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Distance sampling is one of the most commonly used methods for estimating density and abundance. Conventional methods are based on the distances of detected animals from the center of point transects or the center line of line transects. These distances are used to model a detection function: the probability of detecting an animal, given its distance from the line or point. The probability of detecting an animal in the covered area is given by the mean value of the detection function with respect to the available distances to be detected. Given this probability, a Horvitz-Thompson- like estimator of abundance for the covered area follows, hence using a model-based framework. Inferences for the wider survey region are justified using the survey design. Conventional distance sampling methods are based on a set of assumptions. In this thesis I present results that extend distance sampling on two fronts. Firstly, estimators are derived for situations in which there is measurement error in the distances. These estimators use information about the measurement error in two ways: (1) a biased estimator based on the contaminated distances is multiplied by an appropriate correction factor, which is a function of the errors (PDF approach), and (2) cast into a likelihood framework that allows parameter estimation in the presence of measurement error (likelihood approach). Secondly, methods are developed that relax the conventional assumption that the distribution of animals is independent of distance from the lines or points (usually guaranteed by appropriate survey design). In particular, the new methods deal with the case where animal density gradients are caused by the use of non-random sampler allocation, for example transects placed along linear features such as roads or streams. This is dealt with separately for line and point transects, and at a later stage an approach for combining the two is presented. A considerable number of simulations and example analysis illustrate the performance of the proposed methods.

Knowledge about cetaceans in the Red Sea is limited with only a handful of sporadic or spatially-limited studies carried out to date. Funded by the Italian Cooperation through a Debt-for-Nature Swap programme and carried out in collaboration with the Egyptian NGO HEPCA, this thesis presents the results from the first ever systematic vessel-based surveys conducted in the southern Egyptian Red Sea from 2010 to 2013 using linetransect methodology. The main aims of the thesis were (a) to estimate cetacean abundance, (b) to determine distribution patterns and habitat use of the cetacean species, (c) to investigate movement patterns for species for which individual recognition techniques were suitable and (d) to identify areas of conservation concern for cetaceans with a particular focus on existing protected areas. Eight species were identified, of which five were commonly encountered (Stenella longirostris, S. attenuata, Tursiops truncatus, T. aduncus, and Grampus griseus) and three were rare (Pseudorca crassidens, Sousa plumbea, Balaenoptera edeni). Estimates of abundance using design-based line transect sampling techniques were obtained for five species: S. attenuata 10,268 (CV=0.26); S. longirostris 6,961 (CV=0.26); T. aduncus 659 (CV=0.69); T. truncatus 509 (CV=0.33), and G. griseus 367 (CV=0.37). Habitat modelling revealed that the two Stenella species were widely distributed across the study area. In contrast, T. truncatus was concentrated in waters around Ras Banas peninsula (in particular Satayah offshore reef), and T. aduncus was mainly found along the coast with possibly separate sub-populations in the northern and southern study area. G. griseus was only encountered in the southern part. The information provided in this study will allow the development of a conservation strategy for the protected areas and will serve as baseline information to carry out future survey work in the Red Sea.

No description available.

A urbanização e a expansão das fronteiras agrícolas na região Neotropical estão entre as principais forças causadoras da degradação ambiental em hábitats abertos naturais. Inferências e estimativas de abundância são críticas para quantificação de dinâmicas populacionais e impactos de mudanças ambientais. Contudo, a detecção imperfeita e outros fenômenos que causam inflação de zeros podem induzir erros de estimativas e dificultar a identificação de padrões ecológicos. Examinamos como a consideração desses fenômenos em dados de contagens de indivíduos não marcados pode informar na escolha do método apropriado para estimativas populacionais. Revisamos métodos estabelecidos (modelos lineares generalizados [GLMs] e amostragem de distância [distance sampling]) e emergentes que usam modelos hierárquicos baseados em misturas (N-mixture; modelo de Royle-Nichols [RN], e N-mixture básico, zero inflacionado, espacialmente explicito, visita única, e multiespécies) para estimar a abundância de populações não marcadas. Como estudo de caso, aplicamos o método N-mixture baseado em visitas únicas para modelar dados de contagens de aves de rapina em estradas e investigar como transformações de habitat no Cerrado e Pantanal do Mato Grosso do Sul afetaram as populações de 12 espécies em uma escala regional (>300.000 km2). Os métodos diferem nos pré-requisitos de desenho amostral, e a sua adequabilidade depender da espécie em questão, da escala e objetivos do estudo, e considerações financeiras e logísticas, que devem ser avaliados para que verbas, tempo e esforço sejam utilizados com eficiência. No estudo de caso, a detecção de todas as espécies foi influenciada pela horário de amostragem, com efeitos congruentes com expectativas baseadas no comportamentos de forregeamento e de voo. A vegetação fechada e carcaças também influenciaram a detecção de algumas espécies. A abundância da maioria das espécies foi negativamente influenciada pela conversão de habitats naturais para antrópicos, particularmente pastagens e plantações de soja e cana-de-açúcar, até mesmo para espécies generalistas consideradas como indicadores ruins da qualidade de hábitats. A proteção dos hábitats naturais remanescentes é essencial para prevenir um declínio ainda maior das populações de aves de rapina na área de estudo, especialmente no domínio do Cerrado / Urbanization and the expansion of agricultural frontiers are among the main forces driving the degradation of natural habitats in Neotropical open habitats. Inference and estimates of abundance are critical for quantifying population dynamics and the impacts of environmental change. Yet imperfect detection and other phenomena that cause zero inflation can induce estimation error and obscure ecological patterns. We examine how detection error and zero-inflation in count data of unmarked individuals inform the choice of analytical method for estimating population size. We review established (GLMs and distance sampling) and emerging methods that use N-mixture models (Royle-Nichols model, and basic, zero-inflated, temporary emigration, beta-binomial, generalized open-population, spatially explicit, single-visit and multispecies) to estimate abundance of unmarked populations. As a case study, we employed a single visit N-mixture approach to model roadside raptor count data and investigate how land-use transformations in the Cerrado and Pantanal domains in Brazil have affected the populations of 12 species on a regional scale (>300,000 km2). Methods differ in sampling design requirements, and their suitability will depend on the study species, scale and objectives of the study, and financial and logistical considerations, which should be evaluated to use funds, time and effort efficiently. In the case study, detection of all species was influenced by time of day, with effects that follow expectations based on foraging and flying behavior. Closed vegetation on and carcasses found during surveys also influenced detection of some species. Abundance of most species was negatively influenced by conversion of natural Cerrado and Pantanal habitats to anthropogenic uses, particularly pastures, soybean and sugar cane plantations, even for generalist species usually considered poor habitat-quality indicators. Protection of the remaining natural habitats is essential to prevent further decline of raptor populations in the study area, especially in the Cerrado domain

A urbanização e a expansão das fronteiras agrícolas na região Neotropical estão entre as principais forças causadoras da degradação ambiental em hábitats abertos naturais. Inferências e estimativas de abundância são críticas para quantificação de dinâmicas populacionais e impactos de mudanças ambientais. Contudo, a detecção imperfeita e outros fenômenos que causam inflação de zeros podem induzir erros de estimativas e dificultar a identificação de padrões ecológicos. Examinamos como a consideração desses fenômenos em dados de contagens de indivíduos não marcados pode informar na escolha do método apropriado para estimativas populacionais. Revisamos métodos estabelecidos (modelos lineares generalizados [GLMs] e amostragem de distância [distance sampling]) e emergentes que usam modelos hierárquicos baseados em misturas (N-mixture; modelo de Royle-Nichols [RN], e N-mixture básico, zero inflacionado, espacialmente explicito, visita única, e multiespécies) para estimar a abundância de populações não marcadas. Como estudo de caso, aplicamos o método N-mixture baseado em visitas únicas para modelar dados de contagens de aves de rapina em estradas e investigar como transformações de habitat no Cerrado e Pantanal do Mato Grosso do Sul afetaram as populações de 12 espécies em uma escala regional (>300.000 km2). Os métodos diferem nos pré-requisitos de desenho amostral, e a sua adequabilidade depender da espécie em questão, da escala e objetivos do estudo, e considerações financeiras e logísticas, que devem ser avaliados para que verbas, tempo e esforço sejam utilizados com eficiência. No estudo de caso, a detecção de todas as espécies foi influenciada pela horário de amostragem, com efeitos congruentes com expectativas baseadas no comportamentos de forregeamento e de voo. A vegetação fechada e carcaças também influenciaram a detecção de algumas espécies. A abundância da maioria das espécies foi negativamente influenciada pela conversão de habitats naturais para antrópicos, particularmente pastagens e plantações de soja e cana-de-açúcar, até mesmo para espécies generalistas consideradas como indicadores ruins da qualidade de hábitats. A proteção dos hábitats naturais remanescentes é essencial para prevenir um declínio ainda maior das populações de aves de rapina na área de estudo, especialmente no domínio do Cerrado / Urbanization and the expansion of agricultural frontiers are among the main forces driving the degradation of natural habitats in Neotropical open habitats. Inference and estimates of abundance are critical for quantifying population dynamics and the impacts of environmental change. Yet imperfect detection and other phenomena that cause zero inflation can induce estimation error and obscure ecological patterns. We examine how detection error and zero-inflation in count data of unmarked individuals inform the choice of analytical method for estimating population size. We review established (GLMs and distance sampling) and emerging methods that use N-mixture models (Royle-Nichols model, and basic, zero-inflated, temporary emigration, beta-binomial, generalized open-population, spatially explicit, single-visit and multispecies) to estimate abundance of unmarked populations. As a case study, we employed a single visit N-mixture approach to model roadside raptor count data and investigate how land-use transformations in the Cerrado and Pantanal domains in Brazil have affected the populations of 12 species on a regional scale (>300,000 km2). Methods differ in sampling design requirements, and their suitability will depend on the study species, scale and objectives of the study, and financial and logistical considerations, which should be evaluated to use funds, time and effort efficiently. In the case study, detection of all species was influenced by time of day, with effects that follow expectations based on foraging and flying behavior. Closed vegetation on and carcasses found during surveys also influenced detection of some species. Abundance of most species was negatively influenced by conversion of natural Cerrado and Pantanal habitats to anthropogenic uses, particularly pastures, soybean and sugar cane plantations, even for generalist species usually considered poor habitat-quality indicators. Protection of the remaining natural habitats is essential to prevent further decline of raptor populations in the study area, especially in the Cerrado domain

The area of land farmed in Africa is predicted to double by the year 2050 yet very few African studies have investigated the impact of different farming intensities and regimes on bird communities. This study examined avian species richness and diversity along with the densities of some common bird species on the Jos Plateau, Nigeria, in relation to habitat features on farmland over a gradient of differing farming intensities. The study area exhibited a variety of different levels of farming which differed in the habitat available for birds. Birds normally associated with savanna woodland were more associated with less intensive farming, and open-country birds were more associated with more intensive sites, with more species of birds observed where farming was less intensive. Common species of birds using cultivated land associated with different crops, with acha and millet being the most commonly used. Tree density was the most important variable predicting avian species richness and diversity, with medium tree density predicting the highest species richness and diversity. The densities of two common farmland birds were predicted best by tree density, but varied in their responses to the habitat variables, with common bulbul, a savanna generalist, associating more with less intensive, wooded areas and red-cheeked cordon-bleu, an open savanna granivore, associating with medium intensity, more open farmland. Whinchats were common in open, intensively farmed areas with few trees and good herbaceous vegetation cover. The data presented indicates the importance of retaining natural features of savanna habitat in farmland in order to maintain high avian diversity on farmland. More detailed studies are needed in order to determine the mechanisms involved in the associations observed and collaborations between ecologists and social scientists will be necessary to develop effective policies to limit the impact of the intensification of agriculture in Africa on avian biodiversity.

O mutum-do-sudeste é endêmico da Mata Atlântica de baixada e foi extinto de quase toda sua distribuição original devido ao desmatamento e a caça. Hoje é listado como ameaçado e a falta de conhecimento sobre sua ecologia dificulta o manejo da espécie. Este trabalho teve como objetivo estimar a densidade populacional do mutum-do-sudeste na Reserva Natural Vale (RNV) através do método de transecção linear. Os registros feitos durante as amostragens também foram utilizados para verificar a existência de seleção de habitat por meio da comparação de áreas onde a espécie foi registrada com áreas aleatórias onde nunca obtivemos registros. A estimativa populacional obtida mostrou a existência de uma razão sexual desviada em relação aos machos que parecia estar relacionada a diferenças de comportamento entre os sexos, devido aos poucos registros de fêmeas. Para confirmar nossos resultados, utilizamos dados de armadilhas fotográficas que foram utilizadas para estudar onças na reserva. Estes dados confirmaram um número maior de machos na população, porém menos acentuado do que o encontrado nos transectos, comprovando que o comportamento discreto das fêmeas afetou nossa amostragem. Combinando os dados dos dois métodos obtivemos a estimativa de 1.6 indivíduos/Km2. As análises de seleção de habitat confirmaram a relação positiva do mutum-do-sudeste com matas altas e sub-bosque denso, e mostraram que o mutum-do-sudeste tem menor probabilidade de ocorrência em áreas com abundância de árvores mortas em pé, troncos em decomposição e serapilheira profunda. Tal influencia negativa provavelmente se deve a aspectos relacionados à sua dieta e a baixa tolerância a habitats que sofreram distúrbio. As informações contidas neste trabalho servirão de base para guiar o manejo de populações selvagens e futuros projetos de reintrodução. Além disso, estudos futuros devem considerar as diferenças de comportamento entre os sexos para que os dados sejam analisados de forma correta, evitando assim, erros que podem afetar diretamente o manejo da espécie. / The Red-billed Curassow was formerly found throughout the lowland Brazilian Atlantic Forest but is now extinct across most of its former range due to habitat loss and hunting pressure. Althought classified as globally threatened, there is still a chronic lack of information on Red-billed Curassows\' biology hindering efforts to mitigate the impacts of anthropogenic threats. We investigated population size and habitat relations of Red-billed Curassows at Vale Nature Reserve (VNR) using line transect and presence/absence method. Line transects results showed a male skewed sex ratio that appeared to be related to different behavivour between sexes as we recorded a low number of females. To evaluate any bias in the estimates of sex ratio from line transect we used data from a camera trap survey designed to monitor jaguars at the reserve. Camera trap data confirmed the existence of a male skewed sex ratio in the population but less pronounced than the one found on line transects, showing that different behavior between sexes affected our estimates. Using the sex ratio calculated with camera trap data we were able to estimate 1.6 individuals/Km2. The habitat assessment showed a positive relation of the Red-billed Curassow with taller forests and dense undergrowth. The abundance of snags, decaying log and leaf litter depth, negatively influenced Red-billed Curassows\' occurrence and appear to be related to its mainly frugivorous diet and low tolerance to habitat disturbances. Our study provides critical baseline information about an important population of Red-billed Curassows and will serve to guide management strategies and future reintroduction attempts. It also reveals that survey efforts must take into account sexual differences in behaviour to increase the reliability of modeled estimates. Failing to take these considerations into account may lead to misleading inferences from data, and impact management strategies for a seriously threatened species.

O mutum-do-sudeste é endêmico da Mata Atlântica de baixada e foi extinto de quase toda sua distribuição original devido ao desmatamento e a caça. Hoje é listado como ameaçado e a falta de conhecimento sobre sua ecologia dificulta o manejo da espécie. Este trabalho teve como objetivo estimar a densidade populacional do mutum-do-sudeste na Reserva Natural Vale (RNV) através do método de transecção linear. Os registros feitos durante as amostragens também foram utilizados para verificar a existência de seleção de habitat por meio da comparação de áreas onde a espécie foi registrada com áreas aleatórias onde nunca obtivemos registros. A estimativa populacional obtida mostrou a existência de uma razão sexual desviada em relação aos machos que parecia estar relacionada a diferenças de comportamento entre os sexos, devido aos poucos registros de fêmeas. Para confirmar nossos resultados, utilizamos dados de armadilhas fotográficas que foram utilizadas para estudar onças na reserva. Estes dados confirmaram um número maior de machos na população, porém menos acentuado do que o encontrado nos transectos, comprovando que o comportamento discreto das fêmeas afetou nossa amostragem. Combinando os dados dos dois métodos obtivemos a estimativa de 1.6 indivíduos/Km2. As análises de seleção de habitat confirmaram a relação positiva do mutum-do-sudeste com matas altas e sub-bosque denso, e mostraram que o mutum-do-sudeste tem menor probabilidade de ocorrência em áreas com abundância de árvores mortas em pé, troncos em decomposição e serapilheira profunda. Tal influencia negativa provavelmente se deve a aspectos relacionados à sua dieta e a baixa tolerância a habitats que sofreram distúrbio. As informações contidas neste trabalho servirão de base para guiar o manejo de populações selvagens e futuros projetos de reintrodução. Além disso, estudos futuros devem considerar as diferenças de comportamento entre os sexos para que os dados sejam analisados de forma correta, evitando assim, erros que podem afetar diretamente o manejo da espécie. / The Red-billed Curassow was formerly found throughout the lowland Brazilian Atlantic Forest but is now extinct across most of its former range due to habitat loss and hunting pressure. Althought classified as globally threatened, there is still a chronic lack of information on Red-billed Curassows\' biology hindering efforts to mitigate the impacts of anthropogenic threats. We investigated population size and habitat relations of Red-billed Curassows at Vale Nature Reserve (VNR) using line transect and presence/absence method. Line transects results showed a male skewed sex ratio that appeared to be related to different behavivour between sexes as we recorded a low number of females. To evaluate any bias in the estimates of sex ratio from line transect we used data from a camera trap survey designed to monitor jaguars at the reserve. Camera trap data confirmed the existence of a male skewed sex ratio in the population but less pronounced than the one found on line transects, showing that different behavior between sexes affected our estimates. Using the sex ratio calculated with camera trap data we were able to estimate 1.6 individuals/Km2. The habitat assessment showed a positive relation of the Red-billed Curassow with taller forests and dense undergrowth. The abundance of snags, decaying log and leaf litter depth, negatively influenced Red-billed Curassows\' occurrence and appear to be related to its mainly frugivorous diet and low tolerance to habitat disturbances. Our study provides critical baseline information about an important population of Red-billed Curassows and will serve to guide management strategies and future reintroduction attempts. It also reveals that survey efforts must take into account sexual differences in behaviour to increase the reliability of modeled estimates. Failing to take these considerations into account may lead to misleading inferences from data, and impact management strategies for a seriously threatened species.

No description available.