A distance-based least-square method for dating speciation events

Distance-based phylogenetic methods are widely used in biomedical research. However, there has been little development of rigorous statistical methods and software for dating speciation and gene duplication events by using evolutionary distances. Here we present a simple, fast and accurate dating method based on the least-squares (LS) method that has already been widely used in molecular phylogenetic reconstruction. Dating methods with a global clock or two different local clocks are presented. Single or multiple fossil calibration points can be used, and multiple data sets can be integrated in a combined analysis. Variation of the estimated divergence time is estimated by resampling methods such as bootstrapping or jackknifing. Application of the method to dating the divergence time among seven ape species or among 35 mammalian species including major mammalian orders shows that the estimated divergence time with the LS criterion is nearly identical to those obtained by the likelihood method or Bayesian inference.

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► A new distance-based method for dating speciation events is numerically illustrated.
► The method is based on the least-squares criterion and implemented in DAMBE.
► The method allows global and local clocks with one or multiple calibration points.
► Interval estimates of dates are assesses by resampling methods.
► The method allows dating with both sequences and distance matrices.