Detecting bottlenecks and selective sweeps from DNA sequence polymorphism

Genetics

Volumn 155, Issue 2, 2000, Pages 981-987

  Galtier, Nicolas ^a,b   Depaulis, Frantz ^a   Barton, Nicholas H ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIV MONTPELLIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME INVERSION; DEMOGRAPHY; DNA POLYMORPHISM; DNA SEQUENCE; DROSOPHILA MELANOGASTER; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL;

DNA; LIKELIHOOD FUNCTIONS; POLYMORPHISM, GENETIC; REPRODUCIBILITY OF RESULTS;

EID: 0034086970     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (29)

1. BARTON, N. H., 1998 The effect of hitch-hiking on neutral genealogies. Genet. Res. 72: 123-133.
2. BENASSI, V., F. DEPAULIS, G. K. MEGHLAOUI and M. VEUILLE, 1999 Partial sweeping of variation at the Fbp2 locus in a West-African population of Drosophila melanogaster. Mol. Biol. Evol. 16: 347-353.
3. CHARLESWORTH, D., and B. CHARLESWORTH, 1995 Quantitative genetics in plants: the effect of breeding systems on genetic variability. Evolution 49: 911-920.
4. CHARLESWORTH, B., D. CHARLESWORTH and M. T. MORGAN, 1995 The pattern of neutral molecular variation under the background selection model. Genetics 141: 1619-1632.
5. CORNUET, J. M., and G. LUIKART, 1996 Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014.
6. DEPAULIS, F., 1998 Auto-stop en liaison aux inversions chromosomiques chez Drosophila melanogaster. Ph.D. thesis, Université Paris 6, France.
7. DEPAULIS, F., L. BRAZIER and M. VEUILLE, 1999 Selective sweep at the Drosophila melanogaster Suppressor of Hairless locus and its association with the In(2L)t inversion polymorphism. Genetics 152: 1017-1024.
8. GILLESPIE, J. H., 1991 The Causes of Molecular Evolution. Oxford University Press, Oxford.
9. GRIFFITHS, R. C., and S. TAVARE, 1994a Simulating probability distributions in the coalescent. Theor. Popul. Biol. 46: 131-159.
10. GRIFFITHS, R. C., and S. TAVARE, 1994b Sampling theory for neutral alleles in a varying environment. Philos. Trans. R. Soc. Lond. B Biol. Sci. 344: 403-410.
11. GRIFFITHS, R. C., and S. TAVARE, 1995 Unrooted genealogical tree probabilities in the infinitely-many-sites model. Math. Biosci. 127: 77-98.
12. HASTINGS, W. K., 1970 Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109.
13. HUDSON, R. R., 1991 Gene genealogies and the coalescent process, pp. 1-14 in Oxford Surveys in Evolutionary Biology, Vol. 7, edited by D. FUTUYMA and J. ANTONOVICS. Oxford University Press, London.
14. HUDSON, R. R., M. KREITMAN and M. AGUADE, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
15. KINGMAN, J. F. C., 1982 The coalescent. Stoch. Proc. Appl. 13: 235-218.
16. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 1995 Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.
17. LI, W. H., 1993 So, what about the molecular clock hypothesis? Curr. Opin. Genet. Dev. 3: 896-901.
18. LIU, F., L. ZHANG and D. CHARLESWORTH, 1998 Genetic diversity in Leavenworthia populations with different inbreeding levels. Proc. R. Soc. Lond. Ser. B. 265: 293-301.
19. MARUYAMA, T., and P. A. FUERST, 1985 Population bottlenecks and non-equilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics 111: 675-689.
20. MAYNARD-SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
21. NIELSEN, R., 1998 Maximum likelihood estimation of population divergence times and population phytogenies under the infinite sites model. Theor. Popul. Biol. 53: 143-151.
22. O'BRIEN, S. J., and J. F. EVERMANN, 1988 Interactive influence of infectious disease and genetic diversity in natural populations. Trends Ecol. Evol. 3: 254-259.
23. PRESS, W. H., S. A. TEUKOLSKY, W. T. VETTERLING and B. P. FLANNERY, 1992 Numerical Recipes in C, Ed. 2. Cambridge University Press, Cambridge, United Kingdom.
24. RICH, S. M., M. C. LIGHT, R. R. HUDSON and F. J. AYALA, 1998 Malaria's Eve: evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum. Proc. Natl. Acad. Sci. USA 95: 4425-4430.
25. ROGERS, A. R., and H. HARPENDING, 1992 Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9: 552-569.
26. SATTOU, N., and M. NEI, 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
27. TAJIMA, F., 1989 Statistical methods for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
28. WAKELEY, J., and J. HEY, 1997 Estimating ancestral population parameters. Genetics 145: 847-855.
29. WILSON, I. J., and D. J. BALDING, 1998 Genealogical inference from microsatellite data. Genetics 150: 499-510.