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When diversification models and relaxed-clock models are combined in a Bayesian analysis, it is possible to estimate divergence times on a relative time scale.
External evidence, however, is needed to estimate absolute node ages. Calibration methods (also called “node dating”) are the most widely used approaches for dating trees (Ho and Phillips 2009) where absolute branch times are estimated using prior densities for the ages of a subset of divergences in the tree.
Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions.
The fossil record is frequently used to convert the timescale of inferred phylogenies to absolute time (Zuckerkandl and Pauling 1962; 1965). To date species divergences on an absolute time scale, Bayesian approaches must include three important components to decouple the confounded rate and time parameters: (i) a model describing how substitution rates are distributed across lineages; (ii) a tree prior characterizing the distribution of speciation events over time and the tree topology; and (iii) a way to incorporate information from the fossil or geological record to scale the relative times and rates to absolute values.
Exactly how to incorporate information from the fossil record into a phylogenetic analysis remains an active area of research. Relaxed molecular clock models act as prior distributions on lineage-specific substitution rates and their introduction has greatly improved divergence dating methods (Thorne et al. 2006; Rannala and Yang 2007; Drummond and Suchard 2010; Heath et al. These models do not assume a strict molecular clock, instead they allow each branch in the tree to have its own rate of molecular evolution drawn from a prior distribution of rates across branches.
We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework.
This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa.