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Maximum-Likelihood Estimation of Coalescence Times in Genealogical Trees

Authors
  • Loukia Meligkotsidou
  • Paul Fearnhead
Publisher
Copyright © 2005 by the Genetics Society of America
Publication Date
Dec 01, 2005
Source
PMC
Keywords
Disciplines
  • Computer Science
  • Logic
  • Mathematics
  • Medicine
License
Unknown

Abstract

We develop a method for maximum-likelihood estimation of coalescence times in genealogical trees, based on population genetics data. For this purpose, a Viterbi-type algorithm is constructed to maximize the joint likelihood of the coalescence times. Marginal confidence intervals for the coalescence times based on the profile likelihoods are also computed. Our method of finding MLEs and calculating C.I.'s appears to be more accurate than alternative numerical maximization methods, and maximum-likelihood inference appears to be more accurate than other existing model-free approaches to estimating coalescent times. We demonstrate the method on two different data sets: human Y chromosome DNA data and fungus DNA data.

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