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The tree prior distribution describes the diversification process where fossil and extant species are treated as samples from this process.
The second major concern about node calibration is that the fossilization process is modeled only indirectly and in isolation from other forms of data.Typically the oldest fossil in the clade is chosen as the minimum clade age but there is no agreed upon method of specifying the prior density beyond that.One way to specify a prior calibration density is through using the fossil sampling rate that can be estimated from fossil occurrence data (Foote and Raup 1996).In the total-evidence approach to dating (Lee et al. 2012a), one specifies a probabilistic model that encompasses the fossil data, molecular data and morphological data and then jointly estimates parameters of that model, including a dated phylogeny, in a single analysis using all available data.It builds on previously described methods for combining molecular and morphological data to infer phylogenies (Nylander et al.
Advances in molecular biology and computer science have enabled increasingly sophisticated methods for inferring phylogenetic trees.