity in farmed landscapes that is important to monitor. New generation satellites such as Sentinel-2 offer new opportunities for grassland’s monitoring thanks to their combined high spatial and temporal resolutions. Conversely, the new type of data provided by these sensors involves big data and high dimensional issues because of the increasing number of pixels to process and the large number of spectro-temporal variables. This thesis explores the potential of the new generation satellites to monitor biodiversity and factors that influence biodiversity in semi-natural grasslands. Tools suitable for the statistical analysis of grasslands using dense satellite image time series (SITS) with high spatial resolution are provided. First, we show that the spectro-temporal response of grasslands is characterized by its variability within and among the grasslands. Then, for the statistical analysis, grasslands are modeled at the object level to be consistent with ecological models that represent grasslands at the field scale. We propose to model the distribution of pixels in a grassland by a Gaussian distribution. Following this modeling, similarity measures between two Gaussian distributions robust to the high dimension are developed for the lassification of grasslands using dense SITS: the High-Dimensional Kullback-Leibler Divergence and the -Gaussian Mean Kernel. The latter outperforms conventional methods used with Support Vector Machines for the classification of grasslands according to their management practices and to their age. Finally, indicators of grassland biodiversity issued from dense SITS are proposed through spectro-temporal heterogeneity measures derived from the unsupervised clustering of grasslands. Their correlation with the Shannon index is significant but low. The results suggest that the spectro-temporal variations measured from SITS at a spatial resolution of 10 meters covering the period when the practices occur are more related to the intensity of management practices than to the species diversity. Therefore, although the spatial and spectral properties of Sentinel-2 seem limited to assess the species diversity in grasslands directly, this satellite should make possible the continuous monitoring of factors influencing biodiversity in grasslands. In this thesis, we provided methods that account for the heterogeneity within grasslands and enable the use of all the spectral and temporal information provided by new generation satellites.

Thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy. School of Animal, Plant and Environmental Science, University of the Witwatersrand, Johannesburg, South Africa. October 2016. / Mining has negative impacts on the environment in many different ways. One method developed to quantify some of these impacts is Landscape Function Analysis (LFA) and this has been accepted by some mining companies and regulators. In brief, LFA aims at quantifying the organization of vegetative and landscape components in a landscape into patches along a transect and quantifying, in a relative manner, three basic processes important to landscape functioning, namely: soil stability or susceptibility to erosion, infiltration or runoff, and nutrient cycling or organic matter decomposition. However, LFA is limited in large heterogeneous environments, such as those around mining operations, due to its localized nature, and the man hours required to collect a representative set of measurements for such large and complex environments. Remote sensing using satellite-acquired data can overcome these limitations by sampling the entire environment in a rapid and objective manner. What is required is a method of connecting these satellite-based measurements to LFA measurements and then being able to extrapolate these measurements across the entire mine surface. The aim of this research was to develop a method to use satellite-based hyperspectral imagery to predict landscape function analysis (LFA) using partial least squares regression (PLSR). This was broken down into three objectives: (1) Collection of the LFA data in the field and validation of the LFA indices against other environmental variables collected at the same time, (2) validation of PLSR models predicting LFA indices and various environmental variables from ground-based spectra, and (3) production of risk maps based on predicting LFA indices and above-ground biomass using PLSR models and Hyperion satellite-based hyperspectral imagery. Although the study was based in grasslands at two mining regions, West Wits and Vaal River, a suitable Hyperion image was only available for Vaal River. A minimum of 374 points were sampled for LFA indices, ground-based spectra, above-ground biomass and soil cores along 2880 m of LFA transect from both mine sites. Soil cores were weighed fresh before sieving with a 2 mm sieve to separate root and stone fractions. The sieved soil fraction was tested for pH, EC, SOM, and for the West Wits samples, organic nitrogen and total extractable inorganic nitrogen. There was one modification to the LFA method where grass patches were collapsed into homogenous units as it was deemed not feasible to sample 180 m transects at grass tuft scales of 10 – 30 cm, but other patch definitions followed the LFA manual (Tongway and Hindley, 2004). Evidence suggested that some of the different patch types, in particular the bare/biological soil crust – bare grass – sparse grass patch types, represented successional stages in a continuum although this was not conclusive. There also was evidence that the presence or absence of cattle play a role in some processes active in these grasslands and erosion is mainly through deflation, rain splash and sheet wash. Generally the environmental variables supported the LFA indices although the nutrient cycling index was representative of above-ground nutrient cycling but not below-ground nutrient cycling. Models derived with PLSR to predict the LFA indices from ground-based spectral measurements were strong at both mine sites (West Wits: LFA stability r2 = 0.63, P < 0.0001; LFA infiltration r2 = 0.75, P < 0.0001; LFA nutrient cycling r2 = 0.73, P < 0.0001; Vaal River: LFA stability r2 = 0.39, P < 0.0001, LFA infiltration r2 = 0.72, P < 0.0001, LFA nutrient cycling r2 = 0.54, P < 0.0001), as were PLSR models predicting above-ground biomass (West Wits above-ground biomass r2 = 0.55, P = 0.0003; Vaal River above-ground biomass r2 = 0.79, P < 0.0001) and soil moisture (West Wits soil moisture r2 = 0.45, P = 0.0017; Vaal River soil moisture r2 = 0.68, P < 0.0001). However, for soil organic matter (r2 = 0.50, P < 0.0001) and EC (r2 = 0.63, P < 0.0001), Vaal River had strong prediction models while West Wits had weak models for these variables (r2 = 0.31, P = 0.019 and r2 = 0.10 and P < 0.18, respectively). For EC, the wide range of soil values at Vaal River in association with gypsum crusts, and low values throughout West Wits explained these model results but for soil organic matter, no clear explanation for these site differences was identified. Patch-based models could accurately discriminate between spectrally well-defined patch types such S. plumosum patches but were less successful with patch types that were spectrally similar such as the bare/biological soil crust – bare grass – sparse grass patch continuum. Clustering similar patch types together before PLSR modelling did improve these patch-based spectral models. To test the method proposed to predict LFA indices from satellite-based hyperspectral imagery, a Hyperion image matching 6 transects at Vaal River was acquired by NASA’s EO-1 satellite and downloaded from the USGS Glovis website. LFA transects were partitioned to match and extract pixel spectra from the Hyperion data cube. Thirty-one spectra were separated into calibration (20) and validation (11) data. PLSR models were derived from the calibration data, tested with validation data to select the optimum model, and then applied to the entire Hyperion data cube to produce prediction maps for five LFA indices and above-ground biomass. The patch area index (PAI) produced particularly strong models (r2 = 0.79, P = 0.0003, n =11) with validation data, whereas the landscape organization index (LOI) produced weak models. It is argued that this difference between these two essentially similar indices is related to the fact that the PAI is a 2-dimensional index and the LOI is a 1-dimensional index. This difference in these two indices allowed the PAI to compensate for some burned pixels on the transects by “seeing” the density pattern of grass tufts and patches whereas the linear nature of the LOI was more susceptible to the changing dimensions of patch structure due to the effects of fire. Although validation models for the three LFA indices of soil stability, infiltration and nutrient cycling were strong (r2 = 0.72, P = 0.004; r2 = 0.66, P = 0.008; r2 = 0.70, P = 0.005, n = 9 respectively), prediction maps were confounded by the presence of fire on some transects. The poor quality of the Hyperion imagery also meant great care had to be taken in the selection of models to avoid poor quality prediction maps. The 31 bands from the VNIR (478 – 885 nm) portion of the Hyperion spectra were generally the best for PLSR modelling and prediction maps, presumably because of better signal-to-noise ratios due to higher energy in the shorter wavelengths. With two satellite-based hyperspectral sensors already operational, namely the US Hyperion and the Chinese HJ-1A HSI, and a number expected to be launched by various space agencies in the next few years, this research presents a method to use the strengths of LFA and hyperspectral imagery to model and predict LFA index values and thereby produce risk maps of large, heterogeneous landscapes such as mining environments. As this research documents a method of partitioning the landscape rather than the pixel spectra into pure endmembers, it makes a valuable contribution to the fields of landscape ecology and hyperspectral remote sensing. / LG2017

O trabalho reflete sobre a paisagem, o ambiente e os espaços livres de Suzano, município situado na bacia do Alto Tietê Cabeceiras, que faz parte da Região Metropolitana de São Paulo. Inicialmente, desenvolve-se a análise de conceitos voltados à ecologia de paisagens e do sistema de espaços livres públicos. Em seguida, faz-se uma aproximação da paisagem e do sistema de espaços livres do município, objetivando compreender a diversidade de suas paisagens, bem como do seu ambiente nos distritos que o compõem. Após esta compreensão retoma-se novamente o conceito voltado à ecologia de paisagens, para que este possa ser utilizado na constituição de uma proposta de sistema de espaços livres públicos para o território, buscando a valorização das suas paisagens, assim como do ambiente. Ao final, verifica-se quais são os entraves existentes na gestão pública, que dificultam a implementação de políticas ambientais no país. / The goal of this dissertation is to study the impact of landscape and open spaces on the environment in urban areas. The focus will be on the city of Suzano, which is located at the basin of Alto Tietê Cabeceiras and is part f the metropolitan region of São Paulo, Brazil. The first part of the study will focus on ecological concepts of landscapes and open spaces of the city. After, we aim to better understand the diversity of the open spaces within these territories and how they shape and mold the terrain and effect the local environment. Once an informed and educated analysis is achieved, the goal is then to establish a proposal to implement an open space program for the surrounding Suzano area that would both bring better quality of life and value to the city and their inhabitants. Finally, we plan to point out what obstacles and barriers might exist in within the government for implementation of these policies.

O controle biológico de pragas agrícolas é um dos serviços ecossistêmicos mais valorizados, dada sua importância para a produção agrícola. Embora vários estudos tenham demonstrado que a abundância e riqueza de predadores aumentam com a quantidade de floresta nativa, os mecanismos subjacentes que modulam a relação entre a cobertura florestal e provisão de controle biológico em diferentes escalas espaciais são ainda pouco conhecidos. Neste trabalho, utilizamos experimentos de exclusão de vertebrados voadores em oito paisagens cafeeiras na Mata Atlântica, num gradiente de cobertura florestal, e quantificamos as consequências para a perda foliar e para a frutificação. A perda foliar mostrou uma relação negativa com a cobertura florestal em paisagens com 2 km de raio, indicando que a herbivoria é melhor controlada em paisagens com alta cobertura florestal, especialmente na presença de aves e morcegos. No entanto, no nível local, 300 m ao redor das plantas de café, a perda foliar e a frutificação responderam diferentemente à cobertura florestal. Em unidades com baixa cobertura florestal local, a exclusão de aves e morcegos aumentou a perda foliar e diminuiu a frutificação em uma média de 13%. Por outro lado, em unidades com alta cobertura florestal local, a exclusão de aves e morcegos não teve efeitos significativos nem na perda foliar, nem na frutificação. Concluímos que os efeitos da exclusão de aves e morcegos na perda foliar e frutificação são modulados por diferentes processos que ocorrem no nível local e da paisagem. Sugerimos que quando a cobertura florestal local é alta (geralmente perto de fragmentos florestais), as aves e os morcegos não se alimentam apenas de herbívoros, mas também de mesopredadores. No entanto, quando a cobertura florestal local é baixa (e.g. longe de fragmentos florestais), os mesopredadores não ocorrem e aves e morcegos passam a prover serviço de controle biológico de pragas, alimentando-se principalmente de herbívoros. Destacamos a importância de empregar uma análise multiescalar em sistemas onde espécies com diferentes capacidades de dispersão proveem um serviço ecossistêmico. / Biological control of agricultural pests is one of the most important ecosystem services given its key role for agricultural production. Although several studies have shown that the abundance and richness of predators increase with the amount of native forest in the landscape, the underlying mechanisms relating forest cover at different spatial scales with the provision of biological control are still poorly understood. We experimentally excluded flying vertebrates (birds and bats) in eight coffee landscapes in the Brazilian Atlantic Forest, encompassing a gradient of forest cover and quantified the consequences for coffee leaf loss and fruit set. Leaf loss showed a negative relation with forest cover at landscape level, in landscapes with 2 km radius, indicating that herbivory is better controlled in landscapes with high forest cover, especially in the presence of birds and bats. However, at local level, 300 m around coffee plants, leaf loss and fruit set responded to forest cover differently. In units with low local forest cover exclusion of birds and bats increased leaf loss and reduced fruit set by 13% in mean. However, in units with high local forest cover, exclusion of birds and bats had no significant effect neither on leaf loss nor in fruit set. We concluded that the effects of birds and bats exclusion on leaf loss and fruit set are modulated by different processes occurring at landscape and local levels. We hypothesized that when local forest cover is high (usually near remnant forest fragments) birds and bats are not only controlling herbivores but may also be reducing mesopredators, while when local forest cover is low (e.g. far from forest fragments), mesopredators do not occur and birds and bats start providing biological pest control by feeding mainly on herbivores. We highlight the importance of employing a multiscale analysis in systems where species with different dispersal abilities are providing an ecosystem service.

O presente trabalho tem o objetivo de contribuir para a discussão acerca de diferentes estratégias de conservação da natureza, confrontando o modelo hegemônico baseado na criação de áreas protegidas com modelos alternativos, surgidos com o intuito de superar os problemas e conflitos ocasionados por este modelo, especialmente quando transposto para a realidade de países tropicais como o Brasil. O que se pretende é demonstrar que, diante de situações complexas de interação entre a sociedade e o meio ambiente, faz-se necessário o emprego de mecanismos voltados para a conservação da paisagem como um todo, a partir do seu uso efetivo e da definição conjunta de critérios pelos diversos atores envolvidos no processo, o que implica em mudanças com relação às instituições e instrumentos a serem utilizados. Para tanto, é feita uma análise comparativa de diferentes iniciativas de conservação em andamento na região do Vale do Rio Negro, no Pantanal de Mato Grosso do Sul, representativas de diferentes abordagens da questão da conservação. Além de ser uma das regiões mais preservadas do Pantanal, o Vale do Rio Negro apresenta um histórico de mobilização social em torno da conservação, o que explica o interesse pela área. A proximidade entre os domínios da cultura e da natureza na região do Pantanal, a ponto de tornar inviável sua compreensão senão a partir de uma referência comum, é também um fator importante para este estudo. A análise específica do caso do Vale do Rio Negro é precedida por uma discussão a respeito da evolução da idéia de conservação da natureza, e da concepção de mundo natural que serviu de base para o seu surgimento. São analisadas ainda tendências atuais em estratégias de conservação. Afim de permitir a compreensão do contexto em que se inserem as diferentes iniciativas de conservação analisadas, é feita também uma análise da paisagem do Pantanal e do Vale do Rio Negro em particular, em seus aspectos físicos, bióticos, históricos e humanos, com ênfase na co-evolução dos seus processos naturais e culturais. / The objective of this paper is to contribute to the discussion about different strategies for nature conservation, confronting the predominant model based in protected areas with other alternatives, developed to overcome the problems and conflicts generated by this model, especially with its implementation in tropical countries such as Brazil. The discussion is expected to demonstrate that, in dealing with situations of complex interaction between society and the environment, there is a need for mechanisms that enable the conservation of the region as a whole, through the effective use of its resources, and the definition of common criteria by the different actors involved in the process, which requires changes in the institutions and instruments to be employed. In order to achieve this objective, a comparative study is made among different initiatives for the conservation of the Rio Negro Valley region, in the Pantanal, each representative of different approaches to the issue of conservation. In addition to being one of the most pristine regions of the Pantanal, the Rio Negro Valley has a background of social mobilization around conservation, which explains the interest for the area. The proximity between cultural and natural processes in the Pantanal, to the point that they cannot be understood separately, is also an important factor to be taken into account by this study. The study of the specific issues on the Rio Negro Valley is preceded by a discussion about the evolution of the idea of nature conservation, and the concept of the natural world that enabled its appearance. Current trends in conservation strategies are also analyzed. In order to provide an understanding of the context in which the different conservation initiatives are inserted, the landscape of the Pantanal region – and the Rio Negro Valley in particular – is also analyzed in its physical, biological, historic and human aspects, emphasizing the co-evolution of its natural and cultural processes.

Apesar de vários estudos terem demonstrado que a presença de abelhas resulta em aumento da produtividade de culturas agrícolas, os mecanismos que determinam a eficácia da polinização em escalas espaciais mais amplas ainda são desconhecidos. Avaliamos a influência da composição e configuração da paisagem sobre a composição da comunidade de abelhas e a polinização do café (Coffea arábica). Nosso estudo foi realizado em uma das regiões cafeeiras mais importantes do Brasil, em nove paisagens compostas de cafezais e diferentes quantidades de remanescentes de Mata Atlântica. Utilizando experimentos de exclusão floral, avaliamos a polinização em 15 pés de café por paisagem. A eficiência da polinização foi medida através da contagem e pesagem dos frutos formados. Também coletamos e identificamos os visitantes florais. Nossas análises foram feitas no nível de paisagem, com 1 e 2 km de raio, e no nível do pé de café, com 300 m de raio em torno de cada árvore. Foram coletados 241 indivíduos de abelhas e identificadas um total de 22 espécies. A abelha Apis mellifera (Apini) foi a espécie mais abundante, seguida de Trigona spinipes (Meliponini). A abundância A. mellifera foi afetada pela composição da matriz na paisagem e a composição da comunidade de abelhas nativas mudou com a distância ao fragmento florestal mais próximo. A presença das abelhas, por sua vez, resultou em um aumento 28% na produção de frutos. A abundância de A. mellifera afetou positivamente a frutificação, enquanto a composição da comunidade de abelhas nativas afetou a frutificação de modo diferente no nível da paisagem e do pé de café. Nossos resultados indicam que a estrutura da paisagem afeta a composição da comunidade de visitantes florais e que as flores expostas às abelhas apresentam um aumento na frutificação. Embora nossos resultados não permitam separar claramente os mecanismos responsáveis pelo aumento observado na frutificação, nosso trabalho mostra que o serviço de polinização das abelhas pode ser afetado pela estrutura da paisagem. Estes resultados podem ser utilizados na conservação e planejamento agrícola a fim de maximizar a produção de culturas e, ao mesmo tempo, conservar a biodiversidade e o serviço de polinização. / Although several studies have shown that the presence of bees results in increased crop yields, the mechanisms that determine pollination effectiveness on broader spatial scales are still largely unknown. We evaluated the influence of landscape composition and configuration over bee community composition and coffee (Coffea Arabica) pollination. Our study was undertaken in one of the most important coffee-producing regions of Brazil, and comprised nine landscapes of sun coffee plantations surrounded by different amounts of Atlantic Forest remnants. Using floral exclusion experiments we evaluated pollination effectiveness in 15 coffee trees per landscape. Pollination effectiveness was measured by counting and weighing the fruit set. We also sampled the bees visiting coffee flowers. Our analyses were made at the landscape level, with 1 and 2 km radii, and at the coffee tree level, with 300 m radius around each tree. We collected 241 bee individuals and identified a total of 22 species. The honeybee Apis mellifera (Apini) was the most abundant species followed by Trigona spinipes (Meliponini). Honeybee abundance was affected by landscape matrix composition while native bee community composition changed with distance to the nearest forest fragment. The presence of bees resulted in an increase in coffee fruit set of 28%. A. mellifera abundance positively affected fruit set at both levels, while the composition of the native bee community affected fruit set differently at the landscape level than at the tree level. Landscape structure was found to affect the community composition of floral visitors, and coffee flowers exposed to bees showed an increase in fruit set compared to flowers excluded from pollinators. Although our results do not allow disentangling the mechanisms responsible for the observed increase in fruit set, our work shows that bee pollination services can be affected by landscape structure. These findings can be used in conservation and agricultural planning to maximize crop production while safeguarding biodiversity and the provision of pollination services.

Os estudos de ecologia descritiva de comunidades marinhas bentônicas, tanto as de substratos consolidados (costões rochosos, recifes de corais, recifes de arenitos e bancos de algas calcárias) como as de substratos inconsolidados (areia, silte e sedimentos de baixa granulação), apontam para uma busca, ainda não finalizada, por padrões de distribuição que possam apresentar-se como modelo recorrente, sendo capazes de predizer sobre a composição de uma comunidade local. Como exemplos bem sucedidos, na busca de padrões, sendo marcos históricos no desenvolvimento da ecologia descritiva de comunidades marinhas bentônicas, temos as abordagens da zonação e de níveis de fundo, que buscaram encontrar um meio prático para descrições generalistas em larga escala que se apresentassem universais. No Brasil são caracterizados 3 momentos históricos sobre ecologia descritiva de comunidades marinhas bentônicas de substrato consolidado, que se caracterizam pelo uso de espécies como unidade operacional, recorrendo pouco a abordagens alternativas para ganho de conhecimento sobre grandes áreas. Neste estudo foi utilizado o método alternativo Caracterização fisionômica de comunidades marinhas de substrato consolidado para descrição dessas comunidades no infralitoral e busca por padrões de estruturação gerais visualmente evidentes. Este estudo foi realizado no Parque Estadual da Ilha Anchieta, Ubatuba SP, no infralitoral do costão oeste da Enseada das Palmas, compreendido entre as coordenadas 23°31\'44.37\"S / 045° 3\'38.07\"O e 23°32\'1.62\"S / 045° 3\'39.17\"O. Como principais resultados foram encontrados 24 povoamentos descritos na Abordagem 1, 20 povoamentos no inverno e 23 no verão . Na Abordagem 2, 19, povoamentos no inverno e, na Abordagem 3., 22 no verão. Os resultados quantitativos mostram, discriminados no costão estudado, a formação de 2 grupos gerais, que se mantiveram os mesmos no inverno e no verão, permitindo a conclusão de que há um padrão geral de estruturação da comunidade visualizada. Os povoamentos determinantes na divisão dos 2 grupos foram: Colônia de Palythoa, Tapete de Amphiroa e Jania, Banco de Dichotomaria e Região de Substrato Inconsolidado. Constata-se o mundo natural como um lugar desigual, que se manifesta em manchas ou remendos distintos, apresentando-se de muitas formas e com uma ampla gama de escalas. Os resultados foram vistos sob uma perspectiva exploratória, uma vez que se buscou encontrar padrões de distribuição das comunidades apenas a partir da unidade visual povoamento, sem o registro de dados de condições ambientais. Nessa busca, visualizando tal mosaico de distribuição de formas, cores, estrutura e composição em diferentes escalas encontramos padrões gerais de distribuição da comunidade, aqui representados por 2 grandes grupos, caracterizados por estarem em um nível acima de povoamentos ou supra povoamentos / The studies on descriptive ecology of marine benthic communities, hard bottom (Rocky Shores, Coral Reefs, Sandstone Rock Reefs and Rodolith Beds) as much as soft bottom communities (sand, silt and soft substrate of low granular material), lead to a non finished search for distribution patterns that may present it as a model able to predict about the local communities composition. As successful examples on searching for patterns as historical reference on the developing of descriptive ecology of marine benthic communities we have the zonation and bottom level approaches, that seek for a practical way to describe on a general and large scale universal patterns of distribution. In Brazil we found 3 historical moments about studies dealing with descriptive ecology of hard bottom marine benthic communities, which are characterized by the use of species as an operational unit, taking advantage of few alternative approaches to acquire knowledge about the communities in large areas. In this study the alternative methodology Physiognomic characterization of hard bottom marine benthic communities was applied, to describe such communities in infra-littoral regions and to search for general structural patterns visually evident. This study was made in Anchieta Island State Park, Ubatuba SP, Brazil, on the west rocky shore of Palmas Bay, located between the geographical positions 23°31\'44.37\"S / 045° 3\'38.07\"W and 23°32\'1.62\"S / 045° 3\'39.17\"W. As main results, 24 settlements described by the first approach were found; 20 settlements in winter season and 23 in summer season by the second approach ; 19 settlements in winter season e 22 in summer season by the third approach. The quantitative results show 2 general groups found on the studied rocky shore that were the same both in winter and summer seasons, allowing that we come to the conclusion that there is a general structural pattern visualized in the communities. The determinant settlements to the formation of the 2 groups were Palythoa Colony, Amphiroa and Jania Turf, Dichotomaria Bed and Soft Bottom Region. We face the fact that nature is an unequal place, which manifests this visual difference on patches of different sizes, showing many forms and colors on a huge range of scales. The results were reviewed under an exploratory perspective, searching first for structural patterns of these communities only from the visual unit called settlement, without the data of environmental conditions. On this search, visualizing the distribution of forms, colors, structure and composition mosaic on different scales we found general patterns of communities distribution that here are represented by 2 large groups, characterized by being on a higher level than the one of the settlement

Este estudo mostrou os efeitos da fragmentação sobre a avifauna considerando diferentes aspectos, levando em conta escalas espaciais e temporais distintas e os diferentes elementos que compõem uma paisagem fragmentada. Verificamos a influência das características intrínsecas dos fragmentos, da configuração das paisagens e da variação geográfica sobre as respostas das espécies à fragmentação. Igualmente importante está a variação temporal; modificações da estrutura da paisagem passada têm reflexos na distribuição e abundâncias das aves na paisagem atualmente e a inclusão dessa variável nas análises nos permite avaliar de maneira mais precisa o grau de ameaça que as espécies sofrem nas paisagens alteradas pela ocupação humana. O primeiro capítulo mostra que no Pontal do Paranapanema o tamanho dos fragmentos e a estrutura da vegetação são os fatores principais que afetam a avifauna na região. Isso acontece devido ao grau de isolamentos intenso dos remanescentes, que devem impedir com que a maior parte das espécies florestais se movimentem entre fragmentos, tornando as características intrínsecas dessas áreas mais importantes. Vimos também que uma grande proporção das espécies florestais (~41%) é afetada ou altamente afetada pela redução e fragmentação do habitat, e que, em geral, essas espécies fazem parte de grupos funcionais mais vulneráveis, entre eles: as espécies endêmicas da Mata Atlântica, que estão próximas do limite de distribuição, que estão fora de seus centros de abundância e que têm baixa flexibilidade no uso de florestas. No segundo capítulo, avaliamos o papel de bosques agroflorestais funcionando como trampolins ecológicos (“stepping stones"). Encontramos poucas evidências de que esses elementos influenciem a composição das comunidades de aves na escala da paisagem ou para os remanescentes grandes da região. Espécies generalistas e de áreas abertas foram as mais freqüentemente observadas nos bosques agroflorestais e nos outros elementos de conexão (fragmentos pequenos e corredores ripários), enquanto apenas poucas espécies florestais foram observadas nessas áreas. No entanto, esses elementos são mais ricos em espécies dos que a matriz de pasto, o que mostra a desvantagem desse sistema tradicional de monocultura instalada na região desde o início de sua ocupação. Propomos ainda uma hipótese geral sobre a eficiência dos trampolins ecológicos que ocorre em resistências intermediárias da matriz; quando a matriz é muito resistente, muito contrastante com o habitat natural, como para as espécies florestais em nosso estudo, os indivíduos não conseguem utilizar esses elementos por não conseguirem sair dos fragmentos; em oposição, em matrizes muito permeáveis, provavelmente a necessidade dos trampolins é diminuída porque a movimentações podem ocorrer pela própria matriz; dessa forma, apenas em condições intermediárias os trampolins ecológicos terão uma eficiência ótima, como para as espécies generalistas em nosso estudo; claramente, essa relação é espécie-dependente. Observamos ainda que a distância dos bosques aos remanescentes florestais é determinante na composição, riqueza e abundância de espécies que usam esses elementos. Os trampolins devem ser considerados como alternativa de manejo da paisagem, sobretudo em áreas em que não é possível a implantação de corredores e a matriz tenha uma permeabilidade adequada. No terceiro capítulo, verificamos que a estrutura espacial da paisagem do Pontal de 1978, explica melhor as riquezas de grupos funcionais mais sensíveis do que a estrutura mais atual (2003), evidenciando um tempo de latência da resposta das espécies de cerca de 25 anos. Contrariamente, as espécies não-sensíveis estiveram mais relacionadas com a paisagem mais recente. Esse resultado mostra que as espécies sensíveis ainda não se estabilizaram nos fragmentos e que mais perdas poderão acontecer mesmo sem novos avanços da fragmentação do habitat na região. Processos semelhantes devem acontecer em outras regiões da Mata Atlântica, com o agravante de que, em muitos casos, o tempo de isolamento dos remanescentes é maior e, portanto, esse processo de perda está mais adiantado. No quarto capítulo estimamos quanto é o débito ecológico provocado pelo processo de fragmentação, i.e. quantas espécies devem ser perdidas devido a esse processo; e qual é o tempo de latência para a perda das espécies. Verificamos que o débito é muito alto especialmente para as espécies sensíveis, as endêmicas e as que têm baixa abundância relativa. Muitas dessas espécies já foram perdidas, principalmente nos fragmentos menores e de qualidade inferior, em que o tempo de latência é mais curto; e, muitas outras serão perdidas em um futuro próximo nos fragmentos maiores. O tempo de latência que estimamos é menor do que o encontrado em outro estudo com aves tropicais da África, ilustrando que a urgência para impedir o desaparecimento das espécies é maior do que se pensava. Finalmente, no último capítulo verificamos que as respostas das espécies à fragmentação dependem não somente da configuração da paisagem em uma certa região, mas também da sua localização geográfica. As respostas das espécies podem variar ao longo de sua distribuição geográfica e, em geral, elas são mais vulneráveis quando estão próximas da borda de distribuição, sobretudo as endêmicas. De forma semelhante, aquelas que estão fora dos seus centros de abundância também apresentam uma sensibilidade mais elevada. As espécies com baixa abundância são afetadas independentemente de suas localizações. Verificamos também que em paisagens mais conectadas, a área dos fragmentos tem uma importância secundária e o limiar de tamanho para a ocorrência das espécies mais sensíveis é muito menor nessas situações em comparação com paisagens onde os remanescentes estão muito isolados. / We evaluated the effect of Atlantic Forest fragmentation on bird community, functional groups and populations, in the Pontal do Paranapanema region. Forest bird survey using point counts was conducted during the period of 2002-2004, in 21 patches and seven sites located in a control reserve, the Morro do Diabo State Park (36,000 ha). We identified four degrees of species’ sensitivity to fragmentation: highly affected, affected, not affected and benefited. Four functional groups revealed to be more vulnerable: Atlantic Forest endemic species; those that are near the edge of their geographical distribution; species that have low flexibility on forest type use and species that are outside of their center of abundance. The intrinsic patch parameters, such as size and quality were the most important, affecting a higher number of species, while the degree of isolation explained little about bird parameters variation. This result must be due to the intense isolation imposed to the remnants in the region, caused by the long distance between patches and the low permeability of the matrix, what make the local variables more relevant. This study shows the need to protect and manage the forest remnants to improve habitat quality. Complementarily, landscape management should be conducted to minimize the isolation of forest remnants. The highest priority should be given to the State Park and the largest patches which aggregate the highest diversity. Keywords: fragmentation, Landscape Ecology, conservation, biodiversity, species Sensitivity. The aim of this study was to assess whether stepping stones (agroforest woodlots) can increase landscape connectivity, influencing bird distribution and diversity at landscape and local levels. We also tested which categories of species can use different types of connection elements, and whether this use is influenced by the distance from these elements to forest patches. We studied two fragmented landscapes, with and without stepping stones linking large fragments, and one forested landscape. Using a point count, a bird survey was undertaken in the fragmented landscapes in five different elements: large remnants (>400 ha), agroforest woodlots (0.4-1.1 ha), small patches (0.5 – 7 ha), riparian corridor, and pasture areas (the main matrix). The latter three elements were compared with the stepping stones, in regard to their role in bird movements. The continuous forest was surveyed as a control for large remnants in the fragmented landscapes. We observed no effect of the agroforest systems at the landscape scale or for large forest remnants. Generalist and open-area species were commonly observed in the agroforest system or other connection elements, whereas only a few forest species were present in these connections. The matrix was the poorest element of all. The distance between the woodlots and source areas (large patches) was essential to determine forest species richness and abundance in the agroforest system. We suggest that there is an optimal relationship between the permeability of the matrix and the efficiency of stepping stones, which occurs at intermediate degrees of matrix resistance, and is, clearly, species-dependent. The agroforest system appeared to be more advantageous for conservation than the traditional monoculture system in the region, as they hold higher bird diversity; for this reason, they should be considered as a management alternative, particularly when the corridor implantation is not feasible and the matrix permeability requirement is met. Keywords: Fragmentation, Landscape Ecology, Conservation, Biodiversity, Landscape Management. Landscape dynamic is an important factor effecting biodiversity, especially in humandominated landscapes. The aim of this study was to verify how the historical processes of fragmentation in the Pontal do Paranapanema region, inside the Atlantic Forest domain, influence bird diversity pattern. Maps from the region were produced for each decade: 1957, 1965, 1978, 1984, 1993 and 2003; using different types of information such as Satellite images, topographic maps and aerial photographies. For each map we calculated landscape indices which represent patch size and isolation, and related those metrics with bird community parameters. Birds were surveyed using point count methodology in 21 patches plus seven sites in a control reserve (The Morro do Diabo State Park, with 36,000 ha). Patches varied in size: seven large (>400 ha), seven medium (100 - 200 ha) and seven small (30 – 80 ha). Species richness was calculated for forest and generalist species and for different functional groups. Model selection, based on Akaike’s Information Criterion, was performed to distinguish which landscape indices, older or recent ones, explain better species richness. For non sensitive species the degree of isolation of the most recent landscape (2003) explains better the richness variation, although with a higher uncertainty in model selection. On the contrary, landscape parameters from 1978, especially patch size, were the most important variables to explain the richness of the most sensitive groups of species, what provides an evidence for a time lag of bird response to fragmentation of about 25 years. This time also corresponds to the period of intense fragmentation process in the region, when, the forest cover was reduced to < 30%, the theoretical fragmentation threshold. This time lag is a conservation concern because it indicates that the sensitive species did not get yet into a steady state condition and extinctions might occur in a near future if no landscape management is carried out to revert the negative consequences of fragmentation. This situation must even be more critical for other landscapes in the Atlantic Forest domain where the time since isolation is longer. Keywords: fragmentation, landscape dynamics, conservation, ecological debt. The aim of this study was to estimate the time lag between the fragmentation of an Atlantic forest region and the extinction of sensitive bird species in forest patches and to verify which landscape parameters might be associated with such a delay. We analyzed 21 patches varying in size (30-2,000 ha) and seven sites inside a continuous forest (control, ~36,000 ha). The original, present and future bird richness in each site were estimated using, respectively, data from literature, bird survey using point counts and a species-area relationship. A landscape data set of the historical process of fragmentation in the region was used to estimate patch size and time since isolation and the total forest cover in the landscape before fragmentation had taken place. We estimated a very high bird loss in forest patches, mainly concerning species sensitive to disturbances, endemics for the Atlantic Forest and with low relative abundance. The observed halflife, the time necessary to loose half of the species before the relaxation process, varied, on average, between 20 and 46 years. This period was shorter than those found in another study for birds in an African tropical forest (23 to 80 years), indicating that we have less time to revert this situation than previously predicted. The patch quality and size are both important factors determining the time lag for sensitive species. We have estimated that several species had already gone extinct, particularly in small and low quality patches, and that other ones will disappear in the future, even in the largest patches. Our results allowed us to speculate about other Atlantic Forest landscapes, where longer time since isolation and smaller patches can cause even higher losses. The synchronism of extinctions occurring in many regions probably will increase the list of threatened species in a near future, including many that today seem not likely to be vulnerable. Keywords: Landscape dynamic, conservation, extintion debt, theory of Island Biogeography, species-area relationship. Generally the effect of fragmentation on species focus on the landscape or regional scale, removing the geographic variation effect, nonetheless the addition of this variable might help us understand how species respond to fragmentation in a general form. Based on this idea, we compared the effects of forest fragmentation on bird species sensitive to habitat reduction and segmentation, functional groups and coincident species that occur in three landscapes in two geographically distant regions: the Pontal do Paranapanema region, in the extreme west of the State of São Paulo; and Ibiúna e Caucaia, 700 km to the east of the state. We undertook bird survey, using point count methodology in 37 forest fragment and 11 sites inside two continuous forests. The numbers of sample in each landscape were: Pontal – 21 patches and 7 sites in a control area; and Ibiúna and Caucaia – 8 patches in each landscape and 4 sites in a same control area. In the landscape of Pontal, bird species suffer the most intense effects of fragmentation, although patches are larger than in the other landscapes. The most sensitive species are: endemic, on the limit of distribution, out of abundance center and with low abundance. Many of them are affected only in the Pontal region, result of its geographical location. The spatial structure of landscape explains much of the species diversity and composition variation in the sampled areas. In Pontal and Ibiúna, patch size is the most important variable and, in Caucaia, the high degree of connectivity is the most relevant, making the species less vulnerable. Furthermore, because of its high connectivity, the patch size threshold that defines species loss, is much smaller in Caucaia than in Pontal (50 ha e 300-400 ha, respectively). The comparison of the effects of fragmentation on birds in distinct landscape shows that species responses varies along its distribution, which are constrained to local landscape parameters and bird features. This results show that there is no general recipes for biodiversity conservation, but different strategies must be used according to the regional condition. Keywords: connectivity, fragmentation, Landscape Ecology, conservation, geographical Variation.