Power of Neutrality Tests to Detect Bottlenecks and Hitchhiking

Journal of Molecular Evolution

Volumn 57, Issue SUPPL. 1, 2003, Pages

  Depaulis, Frantz ^a,b   Mousset, Sylvain ^a   Veuille, Michel ^a  

^a UPMC University Paris 06   (France)

^b SORBONNE UNIVERSITÉ   (France)

Author keywords

Bottleneck; Coalescence; Haplotype; Hitchhiking; Neutrality tests; Nucleotide polymorphism

Indexed keywords

CONFERENCE PAPER; GENE MUTATION; GENETIC POLYMORPHISM; HAPLOTYPE; MOLECULAR EVOLUTION; STATISTICAL ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; DROSOPHILA; GENETICS, POPULATION; HAPLOTYPES; MODELS, GENETIC; MUTATION; VARIATION (GENETICS);

EID: 0348011482     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-0027-y     Document Type: Conference Paper

References (30)

1. Andolfatto P, Wall JD, Kreitman M (1999) Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster. Genetics 153:1297-1311
2. Barton NH (1998) The effect of hitch-hiking on neutral genealogies. Genet Res 72:123-133
3. Barton NH (2000) Genetic hitchhiking. Philos Trans R Soc Lond B Biol Sci 355:1553-1562
4. Braverman JM, Hudson RR, Kaplan NL, Langley CH, Stephan W (1995) The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140:783-796
5. Depaulis F, Mousset S, Veuille M (2001) Haplotype tests using coalescent simulations conditional on the number of segregating sites. Mol Biol Evol 18:1136-1138
6. Depaulis F, Mousset S, Veuille M (in press) Detecting selective sweeps with haplotype tests. In: Nurminsky D (ed) Selective sweep. Landes Bioscience, Georgetown, USA
7. Depaulis F, Veuille M (1998) Neutrality tests based on the distribution of haplotypes under an infinite-site model. Mol Biol Evol 15:1788-1790
8. Ewens WJ (1972) The sampling theory of selectively neutral alleles. Theor Pop Biol 3:87-112
9. Fay JC, Wu CI (1999) A human population bottleneck can account for the discordance between patterns of mitochondrial versus nuclear DNA variation. Mol Biol Evol 16:1003-1005
10. Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413
11. Felsenstein J (1992) Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genet Res 59:139-147
12. Fu YX (1996) New statistical tests of neutrality for DNA samples from a population. Genetics 143:557-570
13. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915-925
14. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693-709
15. Galtier N, Depaulis F, Barton NH (2000) Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 155:981-987
16. Hudson RR (1993) The how and why of generating gene genealogies. In: Takahata N, Clarck AG (eds) Mechanism of molecular evolution. Japan Scientific Societies Press, Sinauer Associates, Inc., Sunderland, MA, pp 23-36
17. Hudson RR, Bailey K. Skarecky D, Kwiatowski J, Ayala FJ (1994) Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136:1329-1340
18. Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147-164
19. Hudson RR, Kreitman M, Aguadé M (1987) A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159
20. Kelly JK (1997) A test of neutrality based on interlocus associations. Genetics 146:1197-1206
21. Nordborg M, Tavaré S (2002) Linkage disequilibrium: What history has to tell us. Trends Genet 18:83-90
22. Przeworski M (2002) The signature of positive selection at randomly chosen loci. Genetics 160:1179-1189
23. Schierup MH, Hein J (2000) Recombination and the molecular clock. Mol Biol Evol 17:1578-1789
24. Stephan W, Wiehe THE, Lenz MW (1992) The effect of strongly selected substitutions on neutral polymorphism: Analytical results based on diffusion theory. Theor Popul Biol 41:237-254
25. Strobeck C (1987) Average number of nucleotide differences in a sample from a single subpopulation: A test for population subdivision. Genetics 117:149-154
26. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595
27. Wall JD (1999) Recombination and the power of statistical tests of neutrality. Genet Res 74:65-69
28. Wall JD (2000) A comparison of estimators of the population recombination rate. Mol Biol Evol 17:156-163
29. Wall JD, Hudson RR (2001) Coalescent simulations and statistical tests of neutrality. Mol Biol Evol 18:1134-1135
30. Watterson GA (1975) On the number of segregation sites. Theoret Popul Biol 7:256-276