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, 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 

·       Obtaining insights into functionality, activity and interactions of microbial communities

·       Getting familiar with evolution of prokaryotic and eukaryotic microbes

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, Method, content-based discussions

Programme

Day 1: Introductory lectures to the course, evolutionary genomics lectures, participant poster session with drinks and bites
Day 2: Comparative genomics lectures, method-based discussions

Day 3: Microbial Evolution and Ecology lectures, content-based discussions
Day 4: Functional genomics lectures and presentations

Confirmed Speakers:

1. Sipkema, Detmer: detmer.sipkema@wur.nl
2. Heuvel, Joost van den: joost.vandenheuvel@wur.nl
3. Dick Roelofs (KeyGene)
4. Jolien van Hooff (WU)
   
5. Nico van Straalen (Vrije Universiteit Amsterdam)
6. Mirte Bosse (Vrije Universiteit Amsterdam)
7. Bregje Wertheim (University of Groningen)
8. Erik Schranz (Wageningen University)
9. Berend Snel (Utrecht University)
10. Maurijn van der Zee (Leiden University)
11. Jos Raaijmakers (NIOO-KNAW and Leiden University)

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

Course fee

Fees	Early	Regular
WIMEK/PE&RC/WASS/EPS/VLAG PhDs with TSP	€ 280.00	€ 330.00
PhDs from SENSE	€ 555.00	€ 605.00
All other academic participants	€ 640.00	€ 690.00
Non – academic participants	€ 920.00	€ 970.00

The course fee includes accommodation, coffee, tea, breakfast, lunch, dinner and drinks. In the registration form, you can mention if you do not want to stay in Bosrand overnight though it is highly recommended in order to increase the networking.

Registration

Early bird: 15 November 2024
Regular: 2 December 2024

Registration form: https://fd8.formdesk.com/wageningenuralterra/principles_ecological_genomics_2025

Cancellation conditions

·       Up to Dec 2, cancellation is free of charge.

·       Up to Dec 20,  a fee of 50% of the full costs will be charged.

·       After Dec 20, a fee of 100% of the full costs will be charged.

·       If you do not show at all, a fee of 100% of the full costs and a fine of 100 EUR will be charged.

More information

With regard to logistics:
Elackiya Sithamparanathan (WIMEK-SENSE)  elackiya.sithamparanathan@wur.nl

With regard to contents:
Detmer Sipkema detmer.sipkema@wur.nl

Former occurrences of this course
28 Sep – 1 Oct 2021 | 26-28 Sept 2018   |   8-10 Apr 2015   |   18-22 Febr 2013   |   14-18 Febr 2011   |   23-27 Febr 2009   |   13-17 Febr 2006