FIRST SEMESTER (M1S1)

Master Biodiversity, Ecology and Evolution International Pathway "Evolutionary Biology"

COURSE TITLE: Evolutionary Biology and Population, Communities and Networks Dynamics (UE)

NUMBER of ECTS: 9

Number of hours: Lectures: 15h, Practicals: 18h, Tutorials: 8h

Personal workload (hours expected to be dedicated to, including supervised projects): 67 hours

 

Description of the module

General aims

The module entitled « Evolutionary Biology » provides an entry to the dynamic field of studies of evolution for undergraduates majoring in the life sciences. The module’s aim is to provide a good understanding of microevolutionary processes and their consequences in various fields of research such as behavioural ecology or the evolution of gene frequencies in space and time. Ecological consequences are highlighted in the module named « Population dynamics ».

 

Content summary

The module provides basic and more advanced knowledge on key concepts related to the neo-Darwinian synthesis, to the evolution of populations with finite sizes, to the estimation of patterns of gene flow within and among populations located in fragmented habitats, to the action of natural selection leading to adaptive evolution, to the evolution of quantitative characters through phenotypic plasticity, to the cost of sex and/or to kin selection relying on genetic relatedness among individuals. Therefore, the undergraduates will be expected to get fundamental theoretical knowledge and applied skills in evolutionary biology.

 

Expected knowledge and skills

- Describing and predicting the genetic and genotypic structure under various models of populations in disequilibrium.

- Analysing the genetic relatedness and the inbreeding coefficient.

- Estimating the levels of genetic differentiation among populations and interpreting the results in terms of patterns of gene flow.

- Estimating the effective population size through direct and indirect methods.

- Understanding the societal impact of studying neutral and adaptive microevolutionary forces and linking science with practice to protect biodiversity.

- Additional skills: setting up an experimental design, writing a scientific report, performing phenotypic measures in the field, programming and statistically analysing empirical data using R.

Number of hours: Lectures: 20h, Practicals: 12h, Tutorials: 8h

Personal workload (hours expected to be dedicated to, including supervised projects): 68 hours

 

Description of the module

General aims

There are two main objectives:

1- Being able to decipher and understand the ecological mechanisms underlying the variation in population and communities sizes, and in ecological networks organization: the role of space, intraspecific and interspecific interactions, the different time scales, the importance of stochasticity. Much effort will be devoted to describing and understanding a large variety of methods and approaches, both experimental and theoretical.

2- Learn how to estimate populations and communities sizes and their variation, and use that information for ecosystem management purposes: population viability analysis, ecosystem services protection, measuring the effect of anthropogenic disturbance on biodiversity

 

Content summary

- Role of intraspecific and interspecific interactions for populations and communities’ dynamics (competition, mutualism, predation)

- Role of chance (Neutral theory of biodiversity)

- Dynamics of communities in space and metacommunities

- Ecological networks and communities’ stability

- Methods for estimating population sizes and ecological parameters (death and birth rates, dispersal rates, transition rates)

- Population viability analyses: methods and robustness assessment

- The relationship between biodiversity and ecosystem services

- Evolutionary vs. ecological timescales

 

Expected knowledge and skills

- Deciphering mechanisms underlying the evolution of ecological systems

- Applying experimental and modeling methods to address ecological questions

- Comparing and choosing solutions for ecosystems and natural resources management

- Master informatic tools for addressing ecological questions and problems

- Understanding, developing and using adapted tools to address multidimensional problems

- Searching solutions on their own in various resources: literature, software, internet

- Handling informatics tools for data analysis, modeling and problem solving

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam

80%

Continuous assessment

20%

 

COURSE TITLE: Conservation Genetics (Xavier Vekemans, Professor) (UE)

NUMBER of ECTS: 3

Number of hours: Lectures: 11h, Practicals: 6h, Tutorials: 10h

Personal workload (hours expected to be dedicated to, including supervised projects): 45 hours

Description of the module

General aims

To understand the concepts of ecology, evolutionary biology, and evolutionary genomics on which conservation genetics is based. To become familiar with the methodological approaches used for the estimation of intraspecific biodiversity, and for the conservation of threatened species. To analyze and contextualize the results of a conservation biology publication.             

 

Content summary

Introduction to Conservation Biology and Conservation Genetics: objectives of the field of conservation biology; descriptors of the organization of intraspecific biodiversity; genetic and demographic causes of extinction; presentation of conservation methods. Application with the analysis of data sets during practical work. Analysis of the results of a conservation biology publication and oral presentation.

 

Expected knowledge and skills

- Being able to make an inventory of possible strategic choices to be implemented in a conservation program, and using decision-making tools to guide these choices.

- Using objective criteria to determine the level of threat to a species.

- Additional and transversal skills: data analysis with R, understanding a scientific article in English; critical analysis of an article; oral presentation.

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (written exam)

70%

Continuous assessment (Analysis of a scientific publication and oral presentation)

30%

 

COURSE TITLE: Introduction to Omics Data (Céline Poux, Associate Professor) (UE)

NUMBER of ECTS: 3

Number of hours: Lectures: 20h, Tutorials: 7h

Personal workload (hours expected to be dedicated to, including supervised projects): 45 hours

 

Description of the module

General aims

- To develop and mobilize knowledge concerning the different types of OMICS data (genomic, transcriptomic, proteomic and lipidomic data), their acquisition and some of their applications, particularly in precision medicine.

- To gain a better understanding of OMICS data analyses in further training and/or in a professional context.

- To develop students' critical thinking skills when reading scientific articles regarding OMICS data acquisition.

 

Content summary

- General Introduction to Genetics and Genomics

- Introduction to OMICS data: DNA and RNA sequencing (Sanger, NGS, 3d generation), sequencing data (from machine output to sequence analyses), applications of sequencing data to theoretical and/or applied scientific questions. Introduction to proteomics and lipidomics data acquisition.

- Use of OMICS data in human health: monogenic/polygenic diseases and precision medicine (GWAS and post-GWAS, large scale NGS DNA sequencing, microarrays, RNA-seq, proteomics)

 

Expected knowledge and skills

- Understanding the different types of DNA/RNA sequencing

- Knowing the applications of sequencing

- Knowing how to manipulate sequencing data

- Knowing how to use sequencing data for precision medicine

- Knowing the basics of proteomics and lipidomics

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (written exam)

60%

Continuous assessment

40%

 

COURSE TITLE: Informatics tools for Biologists (Sébastien Grec, Associate Professor) (UE)

NUMBER of ECTS: 3

Number of hours: Tutorials: 24h

Personal workload (hours expected to be dedicated to, including supervised projects): 48 hours

 

Description of the module

General aims

The objective of the module is to acquire computer skills allowing the processing of file data coming from high-speed analysis tools. For this, three levels of learning are offered:

1) Learn Unix commands and understand the interest of scripts to automate tasks, acquire the basics of bash shell scripting.

2) Acquire bases of a algorithm and programming language: python

3) Introduce a python module dedicated to Bioinformatic analysis: Biopython.

The teaching is done by alternating theoretical and practical parts using open-source numeric tools.

 

Content summary

- Introduction to Unix system and command line

- The Bash language for handling and managing files

- Introduction to bash command lines

- Write a Bash script to automate file management

- Extract file information using Grep and Hawk functions

- Introduction to python language

- Understand what a programming language is

- Python's place in the programming field

- Bases of python programming: Data and variables, operators, input / output, control structures, list and dictionaries, iterative loops, reading and writing files

- Create scripts for handling biological and genomic data

- Introduction to Bio-Python language

- Manipulation of genomic data with Biopython

- Introducing bio python in genomic analysis pipeline

 

Expected knowledge and skills:

- Understanding and navigating into a unix system

- Manipulating files and folders

- Seeking informations into files

- Scripting commands

- Be familiar with the notion of algorithm

- Being able to write a script to manipulate data

- Data manipulation with automated approaches

- To realize a simple code in bio-python language

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (carrying out a final task according to a specification by reinvesting the tools acquired during the training. The project report will be accompanied by an oral presentation)

70%

Continuous assessment (knowledge checks during the course sessions)

30%

 

COURSE TITLE: Statistics Initiation with R (Sylvain Billiard, Associate Professor) (UE)

NUMBER of ECTS: 3

Number of hours: Practicals: 24h

Personal workload (hours expected to be dedicated to, including supervised projects): 48 hours

 

Description of the module

General aims

To introduce the students to the use of an open and generalist software commonly used in ecology.  The students will be taught to use R to analyze data, perform advanced statistical testings, program, files management and figures creation. This teaching is a prerequisite for other modules and courses in the Graduate Program. Students will be taught the basics of data analyses and statistical testing: the different statistical frameworks, their hypotheses and their applications.

 

Content summary

1 – R basics: script, package, functions, calculations

2 – Formatting and reading datasets

3 – Programming basics: loops, logical tests, definition and use of functions

4 – Creation and exportation of figures

5 – Basics: Probabilities, distributions, independence, summary statistics, definition of a statistical test, definition of p-values and the different types of errors.

6 – Introduction to statistical testings with non-parametric models: Chi2 and exact tests

7 – Introduction to statistical testings with parametric models: linear models and non-linear models

8 – Application to ecological and evolutionary data

 

Expected knowledge and skills

Direct abilities:

- Exploit a software for data management and analysis, and programming

- Programming with R

- Figures

- Deciding how to analyze data

- Formulating hypotheses and interpreting results

- Verifying statistical tests quality and evaluating confidence level of the analysis

Indirect abilities:

- Algorithms and programming

- Informatics

- Introduction to data analysis and statistical testings

- Communicating methods and results

- Searching literature and internet resources to achieve a specific goal

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (data analysis with R on computers, evaluation of a written report)

75%

Continuous assessment (realization of a programming project on R on computers, evaluation of the product)

25%

 

COURSE TITLE: Scientific Writing and Communication (Céline Toubin, Professor, Graduate Programme) (UE)

NUMBER of ECTS: 3

Number of hours: Lectures: 10h, Practicals: 10h

Personal workload (hours expected to be dedicated to, including supervised projects): 52 hours

 

Description of the module

General aims and content summary

This teaching is designed to train students for           

    - The search for information in the scientific literature,

    - The implementation of automated monitoring strategies,

    - Evaluation of the quality and relevance of the information found,

    - The organization and archiving for reuse.

It will also involve training students in publishing practices (peer review, publishing house, open archives, etc.), bibliometrics, as well as the associated ethical rules (plagiarism, identification of co-authors, etc.). In addition, students will be taught how to develop their capacity to write a scientific article or report, to help them decide on the best way to present their results, to target the right type of publication and to be able to communicate their results to different types of audiences (article, poster, slide show...).

The module will be complemented by an introduction to rhetoric to stimulate students' argumentation skills.

Expected knowledge and skills

The learner will become familiar with writing and communication techniques, which will enable him/her to develop analytical and synthesis skills in order to maximize his/her chances of communicating his/her results to different audiences (peers, general public).

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Full continuous assessment

100%

 

COURSE TITLE: Languages (UE)

NUMBER of ECTS: 3

Number of hours: Tutorials: 20h

Personal workload (hours expected to be dedicated to, including supervised projects): 52 hours

 

Description of the module

General aims

How to communicate in English in an appropriate way with a professor or a professional from the environmental field.

The goal is to reach a minimum level of autonomy in English in order to work without any difficulties in a company, in a laboratory or during the 2nd year internship.

Content summary

Partial content overlook :

The following themes will be discussed during the English lessons:

- Climate change: causes, short and long consequences. Impact on humans, fauna and flora (cities, agriculture, …etc)

- Natural selection.

- Animal skills & behavior

- Marine biology

Expected knowledge and skills

Skills acquired:

How to synthetize a group of oral and written documents (popularized items) in English on technical and scientific topics.

How to explain and structure them (orally and/or in a written way)

How to participate and/or lead a debate, a discussion in English

How to present a clear and precise answer to a particular problem in English.

How to synthesize a file and to present it in English.

 

Assessment methods: (Continuous assessment, report, oral presentation….. + exams weight)

Continuous assessment / Oral comprehension / written comprehension et speaking (debate, presentations, role playing games)

Final presentation in English of a scientific paper  (see EC2)

 

Description of the module

General aims

How to make a bibliographical study on a topic suggested by the educational teams from the ecology, ecotoxicology and evolution laboratories. This study will be presented orally in front of a jury made of an English teacher and a teacher-researcher from the laboratory teams.

Each student chooses his or her topic on the basis of a review article and makes a synthesis and a state of the art on a precise theme. An opening onto other articles dealing with same scientific fields is strongly advised.

Content summary

Here are some examples of the possible themes:

-Evolution in urban environment.

-Mutualism and cooperation.

-reproduction system and global change.

-Biology and genetics of preservation.

-Decline of pollinators.

-Relation between predators and humans

-Cultural evolution and Darwinism.

-Amphibians, endocrine disruptors and multi-xenobiotic resistance

-Behavioral adaptation among crab larvae

-Effect of microplastics in ballast water.

Expected knowledge and skills

-How to synthetize the information from a review article.

-How to synthetize an additional set of scientific articles in English

-How to expose and present this synthesis orally.

-How to present, in English, a clear, precise and detailed answer to either a highly technical question or, on the contrary, a very basic question.

-How to synthetize a research question or a special issue using a slide show in English.

 

Assessment methods: (Continuous assessment, report, oral presentation….. + exams weight)

Oral presentation of the bibliography project in front of a jury made of an English teacher and a teacher-researcher from the laboratory teams.

Number of hours: Tutorials: 24h

Personal workload (hours expected to be dedicated to, including supervised projects): 48 hours

(in construction)

COURSE TITLE: Student project – Projet de l’étudiant (PE)

NUMBER of ECTS: 3

Number of hours: Lectures: 6h, Practicals: 6h, Tutorials: 8h

Personal workload (hours expected to be dedicated to, including supervised projects): 52 hours

 

Description of the module

General aims

The aim of this module is to illustrate the history of the Earth System and long-term interactions between the Geosphere (large scale physical and chemical processes) and the Biosphere by stressing on some major evolutionary events and their relation to global environmental change.

 

Expected outcomes (knowledge and skills)

- Understand the coupling between the Geosphere and the Biosphere through geological time.

- Understand, analyze, and communicate on this interdisciplinary topic through understanding of scientific papers.

 

Content summary

A historical overview will be presented of the coevolution of the Earth system and its Biosphere, by stressing on the evolution of life in relation to global tectonic, oceanographic and climate change and biogeochemical cycles. The origin of life, its early evolution in Precambrian oceans, the rise of animals during the “Cambrian explosion”, terrestrialisation, Phanerozoïc diversifications and mass-extinctions and the significance of the calcite - aragonite and biogenic silica cycles will be developed as case studies. Students will be asked to prepare a short literature review based on relevant scientific papers.

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam

2/3

Continuous assessment (literature review and analyze)

1/3

 

SECOND SEMESTER (M1S2)

Master Biodiversity, Ecology and Evolution International Pathway "Evolutionary Biology"

COURSE TITLE: From genotype to phenotype (Virginie Cuvillier, Associate Professor) (UE)

NUMBER of ECTS: 3

Number of hours: Lectures: 17.5h, Tutorials: 8h

Personal workload (hours expected to be dedicated to, including supervised projects): 46,5 hours

 

Description of the module

General aims

Better apprehend biological systems complexity and their diversity.

Acquire global knowledge about molecular and physiological processes that contribute to phenotypic diversity.

Combine knowledge from different scientific domains (molecular and cellular biology, physiology, ecophysiology) to better understand phenotypic variation.

 

Content summary

- Genetic regulatory networks: regulation of genetic expression; genetic interactions

- Perception of the variable environment: cellular and molecular consequences

- Integrative biology of organisms: physiological regulatory networks (PRNs) and their applied applications

 

Expected knowledge and skills:

To be able to integrate concepts and knowledge from molecular, cellular and organismal biology

To be able to understand scientific articles, perform critical analysis and oral presentation

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam

60%

Continuous assessment (oral)

40%

 

COURSE TITLE: Theoretical modeling (Sylvain Billiard, Associate Professor) (UE)

NUMBER of ECTS: 3

Number of hours: Lectures/Tutorials: 18h

Personal workload (hours expected to be dedicated to, including supervised projects): 54 hours

 

Description of the module

General aims

Be able to translate an evolutionary or ecological problem into a model in order to address a specific question or make predictions.

 

Content summary

- Stochastic models of evolutionary and ecological dynamics, and their approximations

- Numerical analysis, algorithmic and computer simulations of a stochastic model

- Comparison between data and models prediction

- Inference of biological parameters with a process-based model

 

Expected knowledge and skills:

Direct abilities:

- Modeling a specific problem

- Analyzing a deterministic dynamical system (ODE, stability analysis)

- Writing a stochastic models and approximating invasion probability

Indirect abilities:

- Mathematical training

- Programming for simulations and numerical analysis of a model

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (Oral presentation of the analysis of a simple model)

100%

 

COURSE TITLE: Ecology: from theory to experiments (Anne Duputié, Associate Professor) (UE)

NUMBER of ECTS: 3

Number of hours: Lectures: 11h, Practicals: 16h

Personal workload (hours expected to be dedicated to, including supervised projects): 45 hours

 

Description of the module

General aims

The course is designed to provide an overview of the theoretical and applied aspects of ecology, with a special emphasis on species’ geographic distributions in a changing world. The course includes a project work, in which students will design an experiment and/or plan field work, perform this field work or short experimental project, analyze and interpret their data and write a short report.

 

Content summary

Lectures:

  • How to measure fitness?
  • How are life-history traits connected to species’ geographic distributions?
  • How and at what pace do life-history traits evolve?
  • Contemporary evolution in a changing world
  • Species interactions in relation to environmental gradients
  • Assessing biodiversity using metabarcoding approach

Practicals: Students will lead a project in small groups. For example, they could assess how climate change can affect species’ phenology and geographic distribution (through designing experiments aiming at calibrating phenological models for common plant species). Alternatively, they could assess how intra and interspecific interactions vary along an environmental gradient (e.g., pollution gradient). Or, they could estimate biodiversity in samples from different environmental conditions, using a metabarcoding approach. In either case, students will be expected to perform a bibliographic search, to design their protocol, perform the experiment, analyze their data and write an individual report.

 

Expected knowledge and skills:

Direct:

  • based on examples, understand how environmental constraints drive local adaptation and species assemblages.
  • design a realistic yet scientifically valid protocol
  • perform field work and an experiment in the field of ecology

Indirect:

  • work in a small team
  • perform an efficient bibliographic search
  • mobilize the knowledge acquired in biostatistics and R programming language to analyse data
  • write a report in English

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (Oral presentation)

50%

Continuous assessment (design a protocol, carry out experiments, Report)

50%

 

COURSE TITLE: Experimental approaches in Ecology (Isabelle De Cauwer, Associate Professor) (UE)

NUMBER of ECTS: 3 (Common module with the M1 BEE tronc commun)

Number of hours: Lectures: 7h, Practicals: 20h

Personal workload (hours expected to be dedicated to, including supervised projects): 45 hours

 

Description of the module

General aims

- Formulating a scientific question in ecology and identifying relevant hypotheses,

- Designing an experimental protocol to tackle a question in ecology, while taking into account the logistic / biological constraints,

- Choosing and implementing appropriate statistical analysis with regard to the scientific question.

 

Content summary

At the beginning of the term, students will get tutorials on experimental design, data set manipulation and statistical analysis. Each student will then be assigned a scientific question in ecology and will create an experimental protocol to tackle that question. Finally, students will receive a real-life data set corresponding to the initial scientific question and will analyze it using statistical tools.

 

Expected knowledge and skills:

Direct skills:

- Manipulating data sets in ecology (formatting, producing graphic outputs, carrying out statistical analysis) with various software programs (Excel and R).

Indirect skills:

- Presenting a scientific reasoning, both in synthetic written documents and in oral presentations,

- Developing a critical sense by evaluating the relevance of experimental protocols and statistical analysis carried out by their peers.

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (oral presentation)

50%

Continuous assessment  (small report)

50%

 

COURSE TITLE: Analysis of empirical population genetics data (Isabelle De Cauwer, Associate Professor & Jean-François Arnaud, Professor). (UE)

NUMBER of ECTS: 3 (Common module with the M1 tronc commun)

Number of hours: Lectures: 2h, Practicals: 25h

Personal workload (hours expected to be dedicated to, including supervised projects): 45 hours

 

Description of the module

General aims:

 

- Describing the intra (genotypic structure) and inter-population genetic structure using basic genetic data : the number of alleles, the allelic richness, the observed heterozygosity, the expected heterozygosity.

- Depicting the levels of genetic differentiation among populations using F-statistics.

- Learning how to describe the spatial genetic structure using spatial autocorrelation tools at both intra and inter population level.

- Analyzing contemporary dispersal events through the detection of migrants from first generation using assignment tests.

 

Content summary

 

Based on the practical courses, students have to analyze a real population genetics data set and present the obtained results through a final oral defense. Depending on the academic year, the data set to be analyzed might be:

  • A data set including spatially structured populations of the land snail Helix aspersa (Cornu aspersum) sampled along a roadside in Britanny (Western France) and genotyped using both allozymes and microsatellite loci.
  • A data set including a set of populations of the invasive shore crabs Hemigrapsus sanguineus, located along the coastline of north-western France and genotyped using microsatellite loci.
  • A data set of 4 populations of the sea beet (Beta vulgaris ssp. maritima), located along French and Swedish coastlines, and genotyped using microsatellite loci.
  • A data set of populations of a pioneering Amphibian species (Pelodytes punctatus) located in a post-industrial fragmented habitat in northern France, and genotyped using microsatellite loci.

 

Expected knowledge and skills:

 

- Getting an overview of molecular markers commonly used in molecular ecology.

- Using various software programs to describe the levels of genetic diversity in wild populations and estimate F-statistics.

- Understanding the notion of migration-drift equilibrium using neutral genetic markers.

- Understanding the statistical tools for performing one and two-dimensional spatial autocorrelation analyses using univariate or multivariate approaches.

- Presenting a synthetic scientific reasoning through an oral presentation.

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (oral report in front of a jury)

100%

 

COURSE TITLE: Multivariate statistics (Catherine Crônier, Professor) (UE)

NUMBER of ECTS: 3

Number of hours: Lectures: 3h, Practicals: 6h, Tutorials: 3h

Personal workload (hours expected to be dedicated to, including supervised projects): 60 hours

 

Description of the module

General aims:

Students will get an introduction into multivariate data analysis and its application to problems in biology and paleontology.

Content summary

  • Introduction: matrices, distributions, variance, covariance
  • Data reduction:  ordination and clustering methods
  • Discrimination and classification
  • Multivariate hypothesis testing
  • Application of multivariate data analysis in biology and paleontology

 

Expected knowledge and skills:

  • Knowledge on various ways to analyze multivariate datasets, and therewith on how to use multivariate statistics to test hypotheses in biology and paleontology
  • Formulating hypotheses and interpreting results
  • Communicating methods and results

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Continuous assessment (data analysis, report)

100%

 

COURSE TITLE: Research in “Global Changes & Biodiversity” (Anne Duputié, Associate Professor) (UE)

NUMBER of ECTS: 3

Number of hours: Tutorials: 12h

Personal workload (hours expected to be dedicated to, including supervised projects): 60 hours

 

Description of the module

General aims:

This course will be based on seminars given by a panel of researchers active in the field of ecology and evolutionary ecology, especially in the context of global change.

 

Content summary

1. Interspecific interactions along environmental gradients

2. Geographic range limits and range shifts

3. Tolerance to pollutants

 

Expected knowledge and skills:

Integrative biology; Ecology; Evolutionary Ecology ; Theoretical modeling ; Biostatistics

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Continuous assessment (peer reviewing of recently posted preprints on BiorXiv)

100%

 

COURSE TITLE: 2 months Internship (Isabelle De Cauwer, Associate Professor) (UE)

NUMBER of ECTS: 9

Number of hours: 280h

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam

100%

 

THIRD SEMESTER (M2S3)

Master Biodiversity, Ecology and Evolution International Pathway "Evolutionary Biology"

COURSE TITLE: Population genomics (Camille Roux, Tenured Researcher CNRS) (UE)

NUMBER of ECTS: 3

Number of hours: Lectures/Tutorials: 24h

Personal workload (hours expected to be dedicated to, including supervised projects): 48 hours

 

Description of the module

General aims

    - Simulating genomes from populations experiencing different demographic histories (contraction, expansion, migration).

    - Be able to statistically test alternative scenarios in evolution to understand patterns of polymorphism (intrapopulation) and divergence (interspecies) in genomes.

    - Identify in genomes the targets of natural selection.

 

Content summary

- Measure molecular diversity within populations whose genomes have been sequenced and understand the demographic history responsible for the observed pattern. Students will learn to describe real data sets and simulate different scenarios to identify the most realistic ones.

   - Measure the divergence between different species and understand the demographic events that have occurred since ancestral separation.

   - While demographic history impacts the entire genome, natural selection acts locally on the patterns of polymorphisms by rapidly fixing an advantageous allele, or by maintaining different alleles over long evolutionary periods or by eliminating deleterious mutations. Selection can also eliminate or promote the gene flow from another population. In this module we will see how to identify these different targets of selection.

 

Expected knowledge and skills:

    - Extract information from genomes.

    - Simulate genomes according to different historical and selective hypotheses.

    - Statistically test the relevance of the different scenarios.

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam: Small research project and short presentation

100%

 

COURSE TITLE: Evolutionary genomics (Éléonore Durand, Associate Professor) (UE)

NUMBER of ECTS: 3

Number of hours: Lectures: 18h, Tutorials: 9h

Personal workload (hours expected to be dedicated to, including supervised projects): 45 hours

 

Description of the module

General aims

- To better understand how the genetic information in the genomes is organized. 

- To acquire knowledge about the molecular and evolutionary processes driving genome evolution.

- To be able to understand and discuss comparative genomics studies, including their advantages and drawbacks.

 

Content summary

- How are genomes organized across various organisms (size, content, structure...)?

- What are the molecular and evolutionary processes underlying the genetic diversity and genome dynamics?   Types of mutations, rate of emergence of new mutations and their effects at the molecular, phenotypic and fitness levels, evolution of the mutation rate, genetic signatures of natural selection.

- Where do new genes come from?

- How do non-genic regions evolve? 

- Structural variations

- Evolution of regulatory networks

 

Expected knowledge and skills:

- Describe and understand how genomes are organized and evolve across various organisms (model and non-model species)

- Be able to discuss the molecular and evolutionary processes involved in generating the observed genome architecture

- Know the common methods to identify and analyze variation in genomes

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (written evaluation on theoretical courses, applied courses and/or interpretation of scientific documents)

70%

Continuous assessment (data analysis and small reports or oral presentations)

30%

 

COURSE TITLE: Macroevolution (Céline Poux, Associate Professor) (UE)

NUMBER of ECTS: 3

NUMBER of ECTS: 3

Number of hours: Lectures: 18h, Practicals: 6h

Personal workload (hours expected to be dedicated to, including supervised projects): 48 hours

 

Description of the module

General aims

The objectives of this course are to provide the students with the theoretical and practical tools necessary to understand and study the processes that have shaped the evolutionary history of groups of organisms, including diversification and trait evolution. Another goal is to develop student’s critical thinking skills when reading scientific articles about paleontology and comparative phylogenetics.

 

Content summary

- Macroevolution: contribution of Paleontology:

* Modalities and Tempo of evolution

                1. Speciation: Emergence of species, speciation modalities

                2. The seventh evolutionary models

                3. Synthesis and model comparison to the fossil record

* Evolution and Development: Heterochronies

- Phylogenetic comparative methods to study macroevolution:

                1. Dating methods

                2. Reconstruction of ancestral characters and biogeographic history

                3. Trait evolution modelling

                4. Rate of diversification

- Metabarcoding

- History and Epistemology of Evolutionary Sciences

 

 

Expected knowledge and skills:

- Understand paleontological and comparative studies

- Know the analysis tools used for these studies

- Be able to analyze phylogenetic data

- Understand and discuss the results of the analyses.

- Know the different controversies and major historical events in the history of evolutionary sciences.

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (on theoretical courses, applied courses and/or interpretation of scientific documents).

70%

Continuous assessment (short scientific report on a case study)

30%

 

COURSE TITLE: GLM Statistics (Sylvain Billiard, Associate Professor) (UE)

NUMBER of ECTS: 3

Number of hours: Tutorials: 18h.

Personal workload (hours expected to be dedicated to, including supervised projects): 54 hours

 

Description of the module

General aims

Being able to analyze biological data and address ecological and evolutionary questions with Generalized Linear Models with Random and/or Fixed effects.

 

Content summary

- GLM basics with R: definition of a linear model, likelihood, deviance, likelihood ratio test, residuals analyses, Akaike information criterion, Bayesian information criterion

- The exponential family

- Mixed effects models

- Temporal and spatial datasets

- Variance heterogeneity

- Dealing with non-independence

 

Expected knowledge and skills:

Direct abilities:

- Writing a linear model to address a specific question

- Using the software R and various packages to analyze GLMs

- Evaluating the quality of a statistical models

- Interpretation of the results

Indirect abilities:

- Translating a question into a specific method

- Programming in R

- Improving some mathematical skills applied to statistics analysis

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (Individual report of a real data analysis with GLMs)

100%

 

COURSE TITLE: Introduction to Bioinformatics (Sylvain Legrand, Associate Professor) (UE)

NUMBER of ECTS: 6

Number of hours: Lectures: 27h, Tutorials: 27h

Personal workload (hours expected to be dedicated to, including supervised projects): 90 hours

 

Description of the module

General aims:

The objective of the module is to discover the basics of bioinformatics through an alternation between theoretical and practical parts, using mainly free web tools

 

Content summary:

Databases, sequence alignment, gene prediction, protein sequence analysis, phylogeny

 

Expected knowledge and skills:

- To be able to query databases and make relevant queries

- To understand the data structure

- To be able to choose an alignment software and the parameters adapted to a problem

- To know the algorithmic methods for sequence alignment

- To be able to use Blast software optimally to answer a specific question

- To know the methodology for gene prediction, whether bacterial or eukaryotic

- To know the methodology to analyze a protein sequence: to deduce its potential function, to have an idea of its cellular location

- To understand the main principles of molecular evolution and phylogenetic reconstruction

- To be able to build informative alignments for phylogenetic analysis

- To be able to reconstruct phylogenetic trees in Maximum Likelihood (ML) and Bayesian Inference (BI)

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Final exam (written exam)

50%

Continuous assessment

50%

 

COURSE TITLE: Project Management (Sophie Duquesne, Professor, Graduate Programme) (UE)

NUMBER of ECTS: 3

Number of hours: Lectures: 6h, Tutorials: 14h

Personal workload (hours expected to be dedicated to, including supervised projects): 52 hours

 

Description of the module

General aims:

The aim of this course is to provide young scientists the necessary background to highlight the importance of the management in science. It sensitises young scientists to the central role of project management in their professional careers, and that a science project requires effective management in order to maximise its benefit.

 

Content summary:

Introduction to project management in science

a. Defining science projects

b. Lifecycle of a scientific project

Management of a scientific project

a. Project management processes (project planning and project execution)

b. Concepts and jargon in project management

c. Tools to efficiently manage a scientific project

 

Expected knowledge and skills:

The master student that followed this course will manage to properly build a scientific project defining clearly the objectives and the relevance of the ideas, making a rational work plan, evaluating the risks and challenges to maximize the chance of success and being able to follow the progress of the project and evaluate the results.

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Continuous assessment  (case studies)

100%

 

COURSE TITLE: Bibliographic project (Xavier Vekemans, Professor) (UE)

NUMBER of ECTS: 6

Number of hours: Lectures: 6h, Practicals: 30h

Personal workload (hours expected to be dedicated to, including supervised projects): 108 hours

 

Description of the module

General aims:

To initiate the student in the search for documents and the realization of a bibliographical synthesis of scientific articles. To inform the student about the functioning of the world of scientific publication. To bring the student to practice reading scientific literature in English in a field close to his/her internship subject. To train the student to make a scientific report and a scientific presentation, and to answer questions from a jury.

 

Content summary:

-Introduction to bibliographic search engines; access to bibliographic sources and management of a personal bibliographic database.

-Initiation to the way the world of scientific publishing works

-Choosing a subject and carrying out a personal bibliographical research

-Introduction to written and oral expression tools

-Writing and oral defense of a bibliographical synthesis.

 

Expected knowledge and skills:

- Familiarization with scientific English, and the format of scientific publications

- Access to the main bibliographic sources and search engines

- Create and manage a computerized bibliographic database

- Produce and write a bibliographical synthesis on a theme related to his research internship

- To present orally this bibliographical synthesis, and to answer questions from a jury

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Written report (evaluated by 2 members of the jury)

70%

Oral defense (oral presentation and answers to questions evaluated by all members of the jury)

30%

 

COURSE TITLE: Research in “Evolution of Mating Systems” (Vincent Castric, research director CNRS) (UE)

NUMBER of ECTS: 3

Number of hours: Tutorials: 22h

Personal workload (hours expected to be dedicated to, including supervised projects): 50 hours

 

Description of the module

General aims:

This course will be focused on the study of molecular bases, genomic consequences and ecological determinants of mating system variations in natural populations.

 

Content summary:

The objective of this course is to provide a broad overview of ongoing research on the evolutionary biology of mating systems. It is based on a series of invited conferences by active international researchers in the field around four main topics :

1. How is the diversity of mating systems controlled ?

2. To what extent do mating systems influence general evolutionary processes, such as the efficacy of natural selection or the accumulation of selfish genetic elements in a genome ?

3. Why and to what extent do genomic regions controlling mating systems, such as sex chromosomes, follow distinct evolutionary trajectories ?

4. How do mating systems interfere with other life-history traits ?

In practice, before each 1h conference you will be asked to answer by e-mail three short questions related to technical or conceptual aspects in preparation for the presentation. We will take 30 minutes to discuss your answers to these questions before the invited presentation starts. After the presentation, we will again take 30 minutes to debrief on the main take-home messages.

Expected knowledge and skills:

Integrative biology; Theoretical modeling; Genomics; Evolutionary Ecology

 

EVALUATION MODE (final exam, oral defense, report,...)

Ratio of the final grade

Continuous assessment (individual contributions to peer reviewing of recently posted preprints on BiorXiv)

100%