Master 2 BEE specializing in Tropical Forest Ecology (EFT)

During the first semester, courses provided in the Master 2 EFT are organized around 6 teaching units (UE). In addition to the acquisition of theoretical knowledge, emphasis is placed on the acquisition of practical skills through the realization of research projects, field surveys, meetings with regional partners (Conservation tour), and the writing of scientific articles. This training program provide students with the tools they need to pursue careers in academic research (PhD) or management/conservation of tropical ecosystems. During the second semester, EFT students must complete an internship (4 to 6 months) in an organization/institute in French Guiana or abroad.

UE: Origin & Maintenance of biodiversity

Responsible: Eric Marcon

This teaching unity consists of three courses which aim to provide students with concepts and tools for understanding the origin, coexistence and maintenance of biodiversity, especially in tropical contexts.

1.1 Diversity & Distribution

This course introduces the species abundance distributions that describe biodiversity and the underlying ecological and statistical models. Measures of diversity are then discussed in detail: neutral, phylogenetic, functional diversity and their partitioning. A general theory of diversity measurement based on entropy is developed. Finally, methods for estimating biodiversity from inventory data are applied with R.

Learning outcomes: After completing the course, students should be able to 1) understand how the different theories used to explain the observed patterns of biodiversity were born, 2) understand these theories’ philosophy and mathematical foundations, to see the limits of each of them, 3) understand in which scientific context they emerged, and 4) apply these theories to explain the phenomena of spatial structuring and forest dynamics at the scale of the gene, the species and the community.

Lecturer: Eric Marcon (APT) Duration: 14h

Assessment: Written exam (individual)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo Elective: EM-GloFor

1.2 Ecological genetics

This course is an overview of the use of applied molecular tools to study ecology and evolution in tropical forest ecosystems. It reviews the basics of population genetics, gene expression analyses, and metabarcoding and how they can be used and combined to improve our understanding of the evolutionary pressures modulating biodiversity and the interactions between organisms.

Learning outcomes: After completing the course, students should be able to 1) select and appropriately apply molecular tools for the study of ecological and evolutionary issues, 2) understand and manipulate basic concepts in population genetics and 3) understand the fundamentals of metabarcoding.

Lecturer: Niklas Tysklind (INRAE) Duration: 7,5h

Assessment: Written exam (individual)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo Elective: -

1.3 Biotic interactions

Biotic interactions play a key role in the adaptation and evolution of species. These interactions are the driving force behind speciation, play a vital role in maintaining biodiversity and are a cornerstone of ecosystem functioning. They are therefore at the heart of the structure, function and dynamics of living organisms and ecosystems. The aim of this course is to enable students to acquire and consolidate their knowledge of biotic interactions.

Learning outcomes: After completing the course, students should be able to 1) handle concept of speciation and understand its evolutionary consequences, 2) analyze the diversity of biotic interactions in a given environment and 3) understand the influence of these interactions on biodiversity and ecosystem functioning.

Lecturer: Céline Leroy (IRD) Duration: 6h (+2h fieldwork)

Assessment: Written exam (individual)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo Elective: -

UE: Ecological systems modeling

Responsible: Camille Salmon

This teaching unity comprises two courses components designed to enable students to understand and manipulates well-known models (Linear and Bayesian) allowing the quantitative and statistical study of research data.

2.1 Linear models

This course introduces the fundamental properties of linear models, essential tools in ecological research. Students will learn to select appropriate models for specific questions, write model equations and assumptions, and fit models in R to interpret results. The course covers one-way and two-way ANOVA, simple and multiple regression, covariance analysis, and generalized linear models. While rooted in mathematical theory, it also includes practical exercises.

Learning outcomes: After completing the course, students should be able to 1) identifying the correct model within the generalized linear model family to answer a biological question, 2) being aware of possible confounding effects, 3) understanding precisely the different classical tests proposed, and 4) comparing factors taking into account adjustment factors.

Lecturer: Irene Calderon-Sanou (UG) Duration: 15h

Assessment: Written exam (individual)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo Elective: EM-GloFor

2.2 Bayesian models & Machine learning

This course offers a comprehensive exploration of Bayesian statistics with a focus on ecological applications, emphasizing both theoretical concepts and practical coding skills. Key topics include conjugate priors for analytical simplicity, Markov Chain Monte Carlo (MCMC) techniques for complex models, and hands-on experience coding with JAGS in the R framework. You will also explore hidden hierarchical models, which are essential for understanding latent ecological processes.

Learning outcomes: After completing the course, students should be able to 1) analyse a dataset, build, write and implement a model with Rstan, 2) interpret the results, and be aware of the limitations of these methods, 3) apply machine learning algorithms adapted to different tasks (classification, segmentation…), and 4) wisely split the data set into test, training and validation sets.

Lecturer: Lucia Clarotto (APT) Duration: 19h

Assessment: Written report (group)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo Elective: EM-GloFor

UE: Evolutionary botany & Functional ecology

Responsible: Sabrina Coste

This teaching unit is made up of three courses intended to provide students with the fundamental and required concepts, tools and practical skills in the fields of botany, plant architecture and functional and evolutionary ecology.

3.1 Archi-Bota-Systematics

Understanding how plants develop in time and space is essential for qualifying, quantifying and predicting the functioning of forest ecosystems. The aim of this course is to provide students with a solid background in plant phylogeny and taxonomy, as well as in plant architecture and phenology, so as to provide them with the skills to study the evolution and ontogeny of neotropical trees, both immediately and retrospectively.

Learning outcomes: After completing the course, students should be able to 1) manipulate the central concepts and tools of plant architecture, 2) identify the major tropical botanical families of French Guiana and 3) study plants as multidimensional systems characterized by structure-function-time relationships.

Lecturer: Camille Salmon (APT) & Romain Lehnebach (CIRAD) Duration: 20h

Assessment: Written exam (individual)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo, EM-GloFor Elective: -

3.2 Soil-plant interface

Understanding plant growth and development requires the study of the soil-plant interface, which is crucial because the soil provides the essential nutrients and water required for photosynthesis. The aim of this course is to enable students to acquire and consolidate their knowledge of the interactions between soil organisms and vegetation. The focus will be on the rhizosphere, which represents an interface between the soil, the root and the micro-organisms, where multiple exchanges take place.

Learning outcomes: After completing the course, students should be able to 1) understand the importance of soils and subsoils for ecosystems functioning, 2) explain the interactions between soil, roots and micro-organisms and 3) analyze the chemical compounds involved in these exchanges.

Lecturer: Céline Leroy (IRD) & Irene Calderon-Sanou (UG) Duration: 12h

Assessment: Written exam (individual)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo, EM-GloFor Elective: -

3.3 Plant-atmosphere interface

This course aims to explore structure-function relationships and their diversity in plants. Firstly, the course looks at the hydric functioning of plants and the regulatory mechanisms that exist in situations of hydric constraint, at the oranism and organ levels. Secondly, it looks at photosynthetic assimilation mechanisms in plants, with a focus on phytohormone (ABA) synthesis and stomatal regulation of gas exchange (especially carbon).

Learning outcomes: After completing the course, students should be able to 1) explain the hydric functioning of plants, 2) analyze the different regulatory mechanisms for water, oxygen and carbon in these organisms and 3) understand the importance of photosynthetic assimilation and hormone synthesis in plant functioning.

Lecturer: Sabrina Coste (UG) & Maguy Dulormne (UA) Duration: 12h (+4h fieldwork)

Assessment: Written exam (individual)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo, EM-GloFor Elective: -

UE: Tropical forest managment

Responsible: Stéphane Traissac

This teaching unity consists of two courses which aim to provide students with concepts and tools for understanding the dynamics, functioning, conservation and restauration of tropical forest ecosystems.

4.1 Tropical forests conservation

This course provides students with the basics of conservation in the tropics. It will therefore introduce the notions of: Ethics and policies of conservation management; Fragmentation of tropical forests and design of protected areas; and Species conservation in complex environments, the actors involved and their roles. During this course, students will meet managers of Guyanese natural areas during a 2-day field trip and will have to put into practice their learnings on a case study.

Learning outcomes: After completing the course, students should be able to 1) understand the different aspects of conservation in a complex environment, 2) know the different actors of forests managment and their roles and 3) understand the importance of forest-human interactions.

Lecturer: Stéphane Traissac (APT) Duration: 14h (+12h fieldwork)

Assessment: Oral presentation (group)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo Elective: EM-GloFor

4.2 Tropical forests dynamics

This course presents the community aspect of forest structure and dynamics in the tropics. It reviews general concepts of community ecology, measuring biodiversity, and explores major hypotheses attempting to explain large-scale vascular plant diversity patterns and tree coexistence mechanisms. The course then covers specific plant traits, interactions and abiotic mechanisms intrinsic of tropical forests and allowing the understanding of their structure and dynamics.

Learning outcomes: After completing the course, students should be able to 1) understand the dynamics of a tropical forest (recruitment, growth, mortality of trees), 2) recognize the different stages of a forest, and 3) know the means to observe and study these dynamics.

Lecturer: Stéphane Traissac (APT) & Finn Piatscheck (INRAE) Duration: 18,5h (+3h fieldwork)

Assessment: Written exam (individual)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo, EM-GloFor Elective: -

UE: Professionalization

Responsible: Sabrina Coste

5. Professionalization

This course is designed to give students the tools they need to succeed their professional insertion in the world of public and private research, associations and entrepreneurship. To this end, students meet and exchange experiences with various actors in these professional worlds, who are likely to hire them on completion of the Master's degree. The final exam is a simulated job interview based on a CV, covering letter and meeting.

Learning outcomes: After completing the course, students should be able to 1) find a job proposal suiting their academic profil, 2) write a CV and a cover letter, 2) prepare a job interview.

Lecturer: Various contributors Duration: 15h

Assessment: Written report & Oral presentation (individual)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo Elective: -

UE: Research project

Responsible: Camille Salmon

This teaching unit is made up of four courses and one defense intended to provide students with the fundamental and required concepts, tools and practical skills they need to carried out a research project, from experimental design to scientific article writing meet international standards.

6.1 Module Forêts Tropicales Humides (FR)

This module aims to give students experience of the tropics in general, and the Amazon rainforest of French Guiana in particular. The emphasis is on interdisciplinary training in forest ecology, agriculture, botany, wood science, pedology and geology. This training is based on presentations and field trips by key players in the study, conservation and management of biodiversity in French Guiana.

Learning outcomes: module FTH

Lecturer: Camille Salmon (APT) Duration: September

Assessment: Written report (group)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo Elective: -

6.2 Computer tools for ecological research

This course is an introduction to various tools useful for processing ecological data, answering scientific questions and writing articles that meet international standards. Students will first become familiar with the R software, used with the RStudio interface. Other tools will then be introduced: R Markdow, Mendeley, LateX, Git and GitHub, for writing reports, finding and managing bibliography tracking code versions.

Learning outcomes: After completing the course, students should be able to 1) use R to open a dataset, modify it, access specific parts of it, and write a new dataset, and analyze it with RStudio and link it with other tools (e.g., C++ or Git), 2) write a report with R Markdown, 3) use a software to handle the bibliography, add papers and other types of scientific reports, and add citations to it in their own reports, and 4) use a version control system to handle different versions of a project. Access and submit projects on GitHub.

Lecturer: Various contributors Duration: 16h

Assessment: Written report (group)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo, EM-GloFor Elective: -

6.3 Mathematical tools

6.3.1 Outils Mathématiques Part.1 (FR)

This course provides an introduction to mathematical tools used in scientific data analysis. The main focus is on 1) understanding and manipulating linear and differential equations and matrices, 2) coding them using programming languages such as R and Python, 3) using them to analyze ecological data statistically, and 3) interpreting their raw results.

Lecturer: Loïc Louison (UG) Duration: 6h

Assessment: Written report (group)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo Elective: -

6.3.2 Mathematical tools Part.2

This course provides an introduction to supervised and unsupervised statistical learning techniques used in data analysis. In supervised learning, you will explore methods for regression and classification, such as K-Nearest Neighbors, where models are trained using labeled data to make predictions. In unsupervised learning, the course will cover techniques like clustering (K-means and HAC), dimensionality reduction (PCA) and methods for visualizing relationships between categorical data.

Learning outcomes: After completing the course, students should be able to 1) set up of an appropriate experimentation, 2) design a sampling strategy to get a dataset that can then be used to answer a project questions, and 3) explore their data and reduce the dimension number of their data by using factorial analysis.

Lecturer: Lucia Clarotto (APT) Duration: 10h

Assessment: Written report (group)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo, EM-GloFor Elective: -

6.4 Scientific English

This course offers students, regardless of their current level, the opportunity to perfect their vocabulary, conjugation and syntax for written and spoken English. The emphasis is on writing and communicating in the context of the scientific academic world.

Learning outcomes: After the course, students will have a first experience of 1) oral presentation in English, 2) popularizing science in English and 3) scientific writing in English.

Lecturer: Timothy Chubb (CSG) Duration: 24h

Assessment: Written report & Oral presentation (group)

Compulsory: BEE-BioGET, BEE-EFT Elective: EM-Tropimundo

6.5 Defense

Students have the opportunity to publicly present their research project at a conference-format oral defense before a jury of specialists in the field.

Learning outcomes: After the defense, students will have a first experience of 1) presenting a research project orally, 2) popularizing science and 3) interacting with a jury of their peers.

Lecturer: Various contributors Duration: -

Assessment: Oral presentation (group)

Compulsory: BEE-BioGET, BEE-EFT, EM-Tropimundo Elective: -

Credits (ECTS)

n°	UE courses	BioGET/EFT	Tropimundo	GloFor
1.1	Species Diversity & Distribution	2	2	₂
1.2	Ecological genetics	1	1
1.3	Biotic interactions	1	1
2.1	Linear models	2	2	₂
2.2	Bayesian models & Machine learning	2	2	₂
3.1	Archi-Bota-Systematics	3	3	2
3.2	Soil-Plant interface	1.5	2	1.5
3.3	Plant-Atmosphere interface	1.5	2	1.5
4.1	Tropical forest conservation	2	2.5	₂
4.2	Tropical forest dynamics	2	2.5	2
5.	Professionalization	2	2
6.1	Forêts Tropicales Humides	1	1
6.2	Computer tools for ecological research	2	2	2
6.3	Mathematical tools	2	2	2
6.4	Scientific English	2
6.5	Defense	3	3
		30	30	15

GloFor students must choose 2 elective courses from a choice of 4 courses (total= 4ECTS)