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. 1998 Jul;149(3):1539–1546. doi: 10.1093/genetics/149.3.1539

Inference of population history using a likelihood approach.

G Weiss 1, A von Haeseler 1
PMCID: PMC1460236  PMID: 9649540

Abstract

We introduce an approach to revealing the likelihood of different population histories that utilizes an explicit model of sequence evolution for the DNA segment under study. Based on a phylogenetic tree reconstruction method we show that a Tamura-Nei model with heterogeneous mutation rates is a fair description of the evolutionary process of the hypervariable region I of the mitochondrial DNA from humans. Assuming this complex model still allows the estimation of population history parameters, we suggest a likelihood approach to conducting statistical inference within a class of expansion models. More precisely, the likelihood of the data is based on the mean pairwise differences between DNA sequences and the number of variable sites in a sample. The use of likelihood ratios enables comparison of different hypotheses about population history, such as constant population size during the past or an increase or decrease of population size starting at some point back in time. This method was applied to show that the population of the Basques has expanded, whereas that of the Biaka pygmies is most likely decreasing. The Nuu-Chah-Nulth data are consistent with a model of constant population.

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Selected References

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  1. Anderson S., Bankier A. T., Barrell B. G., de Bruijn M. H., Coulson A. R., Drouin J., Eperon I. C., Nierlich D. P., Roe B. A., Sanger F. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. doi: 10.1038/290457a0. [DOI] [PubMed] [Google Scholar]
  2. Aris-Brosou S., Excoffier L. The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Mol Biol Evol. 1996 Mar;13(3):494–504. doi: 10.1093/oxfordjournals.molbev.a025610. [DOI] [PubMed] [Google Scholar]
  3. Bandelt H. J., Forster P., Sykes B. C., Richards M. B. Mitochondrial portraits of human populations using median networks. Genetics. 1995 Oct;141(2):743–753. doi: 10.1093/genetics/141.2.743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bertorelle G., Slatkin M. The number of segregating sites in expanding human populations, with implications for estimates of demographic parameters. Mol Biol Evol. 1995 Sep;12(5):887–892. doi: 10.1093/oxfordjournals.molbev.a040265. [DOI] [PubMed] [Google Scholar]
  5. Bertranpetit J., Sala J., Calafell F., Underhill P. A., Moral P., Comas D. Human mitochondrial DNA variation and the origin of Basques. Ann Hum Genet. 1995 Jan;59(Pt 1):63–81. doi: 10.1111/j.1469-1809.1995.tb01606.x. [DOI] [PubMed] [Google Scholar]
  6. Donnelly P., Tavaré S. Coalescents and genealogical structure under neutrality. Annu Rev Genet. 1995;29:401–421. doi: 10.1146/annurev.ge.29.120195.002153. [DOI] [PubMed] [Google Scholar]
  7. Fu Y. X. New statistical tests of neutrality for DNA samples from a population. Genetics. 1996 May;143(1):557–570. doi: 10.1093/genetics/143.1.557. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Goldman N. Statistical tests of models of DNA substitution. J Mol Evol. 1993 Feb;36(2):182–198. doi: 10.1007/BF00166252. [DOI] [PubMed] [Google Scholar]
  9. Griffiths R. C., Tavaré S. Sampling theory for neutral alleles in a varying environment. Philos Trans R Soc Lond B Biol Sci. 1994 Jun 29;344(1310):403–410. doi: 10.1098/rstb.1994.0079. [DOI] [PubMed] [Google Scholar]
  10. Handt O., Meyer S., von Haeseler A. Compilation of human mtDNA control region sequences. Nucleic Acids Res. 1998 Jan 1;26(1):126–129. doi: 10.1093/nar/26.1.126. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hasegawa M., Di Rienzo A., Kocher T. D., Wilson A. C. Toward a more accurate time scale for the human mitochondrial DNA tree. J Mol Evol. 1993 Oct;37(4):347–354. doi: 10.1007/BF00178865. [DOI] [PubMed] [Google Scholar]
  12. Hasegawa M., Kishino H., Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985;22(2):160–174. doi: 10.1007/BF02101694. [DOI] [PubMed] [Google Scholar]
  13. Horai S., Hayasaka K. Intraspecific nucleotide sequence differences in the major noncoding region of human mitochondrial DNA. Am J Hum Genet. 1990 Apr;46(4):828–842. [PMC free article] [PubMed] [Google Scholar]
  14. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980 Dec;16(2):111–120. doi: 10.1007/BF01731581. [DOI] [PubMed] [Google Scholar]
  15. Lundstrom R., Tavaré S., Ward R. H. Estimating substitution rates from molecular data using the coalescent. Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5961–5965. doi: 10.1073/pnas.89.13.5961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lundstrom R., Tavaré S., Ward R. H. Modeling the evolution of the human mitochondrial genome. Math Biosci. 1992 Dec;112(2):319–335. doi: 10.1016/0025-5564(92)90030-z. [DOI] [PubMed] [Google Scholar]
  17. Marjoram P., Donnelly P. Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution. Genetics. 1994 Feb;136(2):673–683. doi: 10.1093/genetics/136.2.673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Rambaut A., Grassly N. C. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 1997 Jun;13(3):235–238. doi: 10.1093/bioinformatics/13.3.235. [DOI] [PubMed] [Google Scholar]
  19. Rogers A. R., Fraley A. E., Bamshad M. J., Watkins W. S., Jorde L. B. Mitochondrial mismatch analysis is insensitive to the mutational process. Mol Biol Evol. 1996 Sep;13(7):895–902. doi: 10.1093/molbev/13.7.895. [DOI] [PubMed] [Google Scholar]
  20. Rogers A. R., Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol. 1992 May;9(3):552–569. doi: 10.1093/oxfordjournals.molbev.a040727. [DOI] [PubMed] [Google Scholar]
  21. Rogers A. Error introduced by the infinite-site model. Mol Biol Evol. 1992 Nov;9(6):1181–1184. doi: 10.1093/oxfordjournals.molbev.a040787. [DOI] [PubMed] [Google Scholar]
  22. Slatkin M., Hudson R. R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 1991 Oct;129(2):555–562. doi: 10.1093/genetics/129.2.555. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics. 1983 Oct;105(2):437–460. doi: 10.1093/genetics/105.2.437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989 Nov;123(3):585–595. doi: 10.1093/genetics/123.3.585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Tajima F. The amount of DNA polymorphism maintained in a finite population when the neutral mutation rate varies among sites. Genetics. 1996 Jul;143(3):1457–1465. doi: 10.1093/genetics/143.3.1457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993 May;10(3):512–526. doi: 10.1093/oxfordjournals.molbev.a040023. [DOI] [PubMed] [Google Scholar]
  27. Tavaré S., Balding D. J., Griffiths R. C., Donnelly P. Inferring coalescence times from DNA sequence data. Genetics. 1997 Feb;145(2):505–518. doi: 10.1093/genetics/145.2.505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Tavaré S. Line-of-descent and genealogical processes, and their applications in population genetics models. Theor Popul Biol. 1984 Oct;26(2):119–164. doi: 10.1016/0040-5809(84)90027-3. [DOI] [PubMed] [Google Scholar]
  29. Uzzell T., Corbin K. W. Fitting discrete probability distributions to evolutionary events. Science. 1971 Jun 11;172(3988):1089–1096. doi: 10.1126/science.172.3988.1089. [DOI] [PubMed] [Google Scholar]
  30. Vigilant L., Stoneking M., Harpending H., Hawkes K., Wilson A. C. African populations and the evolution of human mitochondrial DNA. Science. 1991 Sep 27;253(5027):1503–1507. doi: 10.1126/science.1840702. [DOI] [PubMed] [Google Scholar]
  31. Wakeley J., Hey J. Estimating ancestral population parameters. Genetics. 1997 Mar;145(3):847–855. doi: 10.1093/genetics/145.3.847. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Wakeley J. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J Mol Evol. 1993 Dec;37(6):613–623. doi: 10.1007/BF00182747. [DOI] [PubMed] [Google Scholar]
  33. Ward R. H., Frazier B. L., Dew-Jager K., Päbo S. Extensive mitochondrial diversity within a single Amerindian tribe. Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8720–8724. doi: 10.1073/pnas.88.19.8720. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Watterson G. A. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 1975 Apr;7(2):256–276. doi: 10.1016/0040-5809(75)90020-9. [DOI] [PubMed] [Google Scholar]
  35. Wright S. Evolution in Mendelian Populations. Genetics. 1931 Mar;16(2):97–159. doi: 10.1093/genetics/16.2.97. [DOI] [PMC free article] [PubMed] [Google Scholar]

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