Invasive plant species are an increasing global threat to native biodiversity. Effective management depends on accurate predictions of their spread. However, modelling the geographic distribution of invasive species, particularly with methods like correlative species distribution models (SDMs), is challenging. SDMs operate under the assumption that species are in equilibrium with their environment (i.e., they occur in all suitable environments); this assumption is more likely to be violated for a species that is still in the process of colonizing suitable environments. SDMs also assume that environmental constraints are the most important factors determining a species' distribution. However, these assumptions are not commonly assessed, and when violated can have consequences for model reliability. I investigated SDM performance and equilibrium in the invasive Vincetoxicum rossicum vine in northeastern North America. Vincetoxicum rossicum has a long, detailed history of occurrence records in its invaded range, which enabled me to observe trends in equilibrium and model performance over a relatively long time scale. I tested the hypotheses that: 1) invasive species approach equilibrium in environmental and geographic space over time; 2) SDM performance will increase as V. rossicum approaches environmental equilibrium; and 3) range expansion in the early stages of an invasion is primarily a function of dispersal rather than environmental constraints, while the reverse is true in later stages. I found that V. rossicum has reached equilibrium in environmental space, but is still expanding its geographic range. SDM performance was poor in the first 30 years following introduction, but then improved as V. rossicum approached environmental equilibrium. SDMs were outperformed by spatial dispersal models in the earliest time period, however, the reverse was true for all subsequent time periods. Overall, these results suggest that V. rossicum’s distribution is becoming more stable and more predictable over time and that models built using the most recent data for this species, will be the most transferable across time and space. Additionally, my findings highlight the need for researchers modelling invasive species’ distributions to consider the inherent assumptions, biases, and unique features related to SDMs and SDMs of invasive species.

Projecting environmental niche models through time is a common goal when studying species response to climatic change. Species distribution models (SDMs) are commonly used to estimate a species' niche from observed patterns of occurrence and environmental predictors. However, a species niche is also shaped by non-environmental factors--including biotic interactions and dispersal barrier—truncating SDM estimates. Though truncated SDMs may accurately predict present-day species niche, projections through time are often biased by environmental condition change. Modeling niche in a phylogenetic framework leverages a clade's shared evolutionary history to pull species estimates closer towards phylogenetic conserved values and farther away from species specific biases. We propose a new Bayesian model of phylogenetic niche implemented in R. Under our model, species SDM parameters are transformed into biologically interpretable continuous parameters of environmental niche optimum, breadth, and tolerance evolving under multivariate Brownian motion random walk. Through simulation analyses, we demonstrated model accuracy and precision that improved as phylogeny size increased. We also demonstrated our model on a clade of eastern United States Plethodontid salamanders by accurately estimating species niche, even when no occurrence data is present. Our model demonstrates a novel framework where niche changes can be studied forwards and backwards through time to understand ancestral ranges, patterns of environmental specialization, and niche in data deficient species. / Master of Science / As many species face increasing pressure in a changing climate, it is crucial to understand the set of environmental conditions that shape species' ranges--known as the environmental niche--to guide conservation and land management practices. Species distribution models (SDMs) are common tools that are used to model species' environmental niche. These models treat a species' probability of occurrence as a function of environmental conditions. SDM niche estimates can predict a species' range given climate data, paleoclimate, or projections of future climate change to estimate species range shifts from the past to the future. However, SDM estimates are often biased by non-environmental factors shaping a species' range including competitive divergence or dispersal barriers. Biased SDM estimates can result in range predictions that get worse as we extrapolate beyond the observed climatic conditions. One way to overcome these biases is by leveraging the shared evolutionary history amongst related species to "fill in the gaps". Species that are more closely phylogenetically related often have more similar or "conserved" environmental niches. By estimating environmental niche over all species in a clade jointly, we can leverage niche conservatism to produce more biologically realistic estimates of niche. However, currently a methodological gap exists between SDMs estimates and macroevolutionary models, prohibiting them from being estimated jointly. We propose a novel model of evolutionary niche called PhyNE (Phylogenetic Niche Evolution), where biologically realistic environmental niches are fit across a set of species with occurrence data, while simultaneously fitting and leveraging a model of evolution across a portion of the tree of life. We evaluated model accuracy, bias, and precision through simulation analyses. Accuracy and precision increased with larger phylogeny size and effectively estimated model parameters. We then applied PhyNE to Plethodontid salamanders from Eastern North America. This ecologically-important and diverse group of lungless salamanders require cold and wet conditions and have distributions that are strongly affected by climatic conditions. Species within the family vary greatly in distribution, with some species being wide ranging generalists, while others are hyper-endemics that inhabit specific mountains in the Southern Appalachians with restricted thermal and hydric conditions. We fit PhyNE to occurrence data for these species and their associated average annual precipitation and temperature data. We identified no correlations between species environmental preference and specialization. Pattern of preference and specialization varied among Plethodontid species groups, with more aquatic species possessing a broader environmental niche, likely due to the aquatic microclimate facilitating occurrence in a wider range of conditions. We demonstrated the effectiveness of PhyNE's evolutionarily-informed estimates of environmental niche, even when species' occurrence data is limited or even absent. PhyNE establishes a proof-of-concept framework for a new class of approaches for studying niche evolution, including improved methods for estimating niche for data-deficient species, historical reconstructions, future predictions under climate change, and evaluation of niche evolutionary processes across the tree of life. Our approach establishes a framework for leveraging the rapidly growing availability of biodiversity data and molecular phylogenies to make robust eco-evolutionary predictions and assessments of species' niche and distributions in a rapidly changing world.

In this thesis, I have assessed and modelled invasion of alien plant species in the forest of the southeastern United States. There are over 380 recognized invasive plants in southeastern forests and grasslands with 53 ranked as high-to-medium risk to natural communities. I have focused on ten of these: Chinese lespedeza, tall fescue, Japanese honeysuckle, Chinese privet, autumn olive, princesstree, silktree, chinaberry, tree of heaven, tallowtree. Assessing them at differing scales, locally (Chapter 2 and 3), eco-regionally (Chapter 4 and 5) and regionally (Chapters 6 and 7), using field based measurements integrated with remotely sensed and digital datasets, and applying both parametric and non-parametric modelling approaches. Data from field based measurements as well as digitally available sources was evaluated, bringing together freely available data with time consuming, intensively collected data. Once models were developed application to assessing long term impacts was done by integrating potential climate change scenarios. At the local level Chinese lespedeza and Japanese Honeysuckle were the most prevalent, with models at the local level dominated by remotely sensed variables. At an eco-regional level Japanese honeysuckle was the most prevalent with models primarily dominated by environmental variables. At a regional level, where only trees were assessed, potential distributions of the invasive species ranged from 12 to 33 percent of the southeastern forests under current conditions with this dramatically increasing for chinaberry and tallowtree under most climate change scenarios, up as high as 66 percent of southeastern forest sites. In this thesis information on anthropogenic factors added some value to the models, however it was rarely dominant. Roads and land use (proportion of forest or distance to forest) were the most useful anthropogenic variables. In all models evaluated, only six times did any one anthropogenic variable represent more than 25 percent of the models, four of these were at the local scale. At the regional and eco-regional level, roads had a greater than 25 percent contribution to the silktree models, at a local level, distance to forest and distance roads contributed more than 25 percent to three of the species evaluated, sawtooth oak, Japanese honeysuckle and privet. Human activities have the most influence on invasion progression through dispersal (movement and introduction rate) and disturbance of the landscape (increased resource availability). Anthropogenic variables such as roads are likely to be a mechanism of spread, thus the more a model is driven by anthropogenic variables, the more likely the invasive plant is to be in the early stages of invasion process. Thus our results suggest that many of these species have moved through the first stages of invasion. Environmental characteristics play an important role in determining a site’s vulnerability to invasion. At an eco-region and regional scale, environmental characteristics dominated (>50%) all but one model (silktree at the regional scale). At the eco-region level elevation was the dominant variable, and at a regional level minimum temperature was the dominant variable. These have some correlation, with higher elevation often relating to lower temperatures, particularly at a smaller scale. This confirms the validity of matching the climate ranges of native species with the range of potential invasion, and the approach of integrating elevation, latitude and longitude to estimate potential distribution. It also suggests that climate change will influence the distribution and that variation in climate should be integrated into models. Two different modelling approaches, logistic regression and maximum entropy, were used throughout my thesis, and applied to the same data. Agreement between different modelling types adds strength to conclusions, while disagreement can assist in asking further questions. The inclusion in the models of similar variables with the same direction of relationships gives confidence to any inference about the importance of these variables. The geographical agreement between models adds confidence to the probability of occurrence in the area. Alternatively using the same model but different datasets can give you similar information. Overall for all models created by both logistic regression and MaxEnt, the logistic regression had slightly better omission rates and the MaxEnt model had better AUC’s. Logistic regression models also often predicted larger geographical areas of occurrences when the threshold of maximum sensitivity plus specificity was used, thus the lower omission rates is related to the less stringent model that predicts a larger area. The selection of appropriate data to answer the question was shown to be fundamental in Chapter 7. When data were used outside of the area of interest it generalized the models and increased the potential for invasion significantly. There was more value in the intensive surveyed data but this was less dramatic than in using the defined areas of interest to select the data for models.

This research seeks to advance our understanding of how to make better informed species conservation decisions on a global scale and advance our understanding of how species' spatial distributions (their geographic ranges) may be respond to climate change, so we can know which areas should be set aside to ensure their present and future conservation. To understand how species' geographic ranges may change, it's important to first assess how geographic ranges are defined and measured. The quantifiable measurement of a species' geographic range, (its geographic range size), is a key criterion the International Union for the Conservation of Nature uses to determine the conservation status and prioritization of species worldwide. Thus, part one of this thesis evaluates different measures for how geographic range size is commonly quantified in the conservation community, to determine whether some range size measures are more reliable than others.Further, to evaluate how species' geographic ranges may respond to climate change, I examine the climatic factors influencing observable longitudinal range size gradients in the North American tree species range maps from E.L. Little's Atlas of North American Trees.

The Arctic areas are warming more rapidly than other parts of the world. Increasing temperatures are predicted to result in shrubification, higher productivity, declining species diversity and new species invasions to the tundra. Changes in species diversity and plant community composition are likely to alter ecosystem functions with potential consequences for human population also at lower latitudes. Thus, in order to better predict the effects of the rapid arctic warming, we need knowledge on how plant communities respond to a warmer climate. Here, I investigate the effects of climate warming on tundra plant communities and focus on the role of mammalian herbivores in mediating these responses. I examined the role of herbivores by incorporating herbivore manipulations to short- and long-term warming experiments as well as along altitudinal gradients. I measured how individual plants and plant communities respond to warming with and without herbivores. Results of my PhD Thesis illustrate several ways how herbivores modify the responses of plants to warming. I found that herbivores (reindeer, hare, voles, lemmings) may prevent lowland forbs from invading open tundra.  Herbivores might also protect small tundra forbs from being outcompeted by taller and denser vegetation under climate warming. Thus, different herbivore pressures may lead to differing plant abundances and distribution shifts in different areas. Furthermore, my results show that high herbivore pressure can reverse the effects of long-term climate warming very rapidly, even in one year. This finding suggests that well-planned targeted reindeer grazing episodes could potentially be used as a conservation tool to keep selected tundra habitats open. Sudden cessation of grazing may initiate rapid changes in plant community, especially if it coincides with warm temperatures. Taken together, I show that herbivores counteract the effects of climate warming by slowing down or preventing vegetation changes in tundra. Therefore, it is important to consider mammalian herbivores when predicting tundra plant community responses to changing climate.

Studies of the occurrence of montane and boreomontane species in ravines of the sandstone landscape are scarce and the occurrence of these species are explained by the presence of temperature inversion. The question is, which factors limit the occurrence ofthese species in ravines with temperature inversion. The aim of this diploma thesis is to reveal factors that influence the occurrence of Huperzia selago in inverse ravines of sandstone landscape. This work uses a habitat variables recorded directly for populations of H. selago and variables derived from a digital elevation model. These derived variables are also used for creation of two predictive models of geographic distribution of H. selago in the National Park Bohemian Switzerland. When we summarize the most informative variables of predictive models and habitat conditions significantly different from control sites, we get the typical habitat of H. selago. Such sites will likely be found on the rock at the bottom of the valley. Factors that influence the suitability of habitat are: moisture, vegetation type, slope, and distance to the bottom of the valley.

<p>Antillean manatees (Trichechus manatus manatus) were heavily hunted in the past throughout the Wider Caribbean Region (WCR), and are currently listed as endangered on the IUCN Red List of Threatened Species. In most WCR countries, including Haiti and the Dominican Republic, remaining manatee populations are believed to be small and declining, but current information is needed on their status, distribution, and local threats to the species.</p><p>To assess the past and current distribution and conservation status of the Antillean manatee in Hispaniola, I conducted a systematic review of documentary archives dating from the pre-Columbian era to 2013. I then surveyed more than 670 artisanal fishers from Haiti and the Dominican Republic in 2013-2014 using a standardized questionnaire. Finally, to identify important areas for manatees in the Dominican Republic, I developed a country-wide ensemble model of manatee distribution, and compared modeled hotspots with those identified by fishers.</p><p>Manatees were historically abundant in Hispaniola, but were hunted for their meat and became relatively rare by the end of the 19th century. The use of manatee body parts diversified with time to include their oil, skin, and bones. Traditional uses for folk medicine and handcrafts persist today in coastal communities in the Dominican Republic. Most threats to Antillean manatees in Hispaniola are anthropogenic in nature, and most mortality is caused by fisheries. I estimated a minimum island-wide annual mortality of approximately 20 animals. To understand the impact of this level of mortality, and to provide a baseline for measuring the success of future conservation actions, the Dominican Republic and Haiti should work together to obtain a reliable estimate of the current population size of manatees in Hispaniola.</p><p> </p><p>In Haiti, the survey of fishers showed a wider distribution range of the species than suggested by the documentary archive review: fishers reported recent manatee sightings in seven of nine coastal departments, and three manatee hotspot areas were identified in the north, central, and south coasts. Thus, the contracted manatee distribution range suggested by the documentary archive review likely reflects a lack of research in Haiti. Both the review and the interviews agreed that manatees no longer occupy freshwater habitats in the country. In general, more dedicated manatee studies are needed in Haiti, employing aerial, land, or boat surveys. </p><p>In the Dominican Republic, the documentary archive review and the survey of fishers showed that manatees still occur throughout the country, and occasionally occupy freshwater habitats. Monte Cristi province in the north coast, and Barahona province in the south coast, were identified as focal areas. Sighting reports of manatees decreased from Monte Cristi eastwards to the adjacent province in the Dominican Republic, and westwards into Haiti. Along the north coast of Haiti, the number of manatee sighting and capture reports decreased with increasing distance to Monte Cristi province. There was good agreement among the modeled manatee hotspots, hotspots identified by fishers, and hotspots identified during previous dedicated manatee studies. The concordance of these results suggests that the distribution and patterns of habitat use of manatees in the Dominican Republic have not changed dramatically in over 30 years, and that the remaining manatees exhibit some degree of site fidelity. The ensemble modeling approach used in the present study produced accurate and detailed maps of manatee distribution with minimum data requirements. This modeling strategy is replicable and readily transferable to other countries in the Caribbean or elsewhere with limited data on a species of interest.</p><p>The intrinsic value of manatees was stronger for artisanal fishers in the Dominican Republic than in Haiti, and most Dominican fishers showed a positive attitude towards manatee conservation. The Dominican Republic is an upper middle income country with a high Human Development Index. It possesses a legal framework that specifically protects manatees, and has a greater number of marine protected areas, more dedicated manatee studies, and more manatee education and awareness campaigns than Haiti. The constant presence of manatees in specific coastal segments of the Dominican Republic, the perceived decline in the number of manatee captures, and a more conservation-minded public, offer hope for manatee conservation, as non-consumptive uses of manatees become more popular. I recommend a series of conservation actions in the Dominican Republic, including: reducing risks to manatees from harmful fishing gear and watercraft at confirmed manatee hotspots; providing alternative economic alternatives for displaced fishers, and developing responsible ecotourism ventures for manatee watching; improving law enforcement to reduce fisheries-related manatee deaths, stop the illegal trade in manatee body parts, and better protect manatee habitat; and continuing education and awareness campaigns for coastal communities near manatee hotspots. </p><p>In contrast, most fishers in Haiti continue to value manatees as a source of food and income, and showed a generally negative attitude towards manatee conservation. Haiti is a low income country with a low Human Development Index. Only a single dedicated manatee study has been conducted in Haiti, and manatees are not officially protected. Positive initiatives for manatees in Haiti include: protected areas declared in 2013 and 2014 that enclose two of the manatee hotspots identified in the present study; and local organizations that are currently working on coastal and marine environmental issues, including research and education on marine mammals. Future conservation efforts for manatees in Haiti should focus on addressing poverty and providing viable economic alternatives for coastal communities. I recommend a community partnership approach for manatee conservation, paired with education and awareness campaigns to inform coastal communities about the conservation situation of manatees in Haiti, and to help change their perceived value. Haiti should also provide legal protection for manatees and their habitat.</p> / Dissertation

A área de pesquisa denominada Informática para Biodiversidade enfrenta o desafio de suprir a demanda por tecnologia de apoio à conservação da biodiversidade. Dentre as áreas da ecologia que se beneficiam de recursos tecnológicos, a modelagem de distribuição de espécies se destaca pelo número de ferramentas e de algoritmos desenvolvidos para os pesquisadores da área. No entanto, estudos demostram que a modelagem tem se tornado mais complexa, bem como, a necessidade por melhorias da aplicação de novas técnicas e soluções computacionais. A interoperabilidade computacional para os dados de biodiversidade, que incluem os modelos gerados pelas ferramentas de modelagem, é citada pelos autores e pesquisadores da área como uma preocupação que demanda estudos, definição de melhores práticas e soluções de computação. Cada tópico que envolve a modelagem como, algoritmos, parâmetros, dados de ocorrência, camadas ambientais, ferramentas e técnicas para a elaboração de modelos, além dos padrões de metadados e perfis de aplicação, são objetos de estudo para que seja possível a interoperabilidade nesse campo de pesquisa. Este trabalho apresenta, portanto, uma estratégia computacional para apoiar a interoperabilidade entre os modelos gerados pelas ferramentas de modelagem de distribuição de espécies, através do uso de padrões de metadados e pelo desenvolvimento de um perfil de aplicação que apoie essa interoperabilidade. São apresentados dois estudos de caso com o objetivo de validar essas estratégias e uma arquitetura computacional para apoiar comunidades de desenvolvimento de ferramentas de modelagem a buscarem essa interoperabilidade entre os dados fornecidos e processados por elas. As contribuições deste trabalho envolvem a disponibilização de um perfil de aplicação voltado para a área de modelagem de distribuição de espécies, um protótipo de software para processar os modelos gerados pelas ferramentas de modelagem, o incentivo e o uso do digital objetct identification para disponibilização dos dados, além do processo de pesquisa e da validação de metodologias que foram utilizadas para se alcançarem os resultados desta pesquisa. / The research area called Informatics for Biodiversity faces the challenge of meeting the demand for technology to support biodiversity conservation. Among the areas of ecology that benefit from technological resources, the modeling of species distribution is notable for the number of tools and algorithms developed to researchers in this area. However, studies have shown that modeling has become more complex, as well as the need for improvements in the application of new techniques and computational solutions. The computational interoperability for biodiversity data, which includes models generated by modeling tools, is cited by authors and researchers in the field as a concern that demands studies, definition of best practices and computing solutions. Each topic that involves modeling such as algorithms, parameters, occurrence data, environmental layers, tools, techniques for the elaboration of models, standards of metadata and application profiles are objects of study of this dissertation. This thesis presents a computational strategy to support the interoperability between the models generated by the modeling tools of species distribution, through the use of metadata standards and the development of an application profile that supports this interoperability. Two case studies are presented with the objective of validating these strategies and we also present a computational architecture to support communities to develop of modeling tools to seek this interoperability between the data supplied and processed by them. The contributions of this work involve the provision of an application profile for the area of species distribution modeling, a software prototype to process the models generated by the modeling tools, the incentive and use of the digital objetct identification to make data available, and in addition to the process of research and validation of methodologies that were used to summarize the results of this research.

Les régions alpines sont particulièrement sensibles aux changements climatiques en cours. Ainsi, l’ouest des Alpes s’est réchauffé deux fois plus vite que l’hémisphère Nord au cours du XXème siècle. Les rythmes saisonniers des arbres, comme beaucoup d’autres organismes, sont fortement modifiés par le réchauffement climatique. La phénologie et les variations temporelles fines du climat apparaissent comme des composantes incontournables à prendre en compte pour prédire la répartition des espèces. L’objectif principal de ce travail de thèse a été de comprendre la réponse de la phénologie des espèces arborées au réchauffement climatique dans les Alpes et de développer des outils pour évaluer cette réponse dans le futur. Pour atteindre cet objectif nous avons utilisé des données phénologiques (débourrement, floraison, senescence foliaire,) pour le noisetier, le frêne, le bouleau, le mélèze et l’épicéa, issues du programme de sciences participatives Phénoclim.Nos résultats montrent que le réchauffement de l’hiver retarde la levée de la dormance des bourgeons et par conséquent les dates de débourrement et de floraison le long du gradient d’altitude. Cet effet est plus important à basse altitude. La robustesse des projections des modèles de répartition basés sur les processus dépend fortement de la robustesse des modèles phénologiques qu’ils utilisent. En comparant des modèles phénologiques présentant différents niveaux de complexité nous avons montré que les modèles basés sur les processus étaient les plus robustes particulièrement lorsque l’estimation de leurs paramètres reposait sur une estimation directe à l'aide de mesures expérimentales. Les modèles prévoient une réduction des écarts entre les dates de débourrement le long du gradient d'altitude pour toutes les espèces d'ici la fin du 21e siècle. Ceci est dû d’une part à un avancement des dates de débourrement à haute altitude et d’autre part à un retard des dates de débourrement à basse altitude. Nous avons également testé de nouvelles hypothèses sur le déterminisme environnemental de la croissance cellulaire dans les bourgeons, mais aucune des hypothèses testées n’a significativement amélioré les performances des modèles. Nous avons ensuite intégré les modèles phénologiques les plus performants que nous ayons obtenus au modèle d’aire de répartition basé sur les processus PHENOFIT. Nous avons réalisé pour la première fois avec ce modèle des simulations à haute résolution spatiale. Les projections du modèle montrent que les espèces arborées devraient se déplacer vers le haut du gradient d’altitude. Cependant, des phénomènes d’extinction locale pourraient avoir lieu dans les fonds des vallées liés à des dates de floraison trop tardives qui diminuerait le succès reproducteur des individus. Selon les espèces, la limite altitudinale supérieure serait contrôlée par le risque d'exposition au gel tardif des fleurs ou par la longueur de la saison de croissance qui détermine le temps disponible pour la maturation des fruits.L’ensemble de ces résultats nous a permis d’apporter des éléments de réponse sur la dynamique future des écosystèmes forestiers altitudes face au réchauffement climatique. Ils nous ont également permis de montrer que les données du programme Phénoclim étaient de qualité suffisante pour être utilisées dans des travaux de recherche scientifique. / Mountainous regions are particularly exposed to the ongoing climate change. Indeed, in the Western Alps the temperature increased twice faster than in the northern hemisphere during the 20th century. Trees’ annual cycle, as in many other organisms, is largely affected by climate change. Phenology and the fine temporal variations of climate appear key to predict species distribution. The main objective of this PhD thesis work was to understand the response of tree phenology to climate change in the Alps and to develop tools to evaluate this response in future conditions. It has been carried out using the phenological observations (budburst, flowering, leaf senescence) of five tree species (hazel, ash, birch, larch and spruce) of the citizen science program Phenoclim.Our results show that warmer winters slow down bud dormancy break, and consequently the budburst and flowering dates along the elevation gradient. This effect is stronger at low elevation. The robustness of process-based species distribution models depends strongly on the robustness of their process-based phenology sub-model. By comparing different phenology models differing in their level of complexity and we showed that process-based models were the most robust especially when their parameter estimates relied on forward estimation using experimental data. Models project a reduction in the phenological cline along the elevation gradient by the end of the 21th century. This is due, on one hand, to an advancement of the budburst dates at high elevation and on the other hand, to a delay of the budburst dates at low elevation. We also tested several hypotheses on the environmental determinism of bud cell growth. However, none of the hypotheses improved significantly the models’ performance. We then implemented the best phenology models we obtained in the process-based species distribution model PHENOFIT. We carried out for the first time simulations at high spatial resolution. Projections showed that species are expected to move up along the elevation gradient in response to climate change. However, local extinction events may occur in the bottom of the valleys due to late flowering dates that would decrease the reproductive success. Depending on the species, the upper altitudinal limit would be controlled by the risk of flowers’ exposure to late spring frost or to the length of growing season, which determine fruit maturation success.All of these results, allowed us to provide some answers on the future dynamics of high altitude ecosystems in the face of global climate change. They also allowed us to show that the Phenoclim data were of sufficient quality to be used to address important scientific questions.

A relação entre a paisagem e a distribuição da ocorrência e abundância das espécies no espaço é uma das questões centrais em ecologia, com importantes aplicações diretas em tempos de intenso uso da terra e mudanças climáticas por atividades humanas. Contudo, para inferirmos sobre essas relações, temos que descrever a paisagem da forma mais próxima possível de como as espécies realmente a percebem. Uma paisagem pode ser descrita em diferentes níveis hierárquicos de organização do ambiente (e.g. quantidade de um mineral no solo, número de plantas em uma parcela, área de cobertura de floresta...), e cada nível pode ser descrito em diferentes escalas (resolução e extensão de descrição). Os níveis e escalas com maior poder de previsão da ocorrência/abundância de uma espécie são chamados de nível de efeito e escala (extensão) de efeito. Nesta tese, utilizo armadilhas fotográficas e modelos hierárquicos para avaliar relações entre a paisagem e espécies de mamíferos e aves. Meus objetivos são: (1) avaliar se existe relação entre nível e extensão de efeito para prever a abundância de espécies e a área de vida ou massa das mesmas; (2) investigar características do solo que possam ser determinantes da distribuição de mamíferos e aves que consumem solo (geofagia); e (3) a partir de ralações espécie-paisagem, estimar a distribuição da densidade de uma espécie, o veado-catingueiro, para diferentes datas. Não há suporte para que a área de vida ou a massa de uma espécie sejam relevantes para o nível ou extensão em que uma paisagem deva ser descrita a fim de prever a abundância de uma espécie. Isso implica na importância de se avaliar diferentes níveis e extensões de uma paisagem quando na busca por relações espécie-paisagem. Fatores locais, como a argila ou minerais do solo, podem ser importantes para algumas espécies. Descobri que o veado-mateiro e o caititu selecionam solos para consumo com base na quantidade e tipo de argila. O caititu também seleciona solos com base na concentração de microminerais, assim como a juriti-azul, a arara-azul-grande, o mutum, o aracuã e a pomba-galega. Uma descrição da paisagem em nível de composição do solo pode ser relevante para avaliar a distribuição destas e outras espécies. Relações espécie-paisagem podem ser usadas para prever a abundância de espécies no espaço. Estimei a densidade do veado-catingueiro em 1992 (2,07 ind/km2) e em 2011 (7,31 ind/km2), para uma região de pecuária extensiva no nordeste do Pantanal onde foi criada uma reserva em 1997. A densidade desta espécie aumentou 3,5 vezes entre 1992 e 2011, com o fim da pecuária no local. Investigações multinível e multiescala de relações espécie-paisagem ainda são incipientes, embora importantes aplicações destas relações já venham sendo feitas há décadas. / The relationship between the landscape and the distribution of species’ occurrence and abundance is one of the main questions in ecology, with important applications for the current period of intense land use and climate change. However, to infer about these relationships, we have to describe the landscape as closely as possible to how species actually realize it. We can describe landscapes at different hierarchical levels of the environment (e.g. mineral amount in soil, number of plants in a plot, forest cover area…), and each level can be described at different scales (resolution and extent). The best levels and scales to predict species’ occurrence/abundance are known as level of effect and scale (extent) of effect. In this PhD thesis, I use camera traps and hierarchical models to assess relationships between the landscape and mammals or birds. My goals are: (1) to evaluate possible relationships between the level and extent of effect to predict species’ abundance and species’ home range or mass; (2) to investigate soil features important to the distribution of mammals and birds engaged on geophagy (soil consumption); and (3) from species-landscape relations, to estimate the density of a species, the Gray Brocket in space for different dates. There is no support for species’ home range or mass as relevant traits related to the level and scale that a landscape should be described in order to predict species’ abundance. This highlight the importance of evaluating different levels and scales of a landscape when searching for species-landscape relationships. Local factors such as clay or minerals may be important for some species. I found that the Red Brocket and Collared Peccary select soils for consumption based on clay amount and type. The Collared Peccary also selects soil based on the concentration of trace minerals, as well as Blue Ground-dove, Hyacinth Macaw, Bare-faced Curassow, Chaco Chachalaca, and Pale-vented Pigeon. Describing the landscape at soil composition level may be important to evaluate the distribution of these and another species. Species-landscape relationships can be used to predict the abundance of species in space at different dates. I estimated the density of the Gray Brocket in 1992 (2.07 ind/km2) and 2011 (7.31 ind/km2), in a livestock region in northeastern Brazilian Pantanal where a reserve was established in 1997. Gray Brocket density increased 3.5 times between 1992 and 2011, after livestock ban. Multi-level and multi-scale approaches to investigate species-landscape relationships are still emerging, though important applications of such relationships have been done for decades.