title: Measuring genome conservation across taxa: divided strains and united kingdoms.
abstract: Species evolutionary relationships have traditionally been defined by sequence similarities of phylogenetic marker molecules, recently followed by whole-genome phylogenies based on gene order, average ortholog similarity or gene content. Here, we introduce genome conservation--a novel metric of evolutionary distances between species that simultaneously takes into account, both gene content and sequence similarity at the whole-genome level. Genome conservation represents a robust distance measure, as demonstrated by accurate phylogenetic reconstructions. The genome conservation matrix for all presently sequenced organisms exhibits a remarkable ability to define evolutionary relationships across all taxonomic ranges. An assessment of taxonomic ranks with genome conservation shows that certain ranks are inadequately described and raises the possibility for a more precise and quantitative taxonomy in the future. All phylogenetic reconstructions are available at the genome phylogeny server: <http://maine.ebi.ac.uk:8000/cgi-bin/gps/GPS.pl>.
authors.affiliation: Computational Genomics Group, The European Bioinformatics Institute EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.
authors.forename: Victor
authors.initials: V
authors.lastname: Kunin
authors.forename: Dag
authors.initials: D
authors.lastname: Ahren
authors.forename: Leon
authors.initials: L
authors.lastname: Goldovsky
authors.forename: Paul
authors.initials: P
authors.lastname: Janssen
authors.forename: Christos A
authors.initials: CA
authors.lastname: Ouzounis
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D020560:Proteobacteria / Q000145:classification / Q000235:genetics