This paper investigates a neutral model for speciation and extinction, the constant rate birth-death process, and examines the distribution of speciation times in reconstructed trees. The process is conditioned to have n extant species today, and the focus is on the tree distribution of the reconstructed trees—i.e., the trees without the extinct species. While the tree shape distribution is well-known and identical to that of the pure birth process, no analytic results for the speciation times were previously known. The paper provides the distribution for the speciation times and calculates their expectations analytically, thereby characterizing the reconstructed trees completely. These results can be used to date phylogenies.
The paper introduces a point process representation for reconstructed trees, which has been previously used for the critical branching process. It calculates the probability distribution of the age of a tree with n species, assuming a uniform prior on the age of the tree. This enables the derivation of the density function for the time of the k-th speciation event in a tree with n extant species. The paper also discusses the expectation of the speciation times under different models, including the Yule model and the conditioned critical branching process.
The paper shows that the speciation times in a reconstructed tree are independent and identically distributed under certain conditions. It provides analytic results for the expected time of the k-th speciation event in a tree with n species, which can be used for dating phylogenies. The results are implemented in the PhyloTree package for Python. The paper also discusses the properties of the speciation times, including the point process representation, the coalescent process, and the backwards process of the cBDP. The results are applicable to a wide range of models, including the Yule model and the conditioned critical branching process. The paper concludes with applications of the results to phylogenetic dating and the simulation of reconstructed trees.This paper investigates a neutral model for speciation and extinction, the constant rate birth-death process, and examines the distribution of speciation times in reconstructed trees. The process is conditioned to have n extant species today, and the focus is on the tree distribution of the reconstructed trees—i.e., the trees without the extinct species. While the tree shape distribution is well-known and identical to that of the pure birth process, no analytic results for the speciation times were previously known. The paper provides the distribution for the speciation times and calculates their expectations analytically, thereby characterizing the reconstructed trees completely. These results can be used to date phylogenies.
The paper introduces a point process representation for reconstructed trees, which has been previously used for the critical branching process. It calculates the probability distribution of the age of a tree with n species, assuming a uniform prior on the age of the tree. This enables the derivation of the density function for the time of the k-th speciation event in a tree with n extant species. The paper also discusses the expectation of the speciation times under different models, including the Yule model and the conditioned critical branching process.
The paper shows that the speciation times in a reconstructed tree are independent and identically distributed under certain conditions. It provides analytic results for the expected time of the k-th speciation event in a tree with n species, which can be used for dating phylogenies. The results are implemented in the PhyloTree package for Python. The paper also discusses the properties of the speciation times, including the point process representation, the coalescent process, and the backwards process of the cBDP. The results are applicable to a wide range of models, including the Yule model and the conditioned critical branching process. The paper concludes with applications of the results to phylogenetic dating and the simulation of reconstructed trees.