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Alright, now we've got to tweak the tree. As they're going to model expansion of IE out of wherever it started from, they need to establish a rough idea of how quickly languages change. They did this by putting limits on how long certain clades are allowed to be time wise. For example, there is good reason to think that the Romance languages had begun to diverge by the time that the Roman Empire began to break up, so with that in mind, we can constrain the age of the romance clade based on that information. 
They also mention in their supplementary paper that one of the advantages of Bayesian analysis is that they don't have to establish fixed constraints, the constraints themselves can vary.
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Step 3! Now, to work out where Indo-European languages have come from, they used information from a publication called Ethnologue about where the present day languages in their sample are (pre-colonially) spoken (given an approximate geographic range, rather than a point location) and where the ancient languages are believed to have been spoken.