BIODIVERSITY, ECOLOGY AND EVOLUTION

"This UE will take the form of a series of a dozen lectures/seminars on current research themes in vertebrate paleontology and evolutionary biology; biodiversity and paleobiodiversity of continental ecosystems (animal); topographical and climatic barriers vs. dispersal and vicariance; community structuring, trophic chains through time and paleoguilds; role of Geodynamics and contingency (crises). The main objective is to acquire a good knowledge of current research themes/axes in the paleontological/evolutionary community".

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Wherever possible, this UE will take the form of a one-week on-site internship (with accommodation). Placements may change from one year to the next, depending on discoveries and/or partnership proposals (public/private). This internship can therefore take different directions, with a "prospecting" approach and therefore an itinerant field or a more "excavation site" approach and therefore fixed. In all cases, the different objectives listed below will be addressed to perfect this week in the field, so that the different techniques are mastered as well as possible.

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In this course, we'll look at the main theoretical concepts of evolutionary processes through the fossil record. The aim is to reconcile microevolutionary mechanisms with macroevolution. Concepts covered include: species and intraspecific variability, speciation and evolutionary rhythms, adaptive radiation (ecological speciation) in the fossil record, targeted extinctions (migrant-autochthonous competition) or mass extinctions (major biological crises), evolutionary modalities (anagenesis and saltationism) observed in the fossil record, and a comprehensive review of microevolutionary mechanisms.

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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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This course provides the tools needed to analyze paleontological data.

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"The aim is to analyze the phylogenetic, developmental and functional constraints likely to have governed the morphological changes perceptible in the fossil record. The phylogenetic approach will be approached using reconstruction methods applicable to fossils (parsimony; cladistic analysis). Developmental and functional approaches (mainly odontology) will be illustrated by different methodologies developed on the Montpellier campus (notably X-ray microtomography). The critical review of reference articles in the field in question will give rise to an oral presentation followed by questions."

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Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on the changes in developmental mechanisms that explain current and past morphological diversity, and thus opens up an important bridge between biology and paleontology.

In the course of the module, we will use articles to discuss a number of evolutionary issues relevant to Evo-Devo approaches: the question of homology, the establishment and evolution of repeated structures, the genetic bases of development and the links between genome evolution and the evolution of form. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them to the scale of today's major groups and populations.

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Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies within species phylogenies, the ways in which evolutionary histories can be represented in tree form, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of this course. Distance methods highlight the difficulties of separating homology and homoplasy, and the need to build models of character evolution. The maximum parsimony cladistic approach illustrates the use of bootstrapping to estimate the strength of phylogeny nodes, and the impact of taxonomic sampling in detecting multiple substitutions.

Probabilistic approaches are presented and explored in greater depth. The attraction artifact of long branches leads to an introduction to probabilistic reasoning. The maximum likelihood method is used to calculate likelihood, to estimate model parameters by optimality, to construct different character evolution models, and to compare models. Bayesian inference introduces the distinction between density-based and optimality-based approaches. It then shows the a priori use of probability densities, the data-driven estimation of a posteriori distributions of model parameters, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the calculation and interpretation of tree and clade posterior probabilities. The importance of DNA, RNA and protein sequence evolution models and their improvement is emphasized.

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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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"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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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 phylogenetic tree is a central concept in biology for students in the "Biodiversity, Ecology & Evolution", "Biology Agrosciences" and "Eco-epidemiology" majors. To tackle phylogeny, this UE is divided into two successive parts of 22.5h each: "Phylogeny and Evolution (Basics)" (HAB708B) and "Phylogeny and Evolution (Advanced)" (HAB714B).

The following skills will be taught:

(i) History of the notion of evolution [Basics].

(ii) Phylogenetic systematics (characters, rules of taxonomy, molecular barcodes, genomics, alignment, homology and homoplasy, orthology and paralogy) [half in Basics; half in Advanced].

(iii) Phylogenetic representation (networks, trees, roots, dendrograms, topology, branch lengths) [Bases].

(iv) Distance-based phylogenetic inference methods [Advanced].

(v) The cladistic approach and the principle of maximum parsimony [Bases].

(vi) The probabilistic approach, the maximum likelihood principle, and sequence evolution models [Advanced].

(vii) Measures of phylogeny robustness (bootstrap, topology comparison, multigene corroboration, gene and species trees) [Advanced].

(viii) Applications to the phylogeny of some major taxonomic groups (Mammals, Eukaryotes) [Advanced]."

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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 phylogenetic tree is a central concept in biology for students in the "Biodiversity, Ecology & Evolution", "Biology Agrosciences" and "Eco-epidemiology" majors. To tackle phylogeny, this UE is divided into two successive parts of 22.5h each: "Phylogeny and Evolution (Basics)" (HAB708B) and "Phylogeny and Evolution (Advanced)" (HAB714B).

The following skills will be taught:

(i) History of the notion of evolution [Basics].

(ii) Phylogenetic systematics (characters, rules of taxonomy, molecular barcodes, genomics, alignment, homology and homoplasy, orthology and paralogy) [half in Basics; half in Advanced].

(iii) Phylogenetic representation (networks, trees, roots, dendrograms, topology, branch lengths) [Bases].

(iv) Distance-based phylogenetic inference methods [Advanced].

(v) The cladistic approach and the principle of maximum parsimony [Bases].

(vi) The probabilistic approach, the maximum likelihood principle, and sequence evolution models [Advanced].

(vii) Measures of phylogeny robustness (bootstrap, topology comparison, multigene corroboration, gene and species trees) [Advanced].

(viii) Applications to the phylogeny of some major taxonomic groups (Mammals, Eukaryotes) [Advanced]."

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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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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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"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 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 complement the first semester's teaching by developing the issues involved in the evolution of phenotypes and the main associated methodological approaches. Lessons will address the evolution of different types of traits (life-history traits, traits involved in reproductive strategies, traits involved in biotic interactions, quantitative traits). The main approaches covered include game-theoretic formalization, adaptive dynamics, quantitative genetic approaches and the work of confronting theoretical predictions with empirical data. Teaching includes:

1) lectures on the main concepts of evolutionary ecology;

2) tutorials focusing on document studies and exercises".

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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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- Firstly, to provide students with a solid foundation of computer knowledge and skills, enabling them to learn and use the bioinformatics tools used more specifically in evolution and ecology.

- Secondly, to make them aware of the need to produce reproducible results, and to introduce them to the key concepts and tools for doing so.

- Thirdly, to get students to work on concrete examples that can be used during their Master's internship and future professional life.

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"The Darwin Field School takes place over one week with the following objectives:

- Create a group dynamic and integration within the Master 2 DARWIN-BEE class.

- Analyze ecological issues in their technical, scientific and social dimensions (e.g. reintroduction operations).

- Addressing biodiversity management issues in a humanized protected area.

- Oral presentation and comparison of results to an audience; assessment of the course.

Activities in Florac :

- Discover the landscapes of the Causse Méjean.

- Understand the specific missions of the Cévennes National Park and its scientific knowledge acquisition policy.

- Study the example of vultures in the Causses, the capercaillie and the beaver in the CNP, and the chamois in the Gorges du Tarn.

- Work in 3 sub-groups on different scientific and ethical themes.

Activities around Montpellier :

- Study bird migration and Mediterranean coastal ecosystems.

- Practicing urban ecology.

- Discover the fauna of the Mediterranean scrublands, with daytime hikes along the Buèges (entomofauna discovery) and evening hikes (bat and/or moth and nocturnal orthopteran evenings)".

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The module covers the following fundamental themes in evolutionary biology: Micro evolution -Macro evolution, Fitness, Natural and sexual selves, Speciation. Other topics (mutation, epigenetics, evo-devo ...) are presented by the students themselves.

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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 design a research project on one of the major themes in ecology, such as the ecological niche, biogeography, networks of ecological interactions or functional diversity. A short review of the major theories and concepts in these major ecology themes is presented by specialists in the field. This is followed by example(s) illustrating the conceptual bases for formulating a relevant and new research question, and how to answer it using different methodologies, especially experimental ones, derived from the speakers' own research. Having chosen one of these major themes, each student develops an original research project (the size of an M2 internship), conducting bibliographical research and proposing a coherent experimental plan to test the hypotheses. This project is presented to the lecturers and other students.

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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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The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Themes such as health, sociality, culture, local adaptations, language, morality, reproduction and sexual preferences are addressed within the theoretical framework of evolutionary biology and ecology. EU contents: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of nutrition / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

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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. 

See full page

The courses present 4 aspects of Conservation Biology, based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): definition of Conservation Biology. Why conserve biodiversity? Who are the main players in BC and the role of science in BC. 
2. Species conservation: What are the priority species? How can species be conserved? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Theimportance of social acceptability and political commitment. Need for biodiversity indicators and to measure the impact of conservation. 

Students also carry out group work in which they present a BC project, based on the questions: why, what, where, how, how much does it cost and how do we know if it's effective? 

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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.

See full page

Quantitative genetics is a discipline that emerged in the early 20th century to understand the heredity of continuous traits, i.e. the majority of traits of agronomic interest (yield, etc.) or evolutionary interest (life-history traits, morphology). It is therefore an essential tool for understanding, modeling and predicting natural or artificial selection, and the evolution of natural systems or cultivated plants/animals. Its relevance is more relevant than ever at the start of the 21st century, with the advent of genomics (a factor of scientific progress, provided we don't reduce every evolutionary problem to the fiction of a few Mendelian alleles with a strong effect), and the return in force of alternative models of heredity (epigenetics) going beyond the sequence-centric vision inherited from classical molecular biology.

The aim of the module is to provide a culture of quantitative genetics sufficient to (i) understand the classical foundations of the discipline, manipulate the key quantities (genetic variances, heritabilities, genetic correlations) and the statistical techniques for estimating these parameters (ii) understand the power of this technique for posing and understanding fundamental or applied evolutionary problems (agronomic improvement) (iii) understand how this formalization of heredity fits in with the classical Mendelian vision.

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The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Themes such as health, sociality, culture, local adaptations, language, morality, reproduction and sexual preferences are addressed within the theoretical framework of evolutionary biology and ecology. EU contents: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of nutrition / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

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Behavioral Ecology takes an evolutionary approach to the study of behavior, investigating its mechanisms, function and contribution to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps us to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrae, exhibit behaviors.

The module exposes students to the various basic concepts, as well as to the multitude of tools likely to be used (observations and experiments on natural populations or captive individuals, comparative analyses, use of modeling tools, ecophysiology, molecular biology, biochemistry, on-board electronics, etc.). Part of the training is based on specific discussions of the research approaches likely to be employed, the tools used and the limits of the inferences that can be made. Students will be expected to play an active role at all these levels, in particular through critical discussions of articles.

Topics range from the exploration of strategies for food provisioning, mate choice, habitat selection and investment in reproduction, to the study of animal communication and the reasons for group living. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibilities of the contributors and the themes addressed (meaning and relationships between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc.).

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The module addresses the theoretical and empirical advances of recent research in evolutionary genetics through a number of major issues:

- theme 1: genetic burden and evolution of reproductive systems: recombination, sex/asex, auto/allofecundation

- theme 2: kinship structures and their evolutionary consequences: kinship selection, group selection, evolution of cooperation, sex ratios

- theme 3: sustainable interactions between species: parasitism, mutualism, coevolution

- theme 4: traces of evolutionary history in genomes, genomics of adaptation.

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The main aim of this course is to provide the skills needed to understand and use the concepts and methods on which the quantitative study of population phenomena is based. The main methods for analyzing and modeling these phenomena will be approached from both a theoretical (formal calculations) and practical (statistics, simulations) point of view, using examples exploring different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and steady-state regimes, eco-evolutionary coupling), with particular attention to the heterogeneity (spatial, genetic or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent to their study.

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The aim of this EU is to show that biological diversity is functional:

1) for different groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different scales of organization (from organisms to ecosystems). The aim of the lessons is to explain how to approach this functional facet of diversity for the 10+ million organisms present on the planet's surface, taking examples from both highly and less anthropized environments.

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Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies within species phylogenies, the ways in which evolutionary histories can be represented in tree form, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of this course. Distance methods highlight the difficulties of separating homology and homoplasy, and the need to build models of character evolution. The maximum parsimony cladistic approach illustrates the use of bootstrapping to estimate the strength of phylogeny nodes, and the impact of taxonomic sampling in detecting multiple substitutions.

Probabilistic approaches are presented and explored in greater depth. The attraction artifact of long branches leads to an introduction to probabilistic reasoning. The maximum likelihood method is used to calculate likelihood, to estimate model parameters by optimality, to construct different character evolution models, and to compare models. Bayesian inference introduces the distinction between density-based and optimality-based approaches. It then shows the a priori use of probability densities, the data-driven estimation of a posteriori distributions of model parameters, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the calculation and interpretation of tree and clade posterior probabilities. The importance of DNA, RNA and protein sequence evolution models and their improvement is emphasized.

See full page

Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on the changes in developmental mechanisms that explain current and past morphological diversity, and thus opens up an important bridge between biology and paleontology.

In the course of the module, we will use articles to discuss a number of evolutionary issues relevant to Evo-Devo approaches: the question of homology, the establishment and evolution of repeated structures, the genetic bases of development and the links between genome evolution and the evolution of form. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them to the scale of today's major groups and populations.

See full page

See full page

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. 

See full page

The courses present 4 aspects of Conservation Biology, based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): definition of Conservation Biology. Why conserve biodiversity? Who are the main players in BC and the role of science in BC. 
2. Species conservation: What are the priority species? How can species be conserved? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Theimportance of social acceptability and political commitment. Need for biodiversity indicators and to measure the impact of conservation. 

Students also carry out group work in which they present a BC project, based on the questions: why, what, where, how, how much does it cost and how do we know if it's effective? 

See full page

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.

See full page

Quantitative genetics is a discipline that emerged in the early 20th century to understand the heredity of continuous traits, i.e. the majority of traits of agronomic interest (yield, etc.) or evolutionary interest (life-history traits, morphology). It is therefore an essential tool for understanding, modeling and predicting natural or artificial selection, and the evolution of natural systems or cultivated plants/animals. Its relevance is more relevant than ever at the start of the 21st century, with the advent of genomics (a factor of scientific progress, provided we don't reduce every evolutionary problem to the fiction of a few Mendelian alleles with a strong effect), and the return in force of alternative models of heredity (epigenetics) going beyond the sequence-centric vision inherited from classical molecular biology.

The aim of the module is to provide a culture of quantitative genetics sufficient to (i) understand the classical foundations of the discipline, manipulate the key quantities (genetic variances, heritabilities, genetic correlations) and the statistical techniques for estimating these parameters (ii) understand the power of this technique for posing and understanding fundamental or applied evolutionary problems (agronomic improvement) (iii) understand how this formalization of heredity fits in with the classical Mendelian vision.

See full page

The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Themes such as health, sociality, culture, local adaptations, language, morality, reproduction and sexual preferences are addressed within the theoretical framework of evolutionary biology and ecology. EU contents: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of nutrition / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

See full page

Behavioral Ecology takes an evolutionary approach to the study of behavior, investigating its mechanisms, function and contribution to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps us to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrae, exhibit behaviors.

The module exposes students to the various basic concepts, as well as to the multitude of tools likely to be used (observations and experiments on natural populations or captive individuals, comparative analyses, use of modeling tools, ecophysiology, molecular biology, biochemistry, on-board electronics, etc.). Part of the training is based on specific discussions of the research approaches likely to be employed, the tools used and the limits of the inferences that can be made. Students will be expected to play an active role at all these levels, in particular through critical discussions of articles.

Topics range from the exploration of strategies for food provisioning, mate choice, habitat selection and investment in reproduction, to the study of animal communication and the reasons for group living. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibilities of the contributors and the themes addressed (meaning and relationships between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc.).

See full page

See full page

See full page

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. 

See full page

The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Themes such as health, sociality, culture, local adaptations, language, morality, reproduction and sexual preferences are addressed within the theoretical framework of evolutionary biology and ecology. EU contents: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of nutrition / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

See full page

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. 

See full page

The courses present 4 aspects of Conservation Biology, based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): definition of Conservation Biology. Why conserve biodiversity? Who are the main players in BC and the role of science in BC. 
2. Species conservation: What are the priority species? How can species be conserved? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Theimportance of social acceptability and political commitment. Need for biodiversity indicators and to measure the impact of conservation. 

Students also carry out group work in which they present a BC project, based on the questions: why, what, where, how, how much does it cost and how do we know if it's effective? 

See full page

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.

See full page

Quantitative genetics is a discipline that emerged in the early 20th century to understand the heredity of continuous traits, i.e. the majority of traits of agronomic interest (yield, etc.) or evolutionary interest (life-history traits, morphology). It is therefore an essential tool for understanding, modeling and predicting natural or artificial selection, and the evolution of natural systems or cultivated plants/animals. Its relevance is more relevant than ever at the start of the 21st century, with the advent of genomics (a factor of scientific progress, provided we don't reduce every evolutionary problem to the fiction of a few Mendelian alleles with a strong effect), and the return in force of alternative models of heredity (epigenetics) going beyond the sequence-centric vision inherited from classical molecular biology.

The aim of the module is to provide a culture of quantitative genetics sufficient to (i) understand the classical foundations of the discipline, manipulate the key quantities (genetic variances, heritabilities, genetic correlations) and the statistical techniques for estimating these parameters (ii) understand the power of this technique for posing and understanding fundamental or applied evolutionary problems (agronomic improvement) (iii) understand how this formalization of heredity fits in with the classical Mendelian vision.

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The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Themes such as health, sociality, culture, local adaptations, language, morality, reproduction and sexual preferences are addressed within the theoretical framework of evolutionary biology and ecology. EU contents: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of nutrition / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

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Behavioral Ecology takes an evolutionary approach to the study of behavior, investigating its mechanisms, function and contribution to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps us to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrae, exhibit behaviors.

The module exposes students to the various basic concepts, as well as to the multitude of tools likely to be used (observations and experiments on natural populations or captive individuals, comparative analyses, use of modeling tools, ecophysiology, molecular biology, biochemistry, on-board electronics, etc.). Part of the training is based on specific discussions of the research approaches likely to be employed, the tools used and the limits of the inferences that can be made. Students will be expected to play an active role at all these levels, in particular through critical discussions of articles.

Topics range from the exploration of strategies for food provisioning, mate choice, habitat selection and investment in reproduction, to the study of animal communication and the reasons for group living. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibilities of the contributors and the themes addressed (meaning and relationships between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc.).

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The module addresses the theoretical and empirical advances of recent research in evolutionary genetics through a number of major issues:

- theme 1: genetic burden and evolution of reproductive systems: recombination, sex/asex, auto/allofecundation

- theme 2: kinship structures and their evolutionary consequences: kinship selection, group selection, evolution of cooperation, sex ratios

- theme 3: sustainable interactions between species: parasitism, mutualism, coevolution

- theme 4: traces of evolutionary history in genomes, genomics of adaptation.

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The main aim of this course is to provide the skills needed to understand and use the concepts and methods on which the quantitative study of population phenomena is based. The main methods for analyzing and modeling these phenomena will be approached from both a theoretical (formal calculations) and practical (statistics, simulations) point of view, using examples exploring different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and steady-state regimes, eco-evolutionary coupling), with particular attention to the heterogeneity (spatial, genetic or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent to their study.

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The aim of this EU is to show that biological diversity is functional:

1) for different groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different scales of organization (from organisms to ecosystems). The aim of the lessons is to explain how to approach this functional facet of diversity for the 10+ million organisms present on the planet's surface, taking examples from both highly and less anthropized environments.

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Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies within species phylogenies, the ways in which evolutionary histories can be represented in tree form, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of this course. Distance methods highlight the difficulties of separating homology and homoplasy, and the need to build models of character evolution. The maximum parsimony cladistic approach illustrates the use of bootstrapping to estimate the strength of phylogeny nodes, and the impact of taxonomic sampling in detecting multiple substitutions.

Probabilistic approaches are presented and explored in greater depth. The attraction artifact of long branches leads to an introduction to probabilistic reasoning. The maximum likelihood method is used to calculate likelihood, to estimate model parameters by optimality, to construct different character evolution models, and to compare models. Bayesian inference introduces the distinction between density-based and optimality-based approaches. It then shows the a priori use of probability densities, the data-driven estimation of a posteriori distributions of model parameters, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the calculation and interpretation of tree and clade posterior probabilities. The importance of DNA, RNA and protein sequence evolution models and their improvement is emphasized.

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Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on the changes in developmental mechanisms that explain current and past morphological diversity, and thus opens up an important bridge between biology and paleontology.

In the course of the module, we will use articles to discuss a number of evolutionary issues relevant to Evo-Devo approaches: the question of homology, the establishment and evolution of repeated structures, the genetic bases of development and the links between genome evolution and the evolution of form. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them to the scale of today's major groups and populations.

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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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The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Themes such as health, sociality, culture, local adaptations, language, morality, reproduction and sexual preferences are addressed within the theoretical framework of evolutionary biology and ecology. EU contents: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of nutrition / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

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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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The courses present 4 aspects of Conservation Biology, based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): definition of Conservation Biology. Why conserve biodiversity? Who are the main players in BC and the role of science in BC. 
2. Species conservation: What are the priority species? How can species be conserved? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Theimportance of social acceptability and political commitment. Need for biodiversity indicators and to measure the impact of conservation. 

Students also carry out group work in which they present a BC project, based on the questions: why, what, where, how, how much does it cost and how do we know if it's effective? 

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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.

See full page

Quantitative genetics is a discipline that emerged in the early 20th century to understand the heredity of continuous traits, i.e. the majority of traits of agronomic interest (yield, etc.) or evolutionary interest (life-history traits, morphology). It is therefore an essential tool for understanding, modeling and predicting natural or artificial selection, and the evolution of natural systems or cultivated plants/animals. Its relevance is more relevant than ever at the start of the 21st century, with the advent of genomics (a factor of scientific progress, provided we don't reduce every evolutionary problem to the fiction of a few Mendelian alleles with a strong effect), and the return in force of alternative models of heredity (epigenetics) going beyond the sequence-centric vision inherited from classical molecular biology.

The aim of the module is to provide a culture of quantitative genetics sufficient to (i) understand the classical foundations of the discipline, manipulate the key quantities (genetic variances, heritabilities, genetic correlations) and the statistical techniques for estimating these parameters (ii) understand the power of this technique for posing and understanding fundamental or applied evolutionary problems (agronomic improvement) (iii) understand how this formalization of heredity fits in with the classical Mendelian vision.

See full page

The general objective is to present human evolutionary biology, proposing to mobilize the tools of evolutionary biology to better understand human behaviors and those observed in non-human primates in the context of their evolutionary history. Themes such as health, sociality, culture, local adaptations, language, morality, reproduction and sexual preferences are addressed within the theoretical framework of evolutionary biology and ecology. EU contents: Anthropology, human sciences and evolutionary biology / Evolution of cooperation / Cultural evolution / Evolution of nutrition / Evolution of sociality in primates / Family ecology / Medicine, public health and evolution / Evolution of language / Evolutionary demography / The origins of equity.

See full page

Behavioral Ecology takes an evolutionary approach to the study of behavior, investigating its mechanisms, function and contribution to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps us to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrae, exhibit behaviors.

The module exposes students to the various basic concepts, as well as to the multitude of tools likely to be used (observations and experiments on natural populations or captive individuals, comparative analyses, use of modeling tools, ecophysiology, molecular biology, biochemistry, on-board electronics, etc.). Part of the training is based on specific discussions of the research approaches likely to be employed, the tools used and the limits of the inferences that can be made. Students will be expected to play an active role at all these levels, in particular through critical discussions of articles.

Topics range from the exploration of strategies for food provisioning, mate choice, habitat selection and investment in reproduction, to the study of animal communication and the reasons for group living. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibilities of the contributors and the themes addressed (meaning and relationships between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc.).

See full page

The module addresses the theoretical and empirical advances of recent research in evolutionary genetics through a number of major issues:

- theme 1: genetic burden and evolution of reproductive systems: recombination, sex/asex, auto/allofecundation

- theme 2: kinship structures and their evolutionary consequences: kinship selection, group selection, evolution of cooperation, sex ratios

- theme 3: sustainable interactions between species: parasitism, mutualism, coevolution

- theme 4: traces of evolutionary history in genomes, genomics of adaptation.

See full page

The main aim of this course is to provide the skills needed to understand and use the concepts and methods on which the quantitative study of population phenomena is based. The main methods for analyzing and modeling these phenomena will be approached from both a theoretical (formal calculations) and practical (statistics, simulations) point of view, using examples exploring different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and steady-state regimes, eco-evolutionary coupling), with particular attention to the heterogeneity (spatial, genetic or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent to their study.

See full page

The aim of this EU is to show that biological diversity is functional:

1) for different groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different scales of organization (from organisms to ecosystems). The aim of the lessons is to explain how to approach this functional facet of diversity for the 10+ million organisms present on the planet's surface, taking examples from both highly and less anthropized environments.

See full page

Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies within species phylogenies, the ways in which evolutionary histories can be represented in tree form, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of this course. Distance methods highlight the difficulties of separating homology and homoplasy, and the need to build models of character evolution. The maximum parsimony cladistic approach illustrates the use of bootstrapping to estimate the strength of phylogeny nodes, and the impact of taxonomic sampling in detecting multiple substitutions.

Probabilistic approaches are presented and explored in greater depth. The attraction artifact of long branches leads to an introduction to probabilistic reasoning. The maximum likelihood method is used to calculate likelihood, to estimate model parameters by optimality, to construct different character evolution models, and to compare models. Bayesian inference introduces the distinction between density-based and optimality-based approaches. It then shows the a priori use of probability densities, the data-driven estimation of a posteriori distributions of model parameters, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the calculation and interpretation of tree and clade posterior probabilities. The importance of DNA, RNA and protein sequence evolution models and their improvement is emphasized.

See full page

Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on the changes in developmental mechanisms that explain current and past morphological diversity, and thus opens up an important bridge between biology and paleontology.

In the course of the module, we will use articles to discuss a number of evolutionary issues relevant to Evo-Devo approaches: the question of homology, the establishment and evolution of repeated structures, the genetic bases of development and the links between genome evolution and the evolution of form. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them to the scale of today's major groups and populations.

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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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https://www.evobio.eu/summer-school

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Each year, teachers will suggest a number of topics, from which students will choose (the list will be neither binding nor exhaustive: any topic that relates to evolution is fair game). Working in groups of two or three people, the students will be responsible for presenting the topic they have chosen. Each person in a group should participate equally in these presentations. Each group will be given a small selection of recent papers that they will use to begin to explore the topic, or the groups will themselves propose pertinent papers. Among these, the group will distribute (one week before the class session) one-two papers that everyone should read before class. The group will be responsible for presenting the topicto the rest of the class and leading discussion of it. The group presentation should explain why the topic is interesting and present the state of the art, outlining points ofcontroversy and defining big open questions. The presentation format will be defined by the group, keeping in mind that it should open discussions. For the last session(s) at the end of the course, students will give short individual presentations providing a recap of some aspect(s) of another group's topic. In addition to the main hot topic presentations, there will be a brief 'writing summaries' exercise at the beginning of the course, and regular "news & views" briefings of recent articles picked by the students from journals of their choice.

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https://www.umontpellier.fr/en/research

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Starting from scratch for analysing biological data: describing, testing and modelling simple experimental protocols;

Getting to know fundamental properties of linear models dealing with simple regressions and simple ANOVAs;

Incorporating into models the essence of biological data: co-linearity, dependence, spatial structure, laws that are not normal....

Representing data and results from models.

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Modelling is a methodology that is frequently used in biological sciences nowadays, in particular in ecological and evolutionary studies. However, models usually frighten students. The aim of this initiation is to show that modelling is by no means more inaccessible than other techniques in biology. The goal is to give students a feel of how a model is constructed, to be able to spot the key assumptions behind a result, and to test their validity. The course will seek to familiarize the students with several basic modelling techniques and tools.

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This one week course will be offered at least in winter 2020 (and in following years if independent funding can be secured). It will be organised as a retreat during which students will write in small groups grant proposals on Evolutionary Biology topics.

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The course discusses cases where evolutionary biology based implementations provide invaluable insight in applied issues such as vector control, conservation biology or fish stock management.

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"The objectives of this course are threefold: (i) to remind students of the theoretical bases of some essential concepts of population genetics theory; (ii) to detail some "classical" inference methods (e.g., F-statistics) and more "modern" approaches (based, e.g., on coalescent theory); (iii) to show how demographic history may be inferred from the analysis of genetic polymorphisms."

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The objective of this course is to provide the theoretical background for understanding, and potentially being able to use and apply the principles of how selection will affect the evolution of populations. Y. Michalakis describes the basics of selection theory and shows with elementary algebra that it is possible to derive some fundamental results in Population Genetics, such as Fisher's Fundamental Theorem. He also gives an introduction to mutation-_selection balance and two--locus theory. The latter topics are put in perspective in the courses by T. Lenormand on the evolution of sexual reproduction, migration and local adaptation. T. Lenormand also presents the theory that allows understanding the dynamics of adaptation. G. Martin's courses explain how stochastic effects interact with selection to influence the fate of adaptive mutations.

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https://www.evobio.eu/semester-3-4

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https://www.evobio.eu/summer-school

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"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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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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ORPAL is an APP course (1/3 fieldwork and 2/3 laboratory work). Work is carried out in pairs or trios under the responsibility of a supervisor, and covers the entire research process, from defining the problem, field sampling and data acquisition to interpretation, writing a scientific article (see https://biologie-ecologie.com/exemples-travaux/) and oral presentation of results.

The ORPAM program begins in the first weeks of teaching. It begins with a 3-day field school (24h - integration internship) and continues with a mini-laboratory internship (24h). The course ends with the writing of a popular scientific article and an oral presentation of the results.

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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 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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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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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 complement the first semester's teaching by developing the issues involved in the evolution of phenotypes and the main associated methodological approaches. Lessons will address the evolution of different types of traits (life-history traits, traits involved in reproductive strategies, traits involved in biotic interactions, quantitative traits). The main approaches covered include game-theoretic formalization, adaptive dynamics, quantitative genetic approaches and the work of confronting theoretical predictions with empirical data. Teaching includes:

1) lectures on the main concepts of evolutionary ecology;

2) tutorials focusing on document studies and exercises".

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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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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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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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Ecophysiology is a discipline at the interface between organismal biology and ecology. Integrative ecophysiology focuses in particular on the question of change of scale. In other words, the aim of this course is to illustrate how the study of acclimatization/adaptation mechanisms on an individual (or even sub-individual) scale can explain the structure of populations, the distribution of species and the functioning of ecosystems. The responses of organisms and populations to the main abiotic structuring parameters (such as temperature, salinity, oxygen availability, pollutants) will be considered, as well as their interactive effects. The role of interactions between organisms will also be addressed. In this course, animals, plants and micro-organisms will be considered, and different types of approach will be illustrated: field observations, in situ or laboratory experiments.

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The main aim of this course is to provide the skills needed to understand and use the concepts and methods on which the quantitative study of population phenomena is based. The main methods for analyzing and modeling these phenomena will be approached from both a theoretical (formal calculations) and practical (statistics, simulations) point of view, using examples exploring different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and steady-state regimes, eco-evolutionary coupling), with particular attention to the heterogeneity (spatial, genetic or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent to their study.

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This course aims to provide a better understanding of the main types of pollutants (organic vs. inorganic), their source(s), their fate in the environment and how they interact with living organisms (bioaccumulation, biotransformation, effects). The methods used in depollution and bioremediation will be discussed. Particular emphasis will be placed on the contribution of terrestrial and aquatic plants to phytoremediation, and on the role of micro-organisms (bacteria, fungi) in biodegradation, biotransformation or biosequestration mechanisms. This course will be illustrated by a number of case studies, covering examples of chronic and acute/accidental pollution of water, air and soil. In particular, the treatment of pollution linked to the mining, oil, plastics and phyto-pharmaceutical industries will be covered, as will the treatment of liquid effluents (wastewater, industrial effluents). A field trip to Saint-Laurent-Le-Minier will illustrate a current phytoremediation project on a former mining site.

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The aim of this EU is to show that biological diversity is functional:

1) for different groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different scales of organization (from organisms to ecosystems). The aim of the lessons is to explain how to approach this functional facet of diversity for the 10+ million organisms present on the planet's surface, taking examples from both highly and less anthropized environments.

See full page

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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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The module aims to provide theoretical and practical knowledge of statistical analysis of spatial and temporal constraints: classification and ordering under constraints, '2-table ordering methods and statistical tests: canonical analyses (AFD, CCA, RDA, CAP), 'statistical tests on distance matrices, comparison of matrices (PERMANOVA, Mantel, Procrustes).

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The courses present 4 aspects of Conservation Biology, based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): definition of Conservation Biology. Why conserve biodiversity? Who are the main players in BC and the role of science in BC. 
2. Species conservation: What are the priority species? How can species be conserved? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Theimportance of social acceptability and political commitment. Need for biodiversity indicators and to measure the impact of conservation. 

Students also carry out group work in which they present a BC project, based on the questions: why, what, where, how, how much does it cost and how do we know if it's effective? 

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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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"I - Physical characterization and biogeochemical cycles of coastal marine ecosystems II - Biodiversity and functioning of coastal marine ecosystems III Coastal and marine law; Uses, conflicts and integrated management of the coastal zone. This course offers students a systemic approach to the study of coastal marine ecosystems from a highly multidisciplinary perspective. The physical structure of these ecosystems will be addressed through courses on their geomorphology and hydrology, with a particular focus on hydric couplings with the open sea and their watersheds. Their biogeochemistry will be addressed, in particular to describe carbon and nutrient flows through the water and sediment compartments. Several aspects of their biodiversity will be illustrated to describe the importance of these ecosystems as living environments for the species they support, and in particular the role of this biodiversity in their functioning. The coastal zone is densely populated by man (40% of the world's population). Particular attention will be paid to human uses (e.g. aquaculture) and their territorial planning, including the evaluation of their ecosystem services in an economic context, management and protection measures (e.g. Marine Protected Areas, Natura 2000), and professionals involved in the management of these environments will present practical feedback. Finally, the implications of the Law of the Sea for the management of coastal zones will be discussed. "

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The module covers the identification, quantification and modeling of interactions between climate, marine species and their exploitation.

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Behavioral Ecology takes an evolutionary approach to the study of behavior, investigating its mechanisms, function and contribution to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps us to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrae, exhibit behaviors.

The module exposes students to the various basic concepts, as well as to the multitude of tools likely to be used (observations and experiments on natural populations or captive individuals, comparative analyses, use of modeling tools, ecophysiology, molecular biology, biochemistry, on-board electronics, etc.). Part of the training is based on specific discussions of the research approaches likely to be employed, the tools used and the limits of the inferences that can be made. Students will be expected to play an active role at all these levels, in particular through critical discussions of articles.

Topics range from the exploration of strategies for food provisioning, mate choice, habitat selection and investment in reproduction, to the study of animal communication and the reasons for group living. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibilities of the contributors and the themes addressed (meaning and relationships between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc.).

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The aim of this resolutely trans-disciplinary course is to provide the skills needed to effectively manage and exploit data of various origins and types, particularly those with a spatial component. The course is divided into three complementary sections. The first deals with the issues inherent in data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second covers geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third axis presents the diversity of spatial analysis tools for quantitative exploitation of spatial data, from metrics to statistical tests.

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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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Ecophysiology is a discipline at the interface between organismal biology and ecology. Integrative ecophysiology focuses in particular on the question of change of scale. In other words, the aim of this course is to illustrate how the study of acclimatization/adaptation mechanisms on an individual (or even sub-individual) scale can explain the structure of populations, the distribution of species and the functioning of ecosystems. The responses of organisms and populations to the main abiotic structuring parameters (such as temperature, salinity, oxygen availability, pollutants) will be considered, as well as their interactive effects. The role of interactions between organisms will also be addressed. In this course, animals, plants and micro-organisms will be considered, and different types of approach will be illustrated: field observations, in situ or laboratory experiments.

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The main aim of this course is to provide the skills needed to understand and use the concepts and methods on which the quantitative study of population phenomena is based. The main methods for analyzing and modeling these phenomena will be approached from both a theoretical (formal calculations) and practical (statistics, simulations) point of view, using examples exploring different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and steady-state regimes, eco-evolutionary coupling), with particular attention to the heterogeneity (spatial, genetic or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent to their study.

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This course aims to provide a better understanding of the main types of pollutants (organic vs. inorganic), their source(s), their fate in the environment and how they interact with living organisms (bioaccumulation, biotransformation, effects). The methods used in depollution and bioremediation will be discussed. Particular emphasis will be placed on the contribution of terrestrial and aquatic plants to phytoremediation, and on the role of micro-organisms (bacteria, fungi) in biodegradation, biotransformation or biosequestration mechanisms. This course will be illustrated by a number of case studies, covering examples of chronic and acute/accidental pollution of water, air and soil. In particular, the treatment of pollution linked to the mining, oil, plastics and phyto-pharmaceutical industries will be covered, as will the treatment of liquid effluents (wastewater, industrial effluents). A field trip to Saint-Laurent-Le-Minier will illustrate a current phytoremediation project on a former mining site.

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The aim of this EU is to show that biological diversity is functional:

1) for different groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different scales of organization (from organisms to ecosystems). The aim of the lessons is to explain how to approach this functional facet of diversity for the 10+ million organisms present on the planet's surface, taking examples from both highly and less anthropized environments.

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The aim of this resolutely trans-disciplinary course is to provide the skills needed to effectively manage and exploit data of various origins and types, particularly those with a spatial component. The course is divided into three complementary sections. The first deals with the issues inherent in data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second covers geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third axis presents the diversity of spatial analysis tools for quantitative exploitation of spatial data, from metrics to statistical tests.

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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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The module aims to provide theoretical and practical knowledge of statistical analysis of spatial and temporal constraints: classification and ordering under constraints, '2-table ordering methods and statistical tests: canonical analyses (AFD, CCA, RDA, CAP), 'statistical tests on distance matrices, comparison of matrices (PERMANOVA, Mantel, Procrustes).

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The courses present 4 aspects of Conservation Biology, based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): definition of Conservation Biology. Why conserve biodiversity? Who are the main players in BC and the role of science in BC. 
2. Species conservation: What are the priority species? How can species be conserved? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Theimportance of social acceptability and political commitment. Need for biodiversity indicators and to measure the impact of conservation. 

Students also carry out group work in which they present a BC project, based on the questions: why, what, where, how, how much does it cost and how do we know if it's effective? 

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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.

See full page

"I - Physical characterization and biogeochemical cycles of coastal marine ecosystems II - Biodiversity and functioning of coastal marine ecosystems III Coastal and marine law; Uses, conflicts and integrated management of the coastal zone. This course offers students a systemic approach to the study of coastal marine ecosystems from a highly multidisciplinary perspective. The physical structure of these ecosystems will be addressed through courses on their geomorphology and hydrology, with a particular focus on hydric couplings with the open sea and their watersheds. Their biogeochemistry will be addressed, in particular to describe carbon and nutrient flows through the water and sediment compartments. Several aspects of their biodiversity will be illustrated to describe the importance of these ecosystems as living environments for the species they support, and in particular the role of this biodiversity in their functioning. The coastal zone is densely populated by man (40% of the world's population). Particular attention will be paid to human uses (e.g. aquaculture) and their territorial planning, including the evaluation of their ecosystem services in an economic context, management and protection measures (e.g. Marine Protected Areas, Natura 2000), and professionals involved in the management of these environments will present practical feedback. Finally, the implications of the Law of the Sea for the management of coastal zones will be discussed. "

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The module covers the identification, quantification and modeling of interactions between climate, marine species and their exploitation.

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Behavioral Ecology takes an evolutionary approach to the study of behavior, investigating its mechanisms, function and contribution to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps us to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrae, exhibit behaviors.

The module exposes students to the various basic concepts, as well as to the multitude of tools likely to be used (observations and experiments on natural populations or captive individuals, comparative analyses, use of modeling tools, ecophysiology, molecular biology, biochemistry, on-board electronics, etc.). Part of the training is based on specific discussions of the research approaches likely to be employed, the tools used and the limits of the inferences that can be made. Students will be expected to play an active role at all these levels, in particular through critical discussions of articles.

Topics range from the exploration of strategies for food provisioning, mate choice, habitat selection and investment in reproduction, to the study of animal communication and the reasons for group living. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibilities of the contributors and the themes addressed (meaning and relationships between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc.).

See full page

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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. 

See full page

The module aims to provide theoretical and practical knowledge of statistical analysis of spatial and temporal constraints: classification and ordering under constraints, '2-table ordering methods and statistical tests: canonical analyses (AFD, CCA, RDA, CAP), 'statistical tests on distance matrices, comparison of matrices (PERMANOVA, Mantel, Procrustes).

See full page

The courses present 4 aspects of Conservation Biology, based on current scientific research in this discipline:  

1. Introduction to Biodiversity Conservation(BC): definition of Conservation Biology. Why conserve biodiversity? Who are the main players in BC and the role of science in BC. 
2. Species conservation: What are the priority species? How can species be conserved? How do you know if a species is "well conserved"? 
3. Space conservation: What are the priority spaces? How to conserve spaces? 
4. Theimportance of social acceptability and political commitment. Need for biodiversity indicators and to measure the impact of conservation. 

Students also carry out group work in which they present a BC project, based on the questions: why, what, where, how, how much does it cost and how do we know if it's effective? 

See full page

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.

See full page

"I - Physical characterization and biogeochemical cycles of coastal marine ecosystems II - Biodiversity and functioning of coastal marine ecosystems III Coastal and marine law; Uses, conflicts and integrated management of the coastal zone. This course offers students a systemic approach to the study of coastal marine ecosystems from a highly multidisciplinary perspective. The physical structure of these ecosystems will be addressed through courses on their geomorphology and hydrology, with a particular focus on hydric couplings with the open sea and their watersheds. Their biogeochemistry will be addressed, in particular to describe carbon and nutrient flows through the water and sediment compartments. Several aspects of their biodiversity will be illustrated to describe the importance of these ecosystems as living environments for the species they support, and in particular the role of this biodiversity in their functioning. The coastal zone is densely populated by man (40% of the world's population). Particular attention will be paid to human uses (e.g. aquaculture) and their territorial planning, including the evaluation of their ecosystem services in an economic context, management and protection measures (e.g. Marine Protected Areas, Natura 2000), and professionals involved in the management of these environments will present practical feedback. Finally, the implications of the Law of the Sea for the management of coastal zones will be discussed. "

See full page

The module covers the identification, quantification and modeling of interactions between climate, marine species and their exploitation.

See full page

Behavioral Ecology takes an evolutionary approach to the study of behavior, investigating its mechanisms, function and contribution to evolutionary and ecological processes. The work carried out in Behavioral Ecology helps us to understand other phenomena observed in other disciplines of life biology, because all animals, from unicellulars to the most complex vertebrae, exhibit behaviors.

The module exposes students to the various basic concepts, as well as to the multitude of tools likely to be used (observations and experiments on natural populations or captive individuals, comparative analyses, use of modeling tools, ecophysiology, molecular biology, biochemistry, on-board electronics, etc.). Part of the training is based on specific discussions of the research approaches likely to be employed, the tools used and the limits of the inferences that can be made. Students will be expected to play an active role at all these levels, in particular through critical discussions of articles.

Topics range from the exploration of strategies for food provisioning, mate choice, habitat selection and investment in reproduction, to the study of animal communication and the reasons for group living. The historical dimension of the discipline is addressed in the introduction, but also according to the sensibilities of the contributors and the themes addressed (meaning and relationships between 'Animal Behaviour', 'Ethology', Behavioral Ecology etc.).

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The aim is to master the modeling and statistical analysis of ecosystem data. Students should be able to model complex systems (e.g. plants in a cultivated ecosystem, population dynamics, lake ecosystems). They will also need to know what type of statistical model to use to process ecological data, and how to interpret it.

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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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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 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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"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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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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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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Drawing on Ecology concepts and methods, this course aims to introduce students to historical ecology (the study of interactions between man and his environment over variable chronological periods) and its main applications in paleoecology and environmental science: climate change, biodiversity fluctuations, vegetation transformation, forest dynamics, disturbance ecology, bioarchaeology, etc. ORPAL is an APP course (1/3 fieldwork and 2/3 laboratory work). Work is carried out in pairs or trios, under the responsibility of a supervisor, and covers the entire research process, from defining the problem, field sampling and data acquisition to interpretation, writing a scientific article (see https://biologie-ecologie.com/exemples-travaux/) and oral presentation of results. ORPAM takes place during the first weeks of teaching. It begins with a 3-day field school (24h - integration internship) and continues with a mini-laboratory internship (24h). The course ends with the writing of a popular scientific article and an oral presentation of the results.

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The objectives of this EU are twofold. On the one hand, the aim is to review all the major stages in the history of organisms on Earth since its birth. Topics such as the appearance of life, the colonization of continents, the appearance of angiosperms, glacial/interglacial cycles and the domestication of plants will be covered. On the other hand, the aim is to show how paleoecology is part of the modern world, whether in terms of methodological developments (geochemistry, optical, electron and X-ray microscopy, etc.), predictive models for climate change, ecosystem management in the context of global change, or biotechnological developments. The course will be organized as a series of lectures, each given by a specialist in the subject concerned.

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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 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 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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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 UE covers the analysis of man's impact on the climate and the environment.

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Present different methodological approaches in an applied approach, from data acquisition to interpretation. Each approach is covered over half a day (3h), covering data acquisition methods (1.5h TP) and interpretation of results (1.5h TD).

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"The aim of this UE is to present and explain the concepts, issues, operational approach in the field and laboratory, methodological and analytical strategies for inferring and reconstructing fluctuations in wild biodiversity and biodiversity exploited by man over time. It draws on empirical and modelled ecological, palaeoecological, palaeobiogeographical, archaeobiological, archaeological and palethnobiological data. Particular attention will be paid to :

- the functional role of ecological disturbances such as fires in the transformation of plant cover;

- the impact of human evolution on the dynamics of forest ecosystems;

- the exploitation, cultivation / breeding and domestication of plants and animals based on the study of modern and bioarchaeological data. "

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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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In this course, we'll look at the main theoretical concepts of evolutionary processes through the fossil record. The aim is to reconcile microevolutionary mechanisms with macroevolution. Concepts covered include: species and intraspecific variability, speciation and evolutionary rhythms, adaptive radiation (ecological speciation) in the fossil record, targeted extinctions (migrant-autochthonous competition) or mass extinctions (major biological crises), evolutionary modalities (anagenesis and saltationism) observed in the fossil record, and a comprehensive review of microevolutionary mechanisms.

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The aim of this resolutely trans-disciplinary course is to provide the skills needed to effectively manage and exploit data of various origins and types, particularly those with a spatial component. The course is divided into three complementary sections. The first deals with the issues inherent in data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second covers geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third axis presents the diversity of spatial analysis tools for quantitative exploitation of spatial data, from metrics to statistical tests.

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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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"The aim is to analyze the phylogenetic, developmental and functional constraints likely to have governed the morphological changes perceptible in the fossil record. The phylogenetic approach will be approached using reconstruction methods applicable to fossils (parsimony; cladistic analysis). Developmental and functional approaches (mainly odontology) will be illustrated by different methodologies developed on the Montpellier campus (notably X-ray microtomography). The critical review of reference articles in the field in question will give rise to an oral presentation followed by questions."

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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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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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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 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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"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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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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This teaching unit is part of a pre-professionalization program. It is designed to help students reflect on their professional integration through meetings with scientific mediation professionals, involvement in scientific mediation projects at the interface between the world of research and secondary education (assistance with environmental education and sustainable development projects for secondary school classes) and analysis of projects developed by Master 2 students.

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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 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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Scientific and non-scientific mediation increasingly involves digital tools for disseminating information, enabling us to reach a wide audience very quickly. These tools are many and varied, and it's hard to give a simple overview. Nevertheless, in the vast majority of job offers or internships in the field of mediation, knowledge in the use of these digital mediation tools is required.

The aim of this course is to present the main digital mediation tools and to introduce students intending to work in scientific mediation to their use. The course will also discuss the importance of sourcing and verifying data at a time when untruths and even lies are increasingly visible.

The first part of the course will take the form of TD/TP sessions on the main digital tools for scientific mediation. Examples put on line by various mediation organizations will be analyzed in order to detail their strengths and weaknesses.

The second part of the course will focus on practical application. Students will be asked to visit scientific mediation structures (temporary or permanent) and report on them using digital scientific mediation tools. In particular, one of the reports will focus on the scientific activities of the Biology and Ecology teaching department, and will be posted on the department's website.

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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 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 objectives of this EU are twofold. On the one hand, the aim is to review all the major stages in the history of organisms on Earth since its birth. Topics such as the appearance of life, the colonization of continents, the appearance of angiosperms, glacial/interglacial cycles and the domestication of plants will be covered. On the other hand, the aim is to show how paleoecology is part of the modern world, whether in terms of methodological developments (geochemistry, optical, electron and X-ray microscopy, etc.), predictive models for climate change, ecosystem management in the context of global change, or biotechnological developments. The course will be organized as a series of lectures, each given by a specialist in the subject concerned.

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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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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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"Teaching takes the form of an inter-disciplinary project (biology-ecology-geology) combining a field approach, bibliographical studies, meetings with professionals or resource persons and scientific mediation. The aim is to produce a synthetic scientific study of an area, linking its bio-ecological-geological characteristics with its economic, social, historical and/or heritage specificities. Students work in small groups (generally 2; maximum 3), under the supervision of a tutor. They are required to produce a written dissertation (of the scientific mediation type) and a one-day field session, tested with a group of students and teachers. "

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Teaching takes the form of a project based on an essentially bibliographical approach. This is a study of epistemology and the history of science, focusing on the work of a scientist in the Life Sciences or Earth and Universe Sciences. The student must highlight the key points of the scientist's work, placing it in the scientific-historical-political context of his or her era, highlighting advances and controversies, contributions to science and interests in scientific mediation. At the end of their work, carried out under the responsibility of a tutor, students produce a written dissertation, a poster and an oral presentation.

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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.

See full page

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.

See full page

"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)".

See full page

See full page

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.

See full page

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.

See full page

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.)."

See full page

"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.

See full page

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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.

See full page

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.