Plant Biodiversity and Tropical Ecosystem Management (BioGET)

General linear models with one or more random explanatory variables: from translating the figure that answers the biological question to the statistical model, i.e., taking into account numerous effects and knowing how to interpret them.

General properties viewed through regression and one-factor ANOVA (R2, F, ddl, least squares, likelihood, diagnosis, validation, goodness of fit, interpretation of effect sizes); nested and crossed factor ANOVA, multiple regression (concept of parameters and effects, and interaction)

incorporation of the dependence of explanatory random variables, confounding effects (quantitative for multiple regression, and unbalanced designs for ANOVAs)

See the full page

See the full page

Generalized linear mixed models + methodology and experimental protocols to account for biological reality: non-normal distribution and pseudo-replication

Protocol optimization, power, and uncontrolled type I risk: variable transformation, polynomial regression, link function, likelihood, model selection

Deviance and goodness-of-fit analysis

Incorporation of blocks, repeated measurements over time, consideration of spatial and temporal correlation, over-dispersion

Graphical representation of predictions.

See the full page

The objective of this course unit is to provide the necessary statistical foundations for following the more advanced modules in the curriculum; it is therefore a general refresher course. Descriptive statistics are reviewed (quantiles, cumulative frequency polygons, sample estimators), simple tests are presented, essential graphs for univariate and multivariate data are presented, and the general principle of a statistical test, hypothesis testing, the concept of p-value, and Type I and Type II errors are presented. In practical work, students are also brought up to speed in the R environment.

See the full page

The overall objective is to consolidate the foundations in ecology acquired by students and to give them the tools they need to apply them in an integrated way to interpret the functioning of ecological systems. The course includes: 1) lectures on ecological concepts from the population scale to the macroecological scale, using examples of applications that place the discipline in the current ecological and societal context; 2) practical and supervised work focused on tools (sampling strategies, modeling, data analysis); 3) field teaching, during which students are encouraged to ask relevant scientific questions based on their observations in the field and to use their knowledge to answer them in a reasoned manner.

Summary of EU content:

- CM: History of the emergence of concepts in ecology; Population dynamics/metapopulations; Biotic interactions and food webs; Community ecology, metacommunities; Ecosystem ecology/functional ecology; Concepts of macroecology/biogeography; Global change and ecosystem functioning;

- Field: Integrative analysis of ecosystem functioning in situ;

- TD/TP: sampling and experimentation strategies in ecology; modeling in population dynamics/metapopulations, community ecology/metacommunities, food webs; biodiversity measures (alpha, beta, etc.).

See the full page

The overall objective is to consolidate students' foundations in evolutionary biology by addressing both (i) macroevolutionary phenomena and the general methods used to analyze them, and (ii) microevolutionary processes with an emphasis on the population genetics approach. This course unit aims to provide a solid foundation of knowledge in evolutionary biology and to illustrate the applications of the discipline to students' future areas of specialization. The course includes: 1) lectures on the concepts of evolution; 2) practical work in two main forms: 2a. sessions focused on the use of tools (phylogeny) and the mathematical formalization of evolutionary processes (population genetics); and 2b: sessions built around group work, allowing students, depending on their background and professional goals, to explore a particular topic in depth (fundamental question or application of evolutionary biology).

See the full page

English tutorial courses aimed at developing professional autonomy in the English language.

See the full page

This course aims to introduce students to the diversity of plants in tropical environments, from both a botanical and morphological as well as a functional perspective. The course includes an introduction to tropical biodiversity and its observation, the taxonomic and phylogenetic diversity of the major tropical families, the life forms of tropical plants (morphology and anatomy, architecture), their ecophysiology (diversity of phenolic compounds, link with adaptation and distribution), functional ecology (general concepts, responses to environmental gradients, specializations, plant succession), the diversity of biotic interactions, and concepts of coevolution (symbiosis, reproductive systems, dispersal).

See the full page

The individual M1 internship lasts approximately three months and, depending on the program, must be completed in a research laboratory or a non-academic organization. It allows students to gain professional experience in the field of biodiversity, evolution, or ecology. It can be carried out in a local, national, or international organization, on a topic approved by the teaching team so as to fit in with the objectives specific to the program followed by the student.

Assessment: Preparation for the internship is assessed on the basis of a written document and a presentation of the internship project. The internship work is assessed during a public presentation before a panel, during which the content of the dissertation and the quality of the responses to the panel's questions are evaluated. The student's behavior and enthusiasm during the internship are assessed by the internship supervisor.

See the full page

See the full page

Teaching unit aimed at linking theoretical ecology, its operational implementation, and territorial issues as seen by societal actors. Built on a format combining theoretical courses covering the elements necessary for understanding field issues (ecosystem dynamics, anthropization, socio-ecosystem resilience, in situ conservation, etc.), this teaching unit includes several field blocks (each consisting of a preparatory tutorial/practical and an "active" field trip). The territories visited will provide an opportunity to meet members of society (managers, elected officials, associations, shepherds, etc.) whose position allows us to understand how ecological issues govern their actions and how, in turn, their actions impact biodiversity, its dynamics, and its distribution.

See the full page

How is biodiversity distributed across the Earth? What ecological, evolutionary, and historical factors determine these patterns of biodiversity distribution? What changes have human activities brought about in the global distribution of biodiversity? In this course, we will study the role of spatial and temporal variations in the environment on a global scale on the dynamics of biodiversity. In particular, we will examine the influence of long-term climate cycles on the past and present diversity of organisms. We will also address the impact of human activities and global changes on biodiversity on a planetary scale.

See the full page

This module provides an introduction to ethnobotany and ethnoecology in order to understand the material and immaterial dimensions of the relationships between humans and their environment, with a particular focus on the plant world. We will focus in particular on local naming and classification systems, perceptions and representations of nature, resource management practices and uses, and biocultural, ecological, and evolutionary interactions. Ethnobotany and ethnoecology are disciplines at the interface of anthropology, botany, and ecology, which may also borrow tools and concepts from linguistics, archaeology, geography, and agronomy. This module complements the "Ethnoecology and Sustainable Development" module (Master 2) by providing the theoretical and methodological foundations of ethnobotany.

See the full page

The objective of this course is to consolidate students' foundations in ecology and/or evolution by inviting them to define a research topic and question(s), formulate relevant hypotheses with supporting arguments, and justify a data acquisition and analysis strategy for testing them.

Summary of EU content:

- Independent work under supervision: identification of a relevant scientific question; bibliographic review to establish the state of the art and justify scientific hypotheses; proposal and justification of a methodological approach (materials and methods) to test the proposed hypotheses.

Types of topics:

Topics may cover any issue identified by students (in groups of 3/4) and approved by the teaching team, and may be based on different approaches to suit the requirements of different courses. For example, students may propose a field sampling or experimentation strategy, a meta-analysis of literature data, an analysis of sequences retrieved from GenBank, an analysis of occurrence data retrieved from GBIF, etc.

In all cases, projects must involve a genuine data acquisition strategy, identified, justified, and described by students in the materials and methods required for M1S2, with a provisional schedule for the project and identification of the tasks that each student will carry out within each group as part of the implementation of the project in M2S3. Projects must also be financially realistic and include a provisional budget, and must be able to be completed within the time available in M2S3.

Assessment methods:

Teaching is based on a problem-based learning approach. Students are assessed on how they progress in developing their approach (40% of the final grade), as well as on their ability to present and defend their project in a final oral exam (60% of the final grade).

See the full page

See the full page

This EU has three objectives:

1) Deepen knowledge of concepts in genetics and evolutionary genomics such as linkage disequilibrium, selection, coalescent theory, detection of natural selection and evolutionary forces acting on genome evolution and the process of genomic speciation.

2) Provide an overview of research topics in evolutionary genomics in the form of educational seminars: molecular evolution, evolutionary genomics of endosymbiosis, chromosomal evolution, and molecular evolution.

3) Finally, the EU is proposing a bioanalysis project using an empirical dataset to understand evolutionary genomics analysis and tackle the increasingly sophisticated bioinformatics aspects of the discipline.

See the full page

This module presents table management and the link between multivariate and univariate analysis: matrix manipulation and common operations; the concepts of projection and distance; translation of descriptive and univariate statistics using multiple regression/ACP/AFD as examples; indices of (dis)similarity, distance; correlation.

See the full page

The aim of this EU is to understand the adaptive biology of organisms by considering individual and population responses to environmental variations. Concrete examples in animal evolutionary ecophysiology will be discussed in the context of global change. The responses of organisms and populations to abiotic parameters (such as temperature, salinity, oxygen availability, pollutants) will be considered, as well as their interactive effects. The course unit will demonstrate the involvement of physiological mechanisms in ecology, from phenotypic and cognitive processes at the intra-individual level to functional variants between individuals and between species. The concepts of intraspecific variability, phenotypic plasticity, and transgenerational effects will also be addressed. This course unit will be illustrated by examples of phenotypic trait analysis (including behavior) within populations. Links with genetic and epigenetic markers will also be discussed. Different approaches (-omics vs. gene/protein target), several experimental designs, and various scales of biological organization will be considered (molecule, gene, phenotype, individual, population, species).

See the full page

The objective of this EU is to enable the implementation of projects defined within the framework of the M1S2 EU project.

Summary of EU content:

- Independent work supervised by student groups: readjustment of project objectives and methodology if necessary, data acquisition, ecological and/or evolutionary analyses and interpretations according to the provisional schedule defined in M1S2, presentation of results at a joint symposium for the different courses.

Assessment methods:

As with the EU M1 project, the EU uses a problem-based learning approach. Students are therefore assessed on an ongoing basis on their progress in completing their project (40% of the final grade), then at the end of the semester on their ability to present the results of their project and discuss them during an oral presentation at a general feedback symposium (60% of the final grade).

See the full page

See the full page

This EU addresses questions surrounding ecosystem management from a social science perspective, particularly that of "science studies." It aims to contribute to the development of a general culture related to the relationship between ecological sciences and societies, and to equip participants with the tools to analyze social issues and underlying socio-scientific controversies. The first part of the course provides the conceptual and methodological framework necessary to present a reflective tool for analyzing the roles of actors and arguments (epistemological, axiological) involved in socio-scientific controversies, and illustrates this tool with current examples. Subsequently, thematic presentations by researchers in ecology illustrate a variety of issues surrounding ecological sciences and serve as a basis for students to apply and acquire the reflective analysis tool. Students are thus assessed on their ability to use this analytical framework to take an individual and reasoned position in controversies related to ecological sciences.

See the full page

The educational objective of this teaching unit is to reposition the major soil types on a global scale, explain their formation, and identify the mineral phases or main abiotic factors likely to regulate biological activity in soils. Based on this analysis, the various soil organisms (microorganisms, micro-, meso- and macrofauna) will be presented, along with their relationships, in order to reposition the cycle of organic matter and mineral elements in the soil at different temporal and spatial scales. The concepts of recycling, biogeochemical cycles and community assembly rules will also be addressed. This course unit is organized around lectures and conferences, as well as tutorials and fieldwork.

See the full page

Module objectives:

Acquire the knowledge necessary to understand recent advances and current debates in the field of tropical plant community ecology, as a basis for evaluating environmental policies and projects.

Module content:

The module provides an introduction to the structure and functioning of tropical forest and savanna ecosystems. It discusses their determinants, characteristics, and some of the implications for management and conservation. It also addresses some of the controversies in ecology surrounding tropical forest ecosystems.

Teaching and learning methods: 

- Course (6 hours)

- Thematic bibliographic analyses by groups (12 hours) and discussion during presentations with external experts (8 hours).

See the full page

The objective of this EU is to support students in developing their career plans and searching for internships, while beginning to prepare for their integration into professional life by providing a comprehensive and personalized overview of possible career paths.

In practical terms, meetings with various stakeholders provide an opportunity to present the doctoral thesis (presentation of the GAIA doctoral school, presentations by doctoral students) and the professional network targeted by the various courses (research professions and non-academic sector). Activities specific to each course then enable students to better target the scientific fields most relevant to their professional projects. Finally, tutorial sessions are designed to prepare students for writing scientific articles in English.

See the full page

See the full page

The objective of this EU is to explore the diversity of life forms and morphological and functional adaptations of plants living in tropical regions. Each of the major biological types will be analyzed (trees, grasses, vines, epiphytes, hemiepiphytes, etc.) in order to understand their architecture and modes of development, and to study the particularities of their functioning.

A comparative analysis will attempt to define the nature of the adaptations that have enabled these plants to occupy all available niches.

Particular emphasis will be placed, from an evolutionary perspective, on studying the biomechanical and conduction properties in situ that characterize some of them.

Another focus will be on tree ontogenesis, addressing architectural concepts related to the processes involved in the development of large tropical tree crowns, including root strategies. The interaction between vegetative structures, reproduction, and secondary growth will be addressed in practical work on tropical material.

The concepts of growth and competition in populations will be addressed using simple examples with concepts of growth modeling.

See the full page

See the full page

This course introduces students to social science research (from developing a topic to writing a report), with an emphasis on qualitative methods. It consists mainly of field research on the general theme of nature management in cities. It aims to introduce students to the social dimensions of environmental management issues, as well as to the methods of producing and processing qualitative data in the social sciences. In this regard, it trains students to develop diagnoses of environmental management situations by working on three main types of skills: (i) Producing and analyzing heterogeneous data (written, oral, observational), (ii) Analyzing multidimensional, complex, and unique situations, (iii) Communicating the complexity of these situations to an audience.

See the full page

See the full page

See the full page

1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

6. Compare scientific hypotheses with model selection (WAIC).

7. Heterogeneity and multilevel models (also known as mixed models). 

See the full page

Strategic Environmental Management Analysis (SEMA) is a theoretical framework that provides a basis for analyzing a management situation based on a clearly expressed environmental concern. It sheds light on the exercise of environmental responsibility in relation to the exercise of other collective responsibilities, within the context of a pluralistic debate.  By identifying the basic structures of environmental management situations, particularly in international contexts, it provides criteria that explain the difficulties faced by public environmental policies in emerging in relation to other areas of public action—particularly development policies – and, on the other hand, identify the scope for promoting change towards greater responsibility for environmental issues. The module is based on two key elements: (1) The presentation of various research-intervention projects using this analytical framework to explain the implementation of the ASGE's working registers, (2) A supervised project combining critical analysis of environmental project documents with the development of an alternative research-intervention study proposal using the ASGE framework, which is presented and discussed collectively at the end of the module.

See the full page

See the full page

Land use changes are responsible for approximately 10% of anthropogenic carbon dioxide emissions. Tropical forest ecosystems can contribute to both pillars of addressing global warming, namely mitigation and adaptation:

-Tropical forests and plantations are important potential carbon sinks, their biomass can provide energy as a substitute for fossil fuels, while reducing deforestation and forest degradation and improving forest management (REDD+) can significantly reduce anthropogenic GHG emissions.

-The ability of human societies that are still predominantly rural to adapt to climate change depends in part on the state of available natural resources, while the necessary adaptation of tropical ecosystems to climate change can be facilitated by human intervention.

As part of the implementation of the United Nations Framework Convention on Climate Change, mechanisms such as the Clean Development Mechanism (CDM) and REDD+, voluntary markets, and ecosystem-based adaptation provide new opportunities for tropical forestry, as well as potential leverage for protecting or restoring tropical forests. The module provides an understanding of the basic concepts of climate change, the role of tropical ecosystems in the global carbon cycle, and technical, political, and economic responses to climate change issues.

Module content:

This module provides basic knowledge on topics such as the carbon cycle, the mechanisms and consequences of climate change, and the technical and political measures for mitigating and adapting to this change. The potential of tropical agroecosystems is assessed on the basis of scientific studies and existing operational projects.

Teaching and learning methods:

-Classes (18 hours)

-TD (3 hours).

See the full page

This course covers the basics of plant architecture and whole-plant development (stem and root) as part of assessing the condition and functioning of trees with a view to managing them in line with objectives. The consideration and management of trees meet different criteria depending on the context (forest, fruit or urban). The following topics will be addressed in a theoretical and practical manner with real-life scenarios. (1) General information on the morphology and architecture of the whole plant, (2) Tree life cycles, growth patterns (3) Trauma (competition, pruning, biological aggressors) and architectural reactivity (4) Practical work on the diagnosis of forest, fruit and urban trees.

See the full page

See the full page

The objectives of this EU are to explore key concepts related to climate change, illustrate important notions in ecology and evolution in light of climate change in many different ecosystems, and summarize the various scientific and societal issues and challenges posed by CC.

See the full page

"Businesses play a central role today in the dynamics of ecosystem degradation, and as such are increasingly called upon to contribute to their protection. How, then, can we improve the way businesses take biodiversity issues into account and their involvement in the territorial management of ecosystems? Furthermore, while conservation science and ecology offer a growing number of indicators and data for assessing biodiversity in its many forms, how can this information be structured so that it provides a basis for strategic and collective action and dialogue among stakeholders?

An approach based on environmental accounting as a management science discipline makes it possible to address these issues of structuring environmental indicators and information systems, the responsibilities of the various actors who interact with ecosystems, and the associated forms of accountability.

The field of ecological accounting and its recent developments in biodiversity aims to transform the accounting systems traditionally used by companies to better take into account the value of natural capital (biodiversity, ecosystems), and thus anchor it at the heart of management processes at different levels of corporate management. Innovation in ecological accounting also exists in other areas (national, ecosystem-wide) and can thus help to create links at different levels of ecosystem governance.

Interactive lectures are punctuated by exercises of varying lengths that put students in an active role:

- reading and lively discussion of scientific articles in the field;

- game for comparative analysis of natural capital accounting tools and models, etc.

-A tutorial on applying ecosystem accounting approaches based on a case study.

See the full page

1. "The way in which the modern West represents nature is the least well-shared thing in the world" (Descola, 2005, p. 56). According to anthropologist Philippe Descola, the category of "Nature," as a reality separate from the human world, is an invention of Europeans that is only one of the possibilities available to societies to account for the living and non-living beings that surround them.

While Philippe Descola contributes to renewing questions about society-environment relations, he nevertheless draws on a long tradition in the humanities and social sciences. Numerous works already explore the various forms of knowledge and social organization to which these relations give rise: ethnoscience, anthropology of technology, economic anthropology, ethnoecology, sociology of science and technology, etc.

This issue is far from being confined to the academic sphere. It also attracts the interest of conservationists (biodiversity, natural resources, etc.) and industry (pharmacology). It also mobilizes so-called "indigenous" populations who are demanding, both locally and internationally, access to resources and the preservation of intangible heritage.

2. Located at the intersection of social sciences and life sciences, these disciplines analyze how human societies use plants, animals, and other components of the environment, but also how their conceptions and representations of their environment(s) guide these uses. This research also explores how human societies organize themselves, perpetuate themselves, change to adapt to new contexts (globalization, global changes), and transmit knowledge about their relationships with nature.

For a long time, these disciplines focused more specifically on the interrelationships between so-called "traditional" societies and their immediate environment. Subsequently, beginning in the 1970s, researchers reconsidered the distinction between so-called "traditional" and "modern" societies in order to better address new contemporary environmental and social transformations.

On the one hand, even the most isolated local communities are affected by events that are decided and take place at different levels (international conventions, economic crises). Their immediate environment is also affected by global phenomena (climate change, erosion of biodiversity, etc.). In turn, their actions can also have international ecological, social, and economic repercussions, for example when these societies organize to bring their demands to international arenas.

On the other hand, modern societies' relationship with their environment is being reconfigured in light of the fact that our planet is becoming increasingly "artificialized" and threatened by serious disruptions and crises. The place of fauna and flora is being reconsidered and is the subject of controversy regarding their rights. Furthermore, the dawn of a new geological era, the Anthropocene, is being invoked to challenge both the natural sciences and the humanities and social sciences on the need to take a different approach to the shared history of the environment and societies.

3. The work of scientists and engineers is being viewed in a new light. In this regard, a new scientific project in the humanities and social sciences aims to reconsider the role of "non-humans" and calls for the development of analytical categories other than those of Nature and Culture. New scales and methods of investigation are also being considered for analyzing global processes.

These recent changes in scale invite researchers in the humanities and social sciences to (re)consider their approach through a reflexive lens: they are no longer mere observers, but can also be active participants in processes, even when they are not directly involved in a social movement.

4. The objective of this module is to introduce these different scientific and operational fields. It aims to provide students with reference points and food for thought, enabling them to develop scientific questions on the relationship between society and the environment, with a view to reflecting on how to address current environmental and social issues. The varied geographical and disciplinary experiences of the speakers will illustrate the approach through a wide range of ecosystem types, sociocultural contexts, and themes. In the time available, we do not claim to cover all themes, approaches, and methods exhaustively. Any student wishing to study this field in greater depth will need to undertake more in-depth training.

See the full page

"The overall objective is to provide students with the basic knowledge necessary to understand international environmental policy and the main paradigms underlying it: international environmental agreements and commitments and their implementation in the Global South; actors on the international stage, the place and role of donors, and the strategies of environmental NGOs; and the standards and instruments they seek to promote."

See the full page

The objective of this EU is to support students in finalizing their professional projects and preparing for life after their master's degree.

The EU is organized on a course-wide basis, with regular discussion sessions between the teaching team and students.

See the full page

The individual M2 internship lasts approximately 5 to 6 months and must be carried out, depending on the course concerned, in a research laboratory or a non-academic organization. It allows students to gain in-depth professional experience in the field of biodiversity, evolution, or ecology. It can be carried out in a local, national, or international organization, on a topic approved by the teaching team so as to fit in with the specific objectives of the program followed by the student.

Assessment: The internship is assessed during a public defense before a jury, during which the content of the thesis and the quality of the responses to the jury's questions are evaluated. The student's behavior and enthusiasm during the internship are assessed by the internship supervisor.

See the full page