Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny

The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists–how can one assign relative dates to the vertices of the tree? In this paper we investigate this problem, assuming a uniform distribution on the order of the inner vertices of the tree (which includes, but is more general than, the popular Yule distribution on trees). We derive fast algorithms for computing the probability that (i) any given vertex in the tree was the j–th speciation event (for each j), and (ii) any one given vertex is earlier in the tree than a second given vertex. We show how the first algorithm can be used to calculate the expected length of any given interior edge in any given tree that has been generated under either a constant-rate speciation model, or the coalescent model.