A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages

Beth Shapiro, Simon Y. W. Ho, Alexei J. Drummond, Marc A. Suchard, Oliver G. Pybus, Andrew Rambaut

Research output: Contribution to journalArticlepeer-review

Abstract

Heterochronous data sets comprise molecular sequences sampled at different points in time. If the temporal range of the sampled sequences is large relative to the rate of mutation, the sampling times can directly calibrate evolutionary rates to calendar time. Here, we extend this calibration process to provide a full probabilistic method that utilizes temporal information in heterochronous data sets to estimate sampling times (leaf-ages) for sequenced for which this information unavailable. Our method is similar to relaxing the constraints of the molecular clock on specific lineages within a phylogenetic tree. Using a combination of synthetic and empirical data sets, we demonstrate that the method estimates leaf-ages reliably and accurately. Potential applications of our approach include incorporating samples of uncertain or radiocarbon-infinite age into ancient DNA analyses, evaluating the temporal signal in a particular sequence or data set, and exploring the reliability of sequence ages that are somehow contentious.

Original languageEnglish
Pages (from-to)879-887
Number of pages9
JournalMolecular Biology and Evolution
Volume28
Issue number2
DOIs
Publication statusPublished - Feb 2011

Keywords

  • heterochronous sequences
  • ancient DNA
  • molecular clock
  • viral evolution
  • measurably evolving populations
  • ANCIENT DNA
  • POPULATION-DYNAMICS
  • MOLECULAR EVOLUTION
  • INFLUENZA-VIRUS
  • CLIMATIC-CHANGE
  • BROWN BEARS
  • PLEISTOCENE
  • HIV-1
  • RATES
  • EXTINCTION

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