17 research outputs found
The conditioned reconstructed process
We investigate a neutral model for speciation and extinction, the constant
rate birth-death process. The process is conditioned to have extant species
today, we look at the tree distribution of the reconstructed trees-- i.e. the
trees without the extinct species. Whereas the tree shape distribution is
well-known and actually the same as under the pure birth process, no analytic
results for the speciation times were known. We provide the distribution for
the speciation times and calculate the expectations analytically. This
characterizes the reconstructed trees completely. We will show how the results
can be used to date phylogenies
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