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A Map of Recent Positive Selection in the Human Genome

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Voight, Benjamin F, Kudaravalli, Sridhar, Wen, Xiaoquan, Pritchard, Jonathan K·2006·PLoS Biology
DOI 10.1371/journal.pbio.0040072
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Abstract

The identification of signals of very recent positive selection provides information about the adaptation of modern humans to local conditions. We report here on a genome-wide scan for signals of very recent positive selection in favor of variants that have not yet reached fixation. We describe a new analytical method for scanning single nucleotide polymorphism (SNP) data for signals of recent selection, and apply this to data from the International HapMap Project. In all three continental groups we find widespread signals of recent positive selection. Most signals are region-specific, though a significant excess are shared across groups. Contrary to some earlier low resolution studies that suggested a paucity of recent selection in sub-Saharan Africans, we find that by some measures our strongest signals of selection are from the Yoruba population. Finally, since these signals indicate the existence of genetic variants that have substantially different fitnesses, they must indicate loci that are the source of significant phenotypic variation. Though the relevant phenotypes are generally not known, such loci should be of particular interest in mapping studies of complex traits. For this purpose we have developed a set of SNPs that can be used to tag the strongest approximately 250 signals of recent selection in each population.

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Research works printed but not linked: 49

  1. 2002, Evolution, consequences and future of plant and animal domestication., Nature, 418, 700, 10.1038/nature01019 · DOI · Paper page
  2. 2004, Human evolutionary genetics: Origins, peoples and disease
  3. 2001, Haplotype diversity and linkage disequilibrium at human G6PD: Recent origin of alleles that confer malarial resistance., Science, 293, 455, 10.1126/science.1061573 · DOI · Paper page
  4. 2002, Complex signatures of natural selection at the Duffy blood group locus., Am J Hum Genet, 70, 369, 10.1086/338628 · DOI · Paper page
  5. 2004, Genetic signatures of strong recent positive selection at the lactase gene., Am J Hum Genet, 74, 1111, 10.1086/421051 · DOI · Paper page
  6. 2004, CYP3A variation and the evolution of salt-sensitivity variants., Am J Hum Genet, 75, 1059, 10.1086/426406 · DOI · Paper page
  7. 2005, Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans., Science, 309, 1717, 10.1126/science.1113722 · DOI · Paper page
  8. 2005, Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens., Science, 309, 1720, 10.1126/science.1116815 · DOI · Paper page
  9. 2003, Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios., Science, 302, 1960, 10.1126/science.1088821 · DOI · Paper page
  10. 2005, A scan for positively selected genes in the genomes of humans and chimpanzees., PLoS Biol, 3, e170, 10.1371/journal.pbio.0030170 · DOI · Paper page
  11. 2003, A genome scan to detect candidate regions influenced by local natural selection in human populations., Mol Biol Evol, 20, 893, 10.1093/molbev/msg092 · DOI
  12. 2004, Population history and natural selection shape patterns of genetic variation in 132 genes., PLoS Biol, 2, e286, 10.1371/journal.pbio.0020286 · DOI · Paper page
  13. 2004, Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa., Mol Biol Evol, 21, 1800, 10.1093/molbev/msh192 · DOI
  14. 2005, Disentangling the effects of demography and selection in human history., Mol Biol Evol, 22, 63
  15. The International HapMap Consortium, 2005, A haplotype map of the human genome., Nature, 437, 1299, 10.1038/nature04226 · DOI · Paper page
  16. 1962, Diabetes mellitus: A “thrifty” genotype rendered detrimental by “progress”?, Am J Hum Genet, 14, 353
  17. 2005, A common inversion under selection in Europeans., Nat Genet, 37, 129, 10.1038/ng1508 · DOI · Paper page
  18. 2005, An evolutionary framework for common diseases: the ancestral-susceptibility model., Trends Genet, 21, 596, 10.1016/j.tig.2005.08.007 · DOI
  19. 2005, Population genetics of CAPN10 and GPR35: Implications for the evolution of type 2 diabetes variants., Am J Hum Genet, 76, 548, 10.1086/428784 · DOI
  20. 2005, Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation., Am J Hum Genet, 76, 449, 10.1086/428594 · DOI · Paper page
  21. 2003, Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data., Genetics, 165, 2213, 10.1093/genetics/165.4.2213 · DOI · Paper page
  22. 1994, Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster., Genetics, 136, 1329, 10.1093/genetics/136.4.1329 · DOI · Paper page
  23. 1995, Haplotype test reveals departure from neutrality in a segment of the white gene of Drosophila melanogaster., Genetics, 141, 1483, 10.1093/genetics/141.4.1483 · DOI
  24. 1999, Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster., Genetics, 153, 1297, 10.1093/genetics/153.3.1297 · DOI
  25. 2001, The use of intraallelic variability for testing neutrality and estimating population growth rate., Genetics, 158, 865, 10.1093/genetics/158.2.865 · DOI · Paper page
  26. 2002, Sequence variation and haplotype structure at the human HFE locus., Genetics, 161, 1609, 10.1093/genetics/161.4.1609 · DOI
  27. 2004, The fine-scale structure of recombination rate variation in the human genome., Science, 304, 581, 10.1126/science.1092500 · DOI · Paper page
  28. 2004, Evidence for substantial fine-scale variation in recombination rates across the human genome., Nat Genet, 36, 700, 10.1038/ng1376 · DOI · Paper page
  29. 2005, A fine-scale map of recombination rates and hotspots across the human genome., Science, 310, 321, 10.1126/science.1117196 · DOI · Paper page
  30. 2005, Microsatellite variation and evolution of human lactase persistence., Hum Genet, 117, 329, 10.1007/s00439-005-1322-z · DOI
  31. 2002, Inferences about human demography based on multilocus analyses of noncoding sequences., Genetics, 161, 1209, 10.1093/genetics/161.3.1209 · DOI
  32. 2005, Interrogating multiple aspects of variation in a full re-sequencing data set to infer human population size changes., PNAS, 102, 18508, 10.1073/pnas.0507325102 · DOI · Paper page
  33. 2001, Linkage disequilibrium in the human genome., Nature, 411, 199, 10.1038/35075590 · DOI · Paper page
  34. 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, 10.1086/341290 · DOI · Paper page
  35. 2003, Natural selection on the olfactory receptor gene family in humans and chimpanzees., Am J Hum Genet, 73, 489, 10.1086/378132 · DOI
  36. 2003, PANTHER: A browsable database of gene products organized by biological function, using curated protein family and subfamily classification., Nucleic Acids Res, 31, 334, 10.1093/nar/gkg115 · DOI · Paper page
  37. OMIM, 2000, Online Mendelian Inheritance in Man. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University and National Center for Biotechnology Information
  38. 2005, Entrez Gene: Gene-centered information at NCBI., Nucleic Acids Res, 33, 54
  39. 2005, Pervasive adaptive evolution in primate seminal proteins., PLoS Genet, 1, e35, 10.1371/journal.pgen.0010035 · DOI
  40. 2005, A centrosomal mechanism involving CDK5RAP2 and CENPJ controls brain size., Nat Genet, 37, 353, 10.1038/ng1539 · DOI · Paper page
  41. 1999, Interaction between the functional polymorphisms of the alcohol-metabolism genes in protection against alcoholism., Am J Hum Genet, 65, 795, 10.1086/302540 · DOI · Paper page
  42. 2002, Generating samples under a Wright-Fisher neutral model of genetic variation., Bioinformatics, 18, 337, 10.1093/bioinformatics/18.2.337 · DOI · Paper page
  43. 2004, SelSim: A program to simulate population genetic data with natural selection and recombination., Bioinformatics, 20, 3673, 10.1093/bioinformatics/bth417 · DOI
  44. 2004, Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms., Genetics, 168, 1699, 10.1534/genetics.104.030171 · DOI
  45. 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, 10.1534/genetics.166.1.351 · DOI · Paper page
  46. 2004, Population genetic analysis of ascertained SNP data., Hum Genomics, 1, 218, 10.1186/1479-7364-1-3-218 · DOI
  47. 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
  48. 2002, A high-resolution recombination map of the human genome., Nat Genet, 31, 241, 10.1038/ng917 · DOI · Paper page
  49. 1989, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism., Genetics, 123, 585, 10.1093/genetics/123.3.585 · DOI · Paper page

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Metadata

Authors
Voight, B. F., Kudaravalli, S., Wen, X., & Pritchard, J. K.
Venue
PLoS Biology
Publisher
Public Library of Science (PLoS)
Published
2006-03-07
Volume
4
Issue
3
Pages
e72
ISSN
  • 1544-9173 (ISSN-L)
  • 1545-7885
DOI
10.1371/journal.pbio.0040072
OpenAlex
W2025253353
Cited by
2,893
References
7
FWCI
89.95
Type
journal article
Language
en
Update notices
Open access
gold
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)

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