Plant Biodiversity and Tropical Ecosystem Management (BioGET)

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

general properties examined through regression and one-way ANOVA (R², F, ddl, least squares, likelihood, diagnostics, validation, goodness of fit, interpretation of effect sizes); ANOVA with nested and crossed factors, multiple regression (concepts of parameters, effects, and interactions)

"accounting for the dependence of explanatory random variables, confounding effects (quantitative for multiple regression, and unbalanced designs for ANOVA)"

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Generalized Linear Mixed Models + Methodology and Experimental Protocols to Account for Biological Reality: Non-Normal Distributions and Pseudo-Replication

Protocol Optimization, Power, and Uncontrolled Type I Risk: Variable Transformation, Polynomial Regression, Link Function, Likelihood, Model Selection

Deviance Analysis and Goodness of Fit

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

Graphical representation of the predictions.

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The objective of this course unit is to provide the necessary foundation in statistics to follow the more advanced modules in the curriculum; it is therefore a general refresher course. Descriptive statistics are reviewed (quantiles, cumulative frequency polygons, sample-based estimators); simple tests are introduced; essential graphs for univariate and multivariate data are presented; and the general principles of statistical testing, hypothesis testing, the concept of the p-value, and Type I and Type II errors are covered. In lab sessions, students also receive training in the R environment.

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The overall objective is to reinforce the students’ foundational knowledge of ecology and to provide them with the tools to apply this knowledge in an integrated manner to interpret the functioning of ecological systems. The curriculum includes: 1) lectures covering ecological concepts ranging from the population level to macroecological scales, supported by practical examples that place the discipline within the current ecological and societal context; 2) practical and guided exercises focused on tools (sampling strategies, modeling, data analysis); 3) fieldwork sessions during which students are encouraged to ask relevant scientific questions based on in-situ observations and to apply their knowledge to answer these questions in a well-reasoned manner.

Summary of the learning unit:

- 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;

- Fieldwork: Integrative analysis of ecosystem functioning in real-world settings;

- Tutorials/Lab Sessions: sampling and experimental strategies in ecology; modeling of population dynamics/metapopulations, community/metacommunity ecology, and food webs; measures of biodiversity (alpha, beta, etc.)."

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"The overall objective is to strengthen students’ foundational knowledge of 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 both to provide a solid common foundation of knowledge in evolutionary biology and to illustrate the discipline’s applications to the students’ future fields of specialization. The course includes: 1) lectures on evolutionary concepts; 2) laboratory sessions in two main formats: 2a. sessions focused on the use of analytical tools (phylogenetics) and on the mathematical formalization of evolutionary processes (population genetics), as well as 2b: sessions structured around group work, allowing students—based on their academic background and career goals—to explore a specific topic in greater depth (a fundamental question or an application of evolutionary biology)."

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English tutorial courses designed to foster professional proficiency in English.

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The objective of this course is to introduce students to the diversity of plants in tropical environments, from both botanical and morphological as well as functional perspectives. The course covers an introduction to tropical biodiversity and its observation, the taxonomic and phylogenetic diversity of major tropical families, the life forms of tropical plants (morphology and anatomy, architecture), their ecophysiology (diversity of phenolic compounds, relationship to 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).

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The M1 individual internship lasts approximately three months and, depending on the student’s program track, must be completed in a research laboratory or a non-academic organization. It allows students to gain professional experience in the fields of biodiversity, evolution, or ecology. It may be carried out at a local, national, or international organization, on a topic approved by the faculty to ensure it aligns with the specific objectives of the student’s program.

Assessment: Preparation for the internship is a graded assignment based on a written document and a presentation of the internship proposal. The internship work is assessed during a public presentation before a panel, during which the content of the report and the quality of the student’s responses to the panel’s questions are evaluated. The student’s conduct and initiative during the internship are assessed by the internship supervisor.

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A course designed to link theoretical ecology, its practical application, and regional challenges as perceived by stakeholders in society. Built around a format that combines theoretical lectures covering the fundamentals necessary for understanding on-the-ground issues (ecosystem dynamics, anthropogenic impacts, socio-ecosystem resilience, in situ conservation, etc.), this course unit includes several field components (each consisting of a preparatory tutorial and an “active” field trip). Visits to these areas will provide opportunities to meet stakeholders (managers, elected officials, nonprofit organizations, shepherds, etc.) whose perspectives help students understand how ecological issues shape their actions and, in turn, how those actions impact biodiversity, its dynamics, and its distribution.

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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 unit, we will study the role of spatiotemporal 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 both past and present organism diversity. We will also address the impact of human activities and global changes on biodiversity on a global scale.

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The courses in this module provide an introduction to ethnobotany and ethnoecology, with the aim of understanding 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 systems of nomenclature and classification, perceptions and representations of nature, resource use and management practices, and biocultural, ecological, and evolutionary interactions. Ethnobotany and ethnoecology are disciplines at the intersection of anthropology, botany, and ecology, and may also draw on tools and concepts from linguistics, archaeology, geography, and agronomy. This module complements the “Ethnoecology and Sustainable Development” module (Master’s 2) by providing the theoretical and methodological foundations of ethnobotany.

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"The objective of this course is to strengthen students' foundations in ecology and/or evolution by encouraging them to identify a research topic and question(s), formulate well-reasoned and relevant hypotheses, and justify a strategy for collecting and analyzing data to test those hypotheses.

Summary of the learning unit:

- Supervised independent work: identifying a relevant scientific question; conducting a literature review to assess the state of the art and justify scientific hypotheses; proposing and justifying a methodological approach (materials and methods) to test the proposed hypotheses.

Topic types:

Topics may address any issue identified by the students (in groups of 3 or 4) and approved by the teaching staff, and may draw on various approaches to align with the learning objectives of the different programs. For example, students may propose a field sampling or experimental strategy, a meta-analysis of data from the literature, an analysis of sequences retrieved from GenBank, an analysis of occurrence data retrieved from GBIF, etc.

In all cases, projects must include a concrete data collection strategy—identified, justified, and described by the students in the “Materials and Methods” section required for the M1S2 course—along with a projected timeline for the project’s progress and a breakdown of the tasks each student will perform within each group as part of the project’s implementation during the M2S3 course. Projects must also be financially realistic and include a projected budget, and they must be capable of being completed within the time available during the M2S3 semester.

Assessment Procedures:

"The course is based on a problem-based learning approach; students are evaluated on their progress in developing their methodology (40% of the grade), as well as on their ability to present and defend their project during a final oral presentation (60% of the overall grade)."

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This learning unit has three objectives:

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

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

3) Finally, the EU is proposing a bioanalysis project based on an empirical dataset to gain an understanding of evolutionary genomics and to tackle the increasingly sophisticated bioinformatics aspects of the discipline.

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"This module introduces array management and the relationship between multivariate and univariate analysis: matrix manipulation and common operations; the concepts of projection and distance; interpretation of descriptive and univariate statistics, using multiple regression, PCA, and AFD as examples; (dis)similarity indices, distance; and correlation."

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The goal of this course unit is to understand the adaptive biology of organisms by examining individual and population responses to environmental variations. Concrete examples from the field of evolutionary animal 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, and pollutants) will be examined, along with their interactive effects. The course will demonstrate the role of physiological mechanisms in ecology, ranging from phenotypic and cognitive processes at the intra-individual level to functional variations 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 with examples of analyses of phenotypic traits (including behavior) within populations. Links to genetic and epigenetic markers will also be discussed. Various approaches (-omics vs. gene/protein targets), several experimental designs, and diverse organizational scales of living organisms will be considered (molecule, gene, phenotype, individual, population, species).

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The objective of this course unit is to facilitate the implementation of the projects defined as part of the M1S2 course unit.

Summary of the learning unit:

- Independent work supervised by student groups: readjustment of project objectives and methodology as needed; data collection; ecological and/or evolutionary analyses and interpretations in accordance with the tentative schedule established in M1S2; presentation of results at a joint symposium for the various tracks.

Assessment Procedures:

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

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This course unit addresses questions surrounding ecosystem management from the perspective of the social sciences, and more specifically “science studies.” It aims to help develop a general understanding of the relationship between ecological sciences and society, and to equip participants with the tools to analyze social issues and the underlying socioscientific controversies. The first part of the course provides the conceptual and methodological framework necessary for introducing a reflective tool for analyzing the interactions of actors and the (epistemological and axiological) arguments involved in socioscientific controversies, and illustrates this tool using current examples. Subsequently, thematic presentations by researchers in ecology highlight a variety of issues surrounding the ecological sciences and serve as a basis for students to apply and master the reflective analytical tool. Students are thus assessed on their ability to use this analytical framework to take an individual and well-reasoned position in controversies related to the ecological sciences.

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The educational objective of this course unit is to provide an overview of the major soil types on a global scale, explain their formation, and identify the mineral phases or primary abiotic factors that may regulate biological activity in soils. Based on this analysis, the various soil organisms (microorganisms, micro-, meso-, and macrofauna) will be presented, along with their interactions, in order to contextualize the cycles of organic matter and mineral elements in the soil across different temporal and spatial scales. The concepts of recycling, the closure of biogeochemical cycles, and the principles governing community assembly will also be addressed. This course unit is organized around lectures and presentations, as well as tutorial sessions and fieldwork.

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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:

This module provides an introduction to the structure and functioning of tropical forest and savanna ecosystems. It examines their determining factors, characteristics, and certain implications for management and conservation. It also addresses some of the ecological controversies surrounding tropical forest ecosystems.

Teaching and Learning Methods: 

- Course (6 hours)

- Thematic literature reviews conducted in groups (12 hours) and discussion during presentation sessions with external experts (8 hours).

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The goal of this course unit is to support students in developing their career plans and searching for internships, while helping them begin to prepare for their transition into the workforce by providing a comprehensive yet personalized overview of possible career paths.

Specifically, sessions with various stakeholders provide an opportunity to present the doctoral thesis (a presentation by the GAIA doctoral school, presentations by doctoral students) and to explore the professional opportunities targeted by the different tracks (research careers and the non-academic sector). Activities specific to each track then help students better identify the scientific fields most closely aligned with their career goals. Finally, tutorial sessions are designed to prepare students for writing scientific articles in English.

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The objective of this course unit is to explore the diversity of life forms and the morphological and functional adaptations of plants living in tropical regions. Each of the major biological types will be analyzed (trees, herbs, vines, epiphytes, hemiepiphytes, etc.) in order to understand their architecture and modes of development, and to study the specific characteristics 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 the study of the biomechanical and in situ conduction properties that characterize some of them.

Another focus will be on tree ontogeny, addressing concepts of architecture related to the processes involved in the development of the large crowns of tropical trees, including root strategies. The interaction between vegetative structures, reproduction, and secondary growth will be explored in laboratory exercises using tropical plant material.

The concepts of growth and competition within a stand will be explored using simple examples that incorporate concepts of growth modeling.

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This course introduces students to social science research (from defining the research question to writing a report), with an emphasis on qualitative methods. It consists primarily of a field study on the general theme of urban nature management. It aims to introduce students to the social dimensions of environmental management issues, as well as to the methods of collecting and analyzing qualitative data in the social sciences. In this regard, it trains students to develop assessments of environmental management situations by focusing on three main types of skills: (i) Generating and analyzing diverse data (written, oral, observational), (ii) Analyzing multidimensional, complex, and unique situations, (iii) Communicating the complexity of these situations to an audience.

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1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

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Strategic Analysis of Environmental Management (SAEM) is a theoretical framework that provides a basis for analyzing a management situation based on a clearly articulated environmental concern. It sheds precise 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, on the one hand, explain the difficulties environmental public policies face in gaining prominence relative to other areas of public policy—particularly development policies — and, on the other hand, make it possible to identify opportunities to promote changes that lead to greater accountability for environmental issues. The module is structured around two key components: (1) The presentation of various action research studies that utilize this analytical framework to illustrate the application of the ASGE’s analytical frameworks, (2) A guided assignment that combines the critical analysis of environmental project documents with the development of a proposal for an alternative action research study using the ASGE framework, which is presented and discussed collectively at the end of the module.

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Land-use changes account for approximately 10% of anthropogenic carbon dioxide emissions. Tropical forest ecosystems can contribute to both pillars of addressing climate change—namely, mitigation and adaptation:

-Tropical forests and plantations are significant 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—which 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 interventions.

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

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 policy measures for mitigating and adapting to climate change. The potential of tropical agroecosystems is assessed based on scientific studies and existing operational projects.

Teaching and Learning Methods:

-Course (18 hours)

-Tutorial (3 hours).

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This course introduces concepts of plant architecture and the development of the entire plant (stem and root) as part of an assessment of tree health and function, with a view to implementing management practices tailored to specific objectives. The assessment and management of trees are guided by different criteria depending on the context (forest, orchard, or urban). The following topics will be covered both theoretically and practically, with hands-on exercises. (1) Overview of morphology and concepts of whole-plant architecture, (2) Tree life cycles and growth stages, (3) Stressors (competition, pruning, pests and diseases) and architectural responses, (4) Hands-on exercises in assessing forest, fruit, and urban trees.

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The objectives of this learning unit are to explore key concepts related to climate change, to illustrate important concepts in ecology and evolution in the context of climate change across a wide range of ecosystems, and to synthesize the various scientific and societal issues and challenges posed by climate change.

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

An approach based on ecological accounting as a discipline within management sciences allows us to address these issues regarding the structuring of ecological indicators and information systems, the assumption of responsibility by the various actors who interact with ecosystems, and the associated forms of accountability.

The field of ecological accounting and its recent developments regarding biodiversity aim to transform the accounting systems traditionally used by firms to better account for the value of natural capital (biodiversity, ecosystems), thereby embedding it at the heart of management processes at various levels of corporate governance. Innovation in ecological accounting also exists at other levels (national, ecosystem-wide) and can thus help create linkages across different scales of ecosystem governance.

Interactive lectures are interspersed with exercises of varying lengths that engage students actively:

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

- a tool for the comparative analysis of natural capital accounting tools and models, etc.

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

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1. “The way the modern West conceives of nature is the least widely shared view 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 a European invention that is merely one of the possibilities available to societies for accounting for the living and non-living beings that surround them.

While Philippe Descola helps to revitalize the discussion of the relationship between society and the environment, he nevertheless draws on a long tradition in the humanities and social sciences. Numerous studies have already explored the various forms of knowledge and social organization that arise from this relationship: ethnoscience, the anthropology of technology, economic anthropology, ethnoecology, the sociology of science and technology, and so on.

This issue is by no means confined to the academic sphere. It also attracts the interest of stakeholders in conservation (biodiversity, natural resources, etc.) and industry (pharmacology). It also mobilizes so-called “indigenous” peoples, who are advocating—both locally and internationally—for access to resources and the preservation of their intangible cultural heritage.

2. Situated at the intersection of the social sciences and the life sciences, these disciplines analyze how human societies use plants, animals, and other components of the environment, as well as how their conceptions and representations of their environment(s) shape 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 reevaluated the distinction between so-called “traditional” and “modern” societies in order to better address new contemporary environmental and social transformations.

Indeed, on the one hand, local communities—even the most isolated ones—are affected by events that are decided and unfold at various levels (international agreements, economic crises). Their immediate environment is also affected by global phenomena (climate change, loss of biodiversity, etc.). Conversely, their actions can also have international ecological, social, and economic repercussions, for example, when these communities organize to voice their demands in international forums.

Furthermore, the relationship that modern societies have with their environment is being reshaped in light of the reality of an increasingly “artificialized” planet threatened by serious disruptions and crises. The role of flora and fauna is being reevaluated, and their rights are the subject of controversy. Furthermore, the onset of a new geological era—the Anthropocene—is cited to challenge both the natural sciences and the humanities and social sciences to reconsider how we view the shared history of the environment and societies.

3. The very work of scientists and engineers is being viewed in a new light. In this regard, a new research project in the humanities and social sciences aims to reexamine 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 to analyze global processes.

These recent shifts in scale prompt researchers in the humanities and social sciences to (re)examine their methodology through a reflective approach: they are no longer mere observers, but can also be active participants in these processes—even when they are not directly involved in a social movement.

4. The objective of this module is to introduce these various scientific and operational fields. It aims to provide students with points of reference and food for thought so that they can formulate scientific questions about the relationship between society and the environment, with a view to reflecting on how to address current environmental and social challenges. The instructors’ diverse geographical and disciplinary backgrounds will help illustrate this approach through a wide range of ecosystem types, sociocultural contexts, and themes. Given the time constraints, we do not intend to provide an exhaustive coverage of all topics, approaches, and methods. Any student wishing to delve deeper into this field should pursue more in-depth training.

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

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The goal of this course unit is to support students as they finalize their career plans and prepare for life after the master’s program.

The EU is organized around the entire program, with regular discussion sessions between the teaching staff and students.

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The M2 individual internship lasts approximately 5 to 6 months and, depending on the student’s track, must be completed 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 may be conducted at a local, national, or international organization on a topic approved by the faculty to ensure it aligns with the specific objectives of the student’s track of study.

Evaluation: The internship is evaluated during a public defense before a panel, during which the content of the thesis and the quality of the student’s responses to the panel’s questions are assessed. The student’s conduct and initiative during the internship are evaluated by the internship supervisor.

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