Maximum-Likelihood Estimation of Coalescence Times in Genealogical Trees
Open Access
- 1 December 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in Genetics
- Vol. 171 (4) , 2073-2084
- https://doi.org/10.1534/genetics.105.043067
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.Keywords
This publication has 16 references indexed in Scilit:
- Importance sampling on coalescent histories. II: Subdivided population modelsAdvances in Applied Probability, 2004
- Genealogical and Evolutionary Inference with the Human Y ChromosomeScience, 2001
- The age of a mutation in a general coalescent treeCommunications in Statistics. Stochastic Models, 1998
- Ancestral Inference in Population GeneticsStatistical Science, 1994
- The “Eve” Hypotheses: A Genetic Critique and ReanalysisAmerican Anthropologist, 1993
- Efficient algorithms for inferring evolutionary treesNetworks, 1991
- The coalescentStochastic Processes and their Applications, 1982
- Evolutionary trees from DNA sequences: A maximum likelihood approachJournal of Molecular Evolution, 1981
- Evolution of Protein MoleculesPublished by Elsevier ,1969
- Error bounds for convolutional codes and an asymptotically optimum decoding algorithmIEEE Transactions on Information Theory, 1967