2023-2024 / MICR0005-1



15h Th

Number of credits

 Master in bio-informatics and modelling (120 ECTS)2 crédits 
 Master in biochemistry and molecular and cell biology (120 ECTS)2 crédits 


Denis Baurain

Language(s) of instruction

French language

Organisation and examination

Teaching in the second semester


Schedule online

Units courses prerequisite and corequisite

Prerequisite or corequisite units are presented within each program

Learning unit contents


1. Course description

Owing to their microscopic size, eukaryotic microbes have been discovered only relatively recently -- that is, not before the late seventeenth century, which saw the spread of the microscope. Before that, the very idea of single-celled organisms was simply unknown.

Since their discovery, various classifications of Life have tried to accommodate unicellular eukaryotes, always as a monolithic group generally referred to as "protists". With the rise of molecular phylogenetics, evolutionary relationships between eukaryotes (microscopic or not) have been widely challenged only to conclude that protists are an artificial group, out of which emerged independently several lineages of multicellular organisms (e.g., animals, plants, red algae and brown algae).

This specialization course based on the knowledge acquired during the BAC3 Microbiology course (part Algology and Mycology) [MICR0711-A] has three aims: (1) to complete the panorama of the eukaryotic groups (e.g., excavates, rhizaria), (2) to deepen the presentation of the mechanisms and trends at work in the evolution of eukaryotes (e.g., endosymbiosis, gene transfer, secondary simplification) and (3) to paint a historical picture of the conceptions pertaining to the classification of Life and especially of unicellular eukaryotes.

2. Table of contents

  • 1. [O3] History of the classification of Life
  • 2. [O1] Diversity of parasitic organisms of animals and crop plants
  • 3. [O1] Plasmodium and the malaria (Apicomplexa, Alveolata)
  • 4. [O1] Trypanosoma and Leishmania (Euglenozoa, Discoba, Excavata)
  • 5. [O1] Giardia, Trichomonas, Dientamoeba and Naegleria (Metamonada and other Discoba)
  • 6. [O1] Cercozoa, foraminifera and radiolarians (Rhizaria)
  • 7. [O1] Entamoeba and other amoebae (Amoebozoa)
  • 8. [O2/3] Evolutionary mechanisms at the origin of eukaryotes and mitochondria
  • 9. [O2] Evolutionary mechanisms behind the plastid and its spread
  • 10. [O2/3] Back to the theory of evolution: the thought of Stephen Jay Gould

Learning outcomes of the learning unit

After this course of Protistology, students will be able to...

  • 1. [O1] Remember the different groups of eukaryotic parasites and the diseases they cause.
  • 2. [O1] Recognize a eukaryotic taxon based on a textual description of its discriminating features.
  • 3. [O1] Exemplify a eukaryotic taxon on the basis of its name.
  • 4. [O1] Classify the archetypes of organisms.
  • 5. [O3] Compare past and present schemes of classification of Life.
  • 6. [O3] Assign an extract of "classificatory" speech to an author or school of thought.
  • 7. [O3] Interpret a phylogenetic tree.
  • 8. [O3] Compare two or more phylogenetic trees.
  • 9. [O1/3] Infer the likely characteristics of an unknown organism or taxon on the basis of a phylogenetic tree with known organisms or taxa.
  • 10. [O2] Explain the evolutionary mechanisms that have led to the current diversity of eukaryotes.
  • 11. [O1/2] Exemplify the evolutionary mechanisms that have led to the current diversity of eukaryotes.
  • 12. [O2/3] Explain the thought of Stephen Jay Gould.
  • 13. [O2/3] Exemplify the thought of Stephen Jay Gould.
  • 14. [O1/2/3] Compare evolutionary scenarios.
  • 15. [O1/2/3] Assign a particular evolutionary scenario to one school of thought.

Prerequisite knowledge and skills

Having attended the BAC3 course of Phycology and Mycology [MICR0720-1] (required part of the biology curriculum) or, alternatively, another course in microbiology (or in general botany) also covering algae and fungi, preferably with a phylogenetic perspective.

Planned learning activities and teaching methods

With the exception of lessons 8 and 9, which are traditional lectures, lessons will only include some theoretical lectures and, if necessary, they will be kept short. The teaching methods are most often "constructivist", so that students are actively appropriating the material and learn to make connections between the various topics of the course.

Lessons 3 to 5, 7 and 10 will be as follows:

  • 1. Brief introductory lecture by the teacher on the topic or organisms of the day.
  • 2. Mining of English-speaking online resource printed from general websites [Centers for Disease Control and Prevention (CDC), World Health Organization (WHO), Tree of Life Web Project (ToL) etc.]. Specifically, students will build identity cards for a variety of parasites, write answers to specific questions or summarize short texts on different topics (e.g., history, pathology, evolution). The work will be done in small groups of 3 or 4 students. During these activities, the teacher will be fully available and will help to overcome the difficulties that arise.
  • 3. General group discussion. In some cases, students may be asked to make oral brief presentations of their discoveries based on group work and small slideshows prepared by the teacher.
  • 4. Integration of the group works into the collaborative syllabus available as Google Docs. These will not be "homework" to be returned systematically, but in the end, each student will be asked to have contributed in one way or another to the syllabus (e.g., corrections, improvements, illustrations). This involvement will represent 10% of the final mark (see below).
Other lessons will use the following teaching methods:

  • Reordering of paragraphs from scientific journal articles presenting the history of the classification of Life in general and in particular of protistology (course 1).
  • Taxonomic analysis and categorization of the main parasitic organisms (computer-assisted interactive work on websites) (course 2) .
  • Fulfilling of phylogenetic trees in which some parts are missing based on textual descriptions from scientific articles (see BAC3 course) (course 6) .
  • Inferring characteristics of different lineages represented in annotated phylogenetic trees (course 6).
  • Rational comparison of partially inconsistent phylogenetic trees (course 6).
To promote associations between the various topics of the course and to facilitate their assimilation, students will have to create (1) a time line (at the end of the course 1), (2) an infographic chart (type Information is beautiful) (course 2), (3) an annotated phylogenetic tree (course 6) and (4) a mind map (courses 8 and 9) summarizing the material presented in class. These assignments will be individual and graded (see below) and will prepare students for the final exam. They will be asked to be as creative as possible.

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

Face-to-face 90-min lectures.

Recommended or required readings

The papers read in the classroom and the slideshows will be made available to students through eCampus.

Exam(s) in session

Any session

- In-person

oral exam

Written work / report

Additional information:

The four personal assignments (time line, infographic chart, annotated phylogenetic tree, mind map) account for 60% of the final grade (4 x 15%), while the rest (40%) will be composed of 30% by oral examination and 10% by the involvement to the collaborative syllabus (courses 3 to 5, 7 and 10).

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.


Prof. Denis Baurain
Institut de Botanique B22 (P70)

Mrs Rosa Gago

Association of one or more MOOCs