Zurich Colloquium for Computational Molecular Evolution (ZC-CME 2012)

One of the fundamental concepts behind Darwin's theory of evolution is “descent with modification”. From a common ancestor, populations and species diverge during the course of evolution, where natural selection is the main driving force. This process is traditionally envisioned through a phylogenetic tree. Since Darwin's ideas were published in his Origin of Species, statisticians, mathematicians, computer scientists, biologists, chemists and physicists have joined their forces developing both methodological and experimental aspects of the field.

Scope

The focus of this seminar series is on statistical and computational methodology to study how genomes of organisms evolve, the driving forces of change at both phenotypic and molecular levels. We aim to encourage and promote the innovation in statistical and computational approaches, and the interdisciplinary character of the field.

Organizers

Maria Anisimova

Please contact me if you would like to join the mailing list for this colloquium.

Funding

This seminar is jointly funded by the CBRG and the SIB.

Program

This is a preliminary program. It is still subject to change since we do not have confirmation from all speakers yet. Only the dates in bold have already been confirmed.

Previous years

The list of speakers/abstracts for previous years are available here: 2011, 2010, 2009, 2008, 2007.

Abstracts

Evolution and gene expression in vertebrates

Dr. Marc Robinson-Rechavi

Department of Ecology and Evolution, University of Lausanne and SIB, Switzerland

Expression patterns are a basic aspect of the description of the function of genes. The evolution of gene expression patterns has been suggested to be a major component of the evolution of gene function. Notably, changes in expression after duplication might be a major factor in the retention of paralogs. Moreover, the breadth or strength of expression seems to be the main determinant of the evolution of gene sequence. On the other hand, it has also been suggested that expression patterns are not very informative concerning gene function, and that they are lowly constrained in evolution. We have developed a database, Bgee (dataBase for gene expression evolution, http://bgee.unil.ch/), which allows large scale comparisons of expression patterns between vertebrate species. This allows us to show that: (i) gene expression forms modules which are conserved between species, and functionally relevant; (ii) the timing of expression during development influences strongly the evolution of vertebrate genes; and (iii) neo- and sub-functionalization can be detected after whole-genome or small-scale duplications, but conservation of expression is the most common pattern for paralogs.

Simulation of molecular data by the coalescent with recombination, migration and demographics

Dr. Miguel Arenas

Institute of Ecology and Evolution, University of Bern and SIB, Switzerland

The simulation of genetic data has been commonly used in molecular evolution for hypothesis testing, to compare and verify analytical methods or tools, to analyze interactions among evolutionary processes and even to estimate evolutionary parameters. Indeed, in order to arrive to meaningful conclusions, it is important that these simulations mimic the process of molecular evolution as realistic as possible. Consequently, there is a continuous need of tools for the simulation of genetic data under diverse evolutionary scenarios. Here I show a program to simulate nucleotide, codon and amino acid data by the coalescent with recombination, migration and demographics. Then I describe some applications of the simulated data such as the effect of recombination on ancestral sequence reconstruction and the coestimation of evolutionary parameters using approximate Bayesian computation.