Relaxed phylogenetics and dating with confidence

PLoS Biol. 2006 May;4(5):e88. doi: 10.1371/journal.pbio.0040088. Epub 2006 Mar 14.


In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of "relaxed phylogenetics." Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacteria / genetics
  • Bayes Theorem
  • Biological Evolution*
  • Computer Simulation
  • Dengue Virus / genetics
  • Fishes / genetics
  • Fungi / genetics
  • Genetic Variation
  • Influenza A virus / genetics
  • Insecta / genetics
  • Markov Chains
  • Marsupialia / genetics
  • Models, Biological
  • Monte Carlo Method
  • Phylogeny*
  • Plants / genetics
  • Primates / genetics
  • Time Factors