Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach

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1366 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)101-109
Number of pages9
JournalMolecular Biology and Evolution
Volume19
Issue number1
StatePublished - 2002
Externally publishedYes

Fingerprint

Molecular Evolution
divergence
embryophytes
roughness
pruning
Embryophyta
Genes
Surface roughness
Phylogeny
smoothing
prediction
phylogeny
methodology
genes
sampling
rate
fold
gene

Keywords

  • Evolutionary rates
  • Molecular clock
  • Penalized likelihood

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Genetics(clinical)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Molecular Biology

Cite this

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