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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J. J Wiens, G. Parra-Olea, M. Garcia-Paris, and D. B Wake Phylogenetic history underlies elevational biodiversity patterns in tropical salamanders Proc R Soc B, April 7, 2007; 274(1612): 919 - 928. [Abstract] [Full Text] [PDF]
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J. M. Waters, D. L. Rowe, S. Apte, T. M. King, G. P. Wallis, L. Anderson, R. J. Norris, D. Craw, and C. P. Burridge Geological Dates and Molecular Rates: Rapid Divergence of Rivers and Their Biotas Syst Biol, April 1, 2007; 56(2): 271 - 282. [Abstract] [Full Text] [PDF]
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 A. B. Smith Intrinsic versus extrinsic biases in the fossil record: contrasting the fossil record of echinoids in the Triassic and early Jurassic using sampling data, phylogenetic analysis, and molecular clocks Paleobiology, March 1, 2007; 33(2): 310 - 323. [Abstract] [Full Text] [PDF]
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M. K. Gonder, H. M. Mortensen, F. A. Reed, A. de Sousa, and S. A. Tishkoff Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages Mol. Biol. Evol., March 1, 2007; 24(3): 757 - 768. [Abstract] [Full Text] [PDF]
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Y.-J. Wang, J.-Q. Liu, and G. Miehe Phylogenetic Origins of the Himalayan Endemic Dolomiaea, Diplazoptilon and Xanthopappus (Asteraceae: Cardueae) Based on Three DNA Regions Ann. Bot., February 1, 2007; 99(2): 311 - 322. [Abstract] [Full Text] [PDF]
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E. D. Akhunov, A. R. Akhunova, and J. Dvorak Mechanisms and Rates of Birth and Death of Dispersed Duplicated Genes during the Evolution of a Multigene Family in Diploid and Tetraploid Wheats Mol. Biol. Evol., February 1, 2007; 24(2): 539 - 550. [Abstract] [Full Text] [PDF]
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K. Roelants, D. J. Gower, M. Wilkinson, S. P. Loader, S. D. Biju, K. Guillaume, L. Moriau, and F. Bossuyt Global patterns of diversification in the history of modern amphibians PNAS, January 16, 2007; 104(3): 887 - 892. [Abstract] [Full Text] [PDF]
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A. Willyard, J. Syring, D. S. Gernandt, A. Liston, and R. Cronn Fossil Calibration of Molecular Divergence Infers a Moderate Mutation Rate and Recent Radiations for Pinus Mol. Biol. Evol., January 1, 2007; 24(1): 90 - 101. [Abstract] [Full Text] [PDF]
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P. G.P Ericson, C. L Anderson, T. Britton, A. Elzanowski, U. S Johansson, M. Kallersjo, J. I Ohlson, T. J Parsons, D. Zuccon, and G. Mayr Diversification of Neoaves: integration of molecular sequence data and fossils Biol Lett, December 22, 2006; 2(4): 543 - 547. [Abstract] [Full Text] [PDF]
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