Skip to main content
PMC home page
Genetics logoLink to Genetics
. 1998 Apr;148(4):1921–1930. doi: 10.1093/genetics/148.4.1921

Signatures of population expansion in microsatellite repeat data.

M Kimmel 1, R Chakraborty 1, J P King 1, M Bamshad 1, W S Watkins 1, L B Jorde 1
PMCID: PMC1460085  PMID: 9560405

Abstract

To examine the signature of population expansion on genetic variability at microsatellite loci, we consider a population that evolves according to the time-continuous Moran model, with growing population size and mutations that follow a general asymmetric stepwise mutation model. We present calculations of expected allele-size variance and homozygosity at a locus in such a model for several variants of growth, including stepwise, exponential, and logistic growth. These calculations in particular prove that population bottleneck followed by growth in size causes an imbalance between allele size variance and heterozygosity, characterized by the variance being transiently higher than expected under equilibrium conditions. This effect is, in a sense, analogous to that demonstrated before for the infinite allele model, where the number of alleles transiently increases after a stepwise growth of population. We analyze a set of data on tetranucleotide repeats that reveals the imbalance expected under the assumption of bottleneck followed by population growth in two out of three major racial groups. The imbalance is strongest in Asians, intermediate in Europeans, and absent in Africans. This finding is consistent with previous findings by others concerning the population expansion of modern humans, with the bottleneck event being most ancient in Africans, most recent in Asians, and intermediate in Europeans. Nevertheless, the imbalance index alone cannot reliably estimate the time of initiation of population expansion.

Full Text

The Full Text of this article is available as a PDF (223.1 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. 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]
  2. Bowcock A. M., Ruiz-Linares A., Tomfohrde J., Minch E., Kidd J. R., Cavalli-Sforza L. L. High resolution of human evolutionary trees with polymorphic microsatellites. Nature. 1994 Mar 31;368(6470):455–457. doi: 10.1038/368455a0. [DOI] [PubMed] [Google Scholar]
  3. Cann R. L., Stoneking M., Wilson A. C. Mitochondrial DNA and human evolution. Nature. 1987 Jan 1;325(6099):31–36. doi: 10.1038/325031a0. [DOI] [PubMed] [Google Scholar]
  4. Chakraborty R., Jin L. Determination of relatedness between individuals using DNA fingerprinting. Hum Biol. 1993 Dec;65(6):875–895. [PubMed] [Google Scholar]
  5. Chakraborty R., Kimmel M., Stivers D. N., Davison L. J., Deka R. Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):1041–1046. doi: 10.1073/pnas.94.3.1041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Deka R., Shriver M. D., Yu L. M., Ferrell R. E., Chakraborty R. Intra- and inter-population diversity at short tandem repeat loci in diverse populations of the world. Electrophoresis. 1995 Sep;16(9):1659–1664. doi: 10.1002/elps.11501601275. [DOI] [PubMed] [Google Scholar]
  7. Di Rienzo A., Peterson A. C., Garza J. C., Valdes A. M., Slatkin M., Freimer N. B. Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3166–3170. doi: 10.1073/pnas.91.8.3166. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Di Rienzo A., Wilson A. C. Branching pattern in the evolutionary tree for human mitochondrial DNA. Proc Natl Acad Sci U S A. 1991 Mar 1;88(5):1597–1601. doi: 10.1073/pnas.88.5.1597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gilbert D. A., Lehman N., O'Brien S. J., Wayne R. K. Genetic fingerprinting reflects population differentiation in the California Channel Island fox. Nature. 1990 Apr 19;344(6268):764–767. doi: 10.1038/344764a0. [DOI] [PubMed] [Google Scholar]
  10. Goldstein D. B., Ruiz Linares A., Cavalli-Sforza L. L., Feldman M. W. An evaluation of genetic distances for use with microsatellite loci. Genetics. 1995 Jan;139(1):463–471. doi: 10.1093/genetics/139.1.463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gyapay G., Morissette J., Vignal A., Dib C., Fizames C., Millasseau P., Marc S., Bernardi G., Lathrop M., Weissenbach J. The 1993-94 Généthon human genetic linkage map. Nat Genet. 1994 Jun;7(2 Spec No):246–339. doi: 10.1038/ng0694supp-246. [DOI] [PubMed] [Google Scholar]
  12. Hanis C. L., Boerwinkle E., Chakraborty R., Ellsworth D. L., Concannon P., Stirling B., Morrison V. A., Wapelhorst B., Spielman R. S., Gogolin-Ewens K. J. A genome-wide search for human non-insulin-dependent (type 2) diabetes genes reveals a major susceptibility locus on chromosome 2. Nat Genet. 1996 Jun;13(2):161–166. doi: 10.1038/ng0696-161. [DOI] [PubMed] [Google Scholar]
  13. Jeffreys A. J., Tamaki K., MacLeod A., Monckton D. G., Neil D. L., Armour J. A. Complex gene conversion events in germline mutation at human minisatellites. Nat Genet. 1994 Feb;6(2):136–145. doi: 10.1038/ng0294-136. [DOI] [PubMed] [Google Scholar]
  14. Jin L., Macaubas C., Hallmayer J., Kimura A., Mignot E. Mutation rate varies among alleles at a microsatellite locus: phylogenetic evidence. Proc Natl Acad Sci U S A. 1996 Dec 24;93(26):15285–15288. doi: 10.1073/pnas.93.26.15285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Jorde L. B., Bamshad M. J., Watkins W. S., Zenger R., Fraley A. E., Krakowiak P. A., Carpenter K. D., Soodyall H., Jenkins T., Rogers A. R. Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data. Am J Hum Genet. 1995 Sep;57(3):523–538. doi: 10.1002/ajmg.1320570340. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Jorde L. B., Rogers A. R., Bamshad M., Watkins W. S., Krakowiak P., Sung S., Kere J., Harpending H. C. Microsatellite diversity and the demographic history of modern humans. Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):3100–3103. doi: 10.1073/pnas.94.7.3100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kimmel M., Chakraborty R. Measures of variation at DNA repeat loci under a general stepwise mutation model. Theor Popul Biol. 1996 Dec;50(3):345–367. doi: 10.1006/tpbi.1996.0035. [DOI] [PubMed] [Google Scholar]
  18. Kimmel M., Chakraborty R., Stivers D. N., Deka R. Dynamics of repeat polymorphisms under a forward-backward mutation model: within- and between-population variability at microsatellite loci. Genetics. 1996 May;143(1):549–555. doi: 10.1093/genetics/143.1.549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lin Z., Cui X., Li H. Multiplex genotype determination at a large number of gene loci. Proc Natl Acad Sci U S A. 1996 Mar 19;93(6):2582–2587. doi: 10.1073/pnas.93.6.2582. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Matise T. C., Perlin M., Chakravarti A. Automated construction of genetic linkage maps using an expert system (MultiMap): a human genome linkage map. Nat Genet. 1994 Apr;6(4):384–390. doi: 10.1038/ng0494-384. [DOI] [PubMed] [Google Scholar]
  21. Nei M., Tajima F., Tateno Y. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol. 1983;19(2):153–170. doi: 10.1007/BF02300753. [DOI] [PubMed] [Google Scholar]
  22. Ohta T., Kimura M. A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res. 1973 Oct;22(2):201–204. doi: 10.1017/s0016672300012994. [DOI] [PubMed] [Google Scholar]
  23. Pena S. D., Chakraborty R. Paternity testing in the DNA era. Trends Genet. 1994 Jun;10(6):204–209. doi: 10.1016/0168-9525(94)90257-7. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Slatkin M. A measure of population subdivision based on microsatellite allele frequencies. Genetics. 1995 Jan;139(1):457–462. doi: 10.1093/genetics/139.1.457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Tautz D. Notes on the definition and nomenclature of tandemly repetitive DNA sequences. EXS. 1993;67:21–28. doi: 10.1007/978-3-0348-8583-6_2. [DOI] [PubMed] [Google Scholar]
  27. Weber J. L. Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics. 1990 Aug;7(4):524–530. doi: 10.1016/0888-7543(90)90195-z. [DOI] [PubMed] [Google Scholar]
  28. Weber J. L., Wong C. Mutation of human short tandem repeats. Hum Mol Genet. 1993 Aug;2(8):1123–1128. doi: 10.1093/hmg/2.8.1123. [DOI] [PubMed] [Google Scholar]
  29. Wehrhahn C. F. The evolution of selectively similar electrophoretically detectable alleles in finite natural populations. Genetics. 1975 Jun;80(2):375–394. doi: 10.1093/genetics/80.2.375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Weissenbach J., Gyapay G., Dib C., Vignal A., Morissette J., Millasseau P., Vaysseix G., Lathrop M. A second-generation linkage map of the human genome. Nature. 1992 Oct 29;359(6398):794–801. doi: 10.1038/359794a0. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES