• 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. Jul 2002; 161(3): 1209–1218.
PMCID: PMC1462170

Inferences about human demography based on multilocus analyses of noncoding sequences.

Abstract

Data from 10 unlinked autosomal noncoding regions, resequenced in 15 individuals from each of three populations, were used in a multilocus analysis to test models of human demography. Each of the 10 regions consisted of approximately 2500 bp. The multilocus analysis, based on summary statistics (average and variance of Tajima's D and Fu and Li's D*), was used to test a family of models with recent population expansion. The African sample (Hausa of Cameroon) is compatible with a constant population size model and a range of models with recent expansion. For this population sample, we estimated confidence sets that showed the limited range of parameter values compatible with growth. For an exponential growth rate as low as 1 x 10(-3)/generation, population growth is unlikely to have started prior to 50,000 years ago. For higher growth rates, the onset of growth must be more recent. On the basis of the average value of Tajima's D, our sample from an Italian population was found to be incompatible with a constant population size model or any simple expansion model. In the Chinese sample, the variance of Tajima's D was too large to be compatible with the constant population size model or any simple expansion model.

Full Text

The Full Text of this article is available as a PDF (134K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Brookfield JF. Importance of ancestral DNA ages. Nature. 1997 Jul 10;388(6638):134–134. [PubMed]
  • Chen FC, Li WH. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am J Hum Genet. 2001 Feb;68(2):444–456. [PMC free article] [PubMed]
  • Di Rienzo A, Wilson AC. Branching pattern in the evolutionary tree for human mitochondrial DNA. Proc Natl Acad Sci U S A. 1991 Mar 1;88(5):1597–1601. [PMC free article] [PubMed]
  • Di Rienzo A, Donnelly P, Toomajian C, Sisk B, Hill A, Petzl-Erler ML, Haines GK, Barch DH. Heterogeneity of microsatellite mutations within and between loci, and implications for human demographic histories. Genetics. 1998 Mar;148(3):1269–1284. [PMC free article] [PubMed]
  • Fay JC, Wu CI. A human population bottleneck can account for the discordance between patterns of mitochondrial versus nuclear DNA variation. Mol Biol Evol. 1999 Jul;16(7):1003–1005. [PubMed]
  • Fay JC, Wu CI. Hitchhiking under positive Darwinian selection. Genetics. 2000 Jul;155(3):1405–1413. [PMC free article] [PubMed]
  • Frisse L, Hudson RR, Bartoszewicz A, Wall JD, Donfack J, Di Rienzo A. Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am J Hum Genet. 2001 Oct;69(4):831–843. [PMC free article] [PubMed]
  • Fu YX, Li WH. Statistical tests of neutrality of mutations. Genetics. 1993 Mar;133(3):693–709. [PMC free article] [PubMed]
  • Gonser R, Donnelly P, Nicholson G, Di Rienzo A. Microsatellite mutations and inferences about human demography. Genetics. 2000 Apr;154(4):1793–1807. [PMC free article] [PubMed]
  • Weiss G, von Haeseler A. Inference of population history using a likelihood approach. Genetics. 1998 Jul;149(3):1539–1546. [PMC free article] [PubMed]
  • Yu A, Zhao C, Fan Y, Jang W, Mungall AJ, Deloukas P, Olsen A, Doggett NA, Ghebranious N, Broman KW, et al. Comparison of human genetic and sequence-based physical maps. Nature. 2001 Feb 15;409(6822):951–953. [PubMed]
  • Zhivotovsky LA, Bennett L, Bowcock AM, Feldman MW. Human population expansion and microsatellite variation. Mol Biol Evol. 2000 May;17(5):757–767. [PubMed]
  • Ingman M, Kaessmann H, Päbo S, Gyllensten U. Mitochondrial genome variation and the origin of modern humans. Nature. 2000 Dec 7;408(6813):708–713. [PubMed]
  • Jeffreys AJ, Kauppi L, Neumann R. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet. 2001 Oct;29(2):217–222. [PubMed]
  • Kimmel M, Chakraborty R, King JP, Bamshad M, Watkins WS, Jorde LB. Signatures of population expansion in microsatellite repeat data. Genetics. 1998 Apr;148(4):1921–1930. [PMC free article] [PubMed]
  • 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. [PMC free article] [PubMed]
  • Nachman MW, Crowell SL. Estimate of the mutation rate per nucleotide in humans. Genetics. 2000 Sep;156(1):297–304. [PMC free article] [PubMed]
  • Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW. Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol Biol Evol. 1999 Dec;16(12):1791–1798. [PubMed]
  • Przeworski Molly. The signature of positive selection at randomly chosen loci. Genetics. 2002 Mar;160(3):1179–1189. [PMC free article] [PubMed]
  • Przeworski M, Hudson RR, Di Rienzo A. Adjusting the focus on human variation. Trends Genet. 2000 Jul;16(7):296–302. [PubMed]
  • Reich DE, Goldstein DB. Genetic evidence for a Paleolithic human population expansion in Africa. Proc Natl Acad Sci U S A. 1998 Jul 7;95(14):8119–8123. [PMC free article] [PubMed]
  • Reich DE, Lander ES. On the allelic spectrum of human disease. Trends Genet. 2001 Sep;17(9):502–510. [PubMed]
  • Rogers AR, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol. 1992 May;9(3):552–569. [PubMed]
  • Sherry ST, Rogers AR, Harpending H, Soodyall H, Jenkins T, Stoneking M. Mismatch distributions of mtDNA reveal recent human population expansions. Hum Biol. 1994 Oct;66(5):761–775. [PubMed]
  • Simonsen KL, Churchill GA, Aquadro CF. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics. 1995 Sep;141(1):413–429. [PMC free article] [PubMed]
  • Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew A, Han JH, et al. Haplotype variation and linkage disequilibrium in 313 human genes. Science. 2001 Jul 20;293(5529):489–493. [PubMed]
  • Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989 Nov;123(3):585–595. [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]
  • Wall JD, Przeworski M. When did the human population size start increasing? Genetics. 2000 Aug;155(4):1865–1874. [PMC free article] [PubMed]
  • Watson E, Bauer K, Aman R, Weiss G, von Haeseler A, Päbo S. mtDNA sequence diversity in Africa. Am J Hum Genet. 1996 Aug;59(2):437–444. [PMC free article] [PubMed]

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

Formats:

Related citations in PubMed

See reviews...See all...

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...