If DNA sequences obtained from fossils are added to the analysis, they may distort the outcome due to different probabilities of substitutions resulting decay processes. I did not find a way to divide the OTUs into subsets like I normally do to different sites/genes using MrBayes
Christian Julian Villabona-Arenas
Are these subsets monophyletic?
The model depends on the data, therefore we select the best-fit model in each case. Perhaps the question is if we can be assumed that the substitutions rate change throughout the tree. In this case, check out BEAST (http://beast2.org/), it enables the integration and statistical analysis of data from heterogeneous sources (such as fossils) and you can assume the data do not share the same evolutionary rate for each branch.
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