Phylogenomics: pitfalls and benefits

25-27 March 2015

Organiser: Dr Christian Parisod (University of Neuchâtel)



Phylogenetic trees provide valuable models of the evolution of traits and molecules, and are thus of central importance for comparative studies in biology. The objective of this course is to address the frontiers of phylogenetics.

We will particularly emphasize two main challenges of current studies.

On the one hand, high-throughput sequencing produces genome-wide datasets whose complexity must be adequately taken into consideration towards truly phylogenomics studies.

On the other hand, reticulate evolutionary histories are commonplace among prokaryotes (e.g. horizontal gene transfer) and eukaryotes (e.g. hybridization and polyploidy), but remain challenging to properly infer.


  • Dr Pascal-Antoine Christin (Univ. Sheffield, UK)
    Researcher working on the evolution of C4 photosynthesis using phylogenomics. He will lecture on approaches addressing the evolutionary forces acting on different traits to investigate the functional diversity of organisms
  • Prof. Christophe Guyeux (Univ. Franche-Comté, France)
    Researcher working on the analysis of discrete dynamical systems. He will lecture on bioinformatics approaches to infer genome evolution in a phylogenetic context
  • Dr Thomas Marcussen (Univ. Oslo, Norway)
    Researcher working on phylogenetic approaches deciphering hybrid and polyploid speciation. He will lecture on recent approaches to accurately infer and date hybridization events from genome-wide datasets
  • Dr Christian Parisod (Univ. Neuchâtel, Switzerland)
    Researcher working on plant genome evolution. He will lecture on molecular processes leading to genome changes and how available high-throughput sequencing technologies can address such challenging variation


The course will first provide a concise overview of the main sequencing technologies now available and, in regards to the processes underlying genome evolution, will discuss possible pitfalls of current approaches. Then, we will discuss how phylogenetic studies can benefit from genome-wide datasets and how to address the challenges brought by myriad of genes with their own history. Finally, we will address how to properly infer reticulate evolution and, in particular, how current approaches can be used to distinguish incomplete lineage sorting from hybridization.
The course will consist of lectures about the research work of our experts as well as presentation of currently available approaches and perspectives. Such introductions will be followed by practical training with selected approaches on real datasets.
Necessary concepts will be introduced, but targeted students should have a keen interest in genome evolution or phylogenetics.

Detailed program

Day 1 - Lectures

Christian Parisod: Genome evolution: challenges of repeats, recombination and hybridization for phylogenetics using high throughput sequencing

Pascal-Antoine Christin: Evolutionary enablers, convergence, and the recurrent assembly of C4 photosynthesis

Christophe Guyeux: Investigating genes effects on phylogeny (topology and bootstraps)

Thomas Marcussen: Inference of dated species networks from gene trees

General instructions for practical

Day 2 – Practical

Practical (leader: Pascal-Antoine Christin): Inferring evolutionary forces and reconciling gene and species trees

Practical (leader: Christophe Gueux): Consistent genome annotation and inference of core vs- pan genomes

Day 3 – Practical

Practical (leader: Thomas Marcussen): Inference of hybridization events from genome-wide datasets

Synthesis and general discussion involving all lecturers

General information

Date : 25-27 March 2015

Schedule : 8.55-17.00 (see detailed program)

Location : University of Neuchâtel, Faculté des sciences, UniMail, bâtiment E , room E213 (meeting) and E003 (computer)

ECTS: 1 ECTS for active participation (Research tools) + 1 ECTS for writing of a short summarizing essay, illustrated with results from practical sessions (Scientific activities)

Evaluation: Full attendance and active participation

Information : Please contact Dr Christian Parisod or the doctoral program coordinator Dr Christiane Bobillier

Registration fee : free

Travel expenses : For participants of the Interuniversity doctoral program in organismal biology (DP-biol ): see reimbursement conditions

MAKE SURE you SIGN the ATTENDANCE LIST EACH and EVERY DAY and TAKE your ATTESTATION of ATTENDANCE at the END of the COURSE (no attestation will be sent by mail)


  • This course is free and open to all PhD students
  • Post-docs and advanced researchers are welcome as long as places are available
  • Maximum 20 participants

Registration through the web only: closed

Please note the cancellation policy (CHF 20).

Deadline: 11 March 2015