Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach

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ID: 290929
2002
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Abstract
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. 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 2- to 10-fold variation across lineages.
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openalex_W1982848324 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Michael J. Sanderson
Journal molecular biology and evolution
Year 2002
DOI
10.1093/oxfordjournals.molbev.a003974
URL
https://academic.oup.com/mbe/article-pdf/19/1/101/23451066/mbev_19_01_0101.pdf
Keywords Keywords not found

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