Localizing recent adaptive evolution in the human genome

PLoS Genetics

Volumn 3, Issue 6, 2007, Pages 0901-0915

  Williamson, Scott H ^a   Hubisz, Melissa J ^a,d   Clark, Andrew G ^b   Payseur, Bret A ^b,e   Bustamante, Carlos D ^a   Nielsen, Rasmus ^c  

^a Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^b Department of Obstetrics Gynecology   (United States)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

^d UNIVERSITY OF CHICAGO   (United States)

^e UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DYSTROPHIN ASSOCIATED PROTEIN COMPLEX;

AFRICAN AMERICAN; ARTICLE; CHINESE; DEMOGRAPHY; EUROPEAN AMERICAN; EVOLUTION; GENETIC RECOMBINATION; HEAT SHOCK; HUMAN; HUMAN GENOME; IMMUNE SYSTEM; NERVOUS SYSTEM DEVELOPMENT; NERVOUS SYSTEM FUNCTION; OLFACTORY RECEPTOR; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; ADAPTATION; GENETICS; GENOME; MOLECULAR EVOLUTION;

ADAPTATION, BIOLOGICAL; EVOLUTION, MOLECULAR; GENOME, HUMAN; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 34347336584     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0030090     Document Type: Article

References (65)

1. Fay JC, Wyckoff GJ, Wu CI (2001) Positive and negative selection on the human genome. Genetics 158: 1227-1234.
2. Smith NGC, Eyre-Walker A (2002) Adaptive protein evolution in Drosophila. Nature 415: 1022-1024.
3. Clark AG, Glanowski S, Nielsen R, Thomas P, Kejariwal A, et al. (2003) Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302: 1960-1963.
4. 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 (6): e170.
5. 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.
6. Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, et al. (2005) Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Natl Acad Sci U S A 102: 7882-7887.
7. Stephens JC, Reich DE, Goldstein DB, Shin HD, Smith MW, 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.
8. 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.
9. Dobzhansky T (1955) A review of some fundamental concepts and problems of population genetics. Cold Spring Harb Symp Quant Biol 20: 1.
10. Lewontin RC (1974) The genetic basis of evolutionary change. New York: Columbia University Press. 346 p.
11. Kimura M (1983) The neutral theory of molecular evolution. New York: Cambridge University Press. 367 p.
12. Gillespie JH (1991) The causes of molecular evolution. New York: Oxford University Press. 336 p.
13. 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.
14. 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.
15. Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4 (3): e72.
16. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
17. Teshima KM, Coop G, Przeworski M (2006) How reliable are empirical genomic scans for selective sweeps? Genome Res 16: 702-712.
18. 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.
19. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, et al. (2005) Whole-genome patterns of common DNA variation in three human populations. Science 18: 1072-1079.
20. Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
21. Kim Y, Stephan W (2002) Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
22. Nielsen R, Williamson SH, Hubisz MT, Kim Y, Clark AG, et al. (2005) Genomic scans for natural selection using ascertained SNP data. Genome Res 15: 1566-1575.
23. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B 85: 289-300.
24. Storey JD, Tibshirani R (2003) Statistical significance for genome-wide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
25. Marth GT, Czabarka E, Murvai J, Sherry ST (2004) The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics 166: 351-372.
26. Ehmsen J, Poon E, Davies K (2002) The dystrophin-associated protein complex. J Cell Sci 115: 2801-2803.
27. Malik HS, Henikoff S (2002) Conflict begets complexity: The evolution of centromeres. Curr Opin Genet Dev 12: 711-718.
28. Malik HS, Bayes JJ (2006) Genetic conflicts during meiosis and the evolutionary origins of centromere complexity. Biochem Soc Trans 34: 569-573.
29. Pardo-Manuel de Villena F, Sapienza C (2001) Female meiosis drives karyotypic evolution in mammals. Genetics 159: 1179-1189.
30. Chevin LM, Hospital F (2006) The hitchiking effect of an autosomal meiotic drive gene. Genetics 173: 1829-1832.
31. Jablonski NG, Chaplin G (2000) The evolution of human skin coloration. J Hum Evol 39: 57-106.
32. Grichnik JM, Burch JA, Burchette J, Shea CR (1998) The SCF/KIT pathway plays a critical role in the control of normal human melanocyte homeostasis. J Invest Dermatol 111: 233-238.
33. Lamason RL, Mohideen MA, Mest JR, Wong AC, Norton HL, et al. (2006) SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310: 1782-1786.
34. Izagirre N, Garcia I, Junquera C, de la Rua C, Alonso S (2006) A scan for signatures of positive selection in candidate loci for skin pigmentation in humans. Mol Biol Evol 23: 1697-1706.
35. Gilad Y, Bustamante CD, Lancet D, Pääbo S (2003) Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am J Hum Genet 73: 489-501.
36. Bajjalieh SM, Peterson K, Linial M, Scheller RH (1994) Brain contains two forms of synaptic vesicle protein 2. Proc Nat Acad Sci U S A 90: 2150-2154.
37. Howell BW, Hawkes R, Soriano P, Cooper JA (1997) Neuronal position in the developing brain is regulated by mouse disabled-1. Nature 389: 733-737.
38. Amieva MR, Vogelmann R, Covacci A, Tompkins LS, Nelson WJ, et al. (2003) Disruption of the epithelial apical-junctional complex by Helicobacter pylori CagA. Science 300: 1430-1434.
39. Stuchell MD, Garrus JE, Muller B, Stray KM, Ghaffarian S, et al. (2004) The human endosomal sorting complex required for transport (ESCRT-I) and its role in HIV-1 budding. J Biol Chem 279: 36059-36071.
40. Cavalli-Sforza L (1973) Analytic review: Some current problems of population genetics. Am J Hum Genet 25: 82-104.
41. Enattah NS, Sahi T, Savilahti E, Terwilliger JD, Peltonen L, et al. (2002) Identification of a variant associated with adult-type hypolactasia. Nat Genet 30: 233-237.
42. 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.
43. Toomajian C, Ajioka RS, Jorde LB, Kushner JP, Kreitman M (2003) A method for detecting recent selection in the human genome from allele age estimates. Genetics 165: 287-297.
44. Feder JN, Gnirke A, Thomas W, Tsuchihashi Z, Ruddy DA, et al. (1996) A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis. Nat Genet 13: 399-408.
45. Peck JR (1994) A ruby in the rubbish: Beneficial mutations, deleterious mutations and the evolution of sex. Genetics 137: 597-606.
46. Osier MV, Pakstis AJ, Soodyall H, Comas D, Goldman D, et al. (2002) A global perspective on genetic variation at the ADH genes reveals unusual patterns of linkage disequilibrium and diversity. Am J Hum Genet 71: 84-99.
47. Rockman MV, Hahn MW, Soranzo N, Zimprich F, Goldstein DB, et al. (2005) Ancient and recent positive selection transformed opioid cis-regulation in humans. PLoS Biol. 3 (12): e387.
48. Rockman MV, Hahn MW, Soranzo N, Loisel DA, Goldstein DB, et al. (2004) Positive selection on MMP3 regulation has shaped heart disease risk. Curr Biol 14: 1531-1539.
49. Mekel-Bobrov N, Gilbert SL, Evans PD, Vallender EJ, Anderson JR, et al. (2005) Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science 309: 1720-1722.
50. Evans PD, Gilbert SL, Mekel-Bobrov N, Vallender EJ, Anderson JR, et al. (2005) Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science 309: 1717-1720.
51. McVean GA, Myers SR, Hunt S, Deloukas P, Bentley DR, et al. (2004) The fine-scale structure of recombination rate variation in the human genome. Science 304: 581-584.
52. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P (2005) A fine-scale map of recombination rates and hotspots across the human genome. Science 310: 321-324.
53. Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, et al. (2005) Calibrating a coalescent simulation. Genome Res 15: 1576-1583.
54. 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.
55. 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.
56. Stajich JE, Hahn MW (2005) Disentangling the effects of demography and selection in human history. Mol Biol Evol 22: 63-73.
57. Tishkoff SA, Williams SM (2002) Genetic analysis of African populations: Human evolution and complex disease. Nat Rev Genet 3: 611-621.
58. Dodson H, Diouf S (2004) In motion: The African-American migration experience. Washington (D. C.): National Geographic. 224 p.
59. Parra EJ, Marcini A, Akey J, Martinson J, Batzer MA, et al. (1998) Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet 63: 1839-1851.
60. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
61. Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R (2005) Ascertainment bias in studies of human genome-wide polymorphism. Genome Res 15: 1496-1502.
62. Nielsen R, Hubisz MJ, Clark AG (2004) Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data. Genetics 168: 2373-2382.
63. Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, et al. (2002) A high-resolution recombination map of the human genome. Nat Genet 31: 241-247.
64. Collins FS, Brooks LD, Chakravarti A (1998) A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8: 1229-1231.
65. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, et al. (2004) The UCSC Table Browser data retrieval tool. Nuc Acids Res 32 (Suppl 1): D493-D496.