Evolutionary Genomics


Course Objective

• Describe different molecular genetic techniques to study
transcriptomes and genomic variation in response to environmental
stimuli and natural selection.
• Understand genome architecture of prokaryotes and eukaryotes.
Comparing genomes to understand evolutionary change in genome
• Analyze experimental data generated by genomics research and knowing
the possibilities for follow-up research.
• Find and analyze genomic data in databases on internet.
• Describe the evolutionary significance of functional genomic
• Explain the evolutionary consequences of such variation for species
abundance, community diversity, and the evolution of speciation.

Course Content

Nowadays, researchers in evolutionary biology and ecology are making
extensive use of molecular techniques. Genomics technology can be used
to advance our understanding of how selection acts on genomic variation
to adapt to local environments, which will in turn affect species
abundance, community diversity, and the evolution of speciation. In this
course we will focus on:
• Regulation of gene expression networks. Which genes are turned on in
response to selection pressure such as environmental change?
• Differences in the molecular basis of fitness among individuals. Is
there intraspecific variation in gene expression in response to
environmental change, and is this variation adaptive?
• Evolutionary consequences of genomic variation. What proportion of
genomic variation is associated with phenotypic change and how does this
affect evolution of species?
Focus will be on molecular adaptation to stressful environments as
driver of adaptive evolution. Adaptive evolution in response to abiotic
and biotic factors will be presented as well as plant-herbivore
interactions in an evolutionary genomic context. We will discuss the
methodology and applications of various genomic analyses including
micro-array, RNAseq, whole genome sequencing, annotation, genome-wide
association studies and phylogenomic analysis.

Teaching Methods

The following working forms with expected amount of hours will be
applied during the course:
- 25 hours Lectures, including some guest lectures of leading
specialists in the field
- Practical transcriptional profiling, four afternoons of each 3 hours,
in total 12 hours.
- Computer exercise Transcriptome analysis, annotation and gene ontology
enrichment analysis. Four afternoons of 3 hours, in total 12 hours.
- Journal club, including paper presentation. one day part, maximum 4
hours. Journal club preparation is estimated to be 8 hours.

Method of Assessment

- A practical report will be written by the student reflecting the
execution of a transcriptional profiling experiment followed by data
analysis and interpretation/discussion of the results. The report
includes, introduction/background, material and methods, results and
discussion. The form of tuition is an assessment of the practical
report, performed by the course coordinator and the course assistant.
It relates to dublin descriptors 1 and 2: knowledge and understanding &
application of knowledge
Weight: 20% of the final grade.
- The Journal club presentation will be assessed using a standardized
rubric performed by a panel of the course lecturer, participating
lecturers and course assistants.
It related to dublin desciptors 3 and 4: critical judgement and
communication. Weight: 20% of the final grade
- The written exam will be assessed by the course coordinator using
model answers.
It relates to dublin descriptors 1 and 5: Knowledge and understanding &
learning skills.
Weight: 60% of final grade and needs to be 5.5 or higher to successfully
pass the course.


Recommended literature:
An Introduction to Ecological Genomics, N.M. van Straalen and D.
Roelofs. Oxford University Press, 2012. ISBN: 9780199594696.
The Origins of Genome Architecture, Michael Lynch, Sinauer Associates,
2007. ISBN: 9780878934843.

Recommended background knowledge

It is highly recommended to have followed and passed the BSc course
'Evolutionary Genetics' AB_1022 (or an equivalent 6 EC).

General Information

Course Code AM_1231
Credits 6 EC
Period P2
Course Level 500
Language of Tuition English
Faculty Faculty of Science
Course Coordinator dr. ir. T.F.M. Roelofs
Examiner dr. ir. T.F.M. Roelofs
Teaching Staff prof. dr. J. Ellers

Practical Information

You need to register for this course yourself

Last-minute registration is available for this course.

Teaching Methods Seminar, Study Group, Lecture, Computer lab, Practical
Target audiences

This course is also available as: