Measuring genome conservation across taxa: divided strains and United Kingdoms

Species evolutionary relationships have traditionally been defined by sequencesimilarities 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 simulta-neously 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 remark-able ability to define evolutionary relationships across all taxonomic ranges. An assessment of taxo-nomic ranks with genome conservation shows that certain ranks are inadequately described and raises the possibility for a more precise and quantitative tax-onomy in the future. All phylogenetic reconstructions areavailable at the genomephylogeny server