M1 - Chronological Environments and Paleoecology (CEPAGE)

"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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