Extracting the evolutionary signal from genomes.

Several methods to analyze aspects of evolution are developed, that depend on the availability of complete genomes. While I consistently find a phylogenetic signal using many approaches, a question that is winning concern is how these evolutionary relationships should be interpreted. Since Darwin’s idea about the tree-like structure of evolution, the dogma has been that evolution is mainly a vertical process, but recently, Doolittle pointed out that especially for prokaryotes, a tree may be insufficient to capture the complex evolutionary paths leading to the current-day genomes. While a tree may fall short as a representation of the evolutionary relationships between genomes, I think that describing a species as its entire genome blurs your vision. To characterize a species, I would look at its core, and disregard the noisy genes that obscure its evolutionary history (chapters 'Genome trees and the nature of genome evolution', 'The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise' and 'Assessment of phylogenomic and orthology approaches for phylogenetic inference'). To identify these cores at many different levels throughout the tree of life, I use the hundreds of complete genomes that have become available. In the chapter 'Signature genes as a phylogenomic tool', I find signature genes for every clade, and show that these can be used for the taxonomic characterization of a sequenced sample, for example an environmental sample. Another type of data that have become available on a large scale are gene expression data. To be able to compare the functional context of genes in distantly related species, we developed the expression context, that relies on the completeness of the genome sequences and on the availability of genome-wide expression experiments (chapter 'A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation')