MEASURING GENOME EVOLUTION

The determination of complete genome sequences provides us with an opp ortunity to describe and analyze evolution at the comprehensive level of genomes. Here we compare nine genomes with respect to their protein coding genes at two levels: (i) we compare genomes as ''bags of genes '' and measure the fraction of orthologs shared between genomes and (i i) we quantify correlations between genes with respect to their relati ve positions in genomes. Distances between the genomes are related to their divergence times, measured as the number of amino acid substitut ions per site in a set of 34 orthologous genes that are shared among a ll the genomes compared. We establish a hierarchy of rates at which ge nomes have changed during evolution. Protein sequence identity is the most conserved, followed by the complement of genes within the genome. Next is the degree of conservation of the order of genes, whereas gen e regulation appears to evolve at the highest rate. Finally, we show t hat some genomes are more highly organized than others: they show a hi gher degree of the clustering of genes that have orthologs in other ge nomes.