A practical genome scan for population-specific strong selective sweeps that have reached fixation

PLoS ONE

Volumn 2, Issue 3, 2007, Pages

  Kimura, Ryosuke ^a,b   Fujimoto, Akihiro ^a   Tokunaga, Katsushi ^a   Ohashi, Jun ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b JAPAN SOCIETY FOR THE PROMOTION OF SCIENCE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; COMPUTER ANALYSIS; COMPUTER SIMULATION; CONTROLLED STUDY; GENE FREQUENCY; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC SELECTION; GENETIC VARIABILITY; GENOME ANALYSIS; HAPLOTYPE; HOMOZYGOSITY; HUMAN; PHENOTYPE; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; BIOLOGICAL MODEL; CHROMOSOME MAP; ETHNIC AND RACIAL GROUPS; GENETICS; HOMOZYGOTE; HUMAN GENOME; MUTATION; PIGMENTATION;

ANIMALS; CHROMOSOME MAPPING; COMPUTER SIMULATION; GENETICS, POPULATION; GENOME, HUMAN; HAPLOTYPES; HOMOZYGOTE; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MUTATION; PIGMENTATION; POPULATION GROUPS; SELECTION, GENETIC;

EID: 55849095847     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000286     Document Type: Article

References (48)

1. Smith JM, Haigh J (1974) The hitch-hiking effect of a favourable gene. Genet Res 23: 23-35.
2. Tishkoff SA, Varkonyi R, Cahinhinan N, Abbes S, Argyropoulos G, et al. (2001) Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293: 455-462.
3. Weir BS, Cockerham CC (1984) Estimating F statistics for the analysis of population structure. Evolution 38: 1358-1370.
4. McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
5. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426.
6. Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, et al. (2003) Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302: 1960-1963.
7. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3: e170.
8. Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, et al. (2005) Natural selection on protein-coding genes in the human genome. Nature 437: 1153-1157.
9. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
10. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133: 693-709.
11. Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
12. Kim Y, Stephan W (2002) Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
13. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12: 1805-1814.
14. Payseur BA, Cutter AD, Nachman MW (2002) Searching for evidence of positive selection in the human genome using patterns of microsatellite variability. Mol Biol Evol 19: 1143-1153.
15. Kayser M, Brauer S, Stoneking M (2003) A genome scan to detect candidate regions influenced by local natural selection in human populations. Mol Biol Evol 20: 893-900.
16. Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, et al. (2004) Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol 2: e286.
17. Storz JF, Payseur BA, Nachman MW (2004) Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa. Mol Biol Evol 21: 1800-1811.
18. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
19. Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, et al. (2005) Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res 15: 1553-1565.
20. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, et al. (2005) Genomic scans for selective sweeps using SNP data. Genome Res 15: 1566-1575.
21. Hanchard NA, Rockett KA, Spencer C, Coop G, Pinder M, et al. (2006) Screening for recently selected alleles by analysis of human haplotype similarity. Am J Hum Genet 78: 153-159.
22. Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4: e72.
23. Wang ET, Kodama G, Baldi P, Moyzis RK (2006) Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci U S A 103: 135-140.
24. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
25. Ohashi J, Naka I, Patarapotikul J, Hananantachai H, Brittenham G, et al. (2004) Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection. Am J Hum Genet 74: 1198-1208.
26. Teshima KM, Coop G, Przeworski M (2006) How reliable are empirical genomic scans for selective sweeps? Genome Res 16: 702-712.
27. Kelley JL, Madeoy J, Calhoun JC, Swanson W, Akey JM (2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Res 16: 980-989.
28. Sabeti PC, Walsh E, Schaffner SF, Varilly P, Fry B, et al. (2005) The case for selection at CCR5-Delta32. PLoS Biol 3: e378.
29. Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, et al. (2005) Calibrating a coalescent simulation of human genome sequence variation. Genome Res 15: 1576-1583.
30. Hamblin MT, Thompson EE, Di Rienzo A (2002) Complex signatures of natural selection at the Duffy blood group locus. Am J Hum Genet 70: 369-383.
31. Yoshiura K, Kinoshita A, Ishida T, Ninokata A, Ishikawa T, et al. (2006) A SNP in the ABCC11 gene is the determinant of human earwax type. Nat Genet 38: 324-330.
32. Lamason RL, Mohideen MA, Mest JR, Wong AC, Norton HL, et al. (2005) SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310: 1782-1786.
33. Soejima M, Tachida H, Ishida T, Sano A, Koda Y (2006) Evidence for recent positive selection at the human AIM1 locus in a European population. Mol Biol Evol 23: 179-188.
34. Stevens J, Plankey MW, Keil JE, Rust PF, Tyroler HA, et al. (1994) Black women have smaller abdominal girths than white women of the same relative weight. J Clin Epidemiol 47: 495-499.
35. Saltin B, Kim CK, Terrados N, Larsen H, Svedenhag J, et al. (1995) Morphology, enzyme activities and buffer capacity in leg muscles of Kenyan and Scandinavian runners. Scand J Med Sci Sports 5: 222-230.
36. Morrison JA, Alfaro MP, Khoury P, Thornton BB, Daniels SR (1996) Determinants of resting energy expenditure in young black girls and young white girls. J Pediatr 129: 637-642.
37. Yanovski JA, Yanovski SZ, Filmer KM, Hubbard VS, Avila N, et al. (1996) Differences in body composition of black and white girls. Am J Clin Nutr 64: 833-839.
38. Ettinger B, Sidney S, Cummings SR, Libanati C, Bikle DD, et al. (1997) Racial differences in bone density between young adult black and white subjects persist after adjustment for anthropometric, lifestyle, and biochemical differences. J Clin Endocrinol Metab 82: 429-434.
39. Hill JO, Sidney S, Lewis CE, Tolan K, Scherzinger AL, et al. (1999) Racial differences in amounts of visceral adipose tissue in young adults: the CARDIA (Coronary Artery Risk Development in Young Adults) study. Am J Clin Nutr 69: 381-387.
40. Harris EF, Hicks JD, Barcroft BD (2001) Tissue contributions to sex and race: differences in tooth crown size of deciduous molars. Am J Phys Anthropol 115: 223-237.
41. Taaffe DR, Cauley JA, Danielson M, Nevitt MC, Lang TF, et al. (2001) Race and sex effects on the association between muscle strength, soft tissue, and bone mineral density in healthy elders: the Health, Aging, and Body Composition Study. J Bone Miner Res 16: 1343-1352.
42. Zhang YY, Liu PY, Lu Y, Davies KM, Dvornyk V, et al. (2005) Race and sex differences and contribution of height: a study on bone size in healthy Caucasians and Chinese. Am J Hum Biol 17: 568-575.
43. Neel JV (1962) Diabetes mellitus: a "thrifty" genotype rendered detrimental by "progress"? Am J Hum Genet 14: 353-362.
44. Innan H, Kim Y (2004) Pattern of polymorphism after strong artificial selection in a domestication event. Proc Natl Acad Sci U S A 101: 10667-10672.
45. Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, et al. (2004) Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet 74: 1111-1120.
46. Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78: 629-644.
47. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, et al. (2005) The effects of artificial selection on the maize genome. Science 308: 1310-1314.
48. Pollinger JP, Bustamante CD, Fledel-Alon A, Schmutz S, Gray MM, et al. (2005) Selective sweep mapping of genes with large phenotypic effects. Genome Res 15: 1809-1819.