Principles of Ecological and Evolutionary Genomics

Short Course Description

Ecological genomics 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 focuses on four topics, each of which is treated by lectures, practical assignments, case studies and participant presentations. Also, participants are encouraged to apply the principles of the course to their own research. To introduce their own work participants are asked to bring and present a research poster.

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

Learning goals

General goals:

• To become acquainted with the state-of-the-art in genomics
• To get an overview of genomics research in the Netherlands and beyond
• To network

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

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
• Understanding the reconstruction and use of phylogenies

Metagenomics

• Getting access to the uncultivated majority of microbes through metagenomic analyses
• Practical: Quality filtering and assembly of (meta) genomic data and generation of metagenome-assembled genomes (MAGs)

Functional genomics

• To learn how to apply basic transcriptomic tools to study gene expression in response to environmental challenges and to reconstruct gene regulatory networks
• To understand gene function and gene expression in relation to environmental challenges

Course methods

Introductory lectures, case studies, poster presentations, computer practicals

Programme

Day 1: Introductory lectures to the course, population genomics lectures, participant poster session with drinks and bites
Day 2: Comparative genomics lectures, population and comparative genomics practical
Day 3: Metagenomics lectures and practical
Day 4: Functional genomics lectures and assignment

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

Course fee

	Early bird	Regular
WIMEK / PE&RC / WASS / WIAS / VLAG / ESP Graduate School PhDs with TSP .	€ 165 .	€ 215 .
PhDs from RSEE .	€ 165 .	€ 215 .
PhDs from SENSE .	€ 330 .	€ 380 .
a) All other PhD candidates b) Postdocs and staff of SENSE / PE&RC / RSEE / WUR Graduate Schools .	€ 370 . .	€ 420 . .
All others .	€ 535 .	€ 585 .
Overnight accommodation for PhD candidates from PE&RC, WIMEK and RSEE* .	€ 70 .	NA .
Overnight accommodation for all other participants* .	€ 142.50 .	NA .

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).

*For people who have to travel to Wageningen we can arrange accommodation. In the registration form you can register for this. Until 1 May we can guarantee accommodation, after 1 May we can arrange accommodation until the location is full.

Registration

Early bird: 28 July 2021
Regular: 13 September 2021
If you want to be sure that we can arrange overnight accommodation for you: 1 May 2021

Registration form

Cancellation conditions

Please note that if you have to cancel for COVID-19 related issues (e.g. travel restrictions) we will be lenient with the 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.

Accommodation

Accommodation 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 proefwageningen.nl. Another option is Short Stay Wageningen. Furthermore Airbnb offers several rooms in the area.

More information

With regard to logistics:

Peter Vermeulen (WIMEK-SENSE) peter1.vermeulen@wur.nl) &
Sabine Vreeburg (PE&RC) sabine.vreeburg@wur.nl

With regard to contents:

Detmer Sipkema detmer.sipkema@wur.nl

Former occurrences of this course

26-28 Sept 2018   |   8-10 Apr 2015   |   18-22 Febr 2013   |   14-18 Febr 2011   |   23-27 Febr 2009   |   13-17 Febr 2006