Adaptation, evolution and diversity

Duration

40h Th, 10h Pr, 30h AUTR

Number of credits

Lecturer

Denis Baurain, Franck Dequiedt, Tom Druet, Moreno Galleni, Marc Hanikenne, Alice Mouton, N..., Claire Remacle, Catherine Sadzot, Annick Wilmotte

Coordinator

Denis Baurain

Language(s) of instruction

French language

Organisation and examination

Teaching in the first semester, review in January

Schedule

Schedule online

Units courses prerequisite and corequisite

Prerequisite or corequisite units are presented within each program

Learning unit contents

The concept of evolution is at the heart of biology and, as T. Dobzhansky said, "Nothing in biology makes sense except in the light of evolution". However, behind the word "evolution" lies a whole continuum of changes inherited over time, caused by natural selection, whose tireless action guarantees the permanent adaptation of organisms to their environment, and whose accumulation has led to the formidable diversity of the living world. These mechanisms act on several time scales and are studied by a wide variety of different disciplines. However, in the context of the BBMC Master's programme, we will focus on those disciplines concerned with observable changes in genomic sequences, including population genetics, quantitative genetics, phylogeny and phylogenomics, the study of molecular and biochemical adaptations, and the study of the diversity and molecular ecology of organisms.


Theory (44h)

Partim I. Populations and Adaptation (24h)

Population genetics (C. Remacle) (4h)

• Populations at equilibrium: Hardy and Weinberg's law
• Mutation, migration, selection

• Mechanisms of adaptation of microorganisms to extreme conditions (thermophilicity, psychrophilicity, piezophilicity, acidophilicity and alkalophilicity) (3h)
• Methods of directed protein evolution (1h)

• Complex traits, heritability, similarity between relatives, basis of directed selection

• Association studies
• Population structure

• Focus on polyploidy
• Examples of extremophilic plants (heavy metals, salinity)

• Extremophiles: strategies for resistance to ionising radiation (Deinococcus, UV-screens), drought, salinity, heavy metals, multiextrêmophile organisms, etc.
• Focus on Archaebacteria as "hotspots" of extremophilicity

• Alignment algorithms (2h)
• Phylogenetic inference (4h)

• Methodological concepts
• Application to large-scale animal phylogeny
• Application to the study of domestication, selection and conservation

• Principles of FAIR and CARE in genomics
• Experimental design and genetic data collection methods
• Responses to anthropogenic changes (hybridisation and introgression, overexploitation, climate change)
• Conservation and management (inbreeding, demography, connectivity, conservation unit)

• Definition of bacterial species
• Generation of genetic diversity in prokaryotes (mutations, recombination, mobile genetic elements, HGT)
• Methods for studying the diversity of microbial communities (polyphasic approach, culture, metagenetics)

• Mechanisms governing the evolution of viruses
• Viral quasispecies
• Host/virus co-evolution

• Problems of population genetics (C. Remacle, 4h)
• Quantitative genetics (F. Dequiedt, 4h)
• Alignment exercises (on paper) (D. Baurain, 2h)

• Quantitative and population genetics (T. Druet, 2h)
• Phylogenetic inference (D. Baurain, 4h)
• Conservation genomics (A. Mouton, 4h)

• Dr. Rob Van Houdt (SCK-CEN) : Bacterial adaptation (2h)
• Dr. Laurent Frantz (LMU): Animal palaeogenomics (2-4h)
• Prof. Maarten Larmuseau (KUL): Genealogy of the Y chromosome / Genetic testing and ethical issues (4h, with M. Hanikenne)

Learning outcomes of the learning unit

The aim of this module is to introduce the basic concepts of the various disciplines listed above. Some of these concepts will be explored in greater depth during tutorials carried out on paper (worked out problems, application of algorithms) and/or illustrated through practical work carried out on computer (use of popular tools for analysing molecular data).

Prerequisite knowledge and skills

This module will build on the concepts covered in the Bac Bio courses and the following BBMC Master's modules:

Toolbox: Nucleic acid analysis

Planned learning activities and teaching methods

• Ex cathedra courses
• Demonstrations
• Tutorials on paper
• Practical work on computer
• Seminars with external speakers

Mode of delivery (face to face, distance learning, hybrid learning)

Face-to-face course


Additional information:

Présential

Recommended or required readings

Slideshows and articles related to the module's theme will be made available to students on the eCampus platform.

Exam(s) in session

Any session

- In-person

written exam ( multiple-choice questionnaire, open-ended questions )


Additional information:

Written exam (MCQ questions, open questions, application exercises). Practical work and seminars may also be assessed.

Work placement(s)

Not applicable

Organisational remarks and main changes to the course

Students should bring their own laptop (a tablet may not be sufficient in some cases). If necessary, a laptop can be loaned, provided the coordinator is notified before the start of the module.

Any absence must be justified and, where appropriate, students are required to put their work in order. If a report is required, it must be completed even in the event of absence. In the event of unjustified absence, the student may not be admitted to the examination.

Contacts

Coordinator of the module

Prof. Denis Baurain

Tél : 04/366.38.64
e-mail : denis.baurain@uliege.be

 
Co-Titulars

Prof. Franck Dequiedt, fdequiedt@uliege.be
Prof. Tom Druet, tom.druet@uliege.be
Prof. Moreno Galleni, mgalleni@uliege.be
Prof. Marc Hanikenne, marc.hanikenne@uliege.be
Dr. Alice Mouton, amouton@uliege.be
Prof. Catherine Sadzot, csadzot@uliege.be
Prof. Claire Remacle, c.remacle@uliege.be
Dr Annick Wilmotte, awilmotte@uliege.be

Association of one or more MOOCs

There is no MOOC associated with this course.