Orientador: Mauro Galetti / Resumo: As palmeiras são consideradas um recurso chave para os mamíferos terrestres tropicais. Entretanto, como as hiper-diversas guildas de frugívoros das florestas tropicais exploram recursos de palmeiras e coexistem, ainda é pouco compreendido. Neste trabalho, avaliamos como três espécies de mamíferos frugívoros terrestres, o queixada (Tayassu pecari), seu parente próximo, o cateto (Pecari tajacu) e a cutia (Dasyprocta azarae) interagem entre si e com os frutos de três espécies de palmeiras em uma floresta tropical da Mata Atlântica do Brasil. Utilizamos armadilhas fotográficas e modelos de ocupação para examinar as interações competitivas entre eles. Ao contrário de nossas expectativas, não encontramos evidências de exclusão competitiva entre esses frugívoros. Os queixadas exploraram principalmente as áreas de grande abundância da palmeira hiper-dominante Euterpe edulis, enquanto as cutias concentraram seu forrageamento em áreas com grande abundância de Syagrus oleracea e, em menor escala, Syagrus romamzoffiana. Os queixadas também responderam positivamente a Syagrus oleracea, mas apenas na ausência de cutias. Os catetos preferiram áreas de alta abundância de Syagrus romamzoffiana onde as outras duas espécies apresentaram baixa detecção ou estavam ausentes. Estes resultados sugerem que, apesar de ocuparem habitats semelhantes, estarem ativos durante as mesmas horas e compartilharem recursos de palmeiras semelhantes, as estratégias comportamentais dessas espécies permitem que elas... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Palm fruits are considered a key resource for tropical terrestrial forest-dwelling mammals. Yet, how hyper-diverse assemblies of frugivores in tropical forests exploit palm resources and coexist despite high diet overlap remains poorly understood. Here, we evaluate how three species of terrestrial frugivorous mammals, the white-lipped peccary (Tayassu pecari), their close relative the collared peccary (Pecari tajacu) and the agouti (Dasyprocta azarae), interact with each other, and with the fruits of three palm species in a tropical Atlantic Forest of Brazil. We used cameras-traps and occupancy models to examine competitive interactions amongst them. Contrary to our expectations, we found no evidence of competitive exclusion amongst these frugivores. White-lipped peccaries primarily exploited areas of large abundance of the hyper-dominant palm Euterpe edulis, whilst agoutis concentrated their foraging on areas with large abundances of Syagrus oleracea and, to a lesser extent, Syagrus romamzoffiana. White-lipped peccaries also responded positively to Syagrus oleracea, but only when agoutis were absent. Collared peccaries preferred areas of high abundance of Syagrus romamzoffiana where the other two species showed low detection or were absent. These results suggest that despite occupying similar habitats, being active during the same hours and sharing similar palm resources in an isolated forest fragment, behavioural strategies of these species allow them to coexist. / Mestre

With the ever-increasing human population, more people reside in urban areas than ever before; this is having marked effects on the landscape and in turn, wildlife. This study uses automatically triggered wildlife cameras to assess the distribution of three carnivore species (coyotes, Canis latrans; red foxes, Vulpes vulpes; and gray foxes, Urocyon cinereoargenteus) around the Pioneer Valley of Massachusetts in relation to a gradient of human development. Cameras were placed at 141 locations within the 320-km2 study area over the course of three field seasons (3,052 trap nights). Relative abundances for fourteen other species and site characteristics (e.g., elevation, forest cover type, distance to urban edge) for each camera location were determined to develop a generalized linear model for the distribution of each species across the study area. Coyote distribution was most affected by the relative abundances of their prey species and not by landscape characteristics or sympatric carnivore species. Coyotes are the top predator in the area and therefore their distribution is correlated with the relative abundances of their prey species, unlike other parts of their range where they are controlled by larger carnivores. Red and gray foxes both had negative relationships with the relative abundance of coyotes as coyotes have been shown to adversely impact fox distributions and access to resources. Both red and gray foxes were also negatively or uncorrelated with increased levels of urbanization, which is both supported and refuted by published literature and is likely system specific.

This thesis presents how deep learning can be utilized for detecting humans ina wildlife setting using image classification. Two different solutions have beenimplemented where both of them use a camera-equipped microprocessor to cap-ture the images. In one of the solutions, the deep learning model is run on themicroprocessor itself, which requires the size of the model to be as small as pos-sible. The other solution sends images from the microprocessor to a more pow-erful computer where a larger object detection model is run. Both solutions areevaluated using standard image classification metrics and compared against eachother. To adapt the models to the wildlife environment,transfer learningis usedwith training data from a similar setting that has been manually collected andannotated. The thesis describes a complete system’s implementation and results,including data transfer, parallel computing, and hardware setup. One of the contributions of this thesis is an algorithm that improves the classifi-cation performance on images where a human is far away from the camera. Thealgorithm detects motion in the images and extracts only the area where thereis movement. This is specifically important on the microprocessor, where theclassification model is too simple to handle those cases. By only applying theclassification model to this area, the task is more simple, resulting in better per-formance. In conclusion, when integrating this algorithm, a model running onthe microprocessor gives sufficient results to run as a camera trap for humans.However, test results show that this implementation is still quite underperform-ing compared to a model that is run on a more powerful computer.

La géophagie désigne l’ingestion volontaire de terre et est répandue à travers le règne animal, l’Homme inclus. Cette large distribution souligne la longue histoire évolutive du comportement et suggère que la terre ingérée confèrerait des bénéfices adaptatifs aux consommateurs. L’Homme possède une longue histoire de la géophagie. Depuis deux dizaines d’années, la géophagie chez les primates non-humains connaît un intérêt scientifique croissant. Elle a été observée chez 27% des espèces de primates reconnues actuellement. Deux hypothèses majeures expliqueraient la géophagie chez les primates :la supplémentation et la protection. Dans le premier cas, la terre ingérée procurerait des éléments essentiels que l’individu ne trouve pas dans d’autres ressources. Dans le second cas, la terre consommée protègerait son tractus gastro-intestinal contre les endoparasites et/ou contre les effets néfastes des composés secondaires contenus dans les items végétaux ingérés. Toutefois, le manque de recherches multidisciplinaires ne facilite pas la compréhension du comportement et de son rôle chez les primates. Cette thèse s’intéresse à la géophagie chez le singe laineux à queue jaune (Lagothrix flavicauda), espèce pour laquelle ce comportement n’avait pas encore été décrit. C’est un des plus grands et un des plus rares primates néo-tropicaux. Ce primate peu étudié est endémique du Pérou et en Danger Critique d’extinction. Il est arboricole et principalement frugivore. Un groupe de singes habitués à la présence de chercheurs a été suivi au site d’étude de La Esperanza, afin de dresser les premières caractéristiques de la géophagie (Chap. 4) :i) toutes les classes d’individus (âge/sexe) consomment de la terre ii) en de rares et brefs événements (15 ± 9 secondes), iii) principalement pendant la saison sèche. Les singes semblent développer des stratégies pour gérer les risques de prédation liés à la terrestrialité qu’implique la géophagie :ils sélectionnent les sites de géophagie selon des paramètres qui pourraient promouvoir leur sécurité ;ils sont plus vigilants ;ils consomment souvent de la terre ex situ, sur une haute branche. La géophagie nécessite donc acquisition de connaissances particulières et nos observations mettent en évidence que l’apprentissage débute très tôt dans la vie de l’individu, la mère jouant un rôle crucial dans le processus de transmission du comportement. Ce travail s’est aussi focalisé sur l’échantillonnage et l’analyse de la composition des terres consommées et contrôles (Chap. 5) :la terre ingérée contient plus d’argile et moins d’éléments essentiels (e.g. Ca, Mg, K, Fe), supportant davantage l’hypothèse de protection, l’argile étant connue pour ses propriétés d’adsorption et d’évacuation des toxines. Enfin, les patterns temporels de la consommation de la terre et des items végétaux ont montré que la géophagie est directement associée à l’augmentation de la consommation de feuilles pendant la saison sèche (Chap. 6). Nos résultats suggèrent que ces primates ingèrent de la terre pour se protéger des composés secondaires pouvant être plus abondants dans les feuilles en saison sèche. Cette étude souligne que des données comportementales détaillées ainsi que des recherches comprenant plusieurs axes d’investigation sont essentielles pour comprendre la façon dont les individus acquièrent les connaissances liées à une pratique si rare. / Geophagy, i.e. the deliberate ingestion of earth, is largely described across the animal kingdom, including in human and non-human primates. Its widespread distribution highlights its long evolutionary history and its widely hypothesized selective benefits. Humans have a long history of geophagy. Since two decades, scientific interest in non-human primate geophagy is growing. The behavior has been described in 27% of the known primate species. In non-human primates, two major adaptive hypotheses are proposed to explain geophagy. The supplementation one argues that earth provides micronutrients individuals cannot find in their diet. The protection one argues that earth protects the gastrointestinal tract from secondary plant compounds and/or parasites. However, multidisciplinary research is lacking to fully understand the geophagy behavior in primates.I studied the geophagy behavior in the yellow-tailed woolly monkey (Lagothrix flavicauda), for which there was no earth consumption data. This monkey is one of the largest and rarest neotropical primates but remains little studied. Yellow-tailed woolly monkeys are Critically Endangered and endemic to northern Peru. They are arboreal and have a primarily frugivorous diet. Their simple gastro-intestinal tract makes digestion of cell walls and secondary plant compounds difficult.One habituated group of yellow-tailed woolly monkeys was studied at La Esperanza study site, allowing to provide the first descriptions of (Chap. 4) i) individuals of all age/sex classes consumed earth ii) in rare and very brief events (15 ± 9 seconds), and iii) mainly occurring during dry seasons. We also examined how these arboreal primates deal with the higher predation pressure linked to this terrestrial behavior: yellow-tailed wooly monkeys selected sites according to some parameters that may ensure their safety; they showed increased vigilance; and they often consumed earth ex situ, on a branch. Geophagy therefore requires the acquisition of specific knowledge and our observations show that learning begins very early in the individual's life, the mother playing a crucial role in the behavior transmission process. This research also focused on sampling and analyzing the composition of consumed and control earths (Chap. 5): earth consumed was richer in clay and poorer in micronutrients (e.g. Ca, Mg, K, Fe), better supporting the protection hypothesis, as clay is known to adsorb and evacuate toxins. Finally, temporal patterns of earth and vegetal items consumptions was also examined and showed geophagy was directly associated with the increased leaf consumption during the dry season (Chap. 6) and, through a geophagy day, earth and leaves consumption were synchronized. This study suggests that these primates eat earth to protect themselves against gastro-intestinal disorders caused by an increased ingestion of secondary compounds that might be more abundant in leaves and during the dry season. It also underlines that detailed behavioral data and multiple axed research are necessary to understand how a rare practice implying specific knowledge and aptitudes emerge in the behavioral repertoire of an individual. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20048号 / 理博第4233号 / 新制||理||1609(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 中川 尚史, 教授 沼田 英治, 教授 中務 真人 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

Predators play a critical role in regulating the structure and function of ecosystems by exhibiting top-down forces on lower trophic levels. Despite their important contributions in maintaining ecosystem health, lethal predator control remains a global wildlife management strategy to reduce predation on livestock, culturally and/or economically important species, and species at risk, as well as to reduce conflict with humans. Predator control has received criticism due in part to a paucity of rigorous research on the community-level impacts of this practice, beyond the target prey species. Specifically, there is a lack of understanding of the behavioural consequences of predator control on the wider ecological community. In this thesis, I used a multi-year camera trap dataset to evaluate how government-mandated grey wolf (Canis lupus) population reduction to conserve boreal woodland caribou (Rangifer tarandus caribou) could impact the resource selection of the carnivore community in northeast Alberta, Canada. In my second chapter, I investigated whether perceived persecution risk due to predator control may alter wolf habitat selection. I found that wolves switched from positively associating with roads before predator control to avoiding anthropogenic linear features and selecting for block features after predator control. These results suggest that lethal control may prompt wolves to prioritize local prey acquisition near block features over movement on linear features. In my third chapter, I examined whether coyote, lynx, and black bear exhibited shifts in co-occurrence with habitat features, competitors, and prey consistent with a release from top-down suppression in response to predator control. I found that predator control triggered unexpected behavioural changes among coyote and lynx consistent with a release from top-down suppression, but not among black bears. Non-apex predator response to predator control may depend on the strength of competition between the apex and non-apex predator, emphasizing the need to consider bottom-up processes when trying to understand the indirect effects of predator control. This research demonstrates that predator control can have trickle-down effects within the larger ecological community, specifically affecting how species utilize resources. As predator control continues to be a recommended wildlife management strategy, it is imperative to continue investigating its unintended consequences throughout the ecological community. / Graduate

The carnivores of Madagascar are likely the least studied of the world's carnivores, thus little is known about threats to their persistence. I provide the first long-term assessment of Madagascar's rainforest carnivore community, including: 1) how multiple forms of habitat degradation (i.e., fragmentation, exotic carnivores, human encroachment, and hunting) affect native and exotic carnivore occupancy; 2) how native and exotic carnivore temporal activity overlap and how body size and niche explain these patterns; 3) how native and exotic carnivores spatially co-occur across the landscape and which variables explain these relationships; and 4) how native and exotic carnivores and humans co-occur with lemurs across Madagascar's largest protected landscape: the Masoala-Makira landscape. From 2008 to 2013 I photographically sampled carnivores and conducted line-transect surveys of lemurs at seven study sites with varying degrees of degradation and human encroachment, including repeat surveys of two sites. As degradation increased, exotic carnivores showed increases in activity and occupancy while endemic carnivore, small mammal, and lemur occupancy and/or activity decreased. Wild/feral cats (Felis sp.) and dogs (Canis familiaris) had higher occupancy (0.37 ± SE 0.08 and 0.61 ± SE 0.07, respectively) than half of the endemic carnivore species across the landscape. Additionally, exotic carnivores had both direct and indirect negative effects on native carnivore occupancy. For example, spotted fanaloka (Fossa fossana) occupancy (0.70 ± SE 0.07) was negatively impacted by both wild/feral cat (beta = -2.65) and Indian civets (beta = -1.20). My results revealed intense pressure from hunting (ex. n = 31 fosa Cryptoprocta ferox consumed per year from 2005-2011 across four villages), including evidence that hunters target intact forest where native carnivore and lemur occupancy and/or activity are highest. I found evidence of high temporal overlap between native and exotic carnivores (ex. temporal overlap between brown-tail vontsira Salanoia concolor and dogs is 0.88), including fosa (Cryptoprocta ferox) avoiding dogs and humans across all seasons. However, I found no evidence of body size or correlates of ecological niche explaining temporal overlap among carnivores. Estimates of spatial co-occurrence among native and exotic carnivores in rainforest habitat revealed strong evidence that native and exotic carnivores occur together less often than expected and that exotic carnivores may be replacing native carnivores in forests close to human settlements. For example, falanouc show a strong increase in occupancy when dogs are absent (0.69 ± SE 0.11) compared to when they are present (0.23 ± SE 0.05). Finally, the two-species interaction occupancy models for carnivores and lemurs, revealed a higher number of interactions among species across contiguous forest where carnivore and lemur occupancy were highest. These various anthropogenic pressures and their effects on carnivore and lemur populations, particularly increases in exotic carnivores and hunting, have wide-ranging, global implications and demand effective management plans to target the influx of exotic carnivores and unsustainable hunting affecting carnivore and primate populations across Madagascar and worldwide. / Ph. D.

Madagascar is one of the world's top conservation priorities due to the intense anthropogenic pressures on its diverse and endemic wildlife. There have been very few studies conducted in the largest protected area complex in Madagascar, the Masoala-Makira landscape (northeastern Madagascar). My goal was to examine the response of ground-dwelling forest birds, tenrecs (Lipotyphla: Tenrecidae) and lemurs to habitat degradation and the presence of exotic predators, and monitor population trends at resurveyed sites from 2008 to 2013. Using camera trap surveys and distance sampling, we observed 26 bird species (n = 4,083 observations), three spiny tenrec species (n = 244 observations) and 12 lemur species (n = 1,172 observations). Out of 13 focal species (seven bird, three tenrec and three lemur species), seven had higher point estimates of occupancy or density at intact forests when compared to intermediately degraded or degraded forest sites. Common tenrecs (Tenrec ecaudatus) and cathemeral lemurs changed their activity patterns, becoming more nocturnal in degraded forests. Feral cat (Felis sp.) trap success was negatively related to the detection of three bird species (red-breasted coua, Coua serriana; scaly ground-roller, Geobiastes squamiger; and Madagascar crested ibis, Lophotibis cristata). At two resurveyed sites (S02 and S05), out of 19 and 17 species, only four and eight species did not show consistent declines in occupancy or encounter rates, respectively, over a six-year period. This research highlights the urgent need for immediate conservation action in the Masoala-Makira protected area complex in order to protect one of the world's biodiversity hotspots. / Master of Science

Noninvasive methods for monitoring wildlife species have revolutionized the way population parameters, such as population density and survival and recruitment rates, are estimated while accounting for imperfect detection using capture-recapture models. Reliable estimates of these parameters are vital information required for making sound conservation decisions; however to date, noninvasive sampling methods have been of limited use for a vast number of species which are difficult to identify to the individual level–a general requirement of capture-recapture models. Capture-recapture models that utilize partial identity information have only recently been introduced and have not been extended to most types of noninvasive sampling scenarios in a manner that uses the spatial location where noninvasive samples were collected to further inform complete identity (i.e. spatial partial identity models). Herein, I extend the recently introduced spatial partial identity models to the noninvasive methods of remote cameras for species that are difficult to identify from photographs and DNA from hair or scat samples. The ability of these novel models to improve parameter estimation and extend study design options are investigated and the methods are made accessible to applied ecologists via statistical software. This research has the potential to greatly improve wildlife conservation decisions by improving our knowledge of parameters related to population structure and dynamics that inform those decisions. Unfortunately, many species of conservation concern (e.g., Florida panthers, Andean bears) are managed without having the necessary information on population status or trends, largely a result of the cost and difficulty of studying species in decline and because of the difficulty of applying statistical models to sparse data, which can produce imprecise and biased estimates of population parameters. By leveraging partial identity information in noninvasive samples, the models I developed will improve these parameter estimates and allow noninvasive methods to be used for more species, leading to more informed conservation decisions, and a more efficient allocation of conservation resources across species and populations. / Ph. D. / Noninvasive methods for monitoring wildlife species have revolutionized the way population parameters, such as population density and survival and recruitment rates, are estimated while accounting for imperfect detection using capture-recapture models. Reliable estimates of these parameters are vital information required for making sound conservation decisions; however to date, noninvasive sampling methods have been of limited use for a vast number of species which are difficult to identify to the individual levela general requirement of capture-recapture models. Capture-recapture models that utilize partial identity information have only recently been introduced and have not been extended to most types of noninvasive sampling scenarios in a manner that uses the spatial location where noninvasive samples were collected to further inform complete identity (i.e. spatial partial identity models). Herein, I extend the recently introduced spatial partial identity models to the noninvasive methods of remote cameras for species that are difficult to identify from photographs and DNA from hair or scat samples. The ability of these novel models to improve parameter estimation and extend study design options are investigated and the methods are made accessible to applied ecologists via statistical software. This research has the potential to greatly improve wildlife conservation decisions by improving our knowledge of parameters related to population structure and dynamics that inform those decisions. Unfortunately, many species of conservation concern (e.g., Florida panthers, Andean bears) are managed without having the necessary information on population status or trends, largely a result of the cost and difficulty of studying species in decline and because of the difficulty of applying statistical models to sparse data, which can produce imprecise and biased estimates of population parameters. By leveraging partial identity information in noninvasive samples, the models I developed will improve these parameter estimates and allow noninvasive methods to be used for more species, leading to more informed conservation decisions, and a more efficient allocation of conservation resources across species and populations.

Widely applicable, quantitative field methods are needed to gather wildlife data for conservation and management initiatives in Turkey. In order to evaluate the use of camera traps in forest habitats of Turkey, we conducted a 5 phase camera trap survey by using 16 passive infrared-triggered cameras with a total sampling effort of 1200 camera trap days in Yaylacik Research Forest, a 50 km2 forest patch of Yenice Forest in Karab&uuml / k during January-May 2006. The camera trap survey confirmed the presence of grey wolf (Canis lupus), brown bear (Ursus arctos), wildcat (Felis silvestris), red fox (Vulpes vulpes), badger (Meles meles), pine marten (Martes martes), roe deer (Capreolus capreolus) and wild boar (Sus scrofa) in the study area. The camera trap survey also revealed the presence of jackal (Canis aureus) and brown hare (Lepus europaeus), whose presence were not known by people living and working in the area. Contrary to the local belief, neither camera trapping survey nor ground survey confirmed the presence of lynx (Lynx lynx) in Yaylacik Research Forest. The wolf was observed to be crepuscular and the wildcat showed a diurnal activity pattern. Wildcat seemed to avoid other carnivores spatially and temporally. Simulation studies suggested that camera trap surveys should last 14 days for wolf, 13 days for wildcat, 10 days for pine marten, and 11 days for roe deer, while it is advisable to conduct longer surveys, probably 15-20 days, for wild boar, red fox and brown bears. The estimated population size for wildcat was 9 (SE=2.28227) with 95% confidence interval of 9 to 25 in the study area. A minimum of 6 brown bears were present in the study area. Our study indicated that the local knowledge about the presence of wildlife should be considered by researchers, but it cannot replace scientific surveys conducted by field biologists. This study was the first attempt to assess the presence, relative abundance, activity patterns and diversity of multiple mammal species by the use of camera trapping methodology in Turkey. The results suggest that camera trap surveys have the potential for gathering wildlife data at larger scales in Turkey, where information gap on large mammals is an obstacle for effective management and conservation of mammals.