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| GENE0443-1 | Phylogenomics
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| Duration : | 12h Th, 12h Pr |
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| Number of credits : |
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| Lecturer : | Denis Baurain |
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Language(s) of instruction :
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| French language |
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Course contents :
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| Molecular phylogenetics is the comparison of gene sequences to establish the relationships between extant species. Born in the late 1960s, this field has completely revolutionized the identification and classification of living things. This revolution has been particularly important for eukaryotic microbes, which often lack comparative characteristics when belonging to distant groups.
Because of its limited length (a few thousand nucleotides or a few hundred amino acids), a single gene (such as the rRNA of the small subunit of the ribosome) does not offer a reliable sampling of the evolutionary process. Therefore, even if different groups of species can be resolved using "single gene" phylogenetic trees, their interrelationships, for which the signal is weaker, are not supported statistically due to the stochastic error affecting short alignments.
Since the early 2000s, a high throughput alternative of molecular phylogenetics has emerged: phylogenomics. Its specificity is to simultaneously analyze dozens or even hundreds of gene alignments, thus resulting in an increase in the signal and in the resolution of phylogenetic trees. Phylogenomics owes its power to a drastic reduction of stochastic error granted by the analysis of thousands of characters. However, this reduction comes at the cost of a parallel increase of systematic error. Caused by the heterogeneity of the evolutionary process, the systematic error is a source of phylogenetic artifacts, some of them well supported, and one of the main issues of phylogenomics.
In this course, the principles, methods, strengths and weaknesses of phylogenomics will be addressed through a selection of milestone research papers. Examples will not be limited to one specific part of the tree of Life but will address the resolution of various levels and parts of it: animals, plants and eukaryotes in general. |
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Learning outcomes of the course :
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| At the end of this course, students will have a good idea of what is phylogenomics. They will be able to explain its pros and cons, discuss its key achievements and cite its major players. |
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Prerequisites and co-requisites/ Recommended optional programme components :
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| Prior knowledge of molecular phylogenetics is required. A suitable level is that of the course [GENE0433-1] 'Evolution and population genetics'. |
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Planned learning activities and teaching methods :
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| A dozen articles dealing with phylogenomics will be distributed to students. These will have to read them on their own and then write a summary (see below). Several consultations will be held with the teacher to clarify difficult concepts, discuss the structure of the written work and monitor its good progress. |
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Mode of delivery (face-to-face ; distance-learning) :
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| Individual work and consultations with the teacher. |
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Recommended or required readings :
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| List of research articles to be defined. |
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Assessment methods and criteria :
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| Writing of an essay summarizing the subject (from 3500 to 4500 words) followed by a private oral defense. Papers may be in French or English and must be received by the teacher at least one week before the defense (of which the date has to be agreed upon by the two parties). |
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Contacts :
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| Prof. Denis Baurain
Institut de Botanique B22 (P70)
denis.baurain@ulg.ac.be
Assistant: Dr. Damien Sirjacobs
Institut de Botanique B22 (P70)
04/366.38.54
D.Sirjacobs@ulg.ac.be |
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