Maximum-Likelihood Estimation of Coalescence Times in Genealogical Trees | Zendy

Loukia Meligkotsidou | Zendy; Paul Fearnhead | Zendy

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Maximum-Likelihood Estimation of Coalescence Times in Genealogical Trees

Author(s) -

Loukia Meligkotsidou,

Paul Fearnhead

Publication year - 2005

Publication title -

genetics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 2.792

H-Index - 246

eISSN - 1943-2631

pISSN - 0016-6731

DOI - 10.1534/genetics.105.043067

Subject(s) - coalescent theory , maximum likelihood , expectation–maximization algorithm , coalescence (physics) , inference , biology , approximate bayesian computation , estimator , population , statistics , confidence interval , mathematics , maximization , algorithm , genetics , computer science , mathematical optimization , gene , artificial intelligence , phylogenetic tree , demography , astrobiology , sociology

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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