MBE Advance Access published online on June 7, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm115
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Research Article |
The Impact of Fossils and Taxon Sampling on Ancient Molecular Dating Analyses
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
Corresponding author: Andrew J. Roger Department of Biochemistry and Molecular Biology, Rm 8-B1 Sir Charles Tupper Building Dalhousie University 5850 College St. Halifax, NS B3H 1X5 Tel: (902) 494-2620 Fax: (902) 494-1355 Email: Andrew.Roger{at}dal.ca
Received for publication March 15, 2007. Revision received May 29, 2007. Accepted for publication May 30, 2007.
The number and complexity of molecular dating studies has increased over the past decade. Along with a broadening acceptance of their utility has come significant controversy over the methods and models that are appropriate, as well as the accuracy of the estimates yielded by molecular clock analyses. Radically different age estimates have been published for the same divergences from analyses of different datasets with different fossil constraints obtained with different methods, and the underlying explanation for these differences is often unclear. Here we utilize two previously published datasets to examine the effect of fossil calibrations and taxon sampling on the age estimates for two deep eukaryote divergences in an attempt to discern the relative impact of these factors. Penalized likelihood, non-parametric rate smoothing, and Bayesian methods were utilized to generate age estimates for the origin of the Metazoa from a 7-gene dataset and for the divergence of Eukaryotes from a 129-gene dataset. From these analyses, it is clear that the fossil calibrations chosen and the method for applying constraints to these nodes have a large impact on age estimates, while the degree of taxon sampling within a dataset is less important in terms of the resulting age estimates. Concerns and recommendations for addressing these two factors when initiating a dating analysis are discussed.
Key Words: molecular dating • fossil constraints • Bayesian analysis • Penalized likelihood • taxon sampling
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