Duration
20h Th, 15h Pr
Number of credits
| Master in biology of organisms and ecology (120 ECTS) | 3 crédits |
Lecturer
Language(s) of instruction
French language
Organisation and examination
Teaching in the first semester, review in January
Schedule
Units courses prerequisite and corequisite
Prerequisite or corequisite units are presented within each program
Learning unit contents
[UPDATED IN 2022] This course aims to provide the bases of phylogenetic methodology required for the understanding of the courses of Taxonomy and phylogeny of animals [BIOL2041-1] and Taxonomy and phylogeny of chlorophyll lines [BIOL2040-1].
- Reminder on (molecular) phylogenetics
- Sequence alignment - global alignment (NW), local alignment (SW, BLAST), multiple alignment (ClustalW) and profiles
- Parsimony - phylogenetic trees, tree length (Fitch's algorithm), character state mapping, search heuristics, statistical support (e.g., bootstrap) and congruence among trees
- Distance methods - distance matrices, W(U)PGMA, NJ and models of sequence evolution
- Probabilistic methods - likelihood (principle, algorithms, models, advantages and model selection), Bayesian inference (principle and algorithms, strict and relaxed molecular clocks)
- Phylogenomics - principle, datasets, supertrees, supermatrices, stochastic and systematic errors, CAT model, applications
Learning outcomes of the learning unit
- Theory: At the end of this course, students will be able to explain the main concepts, methods and algorithms used in phylogenetics. They will have an intuitive understanding of probabilistic methods and will be able to justify their preferential use over other approaches. This requires, above all, to have UNDERSTOOD the course material. In this sense, this course is probably different from some other subjects of the curriculum in biology, in which mere memorization may be enough to pass the examination.
- Exercises: For some algorithms (specified in class), an APPLICATION using pen and paper to solve a toy example may be requested.
- Applications: The practical analysis of a dataset in a phylogenetic context will have been covered during computer practicals. Students will thus be able to concretely reproduce it on their own datasets.
Prerequisite knowledge and skills
The course assumes no prerequisites in computer science, but relies on a basic knowledge of mathematics and molecular genetics. In principle, the necessary level in both subjects is reached at the end of the 3rd year of BA in biology.
Planned learning activities and teaching methods
- Theoretical lectures, demonstrations and supervised exercises: 10 x 2h.
- Computer practicals (Seaview and R): 4 x 4h.
Mode of delivery (face to face, distance learning, hybrid learning)
Face-to-face course
Additional information:
This is a face-to-face course. Attending the lectures is strongly encouraged as they are designed so as to facilitate understanding and assimilation of the course material.
Recommended or required readings
Computer practicals will make use of the following book but students are not expected to buy it: Paradis E. (2012) Analysis of Phylogenetics and Evolution with R, 2nd edition, Springer, 386 pages
http://www.springer.com/978-1-4614-1742-2
http://ape-package.ird.fr/APER.html
Exam(s) in session
Any session
- Remote
written exam ( multiple-choice questionnaire, open-ended questions )
Other : Computer practicals exam (to be confirmed)
Additional information:
The evaluation is an online exam on eCampus (January session) with two parts: 1) knowledge questions (understanding and reformulation of the theory) and 2) know-how questions (algorithms to apply).
- Part 1 contains True/False questions, figures to complete, MCQs, gap-filling texts. The questions are drawn randomly from pools, so that each student is assigned a unique test in terms of combination and order of questions.
- Part 2 corresponds to "hint" exercises in which the questions may have been modified compared to the worked out exercises provided in class. They must be completed on paper and the results transcribed into the examination platform.
Work placement(s)
Organisational remarks and main changes to the course
Taking notes on a laptop or tablet is allowed. However, students are expected not to surf or chat in the classroom.
Course materials and additional documents will be made available on eCampus.
Contacts
Prof. Denis Baurain
Institut de Botanique B22 (P70)
denis.baurain@uliege.be
Mrs Rosa Gago
rgago@uliege.be