Passive acoustic monitoring has been used to investigate many aspects of marine mammal ecology, although methods to estimate absolute abundance and density using acoustic data have only been developed in recent years. The instrument configuration in an acoustic survey determines which abundance estimation methods can be used. Sparsely distributed arrays of instruments are useful because wide geographic areas can be covered. However, instrument spacing in sparse arrays is such that the same vocalisation will not be detected on multiple instruments, excluding the use of some abundance estimation methods. The aim of this thesis was to explore cetacean abundance and density estimation using novel sparse array datasets, applying existing methods where possible, or developing new approaches. The wealth of data collected by sparse arrays was demonstrated by analysing a 10-year dataset collected by the U.S. Navy's Sound Surveillance System in the north-east Atlantic. Spatial and temporal patterns of blue (Balaenoptera musculus) and fin whale (Balaenoptera physalus) vocal activity were investigated using generalised additive models. Distance sampling-based methods were applied to fin whale calls recorded by an array of Ocean Bottom Seismometers in the north-east Atlantic. Estimated call density was 993 calls/1000 km².hr⁻¹ (CV: 0.39). Animal density could not be estimated because the call rate was unknown. Further development of the call localisation method is required so the current density estimate may be biased. Furthermore, analysing a single day of data resulted in a high variance estimate. Finally, a new simulation-based method developed to estimate density from single hydrophones was applied to blue whale calls recorded in the northern Indian Ocean. Estimated call density was 3 calls/1000 km².hr⁻¹ (CV: 0.17). Again, density of whales could not be estimated as the vocalisation rate was unknown. Lack of biological knowledge poses the greatest limitation to abundance and density estimation using acoustic data.

Tous les hôtes ne contribuent pas également à la transmission de parasites. Certains individus ou espèces peuvent par exemple être davantage infectés que d'autres, une observation qui a mené à la proposition de la règle des `20/80', selon laquelle 20 % des individus seraient responsables de 80 % de la transmission. Cependant, les études qui se sont intéressées à l'hétérogénéité de la transmission se sont principalement focalisées sur les sources d'hétérogénéité intrinsèques à l'espèce ou à l'individu, telles que la susceptibilité ou l’infectivité, tandis que les facteurs extrinsèques, comme la connectivité entre espèces au sein de la communauté d'hôtes et le rôle de différents types de mouvements des hôtes ont été relativement négligés. Dans ce contexte, cette thèse aborde le rôle des causes extrinsèques de l'hétérogénéité de transmission sur la propagation d'infections dans les systèmes multi-hôtes, en utilisant notamment les systèmes tiques-oiseaux marins-microparasites comme support empirique à des approches de modélisation théorique. Quatre principales sources d'hétérogénéité dans les systèmes à transmission vectorielles ont ainsi été considérées : (i) l'hétérogénéité de l'abondance des vecteurs, de leur distribution, et l'estimation des paramètres de la dynamique de leurs populations, (ii) l'hétérogénéité de contact entre espèces de communautés multi-hôtes et multi-vecteurs, (iii) l'hétérogénéité de la propagation d'infections en raison de différents types de comportements des hôtes (avec en particulier, l'importance de considérer les mouvements de prospection entre groupes d'hôtes chez les espèces sociales) et (iv) l'hétérogénéité dans les capacités de dispersion et de transmission d'infections entre vecteurs à traits d'histoire de vie contrastés (dispersion en fonction du stade de vie). Nous soulignons d'abord l'importance potentielle d'une estimation fiable des abondances d'ectoparasites, à l'aide d'approches hiérarchiques susceptibles de prendre en compte à la fois l'hétérogénéité de leur probabilité de détection et leur distribution agrégée. Ensuite, nous utilisons une approche permettant d'étudier l'impact des caractéristiques du réseau d'interactions au sein de la communauté d'hôtes sur la transmission et le maintien d'infections. Nos résultats indiquent que la structure de la communauté mais aussi les propriétés locales des espèces modèlent l'émergence d'espèces qui contribuent disproportionnellement à la transmission de l'infection (`superspreader') et d'espèces qui contribuent disproportionnellement au maintien de l'infection (`keystone') dans les communautés d'infections multi-hôtes, multi-vecteurs. Nous avons également exploré le rôle de la contribution de différents comportement de déplacement des hôtes et des traits d'histoire de vie des vecteurs sur la propagation d'agents infectieux. Une revue de la littérature nous a permis de souligner l'importance potentielle, relativement aux autres comportements de déplacement plus communément considérés, des mouvements de prospection entre groupes d'hôtes sur le rôle dans la transmission d'infections. Les résultats d'un travail théorique nous on également permis de montrer l'importance des caractéristiques des traits d'histoire de vie des vecteurs (notamment la durée de repas sanguins) et des contraintes démographiques (effet Allee) sur le potentiel de colonisation des tiques. Cette différence de dispersion en fonction du stade est ainsi susceptible d'avoir une incidence sur la propagation d'infections à transmission vectorielle et la structure génétique des populations de tiques. Dans l'ensemble, les travaux menés ont permis de mettre en évidence l'importance de l'étudie des déterminants des hétérogénéités de transmission et leurs conséquences dans les systèmes à transmission vectorielles, pour une meilleure compréhension de l’écologie et l’évolution des interactions entre hôtes et parasites, avec des implications potentielles pour le contrôle des maladies. / Different hosts may not contribute equally to parasite transmission. For instance, some individuals or species may be more heavily infected than others, an observation that lead to the `20/80' rule, stating that in many cases 20% of individuals are responsible for 80% of the transmission. However, studies on heterogeneity in transmission have primarily focused on intrinsic factors of transmission, such as susceptibility and infectivity, while the impact of extrinsic factors, such as connectivity network among individuals or species of the host community and the role of various host movements has been relatively neglected. This thesis investigates the role of extrinsic transmission heterogeneities on the spread of infectious disease in multi-host systems, using tick-seabird-microparasite system as empirical models for theoretical investigations. Four main causes of heterogeneity in transmission of vector-borne diseases were considered : (i) heterogeneity in vector abundance, distribution, and estimation thereof (ii) heterogeneity in contact among species in a multi-host, multi-vector community, (iii) heterogeneity in infection spread caused by different host mouvement behaviors (notably the potential role of ‘prospecting’ by host individual among host groups), and (iv) heterogeneity in dispersal ability and transmission competence among vectors with different life-history traits (stage-dependent dispersal). First, we highlight the need to accurately estimate ectoparasite abundances with hierarchical modeling approaches that can take into account both heterogeneity in their detection probability and their aggregated distribution among hosts. Next, using network theory to examine the impact of community context on disease transmission and maintenance, we found that network structure (modularity, nestedness) and node-based measures (e.g., centrality) both shape the emergence of ‘super-spreader’ species (i.e., species that contribute disproportionally to disease transmission) and keystone species (i.e., species that contribute disproportionally to disease maintenance) in multi-host, multi-vector pathogens communities. Finally, we explored the contribution of host behavior and vector life-history traits to the spread of infectious agents. By reviewing the recent literature, we highlight the fact that prospecting, relative to various other types of host movement, may be of key importance to disease transmission among host groups, notably in social species. We also show how vector life history characteristics (e.g. length of bloodmeals) and demographic constraints (Allee effects) affect their colonization potential. Soft ticks, which take a single, long bloodmeal at only the larval stage, should have much lower colonization rates than hard ticks, which take a single, long bloodmeal at every life stage. These stage-dependent dispersal discrepancies may have direct consequences for the genetic structure of their populations and the spread of vector-borne infectious agents. Overall, these findings highlight the importance of studying the causes and consequences of transmission heterogeneity in multi-host, multi-vector systems. A series of potentially important sources of heterogeneity in parasite transmission are outlined, together with perspectives of empirical and theoretical studies to further explore their implications for understanding ecology and evolution of host-parasite interactions and for disease management purposes.

Estimates of animal abundance or density are fundamental quantities in ecology and conservation, but for many species such as rare, small mammals, obtaining robust estimates is problematic. In this thesis, I combine elements of two standard abundance estimation methods, capture-recapture and distance sampling, to develop a method called trapping point transects (TPT). In TPT, a "detection function", g(r) (i.e. the probability of capturing an animal, given it is r m from a trap when the trap is set) is estimated using a subset of animals whose locations are known prior to traps being set. Generalised linear models are used to estimate the detection function, and the model can be extended to include random effects to allow for heterogeneity in capture probabilities. Standard point transect methods are modified to estimate abundance. Two abundance estimators are available. The first estimator is based on the reciprocal of the expected probability of detecting an animal, ^P, where the expectation is over r; whereas the second estimator is the expectation of the reciprocal of ^P. Performance of the TPT method under various sampling efforts and underlying true detection probabilities of individuals in the population was investigated in a simulation study. When underlying probability of detection was high (g(0) = 0:88) and between-individual variation was small, survey effort could be surprisingly low (c. 510 trap nights) to yield low bias (c. 4%) in the two estimators; but under certain situations, the second estimator can be extremely biased. Uncertainty and relative bias in population estimates increased with decreasing detectability and increasing between-individual variation. Abundance of the Key Largo woodrat (Neotoma floridana smalli), an endangered rodent with a restricted geographic range, was estimated using TPT. The TPT method compared well to other viable methods (capture-recapture and spatially-explicit capture-recapture), in terms of both field practicality and cost. The TPT method may generally be useful in estimating animal abundance in trapping studies and variants of the TPT method are presented.

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