Erratum: A map of recent positive selection in the human genome (Plos Biology 4,3 DOI:10.1371/journal.pbio.0040072);A map of recent positive selection in the human genome

PLoS Biology

Volumn 4, Issue 3, 2006, Pages 0446-0458

  Voight, Benjamin F ^a   Kudaravalli, Sridhar ^a   Wen, Xiaoquan ^a   Pritchard, Jonathan K ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA; ANALYTIC METHOD; ARTICLE; GENE LOCUS; GENE MAPPING; GENETIC SELECTION; GENETIC TRAIT; GENETIC VARIABILITY; GENOME ANALYSIS; GEOGRAPHIC DISTRIBUTION; HUMAN; PHENOTYPE; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; ALLELE; CHROMOSOME MAP; GENETICS; GENOME; HUMAN CHROMOSOME;

ALLELES; CHROMOSOMES, HUMAN; GENOME, HUMAN; HUMANS; PHYSICAL CHROMOSOME MAPPING; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION (GENETICS);

EID: 33644981509     PISSN: 15457885     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0040072     Document Type: Erratum

References (56)

1. Diamond J (2002) Evolution, consequences and future of plant and animal domestication. Nature 418: 700-707.
2. Jobling MA, Hurles ME, Tyler-Smith C (2004) Human evolutionary genetics: Origins, peoples and disease. New York: Garland Science. 523 p.
3. 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.
4. 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.
5. Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
6. 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.
7. Thompson EE, Kuttab-Boulos H, Witonsky D, Yang L, Roe BA, et al. (2004) CYP3A variation and the evolution of salt-sensitivity variants. Am J Hum Genet 75: 1059-1069.
8. 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.
9. 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.
10. 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.
11. 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. DOI: 10.1371/journal.pbio.0030170
12. Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
13. 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.
14. 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. DOI: 10.1371/journal.pbio.0020286
15. 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.
16. Stajich JE, Hahn MW (2005) Disentangling the effects of demography and selection in human history. Mol Biol Evol 22: 63-73.
17. 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.
18. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
19. Neel JV (1962) Diabetes mellitus: A "thrifty" genotype rendered detrimental by "progress"? Am J Hum Genet 14: 353-362.
20. Stefansson H, Helgason A, Thorleifsson G, Steinthorsdottir V, Masson G, et al. (2005) A common inversion under selection in Europeans. Nat Genet 37: 129-137.
21. Di Rienzo A, Hudson RR (2005) An evolutionary framework for common diseases: the ancestral-susceptibility model. Trends Genet 21: 596-601.
22. Vander Molen J, Frisse LM, Fullerton SM, Qian Y, Del Bosque-Plata L, et al. (2005) Population genetics of CAPN10 and GPR35: Implications for the evolution of type 2 diabetes variants. Am J Hum Genet 76: 548-560.
23. Stephens M, Scheet P (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet 76: 449-462.
24. Li N, Stephens M (2003) Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165: 2213-2233.
25. 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.
26. Kirby DA, Stephan W (1995) Haplotype test reveals departure from neutrality in a segment of the white gene of Drosophila melanogaster. Genetics 141: 1483-1490.
27. 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.
28. Slatkin M, Bertorelle G (2001) The use of intraallelic variability for testing neutrality and estimating population growth rate. Genetics 158: 865-874.
29. Toomajian C, Kreitman M (2002) Sequence variation and haplotype structure at the human HFE locus. Genetics 161: 1609-1623.
30. McVean GA, Myers SR, Hunt S, Deloukas P, Bently DR, et al. (2004) The fine-scale structure of recombination rate variation in the human genome. Science 304: 581-584.
31. Crawford DC, Bhangale T, Li N, Hellenthal G, Rieder MJ, et al. (2004) Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet 36: 700-706.
32. 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.
33. Coelho M, Luiselli D, Bertorelle G, Lopes AI, Seixas S, et al. (2005) Microsatellite variation and evolution of human lactase persistence. Hum Genet 117: 329-339.
34. Pluzhnikov A, Di Rienzo A, Hudson RR (2002) Inferences about human demography based on multilocus analyses of noncoding sequences. Genetics 161: 1209-1218.
35. Voight BF, Adams A, Frisse L, Quan Y, Hudson RR, et al. (2005) Interrogating multiple aspects of variation in a full re-sequencing data set to infer human population size changes. PNAS 102: 18508-18513.
36. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, et al. (2001) Linkage disequilibrium in the human genome. Nature 411: 199-204.
37. Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
38. 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.
39. Gilad Y, Bustamante CD, Lancet D, Paabo S (2003) Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am J Hum Genet 73: 489-501.
40. Maynard Smith J, Haigh J (1974) The hitch-hiking effect of a favourable gene. Genet Res Camb 23: 23-35.
41. Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, et al. (2003) PANTHER: A browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res 31: 334-341.
42. OMIM (2000) Online Mendelian Inheritance in Man. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University and National Center for Biotechnology Information. Available: http://www.ncbi.nlm.nih.gov/entrez/query. fcgi?db=OMIM. Accessed 1 September 2005.
43. Maglott D, Ostell J, Pruitt KD, Tatusova T (2005) Entrez Gene: Gene-centered information at NCBI. Nucleic Acids Res 33: 54-58.
44. Clark NL, Swanson WJ (2005) Pervasive adaptive evolution in primate seminal proteins. PLoS Genet 1: e35. DOI: 10.1371/journal.pgen.0010035
45. Lamason RL, Mohideen M, Mest JR, Wong AC, Norton HL, et al. (2005) SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310: 1782-1786.
46. Bond J, Roberts E, Springell K, Lizarraga SB, Scott S, et al. (2005) A centrosomal mechanism involving CDK5RAP2 and CENPJ controls brain size. Nat Genet 37: 353-355.
47. Chen C, Lu R, Chen Y, Wang M, Chang Y, et al. (1999) Interaction between the functional polymorphisms of the alcohol-metabolism genes in protection against alcoholism. Am J Hum Genet 65: 795-807.
48. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
49. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
50. Spencer CCA, Coop G (2004) SelSim: A program to simulate population genetic data with natural selection and recombination. Bioinformatics 20: 3673-3675.
51. Adams AM, Hudson RR (2004) Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms. Genetics 168: 1699-1712.
52. 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.
53. Nielsen R (2004) Population genetic analysis of ascertained SNP data. Hum Genomics 1: 218-224.
54. 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. In Press.
55. 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.
56. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.