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PLoS One 2013 Jan 01;86:e66245. doi: 10.1371/journal.pone.0066245.
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A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses.

Nowak MD , Smith AB , Simpson C , Zwickl DJ .

Molecular divergence time analyses often rely on the age of fossil lineages to calibrate node age estimates. Most divergence time analyses are now performed in a Bayesian framework, where fossil calibrations are incorporated as parametric prior probabilities on node ages. It is widely accepted that an ideal parameterization of such node age prior probabilities should be based on a comprehensive analysis of the fossil record of the clade of interest, but there is currently no generally applicable approach for calculating such informative priors. We provide here a simple and easily implemented method that employs fossil data to estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade, which can be used to fit an informative parametric prior probability distribution on a node age. Specifically, our method uses the extant diversity and the stratigraphic distribution of fossil lineages confidently assigned to a clade to fit a branching model of lineage diversification. Conditioning this on a simple model of fossil preservation, we estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade. The likelihood surface of missing history can then be translated into a parametric prior probability distribution on the age of the clade of interest. We show that the method performs well with simulated fossil distribution data, but that the likelihood surface of missing history can at times be too complex for the distribution-fitting algorithm employed by our software tool. An empirical example of the application of our method is performed to estimate echinoid node ages. A simulation-based sensitivity analysis using the echinoid data set shows that node age prior distributions estimated under poor preservation rates are significantly less informative than those estimated under high preservation rates.

PubMed ID: 23755303
PMC ID: PMC3673923
Article link: PLoS One

Species referenced: Echinodermata
Genes referenced: ago1b impact irak1bp1 LOC100893907 LOC115925415 LOC576414 LOC583082

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References [+] :
Alfaro, Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. 2009, Pubmed