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Volumn 2, Issue 1, 2011, Pages

Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing

Author keywords

[No Author keywords available]

Indexed keywords

DOPACHROME TAUTOMERASE; STEM CELL FACTOR; TYROSINASE RELATED PROTEIN 1;

EID: 84862182100     PISSN: None     EISSN: 20412223     Source Type: Journal    
DOI: 10.1186/2041-2223-2-24     Document Type: Article
Times cited : (14)

References (69)
  • 1
    • 79959524146 scopus 로고    scopus 로고
    • International HapMap Consortium: A haplotype map of the human genome
    • 10.1038/nature04226, 1880871, 16255080
    • International HapMap Consortium: A haplotype map of the human genome. Nature 2005, 437:1299-1320. 10.1038/nature04226, 1880871, 16255080.
    • (2005) Nature , vol.437 , pp. 1299-1320
  • 8
    • 55849095847 scopus 로고    scopus 로고
    • A practical genome scan for population-specific strong selective sweeps that have reached fixation
    • 10.1371/journal.pone.0000286, 1805687, 17356696
    • Kimura R, Fujimoto A, Tokunaga K, Ohashi J. A practical genome scan for population-specific strong selective sweeps that have reached fixation. PLoS ONE 2007, 2:e286. 10.1371/journal.pone.0000286, 1805687, 17356696.
    • (2007) PLoS ONE , vol.2
    • Kimura, R.1    Fujimoto, A.2    Tokunaga, K.3    Ohashi, J.4
  • 11
    • 34547110828 scopus 로고    scopus 로고
    • A new approach for using genome scans to detect recent positive selection in the human genome
    • 10.1371/journal.pbio.0050171, 1892573, 17579516
    • Tang K, Thornton KR, Stoneking M. A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol 2007, 5:e171. 10.1371/journal.pbio.0050171, 1892573, 17579516.
    • (2007) PLoS Biol , vol.5
    • Tang, K.1    Thornton, K.R.2    Stoneking, M.3
  • 12
    • 33644981509 scopus 로고    scopus 로고
    • A map of recent positive selection in the human genome
    • 10.1371/journal.pbio.0040072, 1382018, 16494531
    • Voight BF, Kudaravalli S, Wen X, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol 2006, 4:e72. 10.1371/journal.pbio.0040072, 1382018, 16494531.
    • (2006) PLoS Biol , vol.4
    • Voight, B.F.1    Kudaravalli, S.2    Wen, X.3    Pritchard, J.K.4
  • 13
    • 30444460720 scopus 로고    scopus 로고
    • Global landscape of recent inferred Darwinian selection for Homo sapiens
    • 10.1073/pnas.0509691102, 1317879, 16371466
    • Wang ET, Kodama G, Baldi P, Moyzis RK. Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci USA 2006, 103:135-140. 10.1073/pnas.0509691102, 1317879, 16371466.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 135-140
    • Wang, E.T.1    Kodama, G.2    Baldi, P.3    Moyzis, R.K.4
  • 15
    • 33748676079 scopus 로고    scopus 로고
    • A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations
    • 10.1093/bioinformatics/btl365, 16845142
    • Zhang C, Bailey DK, Awad T, Liu G, Xing G, Cao M, Valmeekam V, Retief J, Matsuzaki H, Taub M, et al. A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations. Bioinformatics 2006, 22:2122-2128. 10.1093/bioinformatics/btl365, 16845142.
    • (2006) Bioinformatics , vol.22 , pp. 2122-2128
    • Zhang, C.1    Bailey, D.K.2    Awad, T.3    Liu, G.4    Xing, G.5    Cao, M.6    Valmeekam, V.7    Retief, J.8    Matsuzaki, H.9    Taub, M.10
  • 16
    • 65149103048 scopus 로고    scopus 로고
    • Constructing genomic maps of positive selection in humans: where do we go from here?
    • 10.1101/gr.086652.108, 19411596
    • Akey JM. Constructing genomic maps of positive selection in humans: where do we go from here?. Genome Res 2009, 19:711-722. 10.1101/gr.086652.108, 19411596.
    • (2009) Genome Res , vol.19 , pp. 711-722
    • Akey, J.M.1
  • 19
    • 0036964474 scopus 로고    scopus 로고
    • Approximate bayesian computation in population genetics
    • 1462356, 12524368
    • Beaumont MA, Zhang W, Balding DJ. Approximate bayesian computation in population genetics. Genetics 2002, 162:2025-2035. 1462356, 12524368.
    • (2002) Genetics , vol.162 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.2    Balding, D.J.3
  • 20
    • 0041817545 scopus 로고    scopus 로고
    • Estimating the time since the fixation of a beneficial allele
    • 1462667, 12930770
    • Przeworski M. Estimating the time since the fixation of a beneficial allele. Genetics 2003, 164:1667-1676. 1462667, 12930770.
    • (2003) Genetics , vol.164 , pp. 1667-1676
    • Przeworski, M.1
  • 21
    • 52949128377 scopus 로고    scopus 로고
    • An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila
    • 10.1371/journal.pgen.1000198, 2529407, 18802463
    • Jensen JD, Thornton KR, Andolfatto P. An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. PLoS Genet 2008, 4:e1000198. 10.1371/journal.pgen.1000198, 2529407, 18802463.
    • (2008) PLoS Genet , vol.4
    • Jensen, J.D.1    Thornton, K.R.2    Andolfatto, P.3
  • 22
    • 38449113569 scopus 로고    scopus 로고
    • Human pigmentation variation: evolution, genetic basis, and implications for public health
    • Parra EJ. Human pigmentation variation: evolution, genetic basis, and implications for public health. Am J Phys Anthropol 2007, Suppl 45:85-105.
    • (2007) Am J Phys Anthropol , vol.Suppl 45 , pp. 85-105
    • Parra, E.J.1
  • 23
    • 33748171462 scopus 로고    scopus 로고
    • A scan for signatures of positive selection in candidate loci for skin pigmentation in humans
    • 10.1093/molbev/msl030, 16757656
    • Izagirre N, Garcia I, Junquera C, de la Rua C, Alonso S. A scan for signatures of positive selection in candidate loci for skin pigmentation in humans. Mol Biol Evol 2006, 23:1697-1706. 10.1093/molbev/msl030, 16757656.
    • (2006) Mol Biol Evol , vol.23 , pp. 1697-1706
    • Izagirre, N.1    Garcia, I.2    Junquera, C.3    de la Rua, C.4    Alonso, S.5
  • 24
    • 34247097012 scopus 로고    scopus 로고
    • Signatures of positive selection in genes associated with human skin pigmentation as revealed from analyses of single nucleotide polymorphisms
    • 10.1111/j.1469-1809.2006.00341.x, 17233754
    • Lao O, de Gruijter JM, van Duijn K, Navarro A, Kayser M. Signatures of positive selection in genes associated with human skin pigmentation as revealed from analyses of single nucleotide polymorphisms. Ann Hum Genet 2007, 71:354-369. 10.1111/j.1469-1809.2006.00341.x, 17233754.
    • (2007) Ann Hum Genet , vol.71 , pp. 354-369
    • Lao, O.1    de Gruijter, J.M.2    van Duijn, K.3    Navarro, A.4    Kayser, M.5
  • 25
    • 33845645529 scopus 로고    scopus 로고
    • Identifying genes underlying skin pigmentation differences among human populations
    • Myles S, Somel M, Tang K, Kelso J, Stoneking M. Identifying genes underlying skin pigmentation differences among human populations. Hum Genet 2007, 120:613-621.
    • (2007) Hum Genet , vol.120 , pp. 613-621
    • Myles, S.1    Somel, M.2    Tang, K.3    Kelso, J.4    Stoneking, M.5
  • 30
    • 28944447769 scopus 로고    scopus 로고
    • Evidence for recent positive selection at the human AIM1 locus in a European population
    • Soejima M, Tachida H, Ishida T, Sano A, Koda Y. Evidence for recent positive selection at the human AIM1 locus in a European population. Mol Biol Evol 2006, 23:179-188.
    • (2006) Mol Biol Evol , vol.23 , pp. 179-188
    • Soejima, M.1    Tachida, H.2    Ishida, T.3    Sano, A.4    Koda, Y.5
  • 33
    • 33744815615 scopus 로고    scopus 로고
    • How reliable are empirical genomic scans for selective sweeps?
    • 10.1101/gr.5105206, 1473181, 16687733
    • Teshima KM, Coop G, Przeworski M. How reliable are empirical genomic scans for selective sweeps?. Genome Res 2006, 16:702-712. 10.1101/gr.5105206, 1473181, 16687733.
    • (2006) Genome Res , vol.16 , pp. 702-712
    • Teshima, K.M.1    Coop, G.2    Przeworski, M.3
  • 34
    • 34547681436 scopus 로고    scopus 로고
    • Comparisons of site- and haplotype-frequency methods for detecting positive selection
    • 10.1093/molbev/msm078, 17449894
    • Zeng K, Mano S, Shi S, Wu CI. Comparisons of site- and haplotype-frequency methods for detecting positive selection. Mol Biol Evol 2007, 24:1562-1574. 10.1093/molbev/msm078, 17449894.
    • (2007) Mol Biol Evol , vol.24 , pp. 1562-1574
    • Zeng, K.1    Mano, S.2    Shi, S.3    Wu, C.I.4
  • 35
    • 27544474337 scopus 로고    scopus 로고
    • Ascertainment bias in studies of human genome-wide polymorphism
    • 10.1101/gr.4107905, 1310637, 16251459
    • Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R. Ascertainment bias in studies of human genome-wide polymorphism. Genome Res 2005, 15:1496-1502. 10.1101/gr.4107905, 1310637, 16251459.
    • (2005) Genome Res , vol.15 , pp. 1496-1502
    • Clark, A.G.1    Hubisz, M.J.2    Bustamante, C.D.3    Williamson, S.H.4    Nielsen, R.5
  • 36
    • 0042991419 scopus 로고    scopus 로고
    • Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium
    • 10.1016/S0040-5809(03)00005-4, 12689795
    • Nielsen R, Signorovitch J. Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theor Popul Biol 2003, 63:245-255. 10.1016/S0040-5809(03)00005-4, 12689795.
    • (2003) Theor Popul Biol , vol.63 , pp. 245-255
    • Nielsen, R.1    Signorovitch, J.2
  • 37
    • 2942738764 scopus 로고    scopus 로고
    • Balancing claims for balancing selection
    • 10.1016/j.tig.2004.05.002, 15219394
    • Kreitman M, Di Rienzo A. Balancing claims for balancing selection. Trends Genet 2004, 20:300-304. 10.1016/j.tig.2004.05.002, 15219394.
    • (2004) Trends Genet , vol.20 , pp. 300-304
    • Kreitman, M.1    Di Rienzo, A.2
  • 38
    • 20644454389 scopus 로고    scopus 로고
    • Assessing the signatures of selection in PRNP from polymorphism data: results support Kreitman and Di Rienzo's opinion
    • 10.1016/j.tig.2005.05.001, 15913833
    • Soldevila M, Calafell F, Helgason A, Stefansson K, Bertranpetit J. Assessing the signatures of selection in PRNP from polymorphism data: results support Kreitman and Di Rienzo's opinion. Trends Genet 2005, 21:389-391. 10.1016/j.tig.2005.05.001, 15913833.
    • (2005) Trends Genet , vol.21 , pp. 389-391
    • Soldevila, M.1    Calafell, F.2    Helgason, A.3    Stefansson, K.4    Bertranpetit, J.5
  • 39
    • 0029099781 scopus 로고
    • Properties of statistical tests of neutrality for DNA polymorphism data
    • 1206737, 8536987
    • Simonsen KL, Churchill GA, Aquadro CF. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 1995, 141:413-429. 1206737, 8536987.
    • (1995) Genetics , vol.141 , pp. 413-429
    • Simonsen, K.L.1    Churchill, G.A.2    Aquadro, C.F.3
  • 40
    • 8644263161 scopus 로고    scopus 로고
    • A structured ancestral population for the evolution of modern humans
    • 10.1016/j.gde.2004.08.010, 15531162
    • Harding RM, McVean G. A structured ancestral population for the evolution of modern humans. Curr Opin Genet Dev 2004, 14:667-674. 10.1016/j.gde.2004.08.010, 15531162.
    • (2004) Curr Opin Genet Dev , vol.14 , pp. 667-674
    • Harding, R.M.1    McVean, G.2
  • 44
    • 73449149044 scopus 로고    scopus 로고
    • Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data
    • 10.1371/journal.pgen.1000695, 2760211, 19851460
    • Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet 2009, 5:e1000695. 10.1371/journal.pgen.1000695, 2760211, 19851460.
    • (2009) PLoS Genet , vol.5
    • Gutenkunst, R.N.1    Hernandez, R.D.2    Williamson, S.H.3    Bustamante, C.D.4
  • 45
    • 27544497650 scopus 로고    scopus 로고
    • Calibrating a coalescent simulation of human genome sequence variation
    • 10.1101/gr.3709305, 1310645, 16251467
    • Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D. Calibrating a coalescent simulation of human genome sequence variation. Genome Res 2005, 15:1576-1583. 10.1101/gr.3709305, 1310645, 16251467.
    • (2005) Genome Res , vol.15 , pp. 1576-1583
    • Schaffner, S.F.1    Foo, C.2    Gabriel, S.3    Reich, D.4    Daly, M.J.5    Altshuler, D.6
  • 46
    • 67749111629 scopus 로고    scopus 로고
    • Detecting ancient admixture and estimating demographic parameters in multiple human populations
    • 10.1093/molbev/msp096, 2734152, 19420049
    • Wall JD, Lohmueller KE, Plagnol V. Detecting ancient admixture and estimating demographic parameters in multiple human populations. Mol Biol Evol 2009, 26:1823-1827. 10.1093/molbev/msp096, 2734152, 19420049.
    • (2009) Mol Biol Evol , vol.26 , pp. 1823-1827
    • Wall, J.D.1    Lohmueller, K.E.2    Plagnol, V.3
  • 47
    • 9144273249 scopus 로고    scopus 로고
    • The evolution of human skin and skin color
    • Jablonski NG. The evolution of human skin and skin color. Annual Review of Anthropology 2004, 33:585-623.
    • (2004) Annual Review of Anthropology , vol.33 , pp. 585-623
    • Jablonski, N.G.1
  • 50
    • 0347362518 scopus 로고    scopus 로고
    • Informativeness of genetic markers for inference of ancestry
    • 10.1086/380416, 1180403, 14631557
    • Rosenberg NA, Li LM, Ward R, Pritchard JK. Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 2003, 73:1402-1422. 10.1086/380416, 1180403, 14631557.
    • (2003) Am J Hum Genet , vol.73 , pp. 1402-1422
    • Rosenberg, N.A.1    Li, L.M.2    Ward, R.3    Pritchard, J.K.4
  • 51
    • 63149157274 scopus 로고    scopus 로고
    • Molecular genetics of human pigmentation diversity
    • 10.1093/hmg/ddp003, 19297406
    • Sturm RA. Molecular genetics of human pigmentation diversity. Hum Mol Genet 2009, 18:R9-17. 10.1093/hmg/ddp003, 19297406.
    • (2009) Hum Mol Genet , vol.18
    • Sturm, R.A.1
  • 52
    • 0242691208 scopus 로고    scopus 로고
    • A comparison of bayesian methods for haplotype reconstruction from population genotype data
    • 10.1086/379378, 1180495, 14574645
    • Stephens M, Donnelly P. A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 2003, 73:1162-1169. 10.1086/379378, 1180495, 14574645.
    • (2003) Am J Hum Genet , vol.73 , pp. 1162-1169
    • Stephens, M.1    Donnelly, P.2
  • 54
    • 85090878417 scopus 로고    scopus 로고
    • LDheatmap: An R function for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms
    • Code Snippet 3
    • Shin J-H, Blay S, McNeney B, Graham J. LDheatmap: An R function for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms. Journal of Statistical Software 2006, 16. Code Snippet 3.
    • (2006) Journal of Statistical Software , vol.16
    • Shin, J.-H.1    Blay, S.2    McNeney, B.3    Graham, J.4
  • 56
    • 0016491430 scopus 로고
    • On the number of segregating sites in genetical models without recombination
    • 10.1016/0040-5809(75)90020-9, 1145509
    • Watterson GA. On the number of segregating sites in genetical models without recombination. Theor Popul Biol 1975, 7:256-276. 10.1016/0040-5809(75)90020-9, 1145509.
    • (1975) Theor Popul Biol , vol.7 , pp. 256-276
    • Watterson, G.A.1
  • 57
    • 0347513220 scopus 로고    scopus 로고
    • DnaSP, DNA polymorphism analyses by the coalescent and other methods
    • 10.1093/bioinformatics/btg359, 14668244
    • Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003, 19:2496-2497. 10.1093/bioinformatics/btg359, 14668244.
    • (2003) Bioinformatics , vol.19 , pp. 2496-2497
    • Rozas, J.1    Sanchez-DelBarrio, J.C.2    Messeguer, X.3    Rozas, R.4
  • 58
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
    • 1203831, 2513255
    • Tajima FV. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595. 1203831, 2513255.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.V.1
  • 59
    • 0027453041 scopus 로고
    • Statistical tests of neutrality of mutations
    • 1205353, 8454210
    • Fu YX, Li WH. Statistical tests of neutrality of mutations. Genetics 1993, 133:693-709. 1205353, 8454210.
    • (1993) Genetics , vol.133 , pp. 693-709
    • Fu, Y.X.1    Li, W.H.2
  • 60
    • 0033911640 scopus 로고    scopus 로고
    • Hitchhiking under positive Darwinian selection
    • 1461156, 10880498
    • Fay JC, Wu CI. Hitchhiking under positive Darwinian selection. Genetics 2000, 155:1405-1413. 1461156, 10880498.
    • (2000) Genetics , vol.155 , pp. 1405-1413
    • Fay, J.C.1    Wu, C.I.2
  • 61
    • 0030821992 scopus 로고    scopus 로고
    • Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection
    • 1208208, 9335623
    • Fu YX. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147:915-925. 1208208, 9335623.
    • (1997) Genetics , vol.147 , pp. 915-925
    • Fu, Y.X.1
  • 62
    • 0017886236 scopus 로고
    • The homozygosity test of neutrality
    • 1213809, 17248803
    • Watterson GA. The homozygosity test of neutrality. Genetics 1978, 88:405-417. 1213809, 17248803.
    • (1978) Genetics , vol.88 , pp. 405-417
    • Watterson, G.A.1
  • 63
    • 29444451610 scopus 로고    scopus 로고
    • Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes
    • 10.1073/pnas.0507325102, 1311907, 16352722
    • Voight BF, Adams AM, Frisse LA, Qian Y, Hudson RR, Di Rienzo A. Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc Natl Acad Sci USA 2005, 102:18508-18513. 10.1073/pnas.0507325102, 1311907, 16352722.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 18508-18513
    • Voight, B.F.1    Adams, A.M.2    Frisse, L.A.3    Qian, Y.4    Hudson, R.R.5    Di Rienzo, A.6
  • 64
    • 33645229840 scopus 로고    scopus 로고
    • Estimating diversifying selection and functional constraint in the presence of recombination
    • 1456295, 16387887
    • Wilson DJ, McVean G. Estimating diversifying selection and functional constraint in the presence of recombination. Genetics 2006, 172:1411-1425. 1456295, 16387887.
    • (2006) Genetics , vol.172 , pp. 1411-1425
    • Wilson, D.J.1    McVean, G.2
  • 65
    • 0346734143 scopus 로고    scopus 로고
    • Markov chain Monte Carlo without likelihoods
    • 10.1073/pnas.0306899100, 307566, 14663152
    • Marjoram P, Molitor J, Plagnol V, Tavare S. Markov chain Monte Carlo without likelihoods. Proc Natl Acad Sci USA 2003, 100:15324-15328. 10.1073/pnas.0306899100, 307566, 14663152.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 15324-15328
    • Marjoram, P.1    Molitor, J.2    Plagnol, V.3    Tavare, S.4
  • 67
    • 70349507629 scopus 로고    scopus 로고
    • Out of Africa: modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa
    • 10.1073/pnas.0903341106, 2752555, 19706453
    • DeGiorgio M, Jakobsson M, Rosenberg NA. Out of Africa: modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. Proc Natl Acad Sci USA 2009, 106:16057-16062. 10.1073/pnas.0903341106, 2752555, 19706453.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 16057-16062
    • DeGiorgio, M.1    Jakobsson, M.2    Rosenberg, N.A.3
  • 68
    • 0036245438 scopus 로고    scopus 로고
    • Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
    • 10.1038/nrg795, 11988763
    • Rosenberg NA, Nordborg M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet 2002, 3:380-390. 10.1038/nrg795, 11988763.
    • (2002) Nat Rev Genet , vol.3 , pp. 380-390
    • Rosenberg, N.A.1    Nordborg, M.2


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