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Genetics. May 2002; 161(1): 447–459.
PMCID: PMC1462078

Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition.

Abstract

This article proposes a method of estimating the time to the most recent common ancestor (TMRCA) of a sample of DNA sequences. The method is based on the molecular clock hypothesis, but avoids assumptions about population structure. Simulations show that in a wide range of situations, the point estimate has small bias and the confidence interval has at least the nominal coverage probability. We discuss conditions that can lead to biased estimates. Performance of this estimator is compared with existing methods based on the coalescence theory. The method is applied to sequences of Y chromosomes and mtDNAs to estimate the coalescent times of human male and female populations.

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Selected References

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  • Ruvolo M. A new approach to studying modern human origins: hypothesis testing with coalescence time distributions. Mol Phylogenet Evol. 1996 Feb;5(1):202–219. [PubMed]
  • Stumpf MP, Goldstein DB. Genealogical and evolutionary inference with the human Y chromosome. Science. 2001 Mar 2;291(5509):1738–1742. [PubMed]
  • Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics. 1983 Oct;105(2):437–460. [PMC free article] [PubMed]
  • Beerli P, Felsenstein J. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics. 1999 Jun;152(2):763–773. [PMC free article] [PubMed]
  • Takahata N, Lee SH, Satta Y. Testing multiregionality of modern human origins. Mol Biol Evol. 2001 Feb;18(2):172–183. [PubMed]
  • Tavaré S, Balding DJ, Griffiths RC, Donnelly P. Inferring coalescence times from DNA sequence data. Genetics. 1997 Feb;145(2):505–518. [PMC free article] [PubMed]
  • Templeton AR, Weiss KM, Nickerson DA, Boerwinkle E, Sing CF. Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies. Genetics. 2000 Nov;156(3):1259–1275. [PMC free article] [PubMed]
  • Thomson R, Pritchard JK, Shen P, Oefner PJ, Feldman MW. Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7360–7365. [PMC free article] [PubMed]
  • Kuhner MK, Yamato J, Felsenstein J. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics. 1998 May;149(1):429–434. [PMC free article] [PubMed]
  • Tremblay M, Vézina H. New estimates of intergenerational time intervals for the calculation of age and origins of mutations. Am J Hum Genet. 2000 Feb;66(2):651–658. [PMC free article] [PubMed]
  • Kuhner MK, Yamato J, Felsenstein J. Maximum likelihood estimation of recombination rates from population data. Genetics. 2000 Nov;156(3):1393–1401. [PMC free article] [PubMed]
  • Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonné-Tamir B, Bertranpetit J, Francalacci P, et al. Y chromosome sequence variation and the history of human populations. Nat Genet. 2000 Nov;26(3):358–361. [PubMed]

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