Research School for Socio-Economic and
Natural Sciences of the Environment
Research School for Socio-Economic and
Natural Sciences of the Environment

Principles of Ecological and Evolutionary Genomics

Date: 26 September 2018 - 28 September 2018
Location: Wageningen Campus

Short Course Description

Ecological genomics is a quite new scientific discipline, which studies ecological complexity, nutrient cycles, life-history patterns and responses of organisms to environmental stress at the genomic level. Analysis of environmental genomes will improve our understanding of ecosystem functions and biodiversity and may help to define and measure environmental quality. In addition, we assess the role of genetic drift and selection on patterns of genome evolution.

This course is intended for those just embarking on genomics within an ecological setting and teaches the fundamentals of the discipline, while concentrating on ecological questions. The course will focus on four topics, each of which is treated by introductory lectures, assignments, case studies and student presentations.

We have speakers on microbes, fungi, plant and animals, but the concepts taught are universal and many will be applicable to your own species of interest

The four topics are:

  1. Metagenomics (study of genetic material directly from environmental samples)
  2. Functional genomics (understanding the function of genes in a genome)
  3. Comparative genomics (comparing genomes of different organisms)
  4. Population genomics (large-scale comparison of DNA sequences in populations)

During a poster session we will link the course topic to your own PhD topic, so bring your research poster to the course.

Learning goals


  • Getting access to the uncultivated majority of microbes through metagenomic analyses
  • Practical: Quality filtering and assembly of (meta) genomic data

Functional genomics

  • To learn how to apply basic transcriptomic tools to study gene expression in response to environmental challenges
  • To understand gene function and their induction in relation to the environmental challenge

Comparative genomics

  • Understand gene and gene family evolution among groups of organisms
  • Understand gene and gene family evolution among groups of organisms in relation to development and sex determination
  • Understand the evolutionary significance of gene- and genome duplications

Population genomics

  • Describe how genomic data from natural, domesticated and experimental populations can inform on important population genetic concepts such as genetic drift, natural selection, selective sweeps, reproductive isolation, inbreeding and effective population size
  • Describe the coalescence process as a way to model genetic drift
  • Calculate nucleotide diversity (pi) and Watterson's Theta as independent estimators of Theta (4Nu) and Tajima’s D to infer different kinds of selection and changes in effective population size


Course methods

introductory lectures, case studies, poster presentations, computer practicals


General explanation:

The mornings will consist of lectures. Wednesday and Friday afternoon will both begin with lectures, followed by computer practicals; Thursday afternoon will be spend on the computer practical entirely. To make optimal use of the speakers, lecturers and course organisers, the schedule includes a program on Wednesday (poster and mixing session) and Thursday (Comparative Genomics session). This means lunch and dinner hours vary. Friday will end with closing comments, including time for the evaluation of the course.

The programme will be updated as the guest lectures are confirmed.

General information

Intended credits1.0 ECTS
Group sizeminimum 15 - maximum 30
Course frequencyOnce every three years
Course fee

 Early birdRegular
SENSE / PE&RC / WASS PhDs with TSP€ 160€ 185
PhDs from RSEE€ 160€ 185
a) All other PhD candidates
b) Postdocs and staff of SENSE / PE&RC / RSEE / WUR Graduate Schools
€ 360€ 385
All others€ 400€ 425

The course fee include coffee, tea and lunches for all three days, and dinner for Wednesday evening and Thursday evening. It does not include accommodation (see for accommodation options below).

Course coordinatorDetmer Sipkema (
Registration URLRegister now
Registration deadline   Early bird: 29 August 2018
Regular: 17 September 2018
Cancellation conditions

Up to 4 weeks prior to the start of the course, cancellation is free of charge

Up to 2 weeks prior to the start of the course, a fee of €160 will be charged

After this date you will be charged the full fee of € 400, unless:

        You can find someone to replace you in the course and supply the course coordinator with the name and contact information of your replacement. In this case you will only be charged a € 50,- cancellation fee.

        You are a SENSE, PE&RC and RSEE PhD candidate with an approved TSP and have a valid reason to cancel (illness or death in the family 1st or 2nd degree). In this case you will be charged the reduced fee and your supervisor/PI must send a mail indicating the reason for cancellation.

AccommodationAccommodation is not included in the fee of the course, but there are several possibilities in Wageningen. For information on B&B's and hotels in Wageningen please visit Another option is Short Stay Wageningen. Furthermore Airbnb offers several rooms in the area.
More informationPoster
With regard to logistics: Peter Vermeulen (
With regard to contents: Detmer Sipkema (course coordinator,

Former occurrences of this course

  • 8-10 April 2015, Poster.pdf
  • 18-22 February 2013, poster.pdf
  • 14-18 February 2011
  • 23-27 February 2009
  • 13-17 February 2006