1. Mandatory Disciplines
Concetration area: Ecology
Teaching Internship (2 Credit Units, 30 Credit hours)
Syllabus: Training of PhD students in teaching and qualification of undergraduate teaching in Biological Sciences, with emphasis on the teaching-learning process. Participation monitored in theoretical and practical classes of undergraduate courses. Development of didactic material for classes in undergraduate courses. Correction of reports, exercises or tests. Guidance supervised in field activities. Application of pedagogical methods or techniques such as seminars and directed study in ecology, in undergraduate courses with content in the area of Ecology and related areas.
Scientific Writing in Ecological Research for the Doctorate (4 Credit Units, 60 Credit hours)
Syllabus: Basis of scientific writing. Knowledge of scientific method in Ecology. Scientific writing procedures for scientific projects and articles. Types of scientific production. Ethical aspects in writing. Planning of manuscript research and writing. Scientific writing: from question to discussion. Scientific Thought: from question to publication and quotation.
2. Elective Disciplines
Concentration Area: Ecology
Spatial Analysis in Macroecology: theoretical and practical (6 Credit Units, 90 Credit hours)
Syllabus: Introduction to the main methods of spatial analysis with applications in Macroecology. Practices with the main statistical methods of spatial analysis in Macroecology. Spatial patterns of biological diversity and its ecological and evolutionary mechanisms. Using the SAM program (Rangel et al. 2006-2010). Acquisition, processing and analysis of data in geographic ecology. Discussion and follow-up of student research projects.
Biology of Conservation (4 Credit Units, 60 Credit hours)
Syllabus: Biology of conservation and environmental changes related to human activities. Biological diversity. Global patterns of species loss and extinctions. Destruction of habitat. Valuation of biodiversity. Conservation at the population level. Conservation at the community level. Conservation of ecosystems. Conservation of the Amazon. Establishment of protected areas.
Experimental Design in Ecological Studies (4 Credit Units, 60 Credit hours)
Syllabus: Elaboration of experimental designs for hypothesis testing in ecological studies and experiments in ecology. Manipulation of experiments. Types of sampling. Samples, repetitions and pseudo-repetitions. Null models.
Morphological and Functional Diversity of Communities (3 Credit Units, 45 Credit hours)
Syllabus: Main concepts and principles related to morphological and functional diversity. Biological and functional attributes and their quantification. Biological diversity: concepts, scales and measures. Biological diversity in communities and environmental services. Assembly rules: environmental filters, competition, facilitation. Functional attributes: definition, importance and measurement. Functional attributes: divergence, convergence and patterns of organization in communities. Functional Groups: definition and approaches for classification. Functional diversity: definitions, components and measures. Quantification of morphological and functional diversity: applications in Platform R. Functional attributes as indicators of environmental changes: attributes-response, attributes-effect, relations between functional attributes and habitat, linear models and graphical analyses for community data, functional attributes and environmental data.
Behavioral Ecology (3 Credit Units, 45 Credit hours)
Syllabus: Brief history of the study of behavior. Techniques of observation of animal behavior in captivity and in the field. Characterization of the main concepts in Sociobiology. Group selection. Development and modification of social behavior. Individual and social learning. Altruism. Communication. Competition (aggressiveness, territoriality, systems of domination, predator-prey interactions). Sex and reproduction (sexual selection, reproductive strategies, mating systems, parental investment, parental care, parent-child conflict). Behavior and preservation. Description and experimentation in human behavioral ecology. Methods of study in behavior.
Ecology of the Amazon (3 Credit Units, 45 Credit hours)
Syllabus: (i) History of the Amazonian Geology: Shield of the Guianas and Central Brazil, emergence of the Andes, etc. (ii) Climate: - Past and current Climates, seasonal rainfall, wind and temperature, el niño and la niña, and carbon. (iii) Basins: Hydrography and hydrology, mean and seasonal flow, limnological characterization of water, etc . (iv) Pedology (v) Vegetation and Phytophysiognomy: (vi) Ecosystems and Landscapes: IBGE and WWF classification. Presentation of the environments: I - Aquatic - wetlands (floodplain, igapó, fields, mangroves, restinga, rivers, lakes, headwaters, and etc); II - Terrestrial - campina, campinarana, forests, cerrado, savanna.
Ecology of Animal Reproduction (3 Credit Units, 45 Credit hours)
Syllabus: Study of the biological characteristics and / or mechanisms and their relation with the environmental factors during the reproductive cycle of animal species from the Amazon region. Understanding the morphological components and the main processes related to the reproduction of vertebrates. Macroscopic anatomy and general morphology of male and female genitalia, with emphasis on the morphofunctional adaptations found in each group. Gametogenesis, endocrine control and reproductive cycle. Reproductive behavior, ecological aspects and associated environmental factors.
Ecology of Aquatic and Coastal Environments (4 Credit Units, 60 Credit hours)
Syllabus: Description and characterization of the main aquatic and coastal environments and their associated organisms. Physical and chemical properties of water. Analysis of the structure and productivity of aquatic ecosystems. Dynamics of oxygen and salinity of water. Biogeochemical cycles of carbon, nitrogen, phosphorus, sulfur, silica and iron. Biotic and abiotic limiting factors. Description and characterization of planktonic communities (algae, cyanobacteria, zooplankton and ichthyoplankton). Description and characterization of benthic communities (macroalgae, aquatic plants, zoobenthos). Sediment and its associated biota. Anthropogenic impacts on continental aquatic ecosystems. Management and conservation of aquatic ecosystems.
Ecology of Terrestrial Environments (4 Credit Units, 60 Credit hours)
Syllabus: Operation and structuring of terrestrial environments. Introduction of concepts and definitions related to primary production. Terrestrial vegetation and the dynamics of the carbon cycle. Introduction to the concept of biomes. Description of biomass productivity and distribution patterns. Stock and input of nutrients into the soil. Analysis of the main biogeochemical cycles in terrestrial ecosystems.
Field Ecology (6 Credit Units, 90 Credit hours)
Syllabus: Training and qualification of students for the construction of scientific hypotheses in Ecology through activities oriented in the field. Elaboration of testable scientific questions in ecology. Data collection. Result analysis. Preparation of paper reports in scientific article format and correction after evaluation. Development of theoretical and practical tools in ecology. Development and execution of scientific field work with objectivity. Oral and written presentations of the main results of field projects.
Ecology of Natural Communities (5 Credit Units, 75 Credit hours)
Syllabus: Introduction to natural communities and their development. Main concepts, standards and measures of biodiversity. The role of biological interactions, evolutionary history, by chance, and limitation of dispersion in the formation of communities. Coexistence of species, competition vs. facilitation. Models of community organization: spatial dynamics of communities. Diversity and the functioning of ecosystems. Community responses to climate change.
Ecology of Ecosystems (4 Credit Units, 60 Credit hours)
Syllabus: Description of ecosystems as energy flow diagrams. Reflections on the importance of the cycle of elements in ecosystems. Primary Production and Energy in Ecological Systems. Measures of Primary Production. Factors that determine the productivity of ecosystems. Influence of Climate, geology and geomorphology; Global Patterns in Primary Production. Structure and global distribution of Ecosystems. Definitions of various energy efficiencies. Efficiency of assimilation and efficiency of net production. Grass-based herbivorous food chains. Transformations of elements in the Ecosystem. Water cycle. Carbon Cycle. Nutrient cycling. Cycle of Nitrogen, Phosphorus and Sulfur. The role of microorganisms in the cycles of the elements. Chemistry and soil structure. Soil biotic community. Study methods and nutrient cycling. Soil microbiology with emphasis on nitrogen cycling. Mycorrhizae. Applications to soil management. The functioning of ecosystems, the types of community structure and associated species. Assessment of major human impacts on ecosystems. Managed ecosystems. Effects of global changes on ecosystems.
Landscape Ecology (6 Credit Units, 90 Credit hours)
Syllabus: History of Landscape Ecology. Concepts, principles and perceptions. Properties and landscape structure: matrix, fragments and corridors. Scales, hierarchies. Dynamics of natural processes and their anthropic relationships. Operation, transformation and management of landscapes at different scales. Metrics and models. Connectivity and fragmentation of ecosystems. Theories of island biogeography and metapopulation applied to landscape ecology. Scales Dynamics of the Landscape. Fragmentation and thresholds. Structural and functional connectivity. Conservation and landscape ecology. Applications of Landscape Ecology in environmental restoration and recovery of degraded areas. Theoretical and analytical tools in landscape ecology. Landscape structure and biological patterns.
Ecology of Parasites (4 Credit Units, 60 Credit hours)
It aims to ecologically discuss the parasite-host interaction, approaching the dynamics of parasites within host populations, as well as their role as regulators in the population dynamics of their hosts. Important aspects of the ecology, biology and control of arthropod vectors of diseases will be discussed, focusing on factors that determine their distribution and abundance, and that allow their interaction with the human being favoring the dissemination of pathogens.
Phylogenetic Ecology of Communities (3 Credit Units, 45 Credit hours)
Syllabus: Description of the fundamental concepts related to the study of phylogenetic patterns in ecological communities. Presentation of recent advances in the study of phylogenetic ecology of communities. Perspectives of theoretical and methodological advances in phylogenetic ecology of communities. Description of the main methods and discussion of the most recent analytical solutions in phylogenetic ecology of communities. Phylogenetic and functional approaches in ecology. Phylogenetic grouping and repulsion. Phylogenetic diversity. Filombeta Diversity. Phylogenetic composition. Phylogenetic patterns in metacommunities. Phylogenetic trees in ecology. Structure metrics and phylogenetic diversity. Phylogenetic structure of communities. Phylogenetic sign. Phylogenetic niche conservation.
Theoretical Ecology and Macroecology (4 Credit Units, 60 Credit hours)
Syllabus: To introduce and reveal the main known patterns of diversity and their potential causes and processes related to macroecology and macroevolution (Diversity gradients, Patterns of species richness, Macroecology basic concepts and macroecological data, Theories of geographic distribution of species; variation of abundance). Discussions about the use of macroecological knowledge in Biomonitoring, Biogeography of conservation, Spatial analyses, Design of conservation units.
Statistics Applied to Ecological Studies (8 Credit Units, 120 Credit hours)
Syllabus: Introduce basic concepts in statistics and data analysis, allowing the organization, management and description of data sets, planning and operationalization of statistical tests, and finally the interpretation of the results obtained. Main statistical techniques for collecting, arranging and processing data (information). Formulation of hypotheses. General statistics theory and Fisher randomization tests. Experimental design and pseudo-replication. Construction of database. Use of data tabulation programs and statistical analysis. Types of variables and choice of statistical tests. Chi-square T test for independent samples; T test for dependent samples. Simple ANOVA. Kruskall-Wallys. Factorial ANOVA; Correlation of Pearson and Spearman. Simple linear regression. Multiple regression. Logistic regression. Estimators of species richness. Interpretation and presentation of the results in the format of scientific articles.
Multivariate Statistics for Ecological Data (5 Credit Units, 75 Credit hours)
Syllabus: Introduction to multivariate statistics. Main Multivariate Analysis in Ecology: Analysis of Groupings (SAHN), Indicator Species Analysis, Principal Component Analysis (PCA), Principal Coordinate Analysis (PCoA), Distributed Correspondence Analysis (DCA), Non-Metric Multidimensional Scaling (NMDS), Canonical Correspondence Analysis (CCA), Mantel Test, Partial Mantel Test, Similarity Analysis (ANOSIM), Procrustes Analysis and Partial Redundancy Analysis (partial RDA). Main statistical packages for the analysis. Interpretation and discussion of results.
Structure and Dynamics of Populations (4 Credit Units, 60 Credit hours)
Syllabus: Main theoretical concepts and methods of direct application related to the ecology of populations. Population growth, population structure and dynamics, demography, life table, migration / dispersion, competition / predation and stability / chaos. Linear models of population growth: deterministic (Malthusian; Logistic), stochastic (Process of birth and death, Yule-Furry process, Chances of extinction of a population). Population growth matrix model: life table. Theoretical concepts of individual growth models. Von Bertallanffy's Growth Model. Methods for estimating population parameters: abundance (marking and recapture, transection, plot). Survival rates and mortality (life table). Growth Rates (%) Case studies. Structure of population systems and mechanisms of population functioning. Presentation of the main software available for the execution of research in population ecology.
Geotechnologies Applied to Ecology (5 Credit Units, 75 Credit hours)
Syllabus: Introduction to geotechnology: history, concepts and applications. Geotechnologies presented: remote sensing, global positioning systems, digital cartography, geographic information systems. Geodesy and geodetic reference systems. Elements of cartography. Geotechnology tools (for end users): Global Positioning System (GNSS) receivers, Geographic Information Systems. Types of spatial data. Data sources Analysis of digital geographic data. Tool 1: GNSS receivers. Tool 2: WebGIS. Tool 3: Free software for GIS: Import and data conversion; Image analysis and interpretation; Operations with maps; Creating layouts. Applications for ecology: spatial representation of ecological data; Integration of Environmental data; Ecological modelling with GIS.
Soil Impacts and Uses in the Amazon (4 Credit Units, 60 Credit hours)
Syllabus: Presentation of the main patterns of resource use in pre-Columbian civilizations in the Amazon. History of resource use and impacts of land use. Introduction to the main types of anthropic impacts in the Amazon. Patterns of diversity in anthropized environments. Current patterns of land use in the Amazon and its environmental impacts. Climate changes. Modelling of future land use impacts. Practical applications.
Insect-plant interaction (3 Credit Units, 45 Credit hours)
Syllabus: General aspects of insect-plant interactions. Antagonistic interactions (herbivory, mincing insects and gallers, chemical, physical and biotic defenses) and mutualistic (dispersive and defensive mutualism). Adaptive responses (examples of morphological, physiological and behavioral chemical co-adaptations). Case studies.
Introduction to Program R (3 Credit Units, 45 Credit hours)
Syllabus: 1) Introduction: What is R. History of R. Installing R. Using R. Scripts. Editors for the R. Packages; 2) Getting data in R: Getting started. Reading and writing data; 3) How to access variables and manipulation of data in R; 4) Functions in R and its application; 5) Cycles and Functions: Introduction to cycles. Functions; 6) Introduction to basic tools for graphics: plot function. Symbols, colors and size of characters; 7) Graphic Tools: Pie Chart, Bar Chart, Strip Chart, Boxplot, Cleveland dotplots, plot, pairplot, coplot; 8) Introduction to the Lattice package (high-level graphical functions); 9) Common errors in R (problems importing data, use of attach function, etc.); 10) Other useful tools for Ecologists; 11) Data transformations. 12) Simple univariate analyses (t-test, ANOVA); 13) Correlations (Spearman, Pearson); 14) Simple and multiple regression; 15) species richness estimators.
Management and Sustainable Development in Amazonian Ecosystems (4 Credit Units, 60 Credit hours)
Syllabus: Management and conservation in Amazon basin micro-basin systems. Environmentally correct raw materials technologies. Sustainable development. AGENDA 21 Production and consumption. Sustainability economics: principles, challenges and applications. Socio-environmental performance indicators. New challenges for humanity in the 21st century.
Species Distribution Modelling (4 Credit Units, 60 Credit hours)
Syllabus: Introduction to the main ecological theories involving the modelling of potential species distribution. Ecological niche. BAM diagrams. The importance of databases. Climatic databases. Partitioning of occurrence data. Calibration of models. Cutting thresholds. Methods of evaluating distributions. Ensembles and uncertainties inherent in predictions. Major packages of algorithms niches and software available. Making maps and layouts. Results presentation. Discussions regarding the state of the art of potential species distribution modelling. Case studies and main applications.
Special Topics in Ecology I: Assessment of the physical integrity of aquatic environments (3 Credit Units, 45 Credit hours)
Special Topics in Ecology II: Thematic Seminars in Ecology (1 credit unit, 15 Credit hours)
Special Topics in Ecology III: Use of stable isotopes in ecological studies (4 Credit Units, 60 Credit hours)
Special Topics in Ecology IV: Applied Statistics (4 Credit Units, 60 Credit hours)
Special Topics in Ecology V: Applied Ecology of Pollination (2 Credit Units, 30 Credit hours)
Special Topics in Ecology VI: Ecology and Biodiversity (1 credit unit, 15 Credit hours)
Special Topics in Ecology VII: Ecology and Biodiversity (2 Credit Units, 30 Credit hours)
Special Topics in Ecology VIII: Ecological niche modelling (2 Credit Units, 30 Credit hours)
Special Topics in Ecology IX: Landscape genetics (2 Credit Units, 30 Credit hours)