Global climate change is projected to impact multiple levels of biodiversity by imposing strong selection pressures on existing populations, triggering shifts in species distributions, and reorganizing entire communities. The Lower Guineo-Congolian region in central Africa, a reservoir for amphibian diversity, is predicted to be severely affected by future climate change through rising temperatures and greater variability in rainfall. Geospatial modelling can be used to assess how environmental variation shapes patterns of biological variation – from the genomic to the community level – and use these associations to predict patterns of biological change across space and time. The overall goal of this dissertation is to examine potential impacts of climate change on amphibian diversity in central Africa. Geospatial modeling is used to: 1) map the distribution of the amphibian fungal pathogen, Batrachochytrium dendrobatidis (Bd) in a biodiversity hotspot in Cameroon under current and future climate; 2) assess phenotypic and adaptive genomic variation in a widespread frog species, Phrynobatrachus auritus, in order to predict areas where populations may best adapt under climate change; 3) determine how amphibian community composition may shift with climate change and which areas may experience greatest loss of functional groups. Findings show that most Bd samples belong to a globally hypervirulent lineage. However, areas of highest predicted environmental suitability for Bd are predicted to shrink under warming temperatures. Within P. auritus, most phenotypic and genomic turnover occurred across known ecological gradients and are heavily influenced by seasonal precipitation. Current amphibian beta diversity is greatest throughout the Cameroonian highlands and forest-savanna ecotones flanking the central Congolian lowland forests. Greatest shifts in community composition under climate change are predicted to occur in coastal Cameroon and its eastern border whereas the greatest predicted loss of functional richness was in central Gabon. Overall, this dissertation shows that areas of elevated environmentally-associated phenotypic, genomic, and community turnover are associated with key ecological gradients. Regions predicted to experience high genomic mismatch, large shifts in community composition, and high loss of functional richness resulting from climate change may warrant conservation attention.

Ce travail représente une contribution originale à la méthodologie pour le développement de modèles écosystémiques ainsi qu'une première tentative d'une modélisation end-to-end (E2E) de l'écosystème du Courant de Humboldt Nord (ECHN). L'objectif principal du modèle développé dans cette thèse est de construire un outil de gestion écosystémique et d'aide à la décision; raison pour laquelle la crédibilité du modèle est essentielle, laquelle peut-être établie par confrontation aux données. En outre, le ECHN présente une grande variabilité climatique et océanographique à différentes échelles, la source principale de variation inter-annuelle étant l'interruption du cycle d'upwelling saisonnier par l'Oscillation Australe du phénomène El Niño qui a un effet direct sur la survie larvaire et le succès de recrutement des poissons. La pêche peut aussi être fortement variable, en fonction de l'abondance et de l'accessibilité des principales ressources halieutiques. Ce contexte amène deux questions méthodologiques principales que nous explorons dans cette thèse à travers le développement d'un modèle E2E qui couple le modèle OSMOSE, pour la partie haut niveau trophique, au modèle ROMS-PISCES, pour les parties hydrodynamique et biogéochimie:(i) Comment calibrer un modèle écosystémique à partir de séries temporelles de données? (ii) Comment inclure l'impact de la variabilité inter-annuelle de l'environnement et de la pêche? En premier lieu, cette thèse met en évidence plusieurs problèmes liés à la confrontation de modèles écosystémiques complexes aux données et propose une méthodologie pour une calibration séquentielle en plusieurs phases des modèles écosystémiques. Nous proposons deux critères pour classer les paramètres d'un modèle: la dépendance au modèle et la variabilité temporelle des paramètres. A partir de ces critères, et en tenant compte de l'existence d'estimations initiales, on énonce des règles qui permettent de déterminer quels paramètres doivent être estimés, et dans quel ordre, dans le processus de calibration séquentiel. De plus, un nouvel Algorithme Évolutionnaire, conçu pour la calibration de modèles stochastiques et optimisé pour l'estimation du maximum de vraisemblance, a été développé et utilisé pour la calibration du modèle OSMOSE avec des séries temporelles de données.La variabilité environnementale est explicite dans le modèle: le modèle ROMS-PISCES force le modèle OSMOSE et propage les effets bottom-up potentiels dans le réseau trophique à travers les interactions trophiques entre plancton et poisson d'une part, et les changements dans la distribution spatiale du poisson d'autre part. Cette dynamique spatiale des poissons est prise en compte par l'utilisation de modèles de distribution des espèces de type présence/absence, qui sont en général évalués grâce à une matrice de confusion et les indicateurs statistiques qui lui sont associés. Toutefois, quand on considère la prédiction d'un habitat au cours du temps, la variabilité de la distribution spatiale des habitats peut être résumée de manière complémentaire et validée en utilisant les patrons émergents de la forme des distributions spatiales. Nous avons modélisé l'habitat potentiel des principales espèces du ECHN en utilisant plusieurs sources d'information (pêches commerciales, campagnes scientifiques et suivi satellite des navires de pêche) conjointement aux données environnementales issues d'observations satellites et in-situ, de 1992 à 2008. L'habitat potentiel est estimé sur cette période d'étude avec une résolution mensuelle, et le modèle est validé à partir d'informations du système, en utilisant une approche pattern-oriented.Le modèle écosystémique E2E ROMS-PISCES-OSMOSE pour le ECHN est calibré en une approche par maximum de vraisemblance pour ajuster des séries temporelles mensuelles de 1992 à 2008. En conclusion,quelques applications potentielles du modèle pour la gestion des pêches sont présentées et nous discutons leurs limitations et les perspectives. / This work represents an original contribution to the methodology for ecosystem models' development as well as the first attempt of an end-to-end (E2E) model for the Northern Humboldt Current Ecosystem (NHCE). The main purpose of the developed model is to build a tool for ecosystem-based management and decision making, reason why the credibility of the model is essential, and this can be assessed through confrontation to data. Additionally, the NHCE exhibits a high climatic and oceanographic variability at several scales, the major source of interannual variability being the interruption of the upwelling seasonality by the El Nino Southern Oscillation, which has direct effects on larval survival and fish recruitment success. Fishing activity can also be highly variable, depending on the abundance and accessibility of the main fishery resources. This context brings the two main methodological questions addressed in this thesis, through the development of an end-to-end model coupling the high trophic level model OSMOSE to the hydrodynamics and biogeochemical model ROMS-PISCES: i) how to calibrate ecosystem models using time series data and ii) how to incorporate the impact of the interannual variability of the environment and fishing.First, this thesis highlights some issues related to the confrontation of complex ecosystem models to data and proposes a methodology for a sequential multi-phases calibration of ecosystem models. We propose two criteria to classify the parameters of a model: the model dependency and the time variability of the parameters. Then, these criteria along with the availability of approximate initial estimates are used as decision rules to determine which parameters need to be estimated, and their precedence order in the sequential calibration process. Additionally, a new Evolutionary Algorithm designed for the calibration of stochastic models (e.g Individual Based Model) and optimized for maximum likelihood estimation has been developed and applied to the calibration of the OSMOSE model to data time series.The environmental variability is explicit in the model: the ROMS-PISCES model forces the OSMOSE model and drives potential bottom-up effects up the foodweb through plankton and fish trophic interactions, as well as through changes in the spatial distribution of fish. The latter effect was taken into account using presence/absence species distribution models which are traditionally assessed through a confusion matrix and the statistical metrics associated to it. However, when considering the prediction of the habitat against time, the variability in the spatial distribution of the habitat can be summarized and validated using the emerging patterns from the shape of the spatial distributions. We modeled the potential habitat of the main species of the Humboldt Current Ecosystem using several sources of information (fisheries, scientific surveys and satellite monitoring of vessels) jointly with environmental data from remote sensing and in situ observations, from 1992 to 2008. The potential habitat was predicted over the study period with monthly resolution, and the model was validated using quantitative and qualitative information of the system using a pattern oriented approach.The final ROMS-PISCES-OSMOSE E2E ecosystem model for the NHCE was calibrated using our evolutionary algorithm and a likelihood approach to fit monthly time series data of landings, abundance indices and catch at length distributions from 1992 to 2008. To conclude, some applications of the model for fishery management are presented and their limitations and perspectives discussed.

Understanding coral disease dynamics within the heterogeneous populations in which they act is critical for predicting how the structure of reefs may change as a result of enzootic or epizootic levels of these important sources of mortality. This work focused on combining field studies and the development and testing of a spatially-explicit, individual-based epizootiological computer model with the aim of gaining a greater understanding of the dynamics and impact of white plague, a significant source of mortality on reef-building corals in the Caribbean region. Field studies focused on the incidence and distribution of all sources of coral mortality, including suspect white plague in situ, at two locations; the Florida Keys (United States of America) and Little Cayman Island (Cayman Islands, British West Indies). Results indicated that in both regions disease was the most significant source of mortality during the monitoring time periods, and that suspect white plague type II in Cayman is likely contributing to major structural changes. In Florida, observations made during a mass bleaching event indicated that a significant relationship exists between bleaching severity and disease incidence, and that mortality during the event was largely the result of disease and not bleaching. The simulation model was developed using a long-term data set from Little Cayman, and results of calibration indicated that suspect white plague type II on these reefs is transmissible between colonies within a limited field and require a yearly input from an outside source, and that host susceptibility to infection is low and likely not variable among species. Parameters describing the distribution and composition of the coral population were varied, and results indicated a significant effect of colony density, aggregation, and mean size on the impact of disease. Scenario testing of various disease management strategies indicated that should local prevention measures be developed in the future, it is they, and not treatment, that will likely be the most effective in limiting the impact of disease.

Furnas Centrais Elétricas S.A. / A ecologia de reservatórios, que são ecossistemas complexos, dinâmicos e artificiais, vem assumindo destaque no Brasil. O objetivo deste trabalho foi avaliar a viabilidade da aplicação, no reservatório de APM-Manso, de um modelo ecológico tridimensional em estudos sobre a dinâmica fitoplanctônica, simulando a variação temporal do fitoplâncton para cenários distintos de carga de nutrientes. O modelo CAEDYM foi acoplado ao ELCOM e simulação foi realizada em duas etapas: uma hidrodinâmica e outra ecológica. Escolheu-se para as simulações o período de cinco meses, a partir de 1 de setembro de 2005. Foram construídos dois cenários de simulação, o primeiro contendo os valores reais de carga de nutrientes dos principais rios contribuintes medidos em campo, e o segundo com redução na carga nutricional destes rios, simulando um possível processo de substituição de áreas florestadas por áreas de pastagem na bacia do rio Manso. A comunidade fitoplanctônica simulada apresentou rápidas respostas à disponibilidade nutricional do ambiente, e os resultados obtidos corroboraram com diversas teorias sobre as estratégias adaptativas e sobre as dinâmicas algais. Dentre as classes simuladas, Bacillariophyceae e Cryptophyceae se mostraram mais sensíveis às reduções de carga, enquanto Chrolophyceae e Cyanophyceae, apesar de terem suas biomassas reduzidas, sofreram menos com o impacto, sugerindo estarem mais adaptadas à limitação de nutrientes. Os picos chuvosos influenciaram positivamente as taxas de crescimento das Bacillariophyceae apenas no Cenário 1, uma vez que a limitação por nutrientes foi mais decisiva para esta classe no Cenário 2. Observou-se em ambas as simulações uma tendência de substituição na dominância de Cyanophyceae por Chlorophyceae. / The ecology of reservoirs has assumed prominence in Brazil. This study explored the application of a tridimensional ecological modeling on phytoplankton dynamics, in Manso reservoir, simulating the temporal variation of phytoplankton community in two different scenarios of nutrient loading. CAEDYM was coupled to ELCOM, and the simulation was conducted in two stages: one hydrodynamic and other ecological. It was chosen for the simulation the period of five months, from Septemper 1th, 2005. Were constructed two scenarios: the first containing the actual values of nutrient loading of the main river measured in field, and the second with a reduction in nutrient load, simulating a possible replacement process to grazing areas from forested areas in the Manso River basin. The simulation showed rapid responses of phytoplankton to nutritional availability, and the results obtained corroborated with several theories about phytoplankton adaptive strategies and their dynamics. Among the simulated classes, Bacillariophyceae and Cryptophyceae were more sensitive to load reduction, while Chlorophyceae and Cyanophyceae suffered less from the impact, suggesting that they are more adapted to nutrient limitation. Rain positively influenced the growth rates of Bacillariophyceae only in Scenario 1, since the limitation of nutrients was more decisive for this class in Scenario 2. It was observed in both simulations a trend of replacing the dominance of Cyanophyceae with Chlorophyceae.

Furnas Centrais Elétricas S.A. / A ecologia de reservatórios, que são ecossistemas complexos, dinâmicos e artificiais, vem assumindo destaque no Brasil. O objetivo deste trabalho foi avaliar a viabilidade da aplicação, no reservatório de APM-Manso, de um modelo ecológico tridimensional em estudos sobre a dinâmica fitoplanctônica, simulando a variação temporal do fitoplâncton para cenários distintos de carga de nutrientes. O modelo CAEDYM foi acoplado ao ELCOM e simulação foi realizada em duas etapas: uma hidrodinâmica e outra ecológica. Escolheu-se para as simulações o período de cinco meses, a partir de 1 de setembro de 2005. Foram construídos dois cenários de simulação, o primeiro contendo os valores reais de carga de nutrientes dos principais rios contribuintes medidos em campo, e o segundo com redução na carga nutricional destes rios, simulando um possível processo de substituição de áreas florestadas por áreas de pastagem na bacia do rio Manso. A comunidade fitoplanctônica simulada apresentou rápidas respostas à disponibilidade nutricional do ambiente, e os resultados obtidos corroboraram com diversas teorias sobre as estratégias adaptativas e sobre as dinâmicas algais. Dentre as classes simuladas, Bacillariophyceae e Cryptophyceae se mostraram mais sensíveis às reduções de carga, enquanto Chrolophyceae e Cyanophyceae, apesar de terem suas biomassas reduzidas, sofreram menos com o impacto, sugerindo estarem mais adaptadas à limitação de nutrientes. Os picos chuvosos influenciaram positivamente as taxas de crescimento das Bacillariophyceae apenas no Cenário 1, uma vez que a limitação por nutrientes foi mais decisiva para esta classe no Cenário 2. Observou-se em ambas as simulações uma tendência de substituição na dominância de Cyanophyceae por Chlorophyceae. / The ecology of reservoirs has assumed prominence in Brazil. This study explored the application of a tridimensional ecological modeling on phytoplankton dynamics, in Manso reservoir, simulating the temporal variation of phytoplankton community in two different scenarios of nutrient loading. CAEDYM was coupled to ELCOM, and the simulation was conducted in two stages: one hydrodynamic and other ecological. It was chosen for the simulation the period of five months, from Septemper 1th, 2005. Were constructed two scenarios: the first containing the actual values of nutrient loading of the main river measured in field, and the second with a reduction in nutrient load, simulating a possible replacement process to grazing areas from forested areas in the Manso River basin. The simulation showed rapid responses of phytoplankton to nutritional availability, and the results obtained corroborated with several theories about phytoplankton adaptive strategies and their dynamics. Among the simulated classes, Bacillariophyceae and Cryptophyceae were more sensitive to load reduction, while Chlorophyceae and Cyanophyceae suffered less from the impact, suggesting that they are more adapted to nutrient limitation. Rain positively influenced the growth rates of Bacillariophyceae only in Scenario 1, since the limitation of nutrients was more decisive for this class in Scenario 2. It was observed in both simulations a trend of replacing the dominance of Cyanophyceae with Chlorophyceae.

The biodiversity value of a wetland is linked not only to its position in the landscape relative to other wetlands, but also to its habitat characteristics. I monitored amphibian species richness among 12 small, isolated, and undisturbed wetlands (which occur on lands permitted for phosphate mining) in central Florida during the 2005 and 2006 breeding seasons. I used seven habitat and landscape variables to characterize the environments of the wetlands and generalized linear models to determine which of these variables had the greatest influence on the occurrence of seven amphibian species (Anaxyrus terrestris, Gastrophryne carolinensis, Hyla gratiosa, Lithobates capito, L. catesbeianus, L. grylio, and Pseudacris nigrita verrucosa). Significant models for each species incorporated six of the seven habitat and landscape variables: distance to permanent water (2 spp.), distance to nearest wetland (3 spp.), vegetation heterogeneity (2 spp.), hydroperiod (2 spp.), presence/absence of fish (1 sp.), and distance to canopy cover (1 sp.). I suggest that source/sink metapopulation and patchy population dynamics in a given year are affected in part by environmental variables of ephemeral wetlands as they affect individual amphibian species. I suggest that a diversity of environmental conditions among wetlands produces the greatest amphibian biodiversity in this system, and that conservation and restoration efforts should emphasize environmental heterogeneity.

No description available.

Neste trabalho realizou-se o estudo de distribuição, riqueza e conservação do gênero Davilla Vand. (Dilleniaceae) no Neotrópico. Para tal utilizou-se a modelagem de distribuição de espécies com o algoritmo Maxent. Este produz distribuição das espécies no espaço geográfico a partir de dados ambiental e de ocorrência. Foram estudadas as espécies de acordo com o bioma de ocorrência: Mata Atlântica; Cerrado; e Amazônia. Este grupo está representado no Neotrópico por 25 espécies. Para o Cerrado incluiu-se além das espécies do gênero Davilla as demais espécies da família Dilleniaceae. Os resultados indicaram que no Cerrado o grupo está representado por nove espécies de Davilla, além de Curatella americana L. e três espécies de Doliocarpus Rol., destas cinco são endêmicas (Doliocarpus elegans Eichler e 4 Davilla spp.). Para a Mata Atlântica ocorrem 12 espécies de Davilla, oito delas são endêmicas, incluindo uma espécie ameaçada de extinção. Para a Floresta Amazônica são conhecidas nove espécies, cinco delas endêmicas. Duas outras espécies são Neotropicais, portanto, compartilhadas por todos os biomas citados anteriormente. As demais espécies são de ocorrência em pelo menos dois biomas. Para estes três biomas produziu-se a distribuição e a riqueza de espécies visando comparar os resultados com as unidades de conservação, objetivando discutir questões relativas à conservação deste grupo. Os parâmetros conservacionistas como espécies raras, zonas de endemismo, zonas de alta riqueza, áreas de preservação ambiental, foram confrontados objetivando indicar áreas prioritárias para a conservação do grupo e da biodiversidade. Os resultados indicaram existir três centros de diversidade para este grupo. O principal deles está localizado na Mata Atlântica, principalmente nas florestas litorâneas do estado da Bahia. Outro centro de diversidade localiza-se na região central do Cerrado, especialmente nos estados de Goiás e Bahia. A outra área de diversidade localiza-se próximo à foz do Rio Amazonas e ao longo de seu curso. Devido ao hábito predominante das espécies serem lianas, estas são importantes componentes das florestas, das quais usamos este referencial para discutir questões relativas à conservação destes habitats, de suas espécies e da biodiversidade. As informações completas estão apresentadas nos capítulos de acordo com os respectivos biomas abordados. / In this study was realized to study the distribution, richness and conservation of the Davilla Vand. (Dilleniaceae) in the neotropics. For this purpose was used to distribution model of species with Maxent algorithm. This produces species distribution in geographic in space based on environmental and occurrence data. Species in accordance with biome of occurrence were studied: Atlantic Forest; Cerrado; and the Amazon. This group is represented by 25 species in the neotropics. For the Cerrado was included in addition to the Davilla species all species of Dilleniaceae family. The results indicated that in the Cerrado this group is represented by nine species of Davilla, and Curatella americana L. and three species of Doliocarpus Rol., to these five are endemic (Doliocarpus elegans Eichler and 4 Davilla spp.). For Atlantic Forest occur 12 Davilla species, eight of which are endemic, including an endangered species. For the Amazon are known nine species, five of these endemic. Two other neotropical species are therefore shared by all biomes mentioned above. The other species are occurring in at least two biomes. For these three biomes produced the distribution and species richness in order to compare the results with the protected areas, aiming to discuss issues relating to the conservation of this group. Conservationists parameters as rare species, areas of endemism, areas of high species richness, conservation areas, were confronted aiming indicate priority areas for conservation of biodiversity and too this group. The results indicated three centers of diversity for this group. The main one is located in the Atlantic Forest in coastal forests of Bahia. Another center of diversity is located in central region of Cerrado, especially in the states of Goias and Bahia. The other area of diversity is located near the mouth of the Amazon River and along its course. Due to the prevailing habit of the species are lianas, these are important components of forests, of which we use this framework to discuss issues relating to the conservation of these habitats, their species and biodiversity. Full details are presented in chapters according to their biomes addressed.

A abelha Bombus terrestris é um eficiente polinizador, prestando importantes serviços ecossistêmicos na Europa e adjacências, onde é nativa. Suas colônias têm sido criadas em larga escala para polinização agrícola, as quais são comercializadas internacionalmente, inclusive em países fora de sua área de ocorrência nativa. Deliberada ou acidentalmente a espécie tem sido introduzida em ambientes alóctones, em muitos casos tornando-se invasora. Quando invasora, a espécie é um potencial vetor de doenças e um competidor com outras abelhas; vários impactos têm sido relatados em áreas invadidas ao redor do mundo. Na América do Sul, a espécie foi inicialmente introduzida em ambientes naturais no Chile, mas rapidamente a invasão se espalhou; atualmente é encontrada ocupando ambientes naturais na Argentina. A elevada capacidade invasiva da espécie e a alta velocidade de sua expansão, conforme tem sido relatada por pesquisadores, levantou a possibilidade de a espécie alcançar o Brasil por meio de corredores ambientais favoráveis que se conectam com áreas já invadidas, gerando preocupações sobre potenciais impactos aos sistemas naturais e agrícolas. Esta pesquisa empregou uma abordagem interdisciplinar, integrando uma variedade de métodos analíticos oriundos de diferentes áreas da ecologia e os mais avançados recursos de sistemas de informações geográficas para detectar globalmente as áreas susceptíveis à invasão por Bombus terrestris, considerando-se também as mudanças climáticas. Para o sul da América do Sul foram identificados os corredores de invasão que poderão permitir a espécie se espalhar e alcançar Brasil a partir de locais invadidos. Para o Brasil, foram identificados os municípios mais vulneráveis à entrada da espécie, e também aqueles que estão na rota de expansão da invasão Brasil adentro. Para os municípios brasileiros, por sua vez, foram verificadas as culturas agrícolas e as espécies de Bombus nativas que a invasora poderá interagir ao longo da rota de invasão potencial; com estas informações foram apontadas áreas prioritárias, subsidiando o planejamento de monitoramento e ações de controle do processo de invasão, mas também medidas preventivas e mitigadoras de impactos ambientais e econômicos após a invasão, caso venha a ocorrer. / The bee Bombus terrestris is an efficient pollinator, providing important ecosystem services in Europe and surrounding areas, where it is a native species. Their colonies have been reared in large-scale for agricultural pollination, which are internationally traded, including for countries outside its native range. The species has been deliberately or accidentally introduced into non-native environments, becoming invasive in many cases. When invasive, the species is a potential vector of diseases and competes with other bees for resources; many impacts have been reported in invaded countries around the world. In South America, the species was introduced in natural environments of Chile at first, but the invasion was quickly spread; nowadays it is found living in natural environments of Argentina. The high invasiveness of the species and the high speed of its invasive expansion, as has been reported by researchers, raised the possibility of the species reach Brazil through suitable environmental corridors that are connected with areas already invaded, raising the concerns about potential impacts to natural and agricultural systems. An interdisciplinary approach was used in this research, composing a variety of analytical methods from different areas of ecology and applying the most advanced resources of geographic information systems to detect areas susceptible to invasion by Bombus terrestris at global scale, considering also climate change. For the southern South America, the corridors of invasion that could allow the spreading of the species and that potentially reach Brazil were identified. For Brazil, the most susceptible municipalities at the entrance of the species have been identified, and also those that are on the route of expansion inside the country. For Brazilian municipalities, crops and native species of Bombus that the invasive species can interact with along the potential invasion route were verified; with this information, priority areas were identified, supporting the planning of monitoring and control actions of the invasion process, but also preventive and mitigating measures of environmental and economic impacts after the invasion, if it eventually occurs.

This study tested the performance of classification, regression, and ordination techniques to evaluate the spatiotemporal dynamics of threats to big sagebrush ecological sites. The research was focused on invasion by annual exotic grasses and encroachment by woodlands. We sought to identify those areas that have had a persistent coverage of cheatgrass (Bromus tectorum) in big sagebrush ecological sites. We took advantage of the contrast in greenness between multi-temporal (within one year) remotely sensed vegetation indices captured in the spring and summer to find a distinct phenological signature that allowed mapping cheatgrass. We utilized support vector machines (SVM) to classify three temporal scenarios for which field data sets were available. SVM performed very well with accuracies of 70% (producer's) and 95% (user's) for the class of interest (presence of cheatgrass). This was the focus of chapter 2. In chapter 3 we report the development of vegetation continuous fields (VCF) for three years of interest 1996, 2001, and 2007 in order to detect active woodland encroachment. We prepared VCF for shrubs, trees, herbaceous vegetation, and bare ground using a suite of remotely sensed spectral reflectance, vegetation indices, and transformations. We compared the performance of multivariate regression trees (MRT) and random forests (RF) to develop the VCF multi-temporal series. RF outperformed MRT in both accuracy and ability to appropriately map the continuum of percent cover across large landscapes. We estimate that 17,570 hectares of big sagebrush lands showed encroachment by woodlands. Our goal in chapter 4 was to develop a similarity index for large rangeland landscapes. Trend assessments field sites and a long-term annual series (1984 - 2008) of remotely sensed imagery were used in conjunction with multidimensional scaling (MDS) to measure ecological distance to undesired states such as invasion by exotic annuals and encroachment by woodlands. In this chapter our units of analysis were soil-mapping units, which were predominantly composed of one ecological site (>60%). Our MDS results show that different ecological sites can be identified in the reduced MDS statistical space. The observed transitions and trajectories of mountain, Wyoming, and basin big sagebrush sites correlated well with the ecological expectation in semiarid lands. We anticipate that managers can use our protocols to update ecological site descriptions and state and transition models from a remotely sensed perspective.