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Originally published as Genetics Published Articles Ahead of Print on August 5, 2005.
Genetics, Vol. 171, 2073-2084, December 2005, Copyright © 2005
doi:10.1534/genetics.105.043067
Maximum-Likelihood Estimation of Coalescence Times in Genealogical Trees
Loukia Meligkotsidou1 and Paul Fearnhead
Department of Mathematics and Statistics, Lancaster University, Lancaster LA1 4YF, United Kingdom
1 Corresponding author: Department of Mathematics and Statistics, Lancaster University, Lancaster LA1 4YF, United Kingdom.
E-mail: l.meligotsidou{at}lancaster.ac.uk
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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