Genomics in Ecology and Evolution

Faculteit Science and Engineering
Jaar 2021/22
Vakcode WMEV011-05
Vaknaam Genomics in Ecology and Evolution
Niveau(s) master
Voertaal Engels
Periode semester I b (06-12-2021 till 26-12-2021)

Uitgebreide vaknaam Genomics in Ecology and Evolution
Leerdoelen At the end of the course, the student is able to:

1. Understand and summarize the basic theoretical principles and applications of ecological and evolutionary genomics (EEG);

2. Understand and describe “next-generation-sequencing” technologies; compare and contrast applications of the different types of “omics” and markers; apply and synthesize genomic, metagenomic, transcriptomic approaches to EEG questions.

3. Perform some of the basic analysis techniques in EEG (e.g., use of genome browsers, basic annotation, simple comparative analyses of DNA sequences) relevant to evolutionary genomics and prokaryotic metagenomics.

4. Communicate EEG principles and ideas at a more advanced professional level through synthesising a body of theory & research and presenting it (participant and moderator of discussions, making & presentation of a scientific poster based on case studies, and presentation of general principles through a teaching lecture).
Omschrijving Genomic data in all of its forms is reshaping biology. Classic questions about genome evolution, mechanisms of speciation, adaptation, species interactions and conservation are being revisited at the levels of the genome, transcriptome, proteome and metabolome. The course is divided into 2 modules. Module 1 introduces the “omics” way of thinking in an extension of the eco-evolutionary framework; explains “next generation sequencing” technologies and their applications to specific kinds of questions in ecology and evolution; discusses the advantages and limitations of new genomic technologies; and analyzes, through case studies, the interplay of descriptive, inferential and experimental approaches in solving various classes of questions. The first module focuses on functional and evolutionary genomics; mapping and analysis of QTL related to life history traits; sex determination, speciation, epigenetics and host-parasite interactions. The second module focuses on prokaryotic genomes (evolution, size, organization, stability); the importance of horizontal gene transfer (mechanisms, proclivity, impacts on evolution, selection); introduction to metagenomics and functional diversity (soils, marine systems) in microbial ecology; comparative genomics of ecotypes and the emerging significance of “microbiomes” associated with all life systems. During the last week of the course, each student presents a 45-min teaching lecture.
Uren per week
Onderwijsvorm Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC), Werkcollege (T)
(Missing significant portions of one of the modules or assessments means a failure for the course; the student teaching lectures form an integral part of the course and presence is mandatory for these.)
Toetsvorm Practisch werk (PR), Presentatie (P), Verslag (R)
(The final grade is based on the marks given for a poster & poster presentation (25%); a practical assignment in bioinformatics (25%) and a formal student teaching lecture (50%) .Active participation is also judged based on the impressions of each teacher; during discussions and the student lectures that take place at the end of the course.)
Vaksoort master
Coördinator prof. dr. B. Wertheim
Docent(en) prof. dr. L.W. Beukeboom ,prof. dr. J. Falcao Salles , Guest lecturer ,dr. L.P.W.G.M. Jacobus Mgn Van De Zande ,dr. S.J.J. Lequime ,prof. dr. B. Wertheim
Verplichte literatuur
Titel Auteur ISBN Prijs
Assignments with accompanying data sets, pdf files of journal papers, etc.
The Nestor site is used for all communications
Syllabus/Schedule Provides dates times of all activities
Lecture PowerPoints
Entreevoorwaarden This is the fourth of four consecutive, mandatory courses for students in the track Evolutionary Biology
(including those following the MEME programme) in the MSc Ecology and Evolution. The course is also open to a restricted number of selected students from other MSc programmes. The mandatory course series runs from September to December during the first year.
Opmerkingen Register for this course by sending an email to:

Students are expected to have a reasonably thorough background in (population) genetics. Students with no genetic background will have a very difficult time.
Opgenomen in
Opleiding Jaar Periode Type
MSc Ecology and Evolution: Ecology and Conservation  (Electives/optional modules) - semester I b keuze
MSc Ecology and Evolution: Evolutionary Biology  ( Track Evolutionary Biology) - semester I b verplicht
MSc Marine Biology: Research  (Compulsory master courses) - semester I b keuze