Plant Biodiversity and Management of Tropical Ecosystems (BioGET)

"General linear models with 1 or more random explanatory variables: from the translation of 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 seen through regression and 1-factor ANOVA (R2, F, ddl, least squares, likelihood, diagnosis, validation, goodness of fit, interpretation of effect sizes); nested and cross-factor ANOVA, multiple regression (notion of parameter and effects, and interaction)

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

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

Protocol optimization, power and uncontrolled 1st order 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, over-dispersion

Graphical representation of predictions.

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The aim of this course is to provide the statistical foundations needed to follow all the more advanced modules in the curriculum, so it's a general refresher. Descriptive statistics are reviewed (quantile, cumulative frequency polygon, sample estimators), simple tests are introduced, essential graphs for univariate and multivariate data are presented, the general principle of a statistical test, hypothesis design, the notion of p-value, first and second species risk are presented. In practical exercises, students are also brought up to speed in the R environment.

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The general aim is to consolidate the ecological foundations acquired by students, and to give them the tools to mobilize them in an integrative way to interpret the functioning of ecological systems. The course includes: 1) lectures covering the concepts of ecology from population to macro-ecological scales, with examples of applications that place the discipline in the current ecological and societal context; 2) practical work and tutorials focusing on tools (sampling strategies, modelling, data analysis); 3) field courses in which students are invited to ask themselves relevant scientific questions based on observation in a given situation, and to mobilize their knowledge to answer them in a reasoned way.

Summary content of the EU :

- CM: History of the emergence of concepts in ecology; Population dynamics / metapopulations; Biotic interactions and food webs; Ecology of communities, meta-communities; Ecology of ecosystems / functional ecology; Notions of macroecology / biogeography; Global change and ecosystem functioning;

- Field: Integrative analysis of ecosystem functioning in real-life situations ;

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

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"The overall aim is to consolidate students' evolutionary biology foundations, covering both (i) macro-evolutionary phenomena, and the general methods used to analyze them, and (ii) micro-evolutionary processes, with an emphasis on the population genetics approach. The aim of this course is both to provide a common foundation of solid knowledge in evolutionary biology, and to illustrate the applications of the discipline to students' future fields of specialization. Teaching includes: 1) lectures on evolutionary concepts; 2) practical work in two main forms: 2a. sessions focusing on the use of tools (phylogeny) and on the mathematical formalization of evolutionary processes (population genetics), and 2b: sessions built around group work, enabling students, depending on their career path and professional objectives, to delve deeper into a particular theme (fundamental question or application of evolutionary biology)."

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English TD courses aimed at professional autonomy in the English language.

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The aim of this course is to introduce students to the diversity of plants in tropical environments, from a botanical, morphological and functional point of view. Lessons include 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 notions, responses to environmental gradients, specializations, plant succession), the diversity of biotic interactions, notions of coevolution (symbioses, reproductive systems, dispersal).

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The individual M1 internship lasts around three months, and must be carried out in a research laboratory or a non-academic structure, depending on the course concerned. It enables students to gain professional experience in the field of biodiversity, evolution or ecology. It can be carried out in a local, national or international structure, on a subject validated by the teaching staff to fit in with the objectives of the course followed by the student.

Evaluation : The preparation of the internship is a graded exercise based on a written document and a presentation of the internship project. The internship work is assessed at a public presentation before a jury, during which the content of the dissertation and the quality of the answers to the jury's questions are evaluated. The student's behavior and dynamism during the internship are assessed by the internship supervisor.

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A teaching unit designed to link theoretical ecology, its operational implementation and territorial issues as seen by society's stakeholders. Based on a format combining theoretical lectures with a reminder of the elements needed to understand issues in the field (ecosystem dynamics, anthropization, socio-ecosystem resilience, in situ conservation, etc.), this unit comprises several field blocks (each consisting of a preparatory TD/TP and an "active" field trip). The territories visited will provide an opportunity to meet social players (managers, elected representatives, associations, shepherds, etc.) whose position enables us to understand how ecological issues govern their actions, and how in turn their actions impact biodiversity, its dynamics and its distribution.

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How is biodiversity distributed on 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 spatio-temporal variations in the global environment on biodiversity dynamics. In particular, we will examine the influence of long-term climatic cycles on the past and present diversity of organisms. We will also look at the impact of human activities and global change on biodiversity on a planetary scale.

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This module provides an introduction to ethnobotany and ethnoecology, with a view to understanding the material and immaterial dimensions of the relationships between humans and their environment, with a particular focus on the plant world. We will be looking in particular at local systems of nomenclature and classification, perceptions and representations of nature, resource management uses and practices, and biocultural, ecological and evolutionary interactions. Ethnobotany and ethnoecology are disciplines at the interface of anthropology, botany and ecology, which can 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.

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"The aim of this course is to consolidate students' grounding in ecology and/or evolution by inviting them to define a research topic and question(s), by defining relevant hypotheses in a well-argued manner, and by justifying a strategy for acquiring and analyzing the data needed to test them.

Synthetic content of the EU:

- Independent tutored work: identification of a relevant scientific question; bibliographical synthesis 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.

Type of subject:

The topics can be based on any question identified by the students (in groups of 3/4), and validated by the teaching team, and draw on different approaches to suit the expectations of the different courses. For example, students may propose a field or experimental sampling 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 the students in the materials and methods requested in M1S2, with a provisional timetable for the project's progress and identification of the tasks that each student will carry out within each group as part of the project's implementation in M2S3. Projects must also be financially realistic, with a provisional budget, and must be able to be finalized within the time available in M2S3.

Assessment of knowledge:

Teaching is based on a problem-based learning approach, and students are assessed on how they progress in constructing their approach (40% of CC), as well as on their ability to present and defend their project at a final oral (60% of the overall mark)."

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This UE has three objectives:

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

2) Offer an overview of research themes in evolutionary genomics in the form of educational seminars: molecular evolution, evolutionary genomics of endosymbioses, chromosome evolution and molecular evolution.

3) Finally, the EU proposes a project for the bioanalysis of an empirical dataset to understand the analysis of evolutionary genomics and get to grips with the bioinformatics aspects increasingly developed in the discipline.

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"This module introduces table management and the link between multivariate and univariate: matrix manipulation and common operations; notion of projection and distance; translation of descriptive and univariate statistics with multiple regression/ACP/AFD as an example; indices of (dis)similarity, distance; correlation".

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The aim of this course is to understand the adaptive biology of organisms by considering individual and population responses to environmental variations. Concrete examples of 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 will show how physiological mechanisms are involved in ecology, from phenotypic and cognitive processes at the intra-individual level to functional variants between individuals and between species. Intraspecific variability, phenotypic plasticity and transgenerational effects will also be addressed. This course 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. target gene/protein), several experimental set-ups and various scales of organization of living organisms will be considered (molecule, gene, phenotype, individual, population, species).

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The aim of this course is to implement the projects defined in the M1S2 project course.

Synthetic content of the EU:

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

Assessment of knowledge:

As with the M1 Project UE, this UE is based on a problem-based learning approach. Students are therefore assessed as they go along on how they are progressing with their project (40% CC), then at the end of the semester on their ability to present and discuss the results of their project in an oral presentation at a general feedback conference (60% of the overall mark).

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This course approaches the issues surrounding ecosystem management from a social science perspective, with a particular focus on science studies. It aims to help develop a general understanding of the relationship between ecological sciences and society, and to equip participants to analyze the social issues and underlying socio-scientific controversies. The first part of the course provides a conceptual and methodological framework for the presentation of a reflexive tool for analyzing the interplay of actors and arguments (epistemological, axiological) involved in socio-scientific controversies, and illustrates this tool using current examples. Thematic presentations by ecology researchers illustrate a variety of issues surrounding the ecological sciences, and serve as the basis for students' application and acquisition of the reflexive analysis tool. Students are assessed on their ability to mobilize this analytical framework to position themselves individually and argumentatively in ecological science controversies.

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The pedagogical objective of this course is to reposition the main soil types on a global scale, explain their formation and identify the main mineral phases or abiotic factors likely to regulate soil biological activity. Based on this analysis, the different soil organisms (micro-organisms, micro-, meso- and macro-fauna) and their relationships will be presented in order to reposition the cycle of organic matter and mineral elements in the soil on different temporal and spatial scales. The notions of recycling, looping of biogeochemical cycles and community assembly rules will also be addressed. This course is organized around lectures and conferences, as well as fieldwork and practical work.

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Module objectives :

Acquire the knowledge needed to understand recent advances and current debates in the ecology of tropical plant communities, as a basis for assessing environmental policies and projects.

Module content :

The module provides an introduction to the structure and functioning of tropical forest and savanna ecosystems. It discusses the determinants, characteristics and certain consequences in terms of management and conservation. It also addresses some of the ecological controversies surrounding tropical forest ecosystems.

Teaching and learning methods : 

- Course (6 hours)

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

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The aim of this course is to help students build their career plans and find internships, while beginning to prepare for their integration into professional life through a comprehensive and personal vision of possible career paths.

In concrete terms, a series of meetings with various participants introduces the doctoral thesis (presentation of the GAIA doctoral school, presentations by thesis students) and the professional environment targeted by the different career paths (research careers and the non-academic sector). Activities specific to each pathway then enable students to better target the scientific fields most closely aligned with their career plans. Finally, TD sessions are designed to prepare students to write scientific articles in English.

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The aim of this course 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 (trees, grasses, lianas, epiphytes, hemi-epiphytes, etc.) will be analyzed in order to understand their architecture and modes of development, and to study the particularities of their functioning.

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

Particular emphasis will be placed, from an evolutionary perspective, on the study of the bio-mechanical and in situ conductive properties that characterize some of them.

The focus will also be on tree ontogeny, with a focus on architecture and 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 covered in practical work on tropical material.

The notions of growth and competition in a stand will be approached using simple case studies, along with notions of growth modelling.

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This course introduces students to social science research (from constructing a subject to writing a report), with an emphasis on qualitative methods. It consists essentially of a field survey on the general theme of managing nature in the city. It aims to introduce students to the social dimensions of environmental management issues, as well as to the production and processing of qualitative data in the social sciences. In this respect, it trains students to draw up diagnoses of environmental management situations, working on three main types of skills: (i) producing and analyzing heterogeneous data (written, oral, observational), (ii) analyzing multidimensional, complex and singular situations, (iii) conveying the complexity of these situations to an audience.

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1. Bayesian inference: Motivation and simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chains Monte Carlo methods (MCMC)

5. Bayesian analyses in R with the Jags software.  

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

7. Heterogeneity and multilevel models (aka mixed models. 

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Strategic Environmental Management Analysis (SEMA) is a theoretical framework 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 framework of a pluralistic debate. By identifying the basic structures of environmental management situations, particularly in international contexts, it provides the criteria that explain the difficulty of environmental public policies to emerge in relation to other areas of public action - in particular development policies - and that enable us to identify the room for manoeuvre to encourage changes to take greater responsibility for environmental problems. The module is based on two key points: (1) the presentation of various research-intervention projects using this analytical framework, in order to explain the implementation of the ASGE work registers, (2) a supervised project combining the 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.

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Land-use changes are responsible for around 10% of anthropogenic carbon dioxide emissions. Tropical forest ecosystems can play a part in both the mitigation and adaptation aspects of global warming:

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

-The ability of human societies, still essentially 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.

In the context of the implementation of the United Nations Framework Convention on Climate Change, mechanisms such as the Sustainable Development Mechanism (SDM) and REDD+, and voluntary markets, as well as ecosystem-based adaptation to climate change, provide a new outlet for tropical forestry, as well as a potential lever for tropical forest protection or restoration. The 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 political mechanisms 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 :

-Course (18 hours)

-TD (3 hours).

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This course introduces the concepts of plant architecture and whole-plant development (stem and root) as part of a diagnosis of the condition of trees and their functioning, with a view to management adapted to objectives. The consideration and management of trees responds to different criteria depending on the contexts considered (forest, fruit or urban). The following topics will be covered both theoretically and practically, using real-life situations. (1) General information on the morphology and architecture of the whole plant, (2) Tree life trajectories, forms of expectation (3) Trauma (competition, pruning, bio-aggressors) and architectural reactivity (4) Practical work on diagnosing forest, fruit and urban trees.

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The aim of this course is to deepen understanding of key concepts relating to climate change, to illustrate important concepts in ecology and evolution in the light of climate change, in many different ecosystems, and to produce a synthesis of the various scientific and societal questions and issues raised by CC.

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"Today, companies play a central role in the dynamics of ecosystem degradation, and are therefore increasingly called upon to contribute to their protection. How, then, can we improve the way in which companies take account of biodiversity issues, and involve them in localized ecosystem management? In addition, while conservation science and ecology offer a growing number of indicators and data for assessing biodiversity in its many forms, how can we structure this information so that it provides a basis for strategic and collective action, and for dialogue between stakeholders?

An ecological accounting approach, as a management science discipline, enables us to address these issues of structuring ecological indicators and information systems, the responsibilities of the various players who interact with ecosystems, and the associated forms of accountability.

The field of ecological accounting and its recent developments on biodiversity aim 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 on other perimeters (national, ecosystem scale) and can thus help to create articulations at different scales of ecosystem governance.

Interactive lectures are punctuated by exercises of varying length, putting students in an active position:

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

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

-A practical case study of ecosystem accounting approaches.

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1 "The way in which the modern West represents nature is the least 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, was invented by Europeans, and is just one of the ways in which societies can account for the living and non-living beings that surround them.

While Philippe Descola is helping to renew questions concerning the relationship between society and the environment, he is also drawing on a long tradition in the human and social sciences. Numerous works have already explored the various forms of knowledge and social organization to which these relationships give rise: ethnoscience, anthropology of technology, economic anthropology, ethnoecology, sociology of science and technology, and so on.

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

2. Situated at the crossroads of social sciences and life sciences, these disciplines analyze how human societies use plants, animals and other environmental components, and 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 change) and transmit knowledge about their relationships with nature.

For a long time, these disciplines focused more specifically on the interrelations between so-called "traditional" societies and their immediate environment. Then, from the 1970s onwards, researchers reconsidered the distinction between "traditional" and "modern" societies, to better address the new environmental and social transformations taking place today.

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

On the other hand, the relationship that modern societies have with their environment is being reconfigured in the face of an increasingly "artificialized" planet threatened by serious disruptions and crises. The place of flora and fauna is being reconsidered, and their rights are the subject of controversy. Moreover, the entry into a new geological era, the Anthropocene, is being used to call on both the natural sciences and the human and social sciences to take a fresh look at the shared history of the environment and society.

3. The very work of scientists and engineers is apprehended in a new light. A new scientific project in the humanities and social sciences aims to reconsider the role of "non-humans", and calls for analytical categories other than Nature and Culture. New scales and methods of investigation are also envisaged to analyze 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 genuine actors in processes, when they are not directly involved in a social movement.

4. The aim of this module is to introduce these different scientific and operational fields. The aim is to provide students with benchmarks and food for thought, enabling them to construct scientific questions on the relationship between society and the environment, and to reflect on the ways in which current environmental and social issues can be tackled. The speakers' varied geographical and disciplinary backgrounds will illustrate the approach across a wide range of ecosystem types, socio-cultural contexts and themes. In the time available, we cannot claim to cover all the themes, approaches and methods exhaustively. Any student wishing to delve deeper into this field will need to take a more in-depth training course.

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"The general aim is to give students the basic knowledge they need to understand international ecopolitics and the main paradigms that underpin them: international environmental agreements and commitments and their implementation in a Southern context; players on the international scene the place and role of donors and the strategies of environmental NGOs; the standards and instruments they tend to disseminate."

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The aim of this course is to help students finalize their professional projects and prepare for the post-master's period.

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

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The individual M2 internship lasts approximately 5 to 6 months, and must be carried out in a research laboratory or a non-academic structure, depending on the course. It enables 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 structure, on a subject validated by the teaching team to fit in with the objectives of the course followed by the student.

Evaluation: The internship is evaluated at a public presentation before a jury, during which the content of the thesis and the quality of the answers to the jury's questions are assessed. The student's behavior and dynamism during the internship are evaluated by the internship supervisor.

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