• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Aug 2003; 164(4): 1645–1656.
PMCID: PMC1462670

Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.

Abstract

The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be approximately 20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

Full Text

The Full Text of this article is available as a PDF (208K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Kaessmann H, Wiebe V, Weiss G, Päbo S. Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat Genet. 2001 Feb;27(2):155–156. [PubMed]
  • Makova KD, Ramsay M, Jenkins T, Li WH. Human DNA sequence variation in a 6.6-kb region containing the melanocortin 1 receptor promoter. Genetics. 2001 Jul;158(3):1253–1268. [PMC free article] [PubMed]
  • Nielsen R, Wakeley J. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics. 2001 Jun;158(2):885–896. [PMC free article] [PubMed]
  • Ruvolo M. Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets. Mol Biol Evol. 1997 Mar;14(3):248–265. [PubMed]
  • Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics. 1983 Oct;105(2):437–460. [PMC free article] [PubMed]
  • Takahata N, Satta Y, Klein J. Divergence time and population size in the lineage leading to modern humans. Theor Popul Biol. 1995 Oct;48(2):198–221. [PubMed]
  • Bahlo M, Griffiths RC. Inference from gene trees in a subdivided population. Theor Popul Biol. 2000 Mar;57(2):79–95. [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]
  • Wilson IJ, Balding DJ. Genealogical inference from microsatellite data. Genetics. 1998 Sep;150(1):499–510. [PMC free article] [PubMed]
  • Brunet Michel, Guy Franck, Pilbeam David, Mackaye Hassane Taisso, Likius Andossa, Ahounta Djimdoumalbaye, Beauvilain Alain, Blondel Cécile, Bocherens Hervé, Boisserie Jean-Renaud, et al. A new hominid from the Upper Miocene of Chad, Central Africa. Nature. 2002 Jul 11;418(6894):145–151. [PubMed]
  • Wu CI. Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics. 1991 Feb;127(2):429–435. [PMC free article] [PubMed]
  • Yang Z. On the estimation of ancestral population sizes of modern humans. Genet Res. 1997 Apr;69(2):111–116. [PubMed]
  • Yang Z. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. J Mol Evol. 2000 Nov;51(5):423–432. [PubMed]
  • Edwards SV, Beerli P. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution. 2000 Dec;54(6):1839–1854. [PubMed]
  • Yang Ziheng. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics. 2002 Dec;162(4):1811–1823. [PMC free article] [PubMed]
  • Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17(6):368–376. [PubMed]
  • Yu N, Zhao Z, Fu YX, Sambuughin N, Ramsay M, Jenkins T, Leskinen E, Patthy L, Jorde LB, Kuromori T, et al. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol Biol Evol. 2001 Feb;18(2):214–222. [PubMed]
  • Zhao Z, Jin L, Fu YX, Ramsay M, Jenkins T, Leskinen E, Pamilo P, Trexler M, Patthy L, Jorde LB, et al. Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proc Natl Acad Sci U S A. 2000 Oct 10;97(21):11354–11358. [PMC free article] [PubMed]
  • Fu YX. Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences. Genetics. 1994 Dec;138(4):1375–1386. [PMC free article] [PubMed]
  • Hacia JG. Genome of the apes. Trends Genet. 2001 Nov;17(11):637–645. [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America

Formats:

Cited by other articles in PMC

See all...

Links

  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...