In this section we describe recently developed mathematical models and computational methods that treat all data under the equanimous gaze of Bayesian probability.
It is important to note here that both molecular sequences and morphological fossils, including in both cases the circumstances of their observation, must be considered data. It is only be treating them uniformly as data that the total evidence can be correctly synthesized into an unbiased picture. I will contrast this to previous attempts at applying Bayesian inference to the problem of dating species divergences with rocks and clocks. In many past attempts fossil data was pre-processed into prior knowledge in inaccurate and biasing ways. In general the concept of “calibrating” and “dating” molecular phylogenies with fossil data has ignored the role of fossil observations as data. By treating fossils as data in an integrated analysis it is also possible to exploit novel new inferences, such as to date fossils based on their morphological affinities in cases where geological dating is very uncertain.