# Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.

@article{Sanderson2002EstimatingAR, title={Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.}, author={Michael J. Sanderson}, journal={Molecular biology and evolution}, year={2002}, volume={19 1}, pages={ 101-9 } }

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. In this study, a semiparametric 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… Expand

#### 1,794 Citations

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A heuristic rate2smoothing algorithm is implemented ( the AHRS algorithm) to automate the assignment of branches to rate groups and the likelihood algorithm is improved to accommodate missing sequences at some loci in the combined analysis. Expand

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This study tested the accuracy of several relaxed-clock methods (penalized likelihood and Bayesian inference using various models of rate change) using nucleotide sequences simulated on a nine-taxon tree, and provided a strong recommendation for using the exponential model of ratechange if a conservative approach to divergence time estimation is required. Expand

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- Biology
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R8s version 1.5 is a program which uses parametric, nonparametric and semiparametric methods to relax the assumption of constant rates of evolution to obtain better estimates of rates and times. Expand

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—Bayesian methods for estimating evolutionary divergence times are extended to multigene data sets, and a technique is described for detecting correlated changes in evolutionary rates among genes.… Expand

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