Probability Distribution of Tree Age for the Simple Birth–Death Process, with Applications to Distributions of Number of Ancestral Lineages and Divergence Times for Pairs of Taxa in a Yule Tree.

In this contribution, a general expression is derived for the probability density of the time to the most recent common ancestor (TMRCA) of a simple birth–death tree, a widely used stochastic null-model of biological speciation and extinction, conditioned on the constant birth and death rates and number of extant lineages. This density is contrasted with a previous result which was obtained using a uniform prior for the time of origin. The new distribution is applied to two problems of phylogenetic interest. First, that of the probability of the number of taxa existing at any time in the past in a tree of a known number of extant species, and given birth and death rates, and second, that of determining the TMRCA of two randomly selected taxa in an unobserved tree that is produced by a simple birth-only, or Yule, process. In the latter case, it is assumed that only the rate of bifurcation (speciation) and the size, or number of tips, are known. This is shown to lead to a closed-form analytical expression for the probability distribution of this parameter, which is arrived at based on the known mathematical form of the age distribution of Yule trees of a given size and branching rate, which is derived here de novo, and a similar distribution which additionally is conditioned on tree age. The new distribution is the exact Yule prior for divergence times of pairs of taxa under the stated conditions and is potentially useful in statistical (Bayesian) inference studies of phylogenies. [ABSTRACT FROM AUTHOR]