Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation

In this paper we present a method for estimating population divergence times by maximum likelihood in models without mutation. The maximum-likelihood estimator is compared to a commonly applied estimator based on Wright's F-ST statistic. Simulations suggest that the maximum-likelihood estimator is less biased and has a lower variance than the F-ST-based estimator. The maximum-likelihood estimator provides a statistical framework for the analysis of population history given genetic data. We demonstrate how maximum-likelihood estimates of the branching pattern of divergence of multiple populations may be obtained.We also describe how the method may be applied to test hypotheses such as whether populations have maintained equal population sizes. We illustrate the method by applying it to two previously published sets of human restriction fragment length polymorphism (RFLP) data.