Genomic signatures of positive selection in humans and the limits of outlier approaches

Genome Research

Volumn 16, Issue 8, 2006, Pages 980-989

  Kelley, Joanna L ^a   Madeoy, Jennifer ^a   Calhoun, John C ^a   Swanson, Willie ^a   Akey, Joshua M ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE CLUSTER; GENE LOCUS; GENETIC SELECTION; GENETIC VARIABILITY; GENOMICS; GENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

GENOME, HUMAN; HUMANS; MULTIGENE FAMILY; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION (GENETICS);

EID: 33746693757     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.5157306     Document Type: Article

References (52)

1. Akey, J.M., Zhang, G., Zhang, K., Jin, L., and Shriver, M.D. 2002. Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12: 1805-1814.
2. Akey, J.M., Zhang, K., Xiong, M., and Jin, L. 2003. The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. Mol. Biol. Evol. 20: 232-242.
3. Akey, J.M., Eberle, M.A., Rieder, M.J., Carlson, C.S., Shriver, M.D., Nickerson, D.A., and Kruglyak, L. 2004. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol. 2: e286.
4. Andolfatto, P. 2001. Adaptive hitchhiking effects on genome variability. Curr. Opin. Genet. Dev. 11: 635-641.
5. Bamshad, M. and Wooding, S.P. 2003. Signatures of natural selection in the human genome. Nat. Rev. Genet. 4: 99-111.
6. Bersaglieri, T., Sabeti, P.C., Patterson, N., Vanderploeg, T., Schaffner, S.F., Drake, J.A., Rhodes, M., Reich, D.E., and Hirschhorn, J.N. 2004. Genetic signatures of strong recent positive selection at the lactase gene. Am. J. Hum. Genet. 74: 1111-1120.
7. Bowcock, A.M., Kidd, J.R., Mountain, J.L., Hebert, J.M., Carotenuto, L., Kidd, K.K., and Cavalli-Sforza, L.L. 1991. Drift, admixture, and selection in human evolution: A study with DNA polymorphisms. Proc. Natl. Acad. Sci. 88: 839-843.
8. Bustamante, C.D., Fledel-Alon, A., Williamson, S., Nielsen, R., Hubisz, M.T., Glanowski, S., Tanenbaum, D.M., White, T.J., Sninsky, J.J., Hernandez, R.D., et al. 2005. Natural selection on protein-coding genes in the human genome. Nature 437: 1153-1157.
9. Carlson, C.S., Thomas, D.J., Eberle, M.A., Swanson, J.E., Livingston, R.J., Rieder, M.J., and Nickerson, D.A. 2005. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res. 15: 1553-1565.
10. Cavalli-Sforza, L.L. 1966. Population structure and human evolution. Proc. R. Soc. Lond. B. 164: 362-379.
11. Clark, A.G., Glanowski, S., Nielsen, R., Thomas, P.D., Kejariwal, A., Todd, M.A., Tanenbaum, D.M., Civello, D., Lu, F., Murphy, B., et al. 2003. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302: 1960-1963.
12. Clark, A.G., Hubisz, M.J., Bustamante, C.D., Williamson, S.H., and Nielsen, R. 2005. Ascertainment bias in studies of human genome-wide polymorphism. Genome Res. 15: 1496-1502.
13. Fullerton, S.M., Bartoszewicz, A., Ybazeta, G., Horikawa, Y., Bell, G.I., Kidd, K.K., Cox, N.J., Hudson, R.R., and Di Rienzo, A. 2002. Geographic and haplotype structure of candidate type 2 diabetes susceptibility variants at the calpain-10 locus. Am. J. Hum. Genet. 70: 1096-1106.
14. Hamblin, M.T., Thompson, E.E., and Di Rienzo, A. 2002. Complex signatures of natural selection at the Duffy blood group locus. Am. J. Hum. Genet. 70: 369-383.
15. Hinds, D.A., Stuve, L.L., Nilsen, G.B., Halperin, E., Eskin, E., Ballinger, D.G., Frazer, K.A., and Cox, D.R. 2005. Whole-genome patterns of common DNA variation in three human populations. Science 307: 1072-1079.
16. Hirotsune, S., Yoshida, N., Chen, A., Garrett, L., Sugiyama, F., Takahashi, S., Yagami, K., Wynshaw-Boris, A., and Yoshiki, A. 2003. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423: 91-96.
17. Hollox, E.J., Poulter, M., Zvarik, M., Ferak, V., Krause, A., Jenkins, T., Saha, N., Kozlov, A.I., and Swallow, D.M. 2001. Lactase haplotype diversity in the Old World. Am. J. Hum. Genet. 68: 160-172.
18. Hudson, R.R. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
19. The International HapMap Consortium. 2005. A haplotype map of the human genome. Nature 437: 1299-1320.
20. Jeffs, P.S., Holmes, E.C., and Ashburner, M. 1994. The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup. Mol. Biol. Evol. 11: 287-304.
21. Kaplan, N.L., Hudson, R.R., and Langley, C.H. 1989. The "hitchhiking effect" revisited. Genetics 123: 887-899.
22. Kayser, M., Brauer, S., and Stoneking, M. 2003. A genome scan to detect candidate regions influenced by local natural selection in human populations. Mol. Biol. Evol. 20: 893-900.
23. Kong, A., Gudbjartsson, D.F., Sainz, J., Jonsdottir, G.M., Gudjonsson, S.A., Richardsson, B., Sigurdardottir, S., Barnard, J., Hallbeck, B., Masson, G., et al. 2002. A high-resolution recombination map of the human genome. Nat. Genet. 31: 241-247.
24. Lewontin, R.C. and Krakauer, J. 1973. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195.
25. Maynard Smith, J. and Haigh, J. 1974. The hitch-hiking effect of a favourable Ωgene. Genet. Res. 23: 23-35.
26. Nakajima, T., Wooding, S., Sakagami, T., Emi, M., Tokunaga, K., Tamiya, G., Ishigami, T., Umemura, S., Munkhbat, B., Jin, F., et al. 2004. Natural selection and population history in the human angiotensinogen gene (AGT): 736 complete AGT sequences in chromosomes from around the world. Am. J. Hum. Genet. 74: 898-916.
27. Neel, J.V. 1962. Diabetes mellitus: A "thrifty" genotype rendered detrimental by "progress"? Am. J. Hum. Genet. 14: 353-362.
28. Nielsen, R. 2001. Statistical tests of selective neutrality in the age of genomics. Heredity 86: 641-647.
29. Nielsen, R., Hubisz, M.J., and Clark, A.G. 2004. Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data. Genetics 168: 2373-2382.
30. Nielsen, R., Bustamante, C., Clark, A.G., Glanowski, S., Sackton, T.B., Hubisz, M.J, Fledel-Alon, A., Tanenbaum, D.M., Civello, D., White, T.J., et al. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 3: e170.
31. Payseur, B.A., Cutter, A.D., and Nachman, M.W. 2002. Searching for evidence of positive selection in the human genome using patterns of microsatellite variability. Mol. Biol. Evol. 19: 1143-1153.
32. Pluzhnikov, A., Di Rienzo, A., and Hudson, R.R. 2002. Inferences about human demography based on multilocus analyses of noncoding sequences. Genetics 161: 1209-1218.
33. Przeworski, M., Hudson, R.R., and Di Rienzo, A. 2000. Adjusting the focus on human variation. Trends Genet. 16: 296-302.
34. Rana, B.K., Hewett-Emmett, D., Jin, L., Chang, B.H., Sambuughin, N., Lin, M., Watkins, S., Bamshad, M., Jorde, L.B., Ramsay, M., et al. 1999. High polymorphism at the human melanocortin 1 receptor locus. Genetics 151: 1547-1557.
35. Reich, D.E., Cargill, M., Bolk, S., Ireland, J., Sabeti, P.C., Richter, D.J., Lavery, T., Kouyoumjian, R., Farhadian, S.F., Ward, R., et al. 2001. Linkage disequilibrium in the human genome. Nature 411: 199-204.
36. Rockman, M.V., Hahn, M.W., Soranzo, N., Goldstein, D.B., and Wray, G.A. 2003. Positive selection on a human-specific transcription factor binding site regulating IL4 expression. Curr. Biol. 13: 2118-2123.
37. Rosenberg, N.A., Pritchard, J.K., Weber, J.L., Cann, H.M., Kidd, K.K., Zhivotovsky, L.A., and Feldman, M.W. 2002. Genetic structure of human populations. Science 298: 2381-2385.
38. Rozen, S. and Skaletsky, H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132: 365-386.
39. Sabeti, P.C., Reich, D.E., Higgins, J.M., Levine, H.Z., Richter, D.J., Schaffner, S.F., Gabriel, S.B., Platko, J.V., Patterson, N.J., McDonald, G.J., et al. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
40. Sharma, A.M. 1998. The thrifty-genotype hypothesis and its implications for the study of complex genetic disorders in man. J. Mol. Med. 76: 568-571.
41. Shriver, M.D., Kennedy, G.C., Parra, E.J., Lawson, H.A., Sonpar, V., Huang, J., Akey, J.M., and Jones, K.W. 2004. The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Hum. Genomics 1: 274-286.
42. Spencer, C.C. and Coop, G. 2004. SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 20: 3673-3675.
43. Stajich, J.E. and Hahn, M.W. 2005. Disentangling the effects of demography and selection in human history. Mol. Biol. Evol. 22: 63-73.
44. Stephens, J.C., Reich, D.E., Goldstein, D.B., Shin, H.D., Smith, M.W., Carrington, M., Winkler, C., Huttley, G.A., Allikmets, R., Schriml, L., et al. 1998. Dating the origin of the CCR5-Δ32 AIDS-resistance allele by the coalescence of haplotypes. Am. J. Hum. Genet. 62: 1507-1515.
45. Storz, J.F., Payseur, B.A., and Nachman, M.W. 2004. Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa. Mol. Biol. Evol. 21: 1800-1811.
46. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
47. Thompson, E.E., Kuttab-Boulos, H., Witonsky, D., Yang, L., Roe, B.A., and Di Rienzo, A. 2004. CYP3A variation and the evolution of salt-sensitivity variants. Am. J. Hum. Genet. 75: 1059-1069.
48. Tishkoff, S.A., Varkonyi, R., Cahinhinan, N., Abbes, S., Argyropoulos, G., Destro-Bisol, G., Drousiotou, A., Dangerfield, B., Lefranc, G., Loiselet, J., et al. 2001. Haplotype diversity and linkage disequilibrium at human G6PD: Recent origin of alleles that confer malarial resistance. Science 293: 455-462.
49. Voight, B.F., Kudaravalli, S., Wen, X., and Pritchard, J.K. 2006. A map of recent positive selection in the human genome. PLoS Biol. 4: e72.
50. Wang, E.T., Kodama, G., Baldi, P., and Moyzis, R.K. 2006. Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc. Natl. Acad. Sci. 103: 135-140.
51. Yano, Y., Saito, R., Yoshida, N., Yoshiki, A., Wynshaw-Boris, A., Tomita, M., and Hirotsune, S. 2004. A new role for expressed pseudogenes as ncRNA: Regulation of mRNA stability of its homologous coding gene. J. Mol. Med. 82: 414-422.
52. Zhou, G., Zhai, Y., Dong, X., Zhang, X., He, F., Zhou, K., Zhu, Y., Wei, H., Yao, Z., Zhong, S., et al. 2004. Haplotype structure and evidence for positive selection at the human IL13 locus. Mol. Biol. Evol. 21: 29-35.