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Genetics. Jun 2000; 155(2): 981–987.
PMCID: PMC1461106

Detecting bottlenecks and selective sweeps from DNA sequence polymorphism.

Abstract

A coalescence-based maximum-likelihood method is presented that aims to (i) detect diversity-reducing events in the recent history of a population and (ii) distinguish between demographic (e.g., bottlenecks) and selective causes (selective sweep) of a recent reduction of genetic variability. The former goal is achieved by taking account of the distortion in the shape of gene genealogies generated by diversity-reducing events: gene trees tend to be more star-like than under the standard coalescent. The latter issue is addressed by comparing patterns between loci: demographic events apply to the whole genome whereas selective events affect distinct regions of the genome to a varying extent. The maximum-likelihood approach allows one to estimate the time and strength of diversity-reducing events and to choose among competing hypotheses. An application to sequence data from an African population of Drosophila melanogaster shows that the bottleneck hypothesis is unlikely and that one or several selective sweeps probably occurred in the recent history of this population.

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Selected References

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  • Kuhner MK, Yamato J, Felsenstein J. Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics. 1995 Aug;140(4):1421–1430. [PMC free article] [PubMed]
  • Bénassi V, Depaulis F, Meghlaoui GK, Veuille M. Partial sweeping of variation at the Fbp2 locus in a west African population of Drosophila melanogaster. Mol Biol Evol. 1999 Mar;16(3):347–353. [PubMed]
  • Liu F, Zhang L, Charlesworth D. Genetic diversity in Leavenworthia populations with different inbreeding levels. Proc Biol Sci. 1998 Feb 22;265(1393):293–301. [PMC free article] [PubMed]
  • Maruyama T, Fuerst PA. Population bottlenecks and nonequilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics. 1985 Nov;111(3):675–689. [PMC free article] [PubMed]
  • Cornuet JM, Luikart G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics. 1996 Dec;144(4):2001–2014. [PMC free article] [PubMed]
  • Smith JM, Haigh J. The hitch-hiking effect of a favourable gene. Genet Res. 1974 Feb;23(1):23–35. [PubMed]
  • Depaulis F, Brazier L, Veuille M. Selective sweep at the Drosophila melanogaster Suppressor of Hairless locus and its association with the In(2L)t inversion polymorphism. Genetics. 1999 Jul;152(3):1017–1024. [PMC free article] [PubMed]
  • Rich SM, Licht MC, Hudson RR, Ayala FJ. Malaria's Eve: evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum. Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4425–4430. [PMC free article] [PubMed]
  • Griffiths RC, 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. [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]
  • Griffiths RC, Tavaré S. Unrooted genealogical tree probabilities in the infinitely-many-sites model. Math Biosci. 1995 May;127(1):77–98. [PubMed]
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. [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]
  • Wakeley J, Hey J. Estimating ancestral population parameters. Genetics. 1997 Mar;145(3):847–855. [PMC free article] [PubMed]
  • Wilson IJ, Balding DJ. Genealogical inference from microsatellite data. Genetics. 1998 Sep;150(1):499–510. [PMC free article] [PubMed]
  • Hudson RR, Kreitman M, Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics. 1987 May;116(1):153–159. [PMC free article] [PubMed]

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