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

Units courses prerequisite and corequisite

Prerequisite or corequisite units are presented within each program

Learning unit contents

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 introduced to the phylogeny of eukaryotes and to its wanderings through a selection of significant articles that have marked the past 30 years of its development. Hence, they will discover who were the Archezoa, why rRNA trees were incorrect, how phylogenomics still stumbles on super-groups and why the history of eukaryotes is so intimately related to the movement of chloroplasts.

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, 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.

Prerequisite knowledge and skills

It would be better to have a working knowledge of "protistology" (e.g., algae and fungi) and molecular phylogenetics. In principle, the required level corresponds to that of the 3rd year of BA in Biology: Microbiology [MICR0711-1] and Ecology and Biodiversity [BIOL0516-3].

Planned learning activities and teaching methods

About 20 articles dealing with eukaryotic phylogeny 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. If several students are interested in the courses, 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.

Mode of delivery (face-to-face ; distance-learning)

Individual work and consultations with the teacher.

Recommended or required readings

List of research articles to be defined.

Assessment methods and criteria

Writing of an essay summarizing the subject (about 15 to 20 pages including figures). Papers may be in French or English and must be received by the teacher at least one week before the end of the academic year.

Work placement(s)

Organizational remarks

Contacts

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