Phylogenetic Comparative Methods in R

1 - 4 October 2023

Location: Wageningen Campus (if this is impossible due to corona measures, otherwise the course will be held online)

Organised by:
The jointly SENSE, PE&RC and RSEE organised course Principles of Ecological and Evolutionary Genomics is open for registration. The main topics are:

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

Important!
As RSEE sponsors GELIFES PhD students who participate in jointly organised courses conform the agreements made with SENSE and PE&RC, please let us know if you intend to register for this course by sending a message to the secretary of RSEE (t.m.de.boer@rug.nl) by email.

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.

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.

General Information