Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model

Theor Popul Biol. 1998 Apr;53(2):143-51. doi: 10.1006/tpbi.1997.1348.


In this paper, a maximum likelihood estimator of population divergence time based on the infinite sites model is developed. It is demonstrated how this estimator may be applied to obtain maximum likelihood estimates of the topology of population phylogenies. This approach addresses several classical problems occurring in the inference of the phylogenetic relationship of populations, most notably the problem of shared ancestral polymorphisms. The method is applied to previously published data sets of human African populations and of Caribbean hawksbill turtles.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • DNA, Mitochondrial / genetics
  • Founder Effect
  • Gene Frequency / genetics
  • Humans
  • Likelihood Functions*
  • Models, Genetic*
  • Mutation / genetics
  • Phylogeny*
  • Polymorphism, Genetic / genetics*
  • Reproducibility of Results
  • Time Factors
  • Turtles / genetics


  • DNA, Mitochondrial