Classes in the program

Mandatory classes

Theoretical foundations in ecology and evolution

The aim of this course is to integrate some of the main concepts in ecology and evolution and to develop critical reading and writing skills. To this end, the course involves 8-10 lecturers and is divided into two modules. In the first module, lecturers and students meet to introduce, review, and discuss texts on major topics in ecology and evolution, such as macroevolution; species concepts and delimitation; neutralism vs. selectionism; speciation; adaptive radiation; behavioral ecology; population ecology; community ecology, phylogeny, and biogeography; landscape ecology; conservation. In the second module, students will be asked to write an essay integrating concepts from ecology and evolution.

Methodology and scientific communication

In this course, postgraduate students will have to integrate theoretical and practical knowledge about the scientific method and its applications in “Ecology and Evolution” with special emphasis on aspects related to rational thinking and science, the formulation of questions, hypotheses and predictions, project planning, fundraising, project execution, the writing of scientific articles and abstracts, the preparation of oral presentations, and scientometrics.

Seminars in ecology and evolution

The aim of this course is to discuss the ongoing projects and results of dissertations both with lecturers and among students. During this course students will make an oral presentation of their project or dissertation in progress and they will be questioned by at least three professors of the program colleagues.

Electives

Application of molecular tools in ecology and evolution

Introduction to the different molecular markers used in the characterization of biological diversity at its different hierarchical levels, their application in the understanding of patterns and inference of evolutionary and ecological processes and in issues relating to the conservation of biodiversity. Genetic analysis - molecular and cytogenetic - of populations (quantification of genetic diversity, methods for demographic inferences and study of population structure). Molecular markers in phylogenetic and phylogeographic studies. Molecular and chromosomal characterization of species, individuals, and sexes to resolve taxonomic uncertainties, delimit species and management units, study hybridization and forensic analysis.

Historical and conceptual aspects of phylogenetic systematics

History of systematics and taxonomic approaches. phylogenetic systematics. principles and methods of phylogenetic inference. Historical, philosophical and methodological aspects of maximum parsimony, maximum likelihood and Bayesian analysis. Integrative taxonomy.

General Bioinformatics

The main objective of the course is to take students on a journey of discovery in the fascinating universe where biology and data science meet. The proposal is to enable students to understand the revolution that the biological sciences have been experiencing, driven by the application of mathematical, computational, and statistical methods. The focus is on exploring the intricate molecular dynamics of living beings, unraveling the mechanisms of species evolution, cutting-edge technologies for measuring molecular phenomena and the vast public repositories of biological data. Students will be immersed in practical learning, with an introduction to data processing techniques, essential tools for extracting relevant biological information. In addition, they will have the opportunity to analyze real examples of bioinformatics problems and solutions, deepening their understanding and developing practical skills to face real-world challenges.

Diversity, classification and evolution of Heteroptera (Insecta: Hemiptera), with emphasis on the Neotropical fauna

Introduction: diversity and general aspects of morphology. History of studies on Heteroptera in the world and in the Neotropical region. Phylogeny and classification: main hypotheses and evolutionary scenarios. Phylogeny, classification, and diversity of the major lineages (infraorders): Enicocephalomorpha, Dipsocoromorpha, Leptopodomorpha, Gerromorpha, Nepomorpha, Cimicomorpha and Pentatomomorpha. Evolution and diversity of the main families in each infraorder. Evolution of Heteroptera in the Neotropical region. Relationships between heteroptera and other organisms. Heteroptera of economic importance. Methods of collection, preparation and mounting. Recognition of families, genera, and main species. Development of a project with a theme related to the subjects covered.

Angiosperm diversity in the Atlantic Forest

The aim of this course is to provide students with theoretical knowledge about the classification and evolution of characters in the Angiosperm group and to enable them to recognize the main families of Angiosperms occurring in the Atlantic Forest. During this course, the following contents will be covered: characterization of Angiosperms; current classification of Angiosperms; characterization of relevant taxonomic groups in the Atlantic Forest; methods of collecting and processing botanical material; use of botanical identification keys; main families of Angiosperms in the Atlantic Forest.

Diversity and interaction of parasites of aquatic organisms

This course aims to study the biodiversity of parasites found infecting aquatic vertebrates, seeking to understand aspects of life cycles, coevolution, distribution, parasite impacts on host populations and parasite-host-environment interaction, both in the natural environment and in farming systems.

Divulgação científica

(1) Why communicate? (2) The importance of the target audience: medias and content; (3) The importance of storytelling (and how to do it); (4) Science journalism (lectured by Dr. Carlos Fioravanti from FAPESP Magazine); (5) Common pitfalls when getting your hands dirty; (6) Scripting science; (7) Disseminating with drawings and colors (lectured by Vanessa Sontag from Illuscientia).

Ecophysiology and animal energetics

Adaptive processes and evolution of physiological traits; physiological principles applied to the study of ecophysiology; metabolic rate and relationships with body mass; energy budget and study methods in metabolic physiology; extreme environments and relationships with metabolic capacity; seasonal changes and their influence on energy balance; effects of man-made environmental changes on the physiological performance of animals.

Behavioral ecology in vertebrates

The objective of this course is to provide the fundamentals for the study of vertebrate behavioral ecology, addressing the main concepts and theoretical aspects of the field. The course will promote a broad discussion of the most recent advances and the future of the field, as well as exploring the development of an experimental design suitable for testing hypotheses in the field or in controlled environments. The importance of natural history as a basis for studies in the field of behavioral ecology will be highlighted, considering ecological and evolutionary processes to explain the occurrence and adaptive value of observed behavioral patterns. In addition, the course aims to understand behavioral aspects in the study of individual intraspecific variation, as well as the use of behavioral patterns in interspecific comparisons.

Landscape ecology and biodiversity conservation planning

Introduction to Landscape Ecology - history, approaches, and definitions; Conceptual paradigms of Landscape Ecology - relationships between Structure-Function-Change, Pattern-Process and Space-Time scales; Methods of sampling and landscape analysis; Applications of Landscape Ecology in biodiversity conservation planning and management.

Comparative phylogeography

This course will cover different applications of phylogeography. Principles of population genetics, phylogenetics and biogeography will be explored to discuss the evolutionary processes that have shaped biodiversity at different spatial scales. In a practical way, the course will allow students to test different demographic hypotheses using simulations and the Approximate Bayesian Computation method. To this end, the course will include an introduction to the R language, population genetics statistics and the coalescent model.

Practical training for the researcher/lecturer and entry into an academic career

Dealing with pedagogical practices in Higher Education.  Critically analyze the process of training graduate students and the various activities of a research professor, from teaching, mentoring, research, fundraising, etc. Address ethical issues related to research, mentoring, the institution, and peers. Understand the selection process for entry into an academic career.

Phylogenetic inference

Background. Designing morphological and molecular phylogeny projects. Data matrix preparation. Bioinformatics principles and program installation. Morphological characters: description and coding. DNA sequences: sampling, choice of regions, alignment, data quality. Maximum Parsimony criterion. Weighting. Outgroup and character bias. Substitution models. Distance methods. Maximum Likelihood Criteria and Bayesian Inference.

Introduction to scientific computing

Operating systems. Hardware notions. Shell: command line operations. Installing and running programs. Text files and regular expressions. Spreadsheets and relational databases. Scripting. Working with remote servers. Clusters and Cloud computing. Practical classes focusing at the students' lines of research.

Introdução a linguagem R

The R programming language is a very useful tool for a variety of scientific purposes, including data organization, descriptive statistics, inferential statistics, plotting figures and graphs, and more. This course focuses on an introduction to the language, aimed at students with no previous experience with R. The course focuses on learning the basic operations and general logic of R, with the aim of providing students with a first access to R, without including statistical content (course open to students from all post-graduate programs of the Unifesp).

Biological Invasions: Processes, Impacts and Management

Introduction to the main concepts of conservation biology. Learn about the origin, processes, and ecological and socio-economic impacts of invasive species. Evaluate the cases of some invasive species in Brazil.

Principles of Planning and Data Analysis in Ecology

1. the importance of statistics in scientific research; 2. hypothesis testing and statistical inference; 3. understanding the P value; 4. the logic of classical frequentist tests; 5. the basics of experimental/sampling design; 6. simple linear models; 7. multiple linear models; 8. generalized linear models (Poisson, binomial); 9. linear mixed models.

Next Generation Sequencing Applied to Ecological and Evolutionary Studies

This theoretical course will cover various topics ranging from the experimental design of ecological and evolutionary studies using Next Generation Sequencing (NGS) data to the evolutionary analyses (phylogenetic and phylogeographic) in which these data can be applied. The different platforms currently available for obtaining NGS data will be presented, together with bioinformatics tools and programs for data processing and analysis, phylogenetic and phylogeographic analyses.

Termofisiologia dos vertebrados

From the fluidity of cell membranes to the geographical distribution of species, the biology of animals is influenced at various levels by temperature. In this course, students will explore the fundamental themes of vertebrate thermophysiology in a dynamic way. Taking a comparative and evolutionary approach, we will examine everything from physical principles to the impact of temperature on populations.