SANDERSON, MICHAEL J. Section of Evolution and Ecology, University of California, Davis, CA 95616. - Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.
Rates of molecular evolution vary widely between lineages, but
quantification of how rates change has proven difficult. Recently
proposed estimation procedures have mainly adopted highly parametric
approaches that model rate evolution explicitly. Here a
semi-parametric smoothing method is developed using penalized
likelihood. A saturated model in which every lineage has a separate
rate is combined with a roughness penalty that discourages rates from
varying too much across a phylogeny. A data-driven cross-validation
criterion is then used to determine an optimal level of smoothing.
This criterion is based on an estimate of the average prediction error
associated with pruning lineages from the tree. The methods are
applied to three data sets of six genes across a sample of land
plants. Optimally smoothed estimates of absolute rates entailed two-
to ten-fold variation across lineages.
Key words: divergence time, molecular clock, penalized likelihood