Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

Extract

The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

At around the same time, Sanderson (1997) published his nonparametric rate-smoothing algorithm, which operates by minimizing the magnitude of rate changes between adjacent branches in the tree. A related method, penalized likelihood, was subsequently implemented in a maximum-likelihood framework (Sanderson 2002). In this approach, large rate changes between neighboring branches are penalized. The degree of penalization is determined by a smoothing parameter, the value of which is obtained objectively through a cross-validation procedure.