Molecular Biology and Evolution 19:101-109 (2002)
© 2002 Society for Molecular Biology and Evolution
Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach
Section of Evolution and Ecology, University of California, Davis
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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N. Wahlberg That Awkward Age for Butterflies: Insights from the Age of the Butterfly Subfamily Nymphalinae (Lepidoptera: Nymphalidae) Syst Biol, October 1, 2006; 55(5): 703 - 714. [Abstract] [Full Text] [PDF]
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C. Yesson and A. Culham Phyloclimatic Modeling: Combining Phylogenetics and Bioclimatic Modeling Syst Biol, October 1, 2006; 55(5): 785 - 802. [Abstract] [Full Text] [PDF]
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A. B. Smith, D. Pisani, J. A. Mackenzie-Dodds, B. Stockley, B. L. Webster, and D. T. J. Littlewood Testing the Molecular Clock: Molecular and Paleontological Estimates of Divergence Times in the Echinoidea (Echinodermata) Mol. Biol. Evol., October 1, 2006; 23(10): 1832 - 1851. [Abstract] [Full Text] [PDF]
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D. M. Crayn, M. Rossetto, and D. J. Maynard Molecular phylogeny and dating reveals an Oligo-Miocene radiation of dry-adapted shrubs (former Tremandraceae) from rainforest tree progenitors (Elaeocarpaceae) in Australia Am. J. Botany, September 1, 2006; 93(9): 1328 - 1342. [Abstract] [Full Text] [PDF]
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Z.-L. Nie, H. Sun, P. M. Beardsley, R. G. Olmstead, and J. Wen Evolution of biogeographic disjunction between eastern Asia and eastern North America in Phryma (Phrymaceae) Am. J. Botany, September 1, 2006; 93(9): 1343 - 1356. [Abstract] [Full Text] [PDF]
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S. L. Pereira and A. J. Baker A Mitogenomic Timescale for Birds Detects Variable Phylogenetic Rates of Molecular Evolution and Refutes the Standard Molecular Clock Mol. Biol. Evol., September 1, 2006; 23(9): 1731 - 1740. [Abstract] [Full Text] [PDF]
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J. Pons, T. G. Barraclough, J. Gomez-Zurita, A. Cardoso, D. P. Duran, S. Hazell, S. Kamoun, W. D. Sumlin, and A. P. Vogler Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects Syst Biol, August 1, 2006; 55(4): 595 - 609. [Abstract] [Full Text] [PDF]
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H. Won and S. S. Renner Dating Dispersal and Radiation in the Gymnosperm Gnetum (Gnetales)--Clock Calibration When Outgroup Relationships Are Uncertain Syst Biol, August 1, 2006; 55(4): 610 - 622. [Abstract] [Full Text] [PDF]
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M. Kullberg, M. A. Nilsson, U. Arnason, E. H. Harley, and A. Janke Housekeeping Genes for Phylogenetic Analysis of Eutherian Relationships Mol. Biol. Evol., August 1, 2006; 23(8): 1493 - 1503. [Abstract] [Full Text] [PDF]
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S. S. Jakob and F. R. Blattner A Chloroplast Genealogy of Hordeum (Poaceae): Long-Term Persisting Haplotypes, Incomplete Lineage Sorting, Regional Extinction, and the Consequences for Phylogenetic Inference Mol. Biol. Evol., August 1, 2006; 23(8): 1602 - 1612. [Abstract] [Full Text] [PDF]
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S. G Brady, S. Sipes, A. Pearson, and B. N Danforth Recent and simultaneous origins of eusociality in halictid bees Proc R Soc B, July 7, 2006; 273(1594): 1643 - 1649. [Abstract] [Full Text] [PDF]
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C. RYDIN, K. R. PEDERSEN, P. R. CRANE, and E. M. FRIIS Former Diversity of Ephedra (Gnetales): Evidence from Early Cretaceous Seeds from Portugal and North America Ann. Bot., July 1, 2006; 98(1): 123 - 140. [Abstract] [Full Text] [PDF]
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A. J Roger and L. A Hug The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation Phil Trans R Soc B, June 29, 2006; 361(1470): 1039 - 1054. [Abstract] [Full Text] [PDF]
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