Inference from gene trees in a subdivided population

Abstract

This paper studies gene trees in subdivided populations which are constructed as perfect phylogenies from the pattern of mutations in a sample of DNA sequences and presents a new recursion for the probability distribution of such gene trees. The underlying evolutionary model is the coalescent process in a subdivided population. The infinitely-many-sites model of mutation is assumed. Ancestral inference questions that are discussed are maximum likelihood estimation of migration and mutation rates; detection of population growth by likelihood techniques; determining the distribution of the time to the most recent common ancestor of a sample of sequences; determining the distribution of the age..