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Compare the two methods of dating fossils

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Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis.In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating.[Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.] In recent years, divergence time estimation has become increasingly prominent in evolutionary biology.Methodological and empirical advances now allow time trees to be estimated more accurately than ever before.For node dating, one thus often ends up discarding most of the information preserved in the fossil record (but see Marshall 2008).

Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis.

Another possibility is to use cross- validation techniques to identify and remove inconsistent calibration nodes (Near and Sanderson 2004; Near et al. A more satisfactory way of addressing fossil affinities is to treat the actual character evidence in a phylogenetic context. Although the fossil placement and minimum calibration constraints on the tree were thus improved, these approaches could not avoid the largely arbitrary assignment of a probability distribution to the calibration points.

Several studies have analyzed fossil and recent taxa together, using combined morphological and molecular data, to study the placement of the fossils and their impact on the topology estimates for the recent taxa (Lee et al. Here, we advocate a different approach to dating phylogenies, which includes fossils alongside extant taxa in a “total-evidence” analysis.

First, the calibration data must be associated with fixed nodes in the tree, despite the fact that we do not know any of the nodes with absolute certainty.

This may result in artifacts in the dating analysis, such as exaggerated confidence in the tree topology and the resulting age estimates.