title: The impact of calibration and clock-model choice on molecular estimates of divergence times.
abstract: Phylogenetic estimates of evolutionary timescales can be obtained from nucleotide sequence data using the molecular clock. These estimates are important for our understanding of evolutionary processes across all taxonomic levels. The molecular clock needs to be calibrated with an independent source of information, such as fossil evidence, to allow absolute ages to be inferred. Calibration typically involves fixing or constraining the age of at least one node in the phylogeny, enabling the ages of the remaining nodes to be estimated. We conducted an extensive simulation study to investigate the effects of the position and number of calibrations on the resulting estimate of the timescale. Our analyses focused on Bayesian estimates obtained using relaxed molecular clocks. Our findings suggest that an effective strategy is to include multiple calibrations and to prefer those that are close to the root of the phylogeny. Under these conditions, we found that evolutionary timescales could be estimated accurately even when the relaxed-clock model was misspecified and when the sequence data were relatively uninformative. We tested these findings in a case study of simian foamy virus, where we found that shallow calibrations caused the overall timescale to be underestimated by up to three orders of magnitude. Finally, we provide some recommendations for improving the practice of molecular-clock calibration.
authors.affiliation: School of Biological Sciences, University of Sydney, NSW 2006, Australia. Electronic address: sebastian.duchene@sydney.edu.au.
authors.forename: Sebastián
authors.initials: S
authors.lastname: Duchêne
authors.affiliation: Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia.
authors.forename: Robert
authors.initials: R
authors.lastname: Lanfear
authors.affiliation: School of Biological Sciences, University of Sydney, NSW 2006, Australia.
authors.forename: Simon Y W
authors.initials: SY
authors.lastname: Ho
mesh_terms: D001499:Bayes Theorem; D002138:Calibration; D003198:Computer Simulation; D019143:Evolution, Molecular; D005580:Fossils; D008957:Models, Genetic; D010802:Phylogeny; D053150:Simian foamy virus / Q000235:genetics
keywords: Bayesian phylogenetics; Calibration; Date estimation; Divergence times; Evolutionary rate; Relaxed molecular clock