Phylogeny of eukaryotes

Duration

30h Th

Number of credits

Lecturer

Denis Baurain

Language(s) of instruction

French language

Organisation and examination

Teaching in the first semester, examination in June

Schedule

Schedule online

Units courses prerequisite and corequisite

Prerequisite or corequisite units are presented within each program

Learning unit contents

[UPDATED IN 2018] The comparison of molecular sequences has been extensively applied to the enigma of the evolution of eukaryotes. For ten years, the trees obtained from the rRNA of the small subunit of the ribosome suggested that most eukaryotes had emerged simultaneously (crown group phylogeny), whereas a few lineages of "protists" would have branched earlier. As these basal lineages appeared mainly composed of parasites lacking mitochondria (e.g., microsporidia), the prevailing hypothesis was that these "Archezoa" actually appeared before the acquisition of the mitochondrion -- which is the result of the endosymbiosis of a bacteria within one of these amitochondriate proto-eukaryotes.
However, at the turn of the millennium, a converging body of evidence eventually convinced phylogeneticists that this tree was incorrect and that Archezoa -- if they had ever existed -- had disappeared today. Among these indices were the finding of degenerated mitochondria (hydrogenosomes and mitosomes) as well as the presence of genes of mitochondrial origin in the nucleus of the so-called Archezoa. Regarding the topology of the rRNA tree, it could be explained by phylogenetic artifacts that wrongly reject fast-evolving species at the base of the tree.
More recently, the advent of phylogenomics (i.e., the comparison of hundreds of genes simultaneously) led to great progress in resolving the tree of eukaryotes, such as grouping nearly all lineages into six super-groups (Opisthokonta, Amoebozoa, Excavata, Plantae, Chromalveolata and Rhizaria), belonging to two mega-groups (unikonts and bikonts) between which would have lied the ultimate origin (= root) of eukaryotes.
This revised topology had a great impact and even percolated into biology textbooks. Alas, new phylogenomic studies suggest that it is still not an accurate representation of the tree of eukaryotes, in part because Chromalveolata are not a real super-group, but appear more fragmented. Now, the working hypothesis considers three mega-groups (unikonts, Excavata and an assemblage of Plantae/Chromalveolata/Rhizaria). Assuming that these groups are real, their internal organization remains to be defined.
In this course, students will be effectively introduced to the phylogeny of eukaryotes and to its wanderings through the writing of a personal critical review of the phylogenetic literature, bearing a historical perspective.

Learning outcomes of the learning unit

At the end of this course, students will be aware of the difficulty to infer the origin and evolution of eukaryotes and eukaryotic lineages, in particular because of phylogenetic artifacts. They will be able to present, argue and contrast the different phylogenetic frameworks proposed during the last 30 years and to cite the key authors, especially for some lineages of interest.

Prerequisite knowledge and skills

It would be better to have a working knowledge of the diversity of Life, including "protistology" (e.g., algae and fungi), and molecular phylogenetics: Biodiversity and ecology [BIOL0518-1], Microbiology [MICR0715-2] and Phylogenetic methods [GENE0448-1].

Planned learning activities and teaching methods

If several students are interested in the course, different subtopics will be defined by the parties to avoid duplicate efforts. Hence, one can choose to study the phylogeny of a specific eukaryotic group (e.g., arthropods, lichens) or to discuss an evolutionary concept in particular (e.g., living fossils, secondary simplification). Whatever the topic at hand, the historical perspective (evolution of ideas) shall be at the heart of the work.
About twenty to thirty articles (or book sections) dealing with the selected evolutionary concept or phylogeny of the chosen eukaryotic group will be collected by the student. S/he will have to read in detail about fifteen of the most relevant in order to write a critical review (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.

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

Individual work and consultations with the teacher.

Organisational adjustments related to the current health context

Meetings with the teacher will be online.

Recommended or required readings

List of research articles to be defined.

Assessment methods and criteria

Below you will find information on the evaluation methods planned for in-person and remote exams as well as those planned for hybrid sessions. Depending on how the health crisis evolves, the chosen method will be communicated to you no later than one month before the start of the exam session.

Writing a critical review of the phylogenetic literature of the chosen subject, the perspective of which is primarily historical (= evolution of the ideas over time, from antiquity to phylogenomics). The essay should have about 10 pages of main text, 1 to 2 boxes on a colored background discussing more technical points and 1 to 3 original figures. The main text must be understandable by a bachelor in biology and its structure should not include more than two levels of titles (unnumbered), as in a popularization review article. The work can be written in French or English and must be sent to the teacher at least a week before the deliberations of the end of the year.

Work placement(s)

Organizational remarks

Contacts

Prof. Denis Baurain Institut de Botanique B22 (P70) denis.baurain@uliege.be
Assistant: Dr. Damien Sirjacobs Institut de Botanique B22 (P70) 04/366.38.54 D.Sirjacobs@uliege.be