MASTER'S IN BIODIVERSITY, ECOLOGY, AND EVOLUTION

"This course will take the form of a series of about a dozen lectures/seminars on current research topics in vertebrate paleontology and evolutionary biology; biodiversity and paleobiodiversity of continental (animal) ecosystems; topographic and climatic barriers versus dispersal and vicariance; community structure, food webs over time, and paleoguilds; and the role of geodynamics and contingency (crises). The main objective is to gain a solid understanding of the current research themes and areas of focus within the paleontological and evolutionary biology communities."

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This course unit will take the form, as far as possible, of a one-week field internship on-site (with accommodations provided). The internship locations may change from year to year depending on new discoveries and/or partnership proposals (public/private). This internship may therefore take different forms, ranging from a “survey” approach—involving travel to various sites—to a more “excavation site” approach—which is stationary. In all cases, the various objectives listed below will be addressed to ensure the success of this field week, so that students can master the various techniques as thoroughly as possible.

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In this course unit, we will explore the main theoretical concepts of evolutionary processes as reflected in the fossil record. We will focus on reconciling microevolutionary and macroevolutionary mechanisms. The concepts covered will include: species and intraspecific variability, speciation and the rates of evolution, adaptive radiations (ecological speciation) in the fossil record, targeted extinctions (competition between migrants and native species) or mass extinctions (major biological crises), evolutionary modes (anagenesis and saltationism) observed in the fossil record, and a comprehensive review of microevolutionary mechanisms.

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

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

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This course provides the tools needed for data analysis in paleontology

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"The objective is to analyze the phylogenetic, developmental, and functional constraints that may have governed the morphological changes observable in the fossil record. The phylogenetic approach will be addressed using reconstruction methods applicable to fossils (parsimony; cladistic analysis). The developmental and functional approaches (primarily odontology) will be illustrated using various methodologies developed on the Montpellier campus (notably X-ray microtomography). A critical review of key articles in the field will be presented orally, followed by a question-and-answer session."

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

Throughout this module, we will use articles to discuss several evolutionary topics relevant to Evo-Devo approaches: the concept of homology, the origin and evolution of repetitive structures, the genetic basis of development, and the links between genomic evolution and morphological evolution. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them at the level of major modern groups as well as at the population level.

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Phylogeny is a search for evolutionary clues. The goal of this module is to highlight the existence of gene phylogenies within species phylogenies, the methods for representing evolutionary histories as trees, and the concept of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the core of this course unit. Distance-based methods highlight the difficulties in distinguishing between homology and homoplasy, as well as the need to construct models of character evolution. The cladistic approach based on maximum parsimony illustrates, on the one hand, the use of bootstrapping to estimate the robustness of phylogenetic nodes and, on the other hand, the impact of taxonomic sampling on the detection of multiple substitutions.

Probabilistic approaches are introduced and then explored in greater depth. The long-branch attraction artifact leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to address the calculation of likelihood, the estimation of model parameters using optimality criteria, the construction of various models of character evolution, and the comparison of models. Bayesian inference, in turn, introduces the distinction between density-based and optimality-based approaches. It then covers the a priori use of probability densities, the estimation of posterior distributions of model parameters based on the data, their approximation using Markov chains with Monte Carlo and Metropolis coupling (MCMCMC), the initialization and convergence phases, and the calculation and interpretation of posterior probabilities for trees and clades. The importance of evolutionary models for DNA, RNA, and protein sequences and their refinement is emphasized.

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

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

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The M2 individual internship lasts approximately 5 to 6 months and, depending on the student’s track, must be completed in a research laboratory or a non-academic organization. It allows students to gain in-depth professional experience in the field of biodiversity, evolution, or ecology. It may be conducted at a local, national, or international organization on a topic approved by the faculty to ensure it aligns with the specific objectives of the student’s track of study.

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

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

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

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

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

Summary of the learning unit:

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

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

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

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

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English tutorial courses designed to foster professional proficiency in English.

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"The phylogenetic tree is a central concept in biology for students in the majors "Biodiversity, Ecology & Evolution," "Agricultural Biology," and "Eco-epidemiology." To introduce students to phylogeny, this course unit is divided into two consecutive parts, each lasting 22.5 hours: “Phylogeny and Evolution (Fundamentals)” (HAB708B) and “Phylogeny and Evolution (Advanced)” (HAB714B).

The following subjects will be taught there:

(i) History of the Concept of Evolution [Basics].

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

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

(iv) Methods of phylogenetic inference based on distances [Advanced].

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

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

(vii) Measures of phylogenetic robustness (bootstrapping, topology comparison, multigene corroboration, gene and species trees) [Advances].

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

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

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

Deviance Analysis and Goodness of Fit

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

Graphical representation of the predictions.

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

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"The phylogenetic tree is a central concept in biology for students in the majors "Biodiversity, Ecology & Evolution," "Agricultural Biology," and "Eco-epidemiology." To introduce students to phylogeny, this course unit is divided into two consecutive parts, each lasting 22.5 hours: “Phylogeny and Evolution (Fundamentals)” (HAB708B) and “Phylogeny and Evolution (Advanced)” (HAB714B).

The following subjects will be taught there:

(i) History of the Concept of Evolution [Basics].

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

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

(iv) Methods of phylogenetic inference based on distances [Advanced].

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

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

(vii) Measures of phylogenetic robustness (bootstrapping, topology comparison, multigene corroboration, gene and species trees) [Advances].

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

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This learning unit has three objectives:

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

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

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

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

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

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

Summary of the learning unit:

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

Topic types:

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

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

Assessment Procedures:

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

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

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"The objective of this course unit is to build upon the material covered in the first semester by exploring issues related to phenotypic evolution and the main methodological approaches associated with it. The course will address the evolution of various types of traits (life history traits, traits involved in reproductive strategies, traits involved in biotic interactions, and quantitative traits). The main approaches covered include game theory formalization, adaptive dynamics, quantitative genetics, and the comparison of theoretical predictions with empirical data. The course includes:

1) lectures on the main concepts of evolutionary ecology;

2) tutorials focused on document analysis and exercises"

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

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- First, to provide students with a foundation of computer science knowledge and skills, thereby giving them a solid basis for learning and using the bioinformatics tools specifically applied in evolution and ecology.

- Second, to raise their awareness of the need to produce reproducible results and introduce them to the key concepts and tools for doing so.

- Third, have students work on concrete examples that they can draw upon during their master's internship and in their future careers.

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

- Foster a sense of community and inclusion in promoting the DARWIN-BEE Master's 2 program.

- Analyze environmental issues from their technical, scientific, and social perspectives (for example, reintroduction programs).

- Addressing biodiversity management issues in a protected area shaped by human activity.

- Give an oral presentation and discuss the results with the group; wrap-up of the internship.

Things to Do in Florac:

- Explore the landscapes of the Causse Méjean.

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

- Study the examples of vultures in the Causses, capercaillies and beavers in the PNC, and chamois in the Gorges du Tarn.

- Work on individual assignments in three small groups, focusing on different scientific and ethical topics.

Things to Do Around Montpellier:

- Study bird migration and the ecosystems of the Mediterranean coast.

- Practice urban ecology.

- Discover the wildlife of the Mediterranean scrublands, with daytime hikes along the Buèges River (to explore the insect life) and evening hikes (to observe bats and/or moths and nocturnal grasshoppers)."

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The module covers the following fundamental topics in evolutionary biology: microevolution, macroevolution, fitness, natural and sexual selection, and speciation. Other topics (mutation, epigenetics, evo-devo, etc.) are presented by the students themselves.

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

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

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The objective of this course unit is to design a research project on one of the major themes in ecology, such as ecological niche, biogeography, ecological interaction networks, or functional diversity. A brief overview of the major theories and concepts within these broad ecological themes is presented by guest lecturers who are specialists in these fields. This overview is followed by one or more examples illustrating the conceptual foundations for formulating a relevant and novel research question and how to address it using various methodologies—particularly experimental ones—drawn from the lecturers’ own research. After selecting one of these major themes, each student develops an original research project (on the scale of a Master’s 2 internship), conducting a literature review and proposing a coherent experimental design to test the hypotheses. This project is presented to the instructors and fellow students.

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1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

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The overall objective is to introduce human evolutionary biology, proposing to apply the tools of evolutionary biology to better understand human behavior and the behavior observed in non-human primates within the context of their evolutionary history. Whether the topics are health, social behavior, culture, local adaptations, language, morality, reproduction, or sexual preferences, they are addressed within the theoretical framework of evolutionary biology and ecology. Course Overview: Anthropology, Humanities, and Evolutionary Biology / The Evolution of Cooperation / Cultural Evolution / The Evolution of Diet / The Evolution of Sociality in Primates / Family Ecology / Medicine, Public Health, and Evolution / The Evolution of Language / Evolutionary Demography / The Origins of Fairness.

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1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

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The courses cover four aspects of conservation biology, drawing on current scientific research in this field:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology. Why conserve biodiversity? Who are the key players in BC, and what is the role of science in BC? 
2. Species Conservation: Which species are priorities? How can we conserve species? How do we know if a species is “well conserved”? 
3. Conservation of Areas: Which areas are priorities? How can we conserve these areas? 
4. Does Conservation Work?The Importance of Social Acceptance and Political Commitment. The Need for Biodiversity Indicators and for Measuring the Impact of Conservation. 

Students also work in groups to present a community library project, addressing the following questions: Why, what, where, how, how much does it cost, and how can we tell if it’s effective? 

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

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Quantitative genetics is a discipline that emerged in the early 20th century to understand the inheritance of continuous traits—that is, the majority of traits of agronomic interest (yield, etc.) or evolutionary interest (life history traits, morphology). It is therefore an indispensable tool for understanding, modeling, and predicting natural or artificial selection, as well as the evolution of natural systems or cultivated plants and animals. Its relevance is more pressing than ever at the dawn of the 21st century, with the emergence of genomics (a driver of scientific progress, provided that evolutionary problems are not reduced to the fiction of a few strong-effect Mendelian alleles), and the resurgence of alternative models of inheritance (epigenetics) that go beyond the sequence-centered perspective inherited from classical molecular biology.

The goal of this module is to provide students with a sufficient foundation in quantitative genetics to (i) understand the classical foundations of the discipline, work with key quantities (genetic variances, heritabilities, genetic correlations), and apply statistical techniques for estimating these parameters; (ii) understand the power of this technique for formulating and understanding fundamental or applied evolutionary problems (agricultural breeding), and (iii) understand how this formalization of inheritance relates to the classical Mendelian view.

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The overall objective is to introduce human evolutionary biology, proposing to apply the tools of evolutionary biology to better understand human behavior and the behavior observed in non-human primates within the context of their evolutionary history. Whether the topics are health, social behavior, culture, local adaptations, language, morality, reproduction, or sexual preferences, they are addressed within the theoretical framework of evolutionary biology and ecology. Course Overview: Anthropology, Humanities, and Evolutionary Biology / The Evolution of Cooperation / Cultural Evolution / The Evolution of Diet / The Evolution of Sociality in Primates / Family Ecology / Medicine, Public Health, and Evolution / The Evolution of Language / Evolutionary Demography / The Origins of Fairness.

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Behavioral ecology approaches the study of behavior from an evolutionary perspective to examine its mechanisms, function, and the role behavior plays in evolutionary and ecological processes. Research in behavioral ecology helps us understand other phenomena observed in other disciplines of biology, since all animals—from single-celled organisms to the most complex vertebrates—exhibit behavior.

The module exposes students to various basic concepts, as well as the wide range of tools that may be used (observations and experiments in natural populations or on captive individuals, comparative analyses, the use of modeling tools, ecophysiology, molecular biology, biochemistry, embedded electronics, etc.). Part of the course focuses on specific discussions of potential research approaches, the tools used, and the limitations of the inferences that can be drawn. Students will be expected to participate actively at these various levels, particularly through critical discussions of research articles.

The topics covered range from the exploration of food-foraging strategies, mate selection, habitat choice, and investment in reproduction to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also depending on the instructors’ perspectives and the specific topics covered (the meanings and relationships between “Animal Behavior,” “Ethology,” “Behavioral Ecology,” etc.).

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The module explores the theoretical and empirical advances in recent research in evolutionary genetics through several key issues:

- Topic 1: Genetic Burden and the Evolution of Reproductive Systems: Recombination, Sexual/Asexual Reproduction, Self-Fertilization/Cross-Fertilization

- Topic 2: Kinship structures and their evolutionary consequences: kin selection, group selection, the evolution of cooperation, and sex ratios

- Topic 3: Long-term interactions between species: parasitism, mutualism, coevolution

- Topic 4: Traces of evolutionary history in genomes; genomics of adaptation.

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The primary objective of this course is to provide students with all the skills necessary to understand and apply the concepts and methods underlying the quantitative study of population phenomena. The main methods for analyzing and modeling these phenomena will be addressed from both a theoretical (formal calculations) and practical (statistics, simulations) perspective, using examples that explore 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 paid to heterogeneity (spatial, genetic, or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent in their study.

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The objective of this teaching unit is to demonstrate that biological diversity serves a functional purpose:

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

2) at different organizational scales (from organisms to ecosystems). The course aims to explain how to approach this functional aspect of diversity for the more than 10 million organisms present on the planet’s surface, using examples from highly and minimally anthropized environments.

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Phylogeny is a search for evolutionary clues. The goal of this module is to highlight the existence of gene phylogenies within species phylogenies, the methods for representing evolutionary histories as trees, and the concept of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the core of this course unit. Distance-based methods highlight the difficulties in distinguishing between homology and homoplasy, as well as the need to construct models of character evolution. The cladistic approach based on maximum parsimony illustrates, on the one hand, the use of bootstrapping to estimate the robustness of phylogenetic nodes and, on the other hand, the impact of taxonomic sampling on the detection of multiple substitutions.

Probabilistic approaches are introduced and then explored in greater depth. The long-branch attraction artifact leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to address the calculation of likelihood, the estimation of model parameters using optimality criteria, the construction of various models of character evolution, and the comparison of models. Bayesian inference, in turn, introduces the distinction between density-based and optimality-based approaches. It then covers the a priori use of probability densities, the estimation of posterior distributions of model parameters based on the data, their approximation using Markov chains with Monte Carlo and Metropolis coupling (MCMCMC), the initialization and convergence phases, and the calculation and interpretation of posterior probabilities for trees and clades. The importance of evolutionary models for DNA, RNA, and protein sequences and their refinement is emphasized.

View the full page

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

Throughout this module, we will use articles to discuss several evolutionary topics relevant to Evo-Devo approaches: the concept of homology, the origin and evolution of repetitive structures, the genetic basis of development, and the links between genomic evolution and morphological evolution. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them at the level of major modern groups as well as at the population level.

View the full page

View the full page

1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

View the full page

The courses cover four aspects of conservation biology, drawing on current scientific research in this field:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology. Why conserve biodiversity? Who are the key players in BC, and what is the role of science in BC? 
2. Species Conservation: Which species are priorities? How can we conserve species? How do we know if a species is “well conserved”? 
3. Conservation of Areas: Which areas are priorities? How can we conserve these areas? 
4. Does Conservation Work?The Importance of Social Acceptance and Political Commitment. The Need for Biodiversity Indicators and for Measuring the Impact of Conservation. 

Students also work in groups to present a community library project, addressing the following questions: Why, what, where, how, how much does it cost, and how can we tell if it’s effective? 

View the full page

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

View the full page

Quantitative genetics is a discipline that emerged in the early 20th century to understand the inheritance of continuous traits—that is, the majority of traits of agronomic interest (yield, etc.) or evolutionary interest (life history traits, morphology). It is therefore an indispensable tool for understanding, modeling, and predicting natural or artificial selection, as well as the evolution of natural systems or cultivated plants and animals. Its relevance is more pressing than ever at the dawn of the 21st century, with the emergence of genomics (a driver of scientific progress, provided that evolutionary problems are not reduced to the fiction of a few strong-effect Mendelian alleles), and the resurgence of alternative models of inheritance (epigenetics) that go beyond the sequence-centered perspective inherited from classical molecular biology.

The goal of this module is to provide students with a sufficient foundation in quantitative genetics to (i) understand the classical foundations of the discipline, work with key quantities (genetic variances, heritabilities, genetic correlations), and apply statistical techniques for estimating these parameters; (ii) understand the power of this technique for formulating and understanding fundamental or applied evolutionary problems (agricultural breeding), and (iii) understand how this formalization of inheritance relates to the classical Mendelian view.

View the full page

The overall objective is to introduce human evolutionary biology, proposing to apply the tools of evolutionary biology to better understand human behavior and the behavior observed in non-human primates within the context of their evolutionary history. Whether the topics are health, social behavior, culture, local adaptations, language, morality, reproduction, or sexual preferences, they are addressed within the theoretical framework of evolutionary biology and ecology. Course Overview: Anthropology, Humanities, and Evolutionary Biology / The Evolution of Cooperation / Cultural Evolution / The Evolution of Diet / The Evolution of Sociality in Primates / Family Ecology / Medicine, Public Health, and Evolution / The Evolution of Language / Evolutionary Demography / The Origins of Fairness.

View the full page

Behavioral ecology approaches the study of behavior from an evolutionary perspective to examine its mechanisms, function, and the role behavior plays in evolutionary and ecological processes. Research in behavioral ecology helps us understand other phenomena observed in other disciplines of biology, since all animals—from single-celled organisms to the most complex vertebrates—exhibit behavior.

The module exposes students to various basic concepts, as well as the wide range of tools that may be used (observations and experiments in natural populations or on captive individuals, comparative analyses, the use of modeling tools, ecophysiology, molecular biology, biochemistry, embedded electronics, etc.). Part of the course focuses on specific discussions of potential research approaches, the tools used, and the limitations of the inferences that can be drawn. Students will be expected to participate actively at these various levels, particularly through critical discussions of research articles.

The topics covered range from the exploration of food-foraging strategies, mate selection, habitat choice, and investment in reproduction to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also depending on the instructors’ perspectives and the specific topics covered (the meanings and relationships between “Animal Behavior,” “Ethology,” “Behavioral Ecology,” etc.).

View the full page

View the full page

The module explores the theoretical and empirical advances in recent research in evolutionary genetics through several key issues:

- Topic 1: Genetic Burden and the Evolution of Reproductive Systems: Recombination, Sexual/Asexual Reproduction, Self-Fertilization/Cross-Fertilization

- Topic 2: Kinship structures and their evolutionary consequences: kin selection, group selection, the evolution of cooperation, and sex ratios

- Topic 3: Long-term interactions between species: parasitism, mutualism, coevolution

- Topic 4: Traces of evolutionary history in genomes; genomics of adaptation.

View the full page

The primary objective of this course is to provide students with all the skills necessary to understand and apply the concepts and methods underlying the quantitative study of population phenomena. The main methods for analyzing and modeling these phenomena will be addressed from both a theoretical (formal calculations) and practical (statistics, simulations) perspective, using examples that explore 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 paid to heterogeneity (spatial, genetic, or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent in their study.

View the full page

The objective of this teaching unit is to demonstrate that biological diversity serves a functional purpose:

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

2) at different organizational scales (from organisms to ecosystems). The course aims to explain how to approach this functional aspect of diversity for the more than 10 million organisms present on the planet’s surface, using examples from highly and minimally anthropized environments.

View the full page

Phylogeny is a search for evolutionary clues. The goal of this module is to highlight the existence of gene phylogenies within species phylogenies, the methods for representing evolutionary histories as trees, and the concept of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the core of this course unit. Distance-based methods highlight the difficulties in distinguishing between homology and homoplasy, as well as the need to construct models of character evolution. The cladistic approach based on maximum parsimony illustrates, on the one hand, the use of bootstrapping to estimate the robustness of phylogenetic nodes and, on the other hand, the impact of taxonomic sampling on the detection of multiple substitutions.

Probabilistic approaches are introduced and then explored in greater depth. The long-branch attraction artifact leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to address the calculation of likelihood, the estimation of model parameters using optimality criteria, the construction of various models of character evolution, and the comparison of models. Bayesian inference, in turn, introduces the distinction between density-based and optimality-based approaches. It then covers the a priori use of probability densities, the estimation of posterior distributions of model parameters based on the data, their approximation using Markov chains with Monte Carlo and Metropolis coupling (MCMCMC), the initialization and convergence phases, and the calculation and interpretation of posterior probabilities for trees and clades. The importance of evolutionary models for DNA, RNA, and protein sequences and their refinement is emphasized.

View the full page

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

Throughout this module, we will use articles to discuss several evolutionary topics relevant to Evo-Devo approaches: the concept of homology, the origin and evolution of repetitive structures, the genetic basis of development, and the links between genomic evolution and morphological evolution. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them at the level of major modern groups as well as at the population level.

View the full page

View the full page

1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

View the full page

The courses cover four aspects of conservation biology, drawing on current scientific research in this field:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology. Why conserve biodiversity? Who are the key players in BC, and what is the role of science in BC? 
2. Species Conservation: Which species are priorities? How can we conserve species? How do we know if a species is “well conserved”? 
3. Conservation of Areas: Which areas are priorities? How can we conserve these areas? 
4. Does Conservation Work?The Importance of Social Acceptance and Political Commitment. The Need for Biodiversity Indicators and for Measuring the Impact of Conservation. 

Students also work in groups to present a community library project, addressing the following questions: Why, what, where, how, how much does it cost, and how can we tell if it’s effective? 

View the full page

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

View the full page

Quantitative genetics is a discipline that emerged in the early 20th century to understand the inheritance of continuous traits—that is, the majority of traits of agronomic interest (yield, etc.) or evolutionary interest (life history traits, morphology). It is therefore an indispensable tool for understanding, modeling, and predicting natural or artificial selection, as well as the evolution of natural systems or cultivated plants and animals. Its relevance is more pressing than ever at the dawn of the 21st century, with the emergence of genomics (a driver of scientific progress, provided that evolutionary problems are not reduced to the fiction of a few strong-effect Mendelian alleles), and the resurgence of alternative models of inheritance (epigenetics) that go beyond the sequence-centered perspective inherited from classical molecular biology.

The goal of this module is to provide students with a sufficient foundation in quantitative genetics to (i) understand the classical foundations of the discipline, work with key quantities (genetic variances, heritabilities, genetic correlations), and apply statistical techniques for estimating these parameters; (ii) understand the power of this technique for formulating and understanding fundamental or applied evolutionary problems (agricultural breeding), and (iii) understand how this formalization of inheritance relates to the classical Mendelian view.

View the full page

The overall objective is to introduce human evolutionary biology, proposing to apply the tools of evolutionary biology to better understand human behavior and the behavior observed in non-human primates within the context of their evolutionary history. Whether the topics are health, social behavior, culture, local adaptations, language, morality, reproduction, or sexual preferences, they are addressed within the theoretical framework of evolutionary biology and ecology. Course Overview: Anthropology, Humanities, and Evolutionary Biology / The Evolution of Cooperation / Cultural Evolution / The Evolution of Diet / The Evolution of Sociality in Primates / Family Ecology / Medicine, Public Health, and Evolution / The Evolution of Language / Evolutionary Demography / The Origins of Fairness.

View the full page

Behavioral ecology approaches the study of behavior from an evolutionary perspective to examine its mechanisms, function, and the role behavior plays in evolutionary and ecological processes. Research in behavioral ecology helps us understand other phenomena observed in other disciplines of biology, since all animals—from single-celled organisms to the most complex vertebrates—exhibit behavior.

The module exposes students to various basic concepts, as well as the wide range of tools that may be used (observations and experiments in natural populations or on captive individuals, comparative analyses, the use of modeling tools, ecophysiology, molecular biology, biochemistry, embedded electronics, etc.). Part of the course focuses on specific discussions of potential research approaches, the tools used, and the limitations of the inferences that can be drawn. Students will be expected to participate actively at these various levels, particularly through critical discussions of research articles.

The topics covered range from the exploration of food-foraging strategies, mate selection, habitat choice, and investment in reproduction to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also depending on the instructors’ perspectives and the specific topics covered (the meanings and relationships between “Animal Behavior,” “Ethology,” “Behavioral Ecology,” etc.).

View the full page

View the full page

View the full page

1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

View the full page

The overall objective is to introduce human evolutionary biology, proposing to apply the tools of evolutionary biology to better understand human behavior and the behavior observed in non-human primates within the context of their evolutionary history. Whether the topics are health, social behavior, culture, local adaptations, language, morality, reproduction, or sexual preferences, they are addressed within the theoretical framework of evolutionary biology and ecology. Course Overview: Anthropology, Humanities, and Evolutionary Biology / The Evolution of Cooperation / Cultural Evolution / The Evolution of Diet / The Evolution of Sociality in Primates / Family Ecology / Medicine, Public Health, and Evolution / The Evolution of Language / Evolutionary Demography / The Origins of Fairness.

View the full page

1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

View the full page

The courses cover four aspects of conservation biology, drawing on current scientific research in this field:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology. Why conserve biodiversity? Who are the key players in BC, and what is the role of science in BC? 
2. Species Conservation: Which species are priorities? How can we conserve species? How do we know if a species is “well conserved”? 
3. Conservation of Areas: Which areas are priorities? How can we conserve these areas? 
4. Does Conservation Work?The Importance of Social Acceptance and Political Commitment. The Need for Biodiversity Indicators and for Measuring the Impact of Conservation. 

Students also work in groups to present a community library project, addressing the following questions: Why, what, where, how, how much does it cost, and how can we tell if it’s effective? 

View the full page

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

View the full page

Quantitative genetics is a discipline that emerged in the early 20th century to understand the inheritance of continuous traits—that is, the majority of traits of agronomic interest (yield, etc.) or evolutionary interest (life history traits, morphology). It is therefore an indispensable tool for understanding, modeling, and predicting natural or artificial selection, as well as the evolution of natural systems or cultivated plants and animals. Its relevance is more pressing than ever at the dawn of the 21st century, with the emergence of genomics (a driver of scientific progress, provided that evolutionary problems are not reduced to the fiction of a few strong-effect Mendelian alleles), and the resurgence of alternative models of inheritance (epigenetics) that go beyond the sequence-centered perspective inherited from classical molecular biology.

The goal of this module is to provide students with a sufficient foundation in quantitative genetics to (i) understand the classical foundations of the discipline, work with key quantities (genetic variances, heritabilities, genetic correlations), and apply statistical techniques for estimating these parameters; (ii) understand the power of this technique for formulating and understanding fundamental or applied evolutionary problems (agricultural breeding), and (iii) understand how this formalization of inheritance relates to the classical Mendelian view.

View the full page

The overall objective is to introduce human evolutionary biology, proposing to apply the tools of evolutionary biology to better understand human behavior and the behavior observed in non-human primates within the context of their evolutionary history. Whether the topics are health, social behavior, culture, local adaptations, language, morality, reproduction, or sexual preferences, they are addressed within the theoretical framework of evolutionary biology and ecology. Course Overview: Anthropology, Humanities, and Evolutionary Biology / The Evolution of Cooperation / Cultural Evolution / The Evolution of Diet / The Evolution of Sociality in Primates / Family Ecology / Medicine, Public Health, and Evolution / The Evolution of Language / Evolutionary Demography / The Origins of Fairness.

View the full page

Behavioral ecology approaches the study of behavior from an evolutionary perspective to examine its mechanisms, function, and the role behavior plays in evolutionary and ecological processes. Research in behavioral ecology helps us understand other phenomena observed in other disciplines of biology, since all animals—from single-celled organisms to the most complex vertebrates—exhibit behavior.

The module exposes students to various basic concepts, as well as the wide range of tools that may be used (observations and experiments in natural populations or on captive individuals, comparative analyses, the use of modeling tools, ecophysiology, molecular biology, biochemistry, embedded electronics, etc.). Part of the course focuses on specific discussions of potential research approaches, the tools used, and the limitations of the inferences that can be drawn. Students will be expected to participate actively at these various levels, particularly through critical discussions of research articles.

The topics covered range from the exploration of food-foraging strategies, mate selection, habitat choice, and investment in reproduction to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also depending on the instructors’ perspectives and the specific topics covered (the meanings and relationships between “Animal Behavior,” “Ethology,” “Behavioral Ecology,” etc.).

View the full page

The module explores the theoretical and empirical advances in recent research in evolutionary genetics through several key issues:

- Topic 1: Genetic Burden and the Evolution of Reproductive Systems: Recombination, Sexual/Asexual Reproduction, Self-Fertilization/Cross-Fertilization

- Topic 2: Kinship structures and their evolutionary consequences: kin selection, group selection, the evolution of cooperation, and sex ratios

- Topic 3: Long-term interactions between species: parasitism, mutualism, coevolution

- Topic 4: Traces of evolutionary history in genomes; genomics of adaptation.

View the full page

The primary objective of this course is to provide students with all the skills necessary to understand and apply the concepts and methods underlying the quantitative study of population phenomena. The main methods for analyzing and modeling these phenomena will be addressed from both a theoretical (formal calculations) and practical (statistics, simulations) perspective, using examples that explore 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 paid to heterogeneity (spatial, genetic, or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent in their study.

View the full page

The objective of this teaching unit is to demonstrate that biological diversity serves a functional purpose:

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

2) at different organizational scales (from organisms to ecosystems). The course aims to explain how to approach this functional aspect of diversity for the more than 10 million organisms present on the planet’s surface, using examples from highly and minimally anthropized environments.

View the full page

Phylogeny is a search for evolutionary clues. The goal of this module is to highlight the existence of gene phylogenies within species phylogenies, the methods for representing evolutionary histories as trees, and the concept of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the core of this course unit. Distance-based methods highlight the difficulties in distinguishing between homology and homoplasy, as well as the need to construct models of character evolution. The cladistic approach based on maximum parsimony illustrates, on the one hand, the use of bootstrapping to estimate the robustness of phylogenetic nodes and, on the other hand, the impact of taxonomic sampling on the detection of multiple substitutions.

Probabilistic approaches are introduced and then explored in greater depth. The long-branch attraction artifact leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to address the calculation of likelihood, the estimation of model parameters using optimality criteria, the construction of various models of character evolution, and the comparison of models. Bayesian inference, in turn, introduces the distinction between density-based and optimality-based approaches. It then covers the a priori use of probability densities, the estimation of posterior distributions of model parameters based on the data, their approximation using Markov chains with Monte Carlo and Metropolis coupling (MCMCMC), the initialization and convergence phases, and the calculation and interpretation of posterior probabilities for trees and clades. The importance of evolutionary models for DNA, RNA, and protein sequences and their refinement is emphasized.

View the full page

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

Throughout this module, we will use articles to discuss several evolutionary topics relevant to Evo-Devo approaches: the concept of homology, the origin and evolution of repetitive structures, the genetic basis of development, and the links between genomic evolution and morphological evolution. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them at the level of major modern groups as well as at the population level.

View the full page

The module explores the theoretical and empirical advances in recent research in evolutionary genetics through several key issues:

- Topic 1: Genetic Burden and the Evolution of Reproductive Systems: Recombination, Sexual/Asexual Reproduction, Self-Fertilization/Cross-Fertilization

- Topic 2: Kinship structures and their evolutionary consequences: kin selection, group selection, the evolution of cooperation, and sex ratios

- Topic 3: Long-term interactions between species: parasitism, mutualism, coevolution

- Topic 4: Traces of evolutionary history in genomes; genomics of adaptation.

View the full page

The primary objective of this course is to provide students with all the skills necessary to understand and apply the concepts and methods underlying the quantitative study of population phenomena. The main methods for analyzing and modeling these phenomena will be addressed from both a theoretical (formal calculations) and practical (statistics, simulations) perspective, using examples that explore 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 paid to heterogeneity (spatial, genetic, or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent in their study.

View the full page

The objective of this teaching unit is to demonstrate that biological diversity serves a functional purpose:

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

2) at different organizational scales (from organisms to ecosystems). The course aims to explain how to approach this functional aspect of diversity for the more than 10 million organisms present on the planet’s surface, using examples from highly and minimally anthropized environments.

View the full page

Phylogeny is a search for evolutionary clues. The goal of this module is to highlight the existence of gene phylogenies within species phylogenies, the methods for representing evolutionary histories as trees, and the concept of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the core of this course unit. Distance-based methods highlight the difficulties in distinguishing between homology and homoplasy, as well as the need to construct models of character evolution. The cladistic approach based on maximum parsimony illustrates, on the one hand, the use of bootstrapping to estimate the robustness of phylogenetic nodes and, on the other hand, the impact of taxonomic sampling on the detection of multiple substitutions.

Probabilistic approaches are introduced and then explored in greater depth. The long-branch attraction artifact leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to address the calculation of likelihood, the estimation of model parameters using optimality criteria, the construction of various models of character evolution, and the comparison of models. Bayesian inference, in turn, introduces the distinction between density-based and optimality-based approaches. It then covers the a priori use of probability densities, the estimation of posterior distributions of model parameters based on the data, their approximation using Markov chains with Monte Carlo and Metropolis coupling (MCMCMC), the initialization and convergence phases, and the calculation and interpretation of posterior probabilities for trees and clades. The importance of evolutionary models for DNA, RNA, and protein sequences and their refinement is emphasized.

View the full page

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

Throughout this module, we will use articles to discuss several evolutionary topics relevant to Evo-Devo approaches: the concept of homology, the origin and evolution of repetitive structures, the genetic basis of development, and the links between genomic evolution and morphological evolution. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them at the level of major modern groups as well as at the population level.

View the full page

View the full page

View the full page

1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

View the full page

The overall objective is to introduce human evolutionary biology, proposing to apply the tools of evolutionary biology to better understand human behavior and the behavior observed in non-human primates within the context of their evolutionary history. Whether the topics are health, social behavior, culture, local adaptations, language, morality, reproduction, or sexual preferences, they are addressed within the theoretical framework of evolutionary biology and ecology. Course Overview: Anthropology, Humanities, and Evolutionary Biology / The Evolution of Cooperation / Cultural Evolution / The Evolution of Diet / The Evolution of Sociality in Primates / Family Ecology / Medicine, Public Health, and Evolution / The Evolution of Language / Evolutionary Demography / The Origins of Fairness.

View the full page

1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

View the full page

The courses cover four aspects of conservation biology, drawing on current scientific research in this field:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology. Why conserve biodiversity? Who are the key players in BC, and what is the role of science in BC? 
2. Species Conservation: Which species are priorities? How can we conserve species? How do we know if a species is “well conserved”? 
3. Conservation of Areas: Which areas are priorities? How can we conserve these areas? 
4. Does Conservation Work?The Importance of Social Acceptance and Political Commitment. The Need for Biodiversity Indicators and for Measuring the Impact of Conservation. 

Students also work in groups to present a community library project, addressing the following questions: Why, what, where, how, how much does it cost, and how can we tell if it’s effective? 

View the full page

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

View the full page

Quantitative genetics is a discipline that emerged in the early 20th century to understand the inheritance of continuous traits—that is, the majority of traits of agronomic interest (yield, etc.) or evolutionary interest (life history traits, morphology). It is therefore an indispensable tool for understanding, modeling, and predicting natural or artificial selection, as well as the evolution of natural systems or cultivated plants and animals. Its relevance is more pressing than ever at the dawn of the 21st century, with the emergence of genomics (a driver of scientific progress, provided that evolutionary problems are not reduced to the fiction of a few strong-effect Mendelian alleles), and the resurgence of alternative models of inheritance (epigenetics) that go beyond the sequence-centered perspective inherited from classical molecular biology.

The goal of this module is to provide students with a sufficient foundation in quantitative genetics to (i) understand the classical foundations of the discipline, work with key quantities (genetic variances, heritabilities, genetic correlations), and apply statistical techniques for estimating these parameters; (ii) understand the power of this technique for formulating and understanding fundamental or applied evolutionary problems (agricultural breeding), and (iii) understand how this formalization of inheritance relates to the classical Mendelian view.

View the full page

The overall objective is to introduce human evolutionary biology, proposing to apply the tools of evolutionary biology to better understand human behavior and the behavior observed in non-human primates within the context of their evolutionary history. Whether the topics are health, social behavior, culture, local adaptations, language, morality, reproduction, or sexual preferences, they are addressed within the theoretical framework of evolutionary biology and ecology. Course Overview: Anthropology, Humanities, and Evolutionary Biology / The Evolution of Cooperation / Cultural Evolution / The Evolution of Diet / The Evolution of Sociality in Primates / Family Ecology / Medicine, Public Health, and Evolution / The Evolution of Language / Evolutionary Demography / The Origins of Fairness.

View the full page

Behavioral ecology approaches the study of behavior from an evolutionary perspective to examine its mechanisms, function, and the role behavior plays in evolutionary and ecological processes. Research in behavioral ecology helps us understand other phenomena observed in other disciplines of biology, since all animals—from single-celled organisms to the most complex vertebrates—exhibit behavior.

The module exposes students to various basic concepts, as well as the wide range of tools that may be used (observations and experiments in natural populations or on captive individuals, comparative analyses, the use of modeling tools, ecophysiology, molecular biology, biochemistry, embedded electronics, etc.). Part of the course focuses on specific discussions of potential research approaches, the tools used, and the limitations of the inferences that can be drawn. Students will be expected to participate actively at these various levels, particularly through critical discussions of research articles.

The topics covered range from the exploration of food-foraging strategies, mate selection, habitat choice, and investment in reproduction to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also depending on the instructors’ perspectives and the specific topics covered (the meanings and relationships between “Animal Behavior,” “Ethology,” “Behavioral Ecology,” etc.).

View the full page

The module explores the theoretical and empirical advances in recent research in evolutionary genetics through several key issues:

- Topic 1: Genetic Burden and the Evolution of Reproductive Systems: Recombination, Sexual/Asexual Reproduction, Self-Fertilization/Cross-Fertilization

- Topic 2: Kinship structures and their evolutionary consequences: kin selection, group selection, the evolution of cooperation, and sex ratios

- Topic 3: Long-term interactions between species: parasitism, mutualism, coevolution

- Topic 4: Traces of evolutionary history in genomes; genomics of adaptation.

View the full page

The primary objective of this course is to provide students with all the skills necessary to understand and apply the concepts and methods underlying the quantitative study of population phenomena. The main methods for analyzing and modeling these phenomena will be addressed from both a theoretical (formal calculations) and practical (statistics, simulations) perspective, using examples that explore 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 paid to heterogeneity (spatial, genetic, or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent in their study.

View the full page

The objective of this teaching unit is to demonstrate that biological diversity serves a functional purpose:

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

2) at different organizational scales (from organisms to ecosystems). The course aims to explain how to approach this functional aspect of diversity for the more than 10 million organisms present on the planet’s surface, using examples from highly and minimally anthropized environments.

View the full page

Phylogeny is a search for evolutionary clues. The goal of this module is to highlight the existence of gene phylogenies within species phylogenies, the methods for representing evolutionary histories as trees, and the concept of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the core of this course unit. Distance-based methods highlight the difficulties in distinguishing between homology and homoplasy, as well as the need to construct models of character evolution. The cladistic approach based on maximum parsimony illustrates, on the one hand, the use of bootstrapping to estimate the robustness of phylogenetic nodes and, on the other hand, the impact of taxonomic sampling on the detection of multiple substitutions.

Probabilistic approaches are introduced and then explored in greater depth. The long-branch attraction artifact leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to address the calculation of likelihood, the estimation of model parameters using optimality criteria, the construction of various models of character evolution, and the comparison of models. Bayesian inference, in turn, introduces the distinction between density-based and optimality-based approaches. It then covers the a priori use of probability densities, the estimation of posterior distributions of model parameters based on the data, their approximation using Markov chains with Monte Carlo and Metropolis coupling (MCMCMC), the initialization and convergence phases, and the calculation and interpretation of posterior probabilities for trees and clades. The importance of evolutionary models for DNA, RNA, and protein sequences and their refinement is emphasized.

View the full page

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

Throughout this module, we will use articles to discuss several evolutionary topics relevant to Evo-Devo approaches: the concept of homology, the origin and evolution of repetitive structures, the genetic basis of development, and the links between genomic evolution and morphological evolution. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them at the level of major modern groups as well as at the population level.

View the full page

View the full page

The module explores the theoretical and empirical advances in recent research in evolutionary genetics through several key issues:

- Topic 1: Genetic Burden and the Evolution of Reproductive Systems: Recombination, Sexual/Asexual Reproduction, Self-Fertilization/Cross-Fertilization

- Topic 2: Kinship structures and their evolutionary consequences: kin selection, group selection, the evolution of cooperation, and sex ratios

- Topic 3: Long-term interactions between species: parasitism, mutualism, coevolution

- Topic 4: Traces of evolutionary history in genomes; genomics of adaptation.

View the full page

The primary objective of this course is to provide students with all the skills necessary to understand and apply the concepts and methods underlying the quantitative study of population phenomena. The main methods for analyzing and modeling these phenomena will be addressed from both a theoretical (formal calculations) and practical (statistics, simulations) perspective, using examples that explore 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 paid to heterogeneity (spatial, genetic, or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent in their study.

View the full page

The objective of this teaching unit is to demonstrate that biological diversity serves a functional purpose:

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

2) at different organizational scales (from organisms to ecosystems). The course aims to explain how to approach this functional aspect of diversity for the more than 10 million organisms present on the planet’s surface, using examples from highly and minimally anthropized environments.

View the full page

Phylogeny is a search for evolutionary clues. The goal of this module is to highlight the existence of gene phylogenies within species phylogenies, the methods for representing evolutionary histories as trees, and the concept of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the core of this course unit. Distance-based methods highlight the difficulties in distinguishing between homology and homoplasy, as well as the need to construct models of character evolution. The cladistic approach based on maximum parsimony illustrates, on the one hand, the use of bootstrapping to estimate the robustness of phylogenetic nodes and, on the other hand, the impact of taxonomic sampling on the detection of multiple substitutions.

Probabilistic approaches are introduced and then explored in greater depth. The long-branch attraction artifact leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to address the calculation of likelihood, the estimation of model parameters using optimality criteria, the construction of various models of character evolution, and the comparison of models. Bayesian inference, in turn, introduces the distinction between density-based and optimality-based approaches. It then covers the a priori use of probability densities, the estimation of posterior distributions of model parameters based on the data, their approximation using Markov chains with Monte Carlo and Metropolis coupling (MCMCMC), the initialization and convergence phases, and the calculation and interpretation of posterior probabilities for trees and clades. The importance of evolutionary models for DNA, RNA, and protein sequences and their refinement is emphasized.

View the full page

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

Throughout this module, we will use articles to discuss several evolutionary topics relevant to Evo-Devo approaches: the concept of homology, the origin and evolution of repetitive structures, the genetic basis of development, and the links between genomic evolution and morphological evolution. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them at the level of major modern groups as well as at the population level.

View the full page

View the full page

1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

View the full page

The courses cover four aspects of conservation biology, drawing on current scientific research in this field:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology. Why conserve biodiversity? Who are the key players in BC, and what is the role of science in BC? 
2. Species Conservation: Which species are priorities? How can we conserve species? How do we know if a species is “well conserved”? 
3. Conservation of Areas: Which areas are priorities? How can we conserve these areas? 
4. Does Conservation Work?The Importance of Social Acceptance and Political Commitment. The Need for Biodiversity Indicators and for Measuring the Impact of Conservation. 

Students also work in groups to present a community library project, addressing the following questions: Why, what, where, how, how much does it cost, and how can we tell if it’s effective? 

View the full page

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

View the full page

Quantitative genetics is a discipline that emerged in the early 20th century to understand the inheritance of continuous traits—that is, the majority of traits of agronomic interest (yield, etc.) or evolutionary interest (life history traits, morphology). It is therefore an indispensable tool for understanding, modeling, and predicting natural or artificial selection, as well as the evolution of natural systems or cultivated plants and animals. Its relevance is more pressing than ever at the dawn of the 21st century, with the emergence of genomics (a driver of scientific progress, provided that evolutionary problems are not reduced to the fiction of a few strong-effect Mendelian alleles), and the resurgence of alternative models of inheritance (epigenetics) that go beyond the sequence-centered perspective inherited from classical molecular biology.

The goal of this module is to provide students with a sufficient foundation in quantitative genetics to (i) understand the classical foundations of the discipline, work with key quantities (genetic variances, heritabilities, genetic correlations), and apply statistical techniques for estimating these parameters; (ii) understand the power of this technique for formulating and understanding fundamental or applied evolutionary problems (agricultural breeding), and (iii) understand how this formalization of inheritance relates to the classical Mendelian view.

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The overall objective is to introduce human evolutionary biology, proposing to apply the tools of evolutionary biology to better understand human behavior and the behavior observed in non-human primates within the context of their evolutionary history. Whether the topics are health, social behavior, culture, local adaptations, language, morality, reproduction, or sexual preferences, they are addressed within the theoretical framework of evolutionary biology and ecology. Course Overview: Anthropology, Humanities, and Evolutionary Biology / The Evolution of Cooperation / Cultural Evolution / The Evolution of Diet / The Evolution of Sociality in Primates / Family Ecology / Medicine, Public Health, and Evolution / The Evolution of Language / Evolutionary Demography / The Origins of Fairness.

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Behavioral ecology approaches the study of behavior from an evolutionary perspective to examine its mechanisms, function, and the role behavior plays in evolutionary and ecological processes. Research in behavioral ecology helps us understand other phenomena observed in other disciplines of biology, since all animals—from single-celled organisms to the most complex vertebrates—exhibit behavior.

The module exposes students to various basic concepts, as well as the wide range of tools that may be used (observations and experiments in natural populations or on captive individuals, comparative analyses, the use of modeling tools, ecophysiology, molecular biology, biochemistry, embedded electronics, etc.). Part of the course focuses on specific discussions of potential research approaches, the tools used, and the limitations of the inferences that can be drawn. Students will be expected to participate actively at these various levels, particularly through critical discussions of research articles.

The topics covered range from the exploration of food-foraging strategies, mate selection, habitat choice, and investment in reproduction to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also depending on the instructors’ perspectives and the specific topics covered (the meanings and relationships between “Animal Behavior,” “Ethology,” “Behavioral Ecology,” etc.).

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

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

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The M2 individual internship lasts approximately 5 to 6 months and, depending on the student’s track, must be completed in a research laboratory or a non-academic organization. It allows students to gain in-depth professional experience in the field of biodiversity, evolution, or ecology. It may be conducted at a local, national, or international organization on a topic approved by the faculty to ensure it aligns with the specific objectives of the student’s track of study.

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

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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 mandatory nor exhaustive: any topic related to evolution is fair game). Working in groups of two or three, 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 to help them begin exploring the topic, or the groups may propose relevant papers themselves. From among these, the group will assign (one week before the class session) one or two papers that everyone should read before class. The group will be responsible for presenting the topic to the rest of the class and leading a discussion on it. The group presentation should explain why the topic is interesting and present the current state of the field, outlining points of controversy and identifying major open questions. The presentation format will be determined by the group, keeping in mind that it should encourage discussion. For the final session(s) at the end of the course, students will give short individual presentations summarizing certain aspects of another group’s topic. In addition to the main presentations on hot topics, there will be a brief “writing summaries” exercise at the beginning of the course, as well as regular “news & views” briefings on recent articles selected 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 to analyze biological data: describing, testing, and modeling simple experimental protocols;

Gaining an understanding of the fundamental properties of linear models used in simple regressions and simple ANOVAs;

Incorporating the essence of biological data into models: collinearity, dependence, spatial structure, non-normal distributions....

Presenting data and results from models.

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Modeling is a methodology that is frequently used in the biological sciences today, particularly in ecological and evolutionary studies. However, models often intimidate students. The purpose of this introductory course is to show that modeling is by no means more difficult to grasp than other techniques in biology. The goal is to give students a sense of how a model is constructed, to help them identify the key assumptions underlying a result, and to test their validity. The course will aim to familiarize students with several basic modeling techniques and tools.

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This one-week course will be offered at least in the winter of 2020 (and in subsequent years if independent funding can be secured). It will be organized as a retreat during which students will work in small groups to write grant proposals on topics in evolutionary biology.

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

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

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The objective of this course is to provide the theoretical background necessary to understand—and potentially be able to use and apply—the principles of how selection affects the evolution of populations. Y. Michalakis describes the basics of selection theory and demonstrates, using elementary algebra, that it is possible to derive some fundamental results in population genetics, such as Fisher’s Fundamental Theorem. He also provides an introduction to mutation-selection balance and two-locus theory. These latter topics are put into perspective in the courses taught by T. Lenormand on the evolution of sexual reproduction, migration, and local adaptation. T. Lenormand also presents the theory that enables an understanding of 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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The M1 individual internship lasts approximately three months and, depending on the student’s program track, must be completed in a research laboratory or a non-academic organization. It allows students to gain professional experience in the fields of biodiversity, evolution, or ecology. It may be carried out at a local, national, or international organization, on a topic approved by the faculty to ensure it aligns with the specific objectives of the student’s program.

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

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The goal of this course unit is to understand the adaptive biology of organisms by examining individual and population responses to environmental variations. Concrete examples from the field of evolutionary animal ecophysiology will be discussed in the context of global change. The responses of organisms and populations to abiotic parameters (such as temperature, salinity, oxygen availability, and pollutants) will be examined, along with their interactive effects. The course will demonstrate the role of physiological mechanisms in ecology, ranging from phenotypic and cognitive processes at the intra-individual level to functional variations between individuals and between species. The concepts of intraspecific variability, phenotypic plasticity, and transgenerational effects will also be addressed. This course unit will be illustrated with examples of analyses of phenotypic traits (including behavior) within populations. Links to genetic and epigenetic markers will also be discussed. Various approaches (-omics vs. gene/protein targets), several experimental designs, and diverse organizational scales of living organisms will be considered (molecule, gene, phenotype, individual, population, species).

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

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"The objective of this course unit is to build upon the material covered in the first semester by exploring issues related to phenotypic evolution and the main methodological approaches associated with it. The course will address the evolution of various types of traits (life history traits, traits involved in reproductive strategies, traits involved in biotic interactions, and quantitative traits). The main approaches covered include game theory formalization, adaptive dynamics, quantitative genetics, and the comparison of theoretical predictions with empirical data. The course includes:

1) lectures on the main concepts of evolutionary ecology;

2) tutorials focused on document analysis and exercises"

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

Summary of the learning unit:

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

Topic types:

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

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

Assessment Procedures:

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

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

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

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

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

Summary of the learning unit:

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

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

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

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

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English tutorial courses designed to foster professional proficiency in English.

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ORPAL is a course offered as a combined program (1/3 fieldwork and 2/3 laboratory practicals). The work, carried out in pairs or groups of three under the supervision of an instructor, covers the entire research process, from defining the research question and collecting samples in the field, data collection, through interpretation, the writing of a scientific article (see https://biologie-ecologie.com/exemples-travaux/), and the oral presentation of the results.

'ORPAM takes place during the first few weeks of the semester. This course unit begins with a 3-day field training session (24 hours—orientation workshop) and continues with a short laboratory workshop (24 hours). The course unit concludes with the writing of a popular science article and an oral presentation of the results.

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

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

Deviance Analysis and Goodness of Fit

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

Graphical representation of the predictions.

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

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

Summary of the learning unit:

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

Assessment Procedures:

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

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

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Ecophysiology is a discipline at the intersection of organismal biology and ecology. Integrative ecophysiology focuses more specifically on the issue of scaling. In other words, the objective of this course unit is to illustrate how the study of acclimation and adaptation mechanisms at the individual (or even sub-individual) level can explain population structure, species distribution, and ecosystem functioning. The responses of organisms and populations to key structuring abiotic parameters (such as temperature, salinity, oxygen availability, and pollutants) will be examined, along with their interactive effects. The role of interactions among organisms will also be addressed. In this course unit, animals, plants, and microorganisms will be examined, and various types of approaches will be illustrated: field observations, in situ experiments, and laboratory experiments.

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The primary objective of this course is to provide students with all the skills necessary to understand and apply the concepts and methods underlying the quantitative study of population phenomena. The main methods for analyzing and modeling these phenomena will be addressed from both a theoretical (formal calculations) and practical (statistics, simulations) perspective, using examples that explore 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 paid to heterogeneity (spatial, genetic, or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent in their study.

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The objective of this teaching unit is to demonstrate that biological diversity serves a functional purpose:

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

2) at different organizational scales (from organisms to ecosystems). The course aims to explain how to approach this functional aspect of diversity for the more than 10 million organisms present on the planet’s surface, using examples from highly and minimally anthropized environments.

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1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

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The module aims to provide theoretical and practical knowledge of statistical analyses of spatial and temporal constraints: classification and ordination under constraints, "two-table ordination methods and statistical tests: canonical analyses (AFD, CCA, RDA, CAP)," "statistical tests on distance matrices, and matrix comparisons (PERMANOVA, Mantel, Procrustes)."

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The courses cover four aspects of conservation biology, drawing on current scientific research in this field:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology. Why conserve biodiversity? Who are the key players in BC, and what is the role of science in BC? 
2. Species Conservation: Which species are priorities? How can we conserve species? How do we know if a species is “well conserved”? 
3. Conservation of Areas: Which areas are priorities? How can we conserve these areas? 
4. Does Conservation Work?The Importance of Social Acceptance and Political Commitment. The Need for Biodiversity Indicators and for Measuring the Impact of Conservation. 

Students also work in groups to present a community library project, addressing the following questions: Why, what, where, how, how much does it cost, and how can we tell if it’s effective? 

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

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"This course unit consists of three main sections: I—Physical Characterization and Biogeochemical Cycles of Coastal Marine Ecosystems; II—Biodiversity and Functioning of Coastal Marine Ecosystems; III—Coastal and Maritime Law; Uses, Conflicts, and Integrated Management of the Coastal Zone. This course unit 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 particular emphasis on water interactions with the open sea and their watersheds. Their biogeochemistry will be examined, notably to describe carbon and nutrient fluxes through the water and sediment compartments. Various aspects of their biodiversity will be illustrated to highlight the importance of these ecosystems as habitats for dependent species, with particular emphasis on the role of this biodiversity in their functioning. The coastal zone is densely populated by humans (40% of the world’s population). Particular attention will be given to human uses (e.g., aquaculture) and their spatial planning, including the assessment of their ecosystem services in an economic context, management and protection measures (e.g., Marine Protected Areas, Natura 2000), and professionals involved in managing these environments will share concrete experiences. Finally, the implications of the law of the sea for the management of the littoral and coastal zones will be covered."

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This module covers topics related to identifying, quantifying, and modeling the interactions between climate, marine species, and their exploitation.

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Behavioral ecology approaches the study of behavior from an evolutionary perspective to examine its mechanisms, function, and the role behavior plays in evolutionary and ecological processes. Research in behavioral ecology helps us understand other phenomena observed in other disciplines of biology, since all animals—from single-celled organisms to the most complex vertebrates—exhibit behavior.

The module exposes students to various basic concepts, as well as the wide range of tools that may be used (observations and experiments in natural populations or on captive individuals, comparative analyses, the use of modeling tools, ecophysiology, molecular biology, biochemistry, embedded electronics, etc.). Part of the course focuses on specific discussions of potential research approaches, the tools used, and the limitations of the inferences that can be drawn. Students will be expected to participate actively at these various levels, particularly through critical discussions of research articles.

The topics covered range from the exploration of food-foraging strategies, mate selection, habitat choice, and investment in reproduction to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also depending on the instructors’ perspectives and the specific topics covered (the meanings and relationships between “Animal Behavior,” “Ethology,” “Behavioral Ecology,” etc.).

View the full page

The goal of this resolutely transdisciplinary course is to provide the skills necessary for the effective management and meaningful use of data from various sources and of various types, particularly data with a spatial component. The course consists of three complementary, sequential modules. The first addresses the challenges inherent in data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second focuses on geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third area presents the diversity of spatial analysis tools that enable the quantitative exploitation of spatial data, whether through metrics or statistical tests.

View the full page

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

View the full page

Ecophysiology is a discipline at the intersection of organismal biology and ecology. Integrative ecophysiology focuses more specifically on the issue of scaling. In other words, the objective of this course unit is to illustrate how the study of acclimation and adaptation mechanisms at the individual (or even sub-individual) level can explain population structure, species distribution, and ecosystem functioning. The responses of organisms and populations to key structuring abiotic parameters (such as temperature, salinity, oxygen availability, and pollutants) will be examined, along with their interactive effects. The role of interactions among organisms will also be addressed. In this course unit, animals, plants, and microorganisms will be examined, and various types of approaches will be illustrated: field observations, in situ experiments, and laboratory experiments.

View the full page

The primary objective of this course is to provide students with all the skills necessary to understand and apply the concepts and methods underlying the quantitative study of population phenomena. The main methods for analyzing and modeling these phenomena will be addressed from both a theoretical (formal calculations) and practical (statistics, simulations) perspective, using examples that explore 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 paid to heterogeneity (spatial, genetic, or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent in their study.

View the full page

The objective of this teaching unit is to demonstrate that biological diversity serves a functional purpose:

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

2) at different organizational scales (from organisms to ecosystems). The course aims to explain how to approach this functional aspect of diversity for the more than 10 million organisms present on the planet’s surface, using examples from highly and minimally anthropized environments.

View the full page

The goal of this resolutely transdisciplinary course is to provide the skills necessary for the effective management and meaningful use of data from various sources and of various types, particularly data with a spatial component. The course consists of three complementary, sequential modules. The first addresses the challenges inherent in data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second focuses on geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third area presents the diversity of spatial analysis tools that enable the quantitative exploitation of spatial data, whether through metrics or statistical tests.

View the full page

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1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

View the full page

The module aims to provide theoretical and practical knowledge of statistical analyses of spatial and temporal constraints: classification and ordination under constraints, "two-table ordination methods and statistical tests: canonical analyses (AFD, CCA, RDA, CAP)," "statistical tests on distance matrices, and matrix comparisons (PERMANOVA, Mantel, Procrustes)."

View the full page

The courses cover four aspects of conservation biology, drawing on current scientific research in this field:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology. Why conserve biodiversity? Who are the key players in BC, and what is the role of science in BC? 
2. Species Conservation: Which species are priorities? How can we conserve species? How do we know if a species is “well conserved”? 
3. Conservation of Areas: Which areas are priorities? How can we conserve these areas? 
4. Does Conservation Work?The Importance of Social Acceptance and Political Commitment. The Need for Biodiversity Indicators and for Measuring the Impact of Conservation. 

Students also work in groups to present a community library project, addressing the following questions: Why, what, where, how, how much does it cost, and how can we tell if it’s effective? 

View the full page

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

View the full page

"This course unit consists of three main sections: I—Physical Characterization and Biogeochemical Cycles of Coastal Marine Ecosystems; II—Biodiversity and Functioning of Coastal Marine Ecosystems; III—Coastal and Maritime Law; Uses, Conflicts, and Integrated Management of the Coastal Zone. This course unit 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 particular emphasis on water interactions with the open sea and their watersheds. Their biogeochemistry will be examined, notably to describe carbon and nutrient fluxes through the water and sediment compartments. Various aspects of their biodiversity will be illustrated to highlight the importance of these ecosystems as habitats for dependent species, with particular emphasis on the role of this biodiversity in their functioning. The coastal zone is densely populated by humans (40% of the world’s population). Particular attention will be given to human uses (e.g., aquaculture) and their spatial planning, including the assessment of their ecosystem services in an economic context, management and protection measures (e.g., Marine Protected Areas, Natura 2000), and professionals involved in managing these environments will share concrete experiences. Finally, the implications of the law of the sea for the management of the littoral and coastal zones will be covered."

View the full page

This module covers topics related to identifying, quantifying, and modeling the interactions between climate, marine species, and their exploitation.

View the full page

Behavioral ecology approaches the study of behavior from an evolutionary perspective to examine its mechanisms, function, and the role behavior plays in evolutionary and ecological processes. Research in behavioral ecology helps us understand other phenomena observed in other disciplines of biology, since all animals—from single-celled organisms to the most complex vertebrates—exhibit behavior.

The module exposes students to various basic concepts, as well as the wide range of tools that may be used (observations and experiments in natural populations or on captive individuals, comparative analyses, the use of modeling tools, ecophysiology, molecular biology, biochemistry, embedded electronics, etc.). Part of the course focuses on specific discussions of potential research approaches, the tools used, and the limitations of the inferences that can be drawn. Students will be expected to participate actively at these various levels, particularly through critical discussions of research articles.

The topics covered range from the exploration of food-foraging strategies, mate selection, habitat choice, and investment in reproduction to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also depending on the instructors’ perspectives and the specific topics covered (the meanings and relationships between “Animal Behavior,” “Ethology,” “Behavioral Ecology,” etc.).

View the full page

View the full page

1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

View the full page

The module aims to provide theoretical and practical knowledge of statistical analyses of spatial and temporal constraints: classification and ordination under constraints, "two-table ordination methods and statistical tests: canonical analyses (AFD, CCA, RDA, CAP)," "statistical tests on distance matrices, and matrix comparisons (PERMANOVA, Mantel, Procrustes)."

View the full page

The courses cover four aspects of conservation biology, drawing on current scientific research in this field:  

1. Introduction to Biodiversity Conservation(BC): Definition of Conservation Biology. Why conserve biodiversity? Who are the key players in BC, and what is the role of science in BC? 
2. Species Conservation: Which species are priorities? How can we conserve species? How do we know if a species is “well conserved”? 
3. Conservation of Areas: Which areas are priorities? How can we conserve these areas? 
4. Does Conservation Work?The Importance of Social Acceptance and Political Commitment. The Need for Biodiversity Indicators and for Measuring the Impact of Conservation. 

Students also work in groups to present a community library project, addressing the following questions: Why, what, where, how, how much does it cost, and how can we tell if it’s effective? 

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

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"This course unit consists of three main sections: I—Physical Characterization and Biogeochemical Cycles of Coastal Marine Ecosystems; II—Biodiversity and Functioning of Coastal Marine Ecosystems; III—Coastal and Maritime Law; Uses, Conflicts, and Integrated Management of the Coastal Zone. This course unit 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 particular emphasis on water interactions with the open sea and their watersheds. Their biogeochemistry will be examined, notably to describe carbon and nutrient fluxes through the water and sediment compartments. Various aspects of their biodiversity will be illustrated to highlight the importance of these ecosystems as habitats for dependent species, with particular emphasis on the role of this biodiversity in their functioning. The coastal zone is densely populated by humans (40% of the world’s population). Particular attention will be given to human uses (e.g., aquaculture) and their spatial planning, including the assessment of their ecosystem services in an economic context, management and protection measures (e.g., Marine Protected Areas, Natura 2000), and professionals involved in managing these environments will share concrete experiences. Finally, the implications of the law of the sea for the management of the littoral and coastal zones will be covered."

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This module covers topics related to identifying, quantifying, and modeling the interactions between climate, marine species, and their exploitation.

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Behavioral ecology approaches the study of behavior from an evolutionary perspective to examine its mechanisms, function, and the role behavior plays in evolutionary and ecological processes. Research in behavioral ecology helps us understand other phenomena observed in other disciplines of biology, since all animals—from single-celled organisms to the most complex vertebrates—exhibit behavior.

The module exposes students to various basic concepts, as well as the wide range of tools that may be used (observations and experiments in natural populations or on captive individuals, comparative analyses, the use of modeling tools, ecophysiology, molecular biology, biochemistry, embedded electronics, etc.). Part of the course focuses on specific discussions of potential research approaches, the tools used, and the limitations of the inferences that can be drawn. Students will be expected to participate actively at these various levels, particularly through critical discussions of research articles.

The topics covered range from the exploration of food-foraging strategies, mate selection, habitat choice, and investment in reproduction to the study of animal communication and the reasons for living in groups. The historical dimension of the discipline is addressed in the introduction, but also depending on the instructors’ perspectives and the specific topics covered (the meanings and relationships between “Animal Behavior,” “Ethology,” “Behavioral Ecology,” etc.).

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The goal is to master the modeling and statistical analysis of ecosystem data. Students will need to be able to model complex systems (such as a plant in a cultivated ecosystem, population dynamics, or a lake ecosystem). They will also need to know which type of statistical model to use for analyzing ecological data and how to interpret it.

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

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

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

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

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

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The M2 individual internship lasts approximately 5 to 6 months and, depending on the student’s track, must be completed in a research laboratory or a non-academic organization. It allows students to gain in-depth professional experience in the field of biodiversity, evolution, or ecology. It may be conducted at a local, national, or international organization on a topic approved by the faculty to ensure it aligns with the specific objectives of the student’s track of study.

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

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

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

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

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

Summary of the learning unit:

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

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

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

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

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English tutorial courses designed to foster professional proficiency in English.

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

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

Deviance Analysis and Goodness of Fit

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

Graphical representation of the predictions.

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

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Drawing on concepts and methods from ecology, this course unit aims to introduce students to and provide hands-on experience with historical ecology (the study of interactions between humans and their environment over varying time periods) and its main applications in paleoecology and environmental sciences: climate change, fluctuations in biodiversity, vegetation changes, forest dynamics, disturbance ecology, bioarchaeology… ORPAL is a course taught through applied practical training (1/3 fieldwork and 2/3 laboratory practicals). The work, carried out in pairs or groups of three under the supervision of an instructor, covers the entire research process, from defining the research question, field sampling, and data collection, all the way through to interpretation, writing a scientific article (see https://biologie-ecologie.com/exemples-travaux/), and an oral presentation of the results. ORPAM takes place during the first few weeks of the semester. This course unit begins with a 3-day field school (24 hours—orientation workshop) and continues with a short laboratory workshop (24 hours). The course unit concludes with the writing of a popular science article and an oral presentation of the results.

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The objectives of this EU initiative are twofold. On the one hand, it aims to trace all the major milestones in the history of organisms on Earth since the planet’s formation. Thus, topics such as the origin of life, the colonization of the continents, the emergence of angiosperms, glacial and interglacial cycles, and the domestication of plants will be addressed. Second, the course aims to demonstrate how paleoecology is relevant to the modern world, whether through methodological advancements (geochemistry, optical microscopy, electron microscopy, X-ray microscopy, etc.), models for predicting climate change, ecosystem management in the context of global change, or developments in biotechnology.  The course will primarily consist of lecture-style sessions (TD), each led by a specialist in the relevant topic.

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

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

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

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

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

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

Summary of the learning unit:

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

Topic types:

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

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

Assessment Procedures:

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

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

Summary of the learning unit:

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

Assessment Procedures:

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

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This unit focuses on analyzing the impact of human activity on the climate and the environment

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Present various methodological approaches in an applied context, from data collection through interpretation. Each approach is covered over half a day (3 hours), focusing on data collection methods (1.5 hours of lab work) and the interpretation of results (1.5 hours of tutorial).

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"The objective of this course is to present and explain the concepts, issues, operational approaches in the field and in the laboratory, and methodological and analytical strategies used to infer and reconstruct fluctuations in wild and human-exploited biodiversity over time. It draws on empirical and modeled datasets from the fields of ecology, paleoecology, paleobiogeography, archaeobiology, archaeology, and paleethnobiology. Particular attention will be paid to:

- the functional role of ecological disturbances, such as wildfires, in changes to vegetation cover;

- the impact of changes in human societies on the dynamics of forest ecosystems;

- the use, cultivation, and domestication of plants and animals based on the analysis of modern and bioarchaeological data."

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

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

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In this course unit, we will explore the main theoretical concepts of evolutionary processes as reflected in the fossil record. We will focus on reconciling microevolutionary and macroevolutionary mechanisms. The concepts covered will include: species and intraspecific variability, speciation and the rates of evolution, adaptive radiations (ecological speciation) in the fossil record, targeted extinctions (competition between migrants and native species) or mass extinctions (major biological crises), evolutionary modes (anagenesis and saltationism) observed in the fossil record, and a comprehensive review of microevolutionary mechanisms.

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The goal of this resolutely transdisciplinary course is to provide the skills necessary for the effective management and meaningful use of data from various sources and of various types, particularly data with a spatial component. The course consists of three complementary, sequential modules. The first addresses the challenges inherent in data compilation and the solutions provided by database management systems (DBMS): from database design to queries. The second focuses on geographic information systems (GIS): from cartographic representation to geoprocessing. Finally, the third area presents the diversity of spatial analysis tools that enable the quantitative exploitation of spatial data, whether through metrics or statistical tests.

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

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"The objective is to analyze the phylogenetic, developmental, and functional constraints that may have governed the morphological changes observable in the fossil record. The phylogenetic approach will be addressed using reconstruction methods applicable to fossils (parsimony; cladistic analysis). The developmental and functional approaches (primarily odontology) will be illustrated using various methodologies developed on the Montpellier campus (notably X-ray microtomography). A critical review of key articles in the field will be presented orally, followed by a question-and-answer session."

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

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

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

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

Module Content:

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

Teaching and Learning Methods:

-Course (18 hours)

-Tutorial (3 hours).

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1. Bayesian inference: Motivation and a simple example. 

2. The likelihood. 

3. A detour to explore priors. 

4. Markov chain Monte Carlo (MCMC) methods

5. Bayesian analyses in R using the Jags software.  

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

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

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1. “The way the modern West conceives of nature is the least widely shared view in the world” (Descola, 2005, p. 56). According to anthropologist Philippe Descola, the category of “Nature,” as a reality separate from the human world, is a European invention that is merely one of the possibilities available to societies for accounting for the living and non-living beings that surround them.

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

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

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

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

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

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

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

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

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

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

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

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The M2 individual internship lasts approximately 5 to 6 months and, depending on the student’s track, must be completed in a research laboratory or a non-academic organization. It allows students to gain in-depth professional experience in the field of biodiversity, evolution, or ecology. It may be conducted at a local, national, or international organization on a topic approved by the faculty to ensure it aligns with the specific objectives of the student’s track of study.

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

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

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

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

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

Summary of the learning unit:

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

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

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

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

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English tutorial courses designed to foster professional proficiency in English.

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This course is part of a pre-professional training program. It aims to help students reflect on their career plans through interactions with professionals in science communication, participation in science communication projects at the intersection of the research world and secondary education (assisting middle school classes in carrying out environmental and sustainable development education projects), and the analysis of projects developed by Master’s 2 students.

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

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

Deviance Analysis and Goodness of Fit

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

Graphical representation of the predictions.

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

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

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

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Mediation (whether scientific or not) increasingly relies on digital tools for disseminating information, which make it possible to reach a wide audience very quickly. These tools are numerous and diverse, and it is difficult to provide a simple overview of them. Nevertheless, the vast majority of job and internship postings in the field of mediation require knowledge of how to use these digital mediation tools.

The course unit proposed here will therefore aim to introduce students pursuing a career in science communication to the main tools of digital communication and provide them with an introduction to using them. The course unit will also provide an opportunity to discuss the importance of citing sources for published data and verifying that data at a time when misinformation and even outright lies are becoming increasingly prevalent.

The first part of the course will take the form of tutorials and lab sessions designed to introduce students to the main digital tools used in science communication. Examples posted online by various science communication organizations will be analyzed to identify their strengths and weaknesses.

The second part of the course will focus on practical application. Students will be required to visit science communication organizations (whether temporary or permanent) and submit reports on their visits using digital science communication tools. In particular, one of the reports will focus on the scientific activities of the Biology and Ecology Department and will be posted on the department’s website.

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