The genome reduction hypothesis and the phylogeny of eukaryotes

The first steps in eukaryotic evolution appear difficult to retrace despite the availability of an increasing amount of data. Current molecular phylogenies suggest that the eukaryotic tree would be better represented as a bush of major lineages whose order of emerge is poorly resolved. Such lack of resolution is often explained by a radiation event that would have left very little ancient signal in eukaryotic molecular markers. We suggest a complementary genomic approach that might help tackling this major issue. It rests on a hypothesis, the genome reduction hypothesis (GRH), suggesting that the divergence of major eukaryotic lineages might have been coupled with independent genomic reduction events, starting from a large and partially redundant chimerical genome. Thus, significant and coherent patterns of shared ancestral gene losses between major eukaryotic lineages might help polarizing the most basal nodes in the eukaryotic phylogeny. We propose a test for the GRH that exploits the increasing availability of complete eukaryotic genomes in public databases.