Genome Trees from Conservation Profiles

Abstract

The concept of the genome tree depends ors the potential evolutionary significance in the clustering of species according to similarities in the gene content of their genomes. Sn this respect, genome trees have often been Identified with species trees. With the rapid expansion of genome sequence data it becomes of increasing importance to develop accurate methods for grasping gSobal trends for the phySogenetic signais that mutually Sink the various genomes. We therefore derive here the methodological concept of gesiome trees based ors protein conservation profites in multiple species. The bask idea in this derivators is that the multi-component "presence-absence" protein conservation profiles permit tracking of common evolutionary histories of genes across muutiple genomes. We show that a significant reduction in informationall redundancy is achieved by considering only the subset of distinct conservation profiies. Beyond these basic ideas, we point out various pitfails and [imitations associated with the data handling, paving the way for further improvements. As an frustration for the methods, we analyze a genome tree based ors the above principles, along with a series of other trees derived from the same data and based on pair-wise comparisons (ancestral duplication-conservation and shared orthoSogs). in all trees we observe a sharp discrimination between the three primary domains of life: Bacteria, Archaea, and Eukarya. The new genome tree, based on conservation profiles, displays a significant correspondence with classically recognized taxonomical groupings, along with a series of departures from such conventional clusterings. Copyright © 2005 Teksia and Yeramian.