Universal pacemaker of genome evolution in animals and fungi and variation of evolutionary rates in diverse organisms

Sagi Snir, Yuri I. Wolf, Eugene V. Koonin

Research output: Contribution to journalArticlepeer-review


Gene evolution is traditionally considered within the framework of the molecular clock (MC) model whereby each gene is characterized by an approximately constant rate of evolution. Recent comparative analysis of numerous phylogenies of prokaryotic genes has shown that a different model of evolution, denoted the Universal PaceMaker (UPM), which postulates conservation of relative, rather than absolute evolutionary rates, yields a better fit to the phylogenetic data. Here, we show that the UPM model is a better fit than the MC for genome wide sets of phylogenetic trees from six species of Drosophila and nine species of yeast, with extremely high statistical significance. Unlike the prokaryotic phylogenies that include distant organisms and multiple horizontalgene transfers, these are simpledata sets that cover groupsof closely related organisms and consist of genetrees with the sametopology as thespecies tree. The results indicate that both lineage-specific and gene-specific rates are important in genome evolution but the lineage-specific contribution is greater. Similar to the MC, the gene evolution rates under the UPM are strongly overdispersed, approximately 2-fold compared with the expectation from sampling error alone. However, we show that neither Drosophila nor yeast genes form distinct clusters in the tree space. Thus, the gene-specific deviations from the UPM, although substantial, are uncorrelated and most likely dependon selective factors that are largelyunique to individualgenes. Thus, the UPM appears to beakey feature of genome evolution across the history of cellular life.

Original languageEnglish
Pages (from-to)1268-1278
Number of pages11
JournalGenome Biology and Evolution
Issue number6
StatePublished - Jun 2014


  • Genome evolution
  • Molecular clock
  • Phylogenetic trees
  • Relative evolution rates

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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