What units are species tree divergences from *BEAST analysis in? 

Let $r_i$ be the estimated relative rate for locus $i$ and let $L_i$ be the number of sites in locus $i$. If *BEAST is run with the mean substitution rate across partitions fixed to 1, and the clock rate fixed to 1, then the following is true:

<math> frac{sum_i r_i L_i}{sum_i L_i} = 1, </math>

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Bayesian evolutionary analysis by sampling trees

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