Genomic insights into positive selection

Trends in Genetics

Volumn 22, Issue 8, 2006, Pages 437-446

  Biswas, Shameek ^a   Akey, Joshua M ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISEASE ASSOCIATION; DNA SEQUENCE; ETHNIC DIFFERENCE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENETIC ANALYSIS; GENETIC SELECTION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMICS; HAPLOTYPE; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; PHENOTYPE; POPULATION SIZE; PRIORITY JOURNAL; REVIEW; SPECIES DIVERSITY;

ANIMALS; EVOLUTION, MOLECULAR; GENETICS, POPULATION; HUMANS; MODELS, GENETIC; SELECTION (GENETICS); SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 33746237567     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2006.06.005     Document Type: Review

References (67)

1. Gillespie J.H. The Causes of Molecular Evolution (1991), Oxford University Press
2. Kimura M. The Neutral Theory of Molecular Evolution (1983), Cambridge University Press
3. Kimura M. Evolutionary rate at the molecular level. Nature 217 (1968) 624-626
4. King J.L., and Jukes T.H. Non-darwinian evolution. Science 164 (1969) 788-798
5. Ohta T. Slightly deleterious mutant substitutions in evolution. Nature 246 (1973) 96-98
6. Kreitman M. Methods to detect selection in populations with applications to the human. Annu. Rev. Genomics Hum. Genet. 1 (2000) 539-559
7. Nielsen R. Statistical tests of selective neutrality in the age of genomics. Heredity 86 (2001) 641-647
8. Smith J.M., and Haigh J. The hitch-hiking effect of a favourable gene. Genet. Res. 23 (1974) 23-35
9. Ronald J., and Akey J.M. Genome-wide scans for loci under selection in humans. Hum. Genomics 2 (2005) 113-125
10. Przeworski M., et al. Adjusting the focus on human variation. Trends Genet. 16 (2000) 296-302
11. Akey J.M., et al. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol. 2 (2004) e286
12. Hinds D.A., et al. Whole-genome patterns of common DNA variation in three human populations. Science 307 (2005) 1072-1079
13. Altshuler D., et al. A haplotype map of the human genome. Nature 437 (2005) 1299-1320
14. Carlson C.S., et al. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res. 15 (2005) 1553-1565
15. Hamblin M.T., et al. Complex signatures of natural selection at the Duffy blood group locus. Am. J. Hum. Genet. 70 (2002) 369-383
16. Lamason R.L., et al. SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310 (2005) 1782-1786
17. Hearn T., et al. ALMS1, a large gene with a tandem repeat encoding 47 amino acids, causes Alstrom syndrome. Nat. Genet. 31 (2002) 79-83
18. Weir B.S., et al. Measures of human population structure show heterogeneity among genomic regions. Genome Res. 15 (2005) 1468-1476
19. Weir B.S., and Hill W.G. Estimating F-statistics. Annu. Rev. Genet. 36 (2002) 721-750
20. Bersaglieri T., et al. Genetic signatures of strong recent positive selection at the lactase gene. Am. J. Hum. Genet. 74 (2004) 1111-1120
21. Wang E.T., et al. Global landscape of recent inferred darwinian selection for Homo sapiens. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 135-140
22. Voight B.F., et al. A map of recent positive selection in the human genome. PLoS Biol. 4 (2006) e72
23. Sabeti P.C., et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 419 (2002) 832-837
24. Innan H., and Kim Y. Pattern of polymorphism after strong artificial selection in a domestication event. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 10667-10672
25. Wright S.I., et al. The effects of artificial selection on the maize genome. Science 308 (2005) 1310-1314
26. Wang R.L., et al. The limits of selection during maize domestication. Nature 398 (1999) 236-239
27. Wang H., et al. The origin of the naked grains of maize. Nature 436 (2005) 714-719
28. Ostrander E.A., et al. The canine genome. Genome Res. 15 (2005) 1706-1716
29. Pollinger J.P., et al. Selective sweep mapping of genes with large phenotypic effects. Genome Res. 15 (2005) 1809-1819
30. Schlotterer C. Hitchhiking mapping-functional genomics from the population genetics perspective. Trends Genet. 19 (2003) 32-38
31. Shiang R., et al. Mutations in the transmembrane domain of FGFR3 cause the most common genetic form of dwarfism, achondroplasia. Cell 78 (1994) 335-342
32. Martinez S., et al. Achondroplastic dog breeds have no mutations in the transmembrane domain of the FGFR-3 gene. Can. J. Vet. Res. 64 (2000) 243-245
33. Lindblad-Toh K., et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438 (2005) 803-819
34. Parker H.G., et al. Genetic structure of the purebred domestic dog. Science 304 (2004) 1160-1164
35. Nielsen R., et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 3 (2005) e170
36. Clark A.G., et al. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302 (2003) 1960-1963
37. Bustamante C.D., et al. Natural selection on protein-coding genes in the human genome. Nature 437 (2005) 1153-1157
38. Spencer C.C., and Coop G. SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 20 (2004) 3673-3675
39. Nielsen R., et al. Genomic scans for selective sweeps using SNP data. Genome Res. 15 (2005) 1566-1575
40. Rockman M.V., et al. Positive selection on MMP3 regulation has shaped heart disease risk. Curr. Biol. 14 (2004) 1531-1539
41. Thompson E.E., et al. CYP3A variation and the evolution of salt-sensitivity variants. Am. J. Hum. Genet. 75 (2004) 1059-1069
42. Nakajima T., et al. Natural selection and population history in the human angiotensinogen gene (AGT): 736 complete ATG sequences in chromosomes from around the world. Am. J. Hum. Genet. 74 (2004) 898-916
43. Fullerton S.M., et al. Geographic and haplotype structure of candidate type 2 diabetes susceptibility variants at the calpain-10 locus. Am. J. Hum. Genet. 70 (2002) 1096-1106
44. Zhou G., et al. Haplotype structure and evidence for positive selection at the human IL13 locus. Mol. Biol. Evol. 21 (2004) 29-35
45. Sakagami T., et al. Local adaptation and population differentiation at the interleukin 13 and interleukin 4 loci. Genes Immun. 5 (2004) 389-397
46. Rockman M.V., et al. Positive selection on a human-specific transcription factor binding site regulating IL4 expression. Curr. Biol. 13 (2003) 2118-2123
47. Neel J.V. Diabetes mellitus: a 'thrifty' genotype rendered detrimental by 'progress'?. Am. J. Hum. Genet. 14 (1962) 353-362
48. Gleibermann L. Blood pressure and dietary salt in human populations. Ecol. Food Nutr. 2 (1973) 143-156
49. Di Rienzo A., and Hudson R.R. An evolutionary framework for common diseases: the ancestral-susceptibility model. Trends Genet. 21 (2005) 596-601
50. Young J.H., et al. Differential susceptibility to hypertension is due to selection during the out-of-Africa Expansion. PloS Genet. 1 (2005) e82
51. Akey J.M., et al. Interrogating a high density SNP map for signatures of natural selection. Genome Res. 12 (2002) 1805-1814
52. Halder I., and Shriver M.D. Measuring and using admixture to study the genetics of complex diseases. Hum. Genomics 1 (2003) 52-62
53. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
54. Fu Y.X., and Li W.H. Statistical test of neutrality of mutations. Genetics 133 (1993) 693-709
55. Fay J.C., and Wu C.I. Hitchhiking under positive darwinian selection. Genetics 155 (2000) 1405-1413
56. Weir B.S., and Cockerham C.C. Estimating F-statistics for the analysis of population structure. Evolution Int. J. Org. Evolution 38 (1984) 1358-1370
57. Hudson R.R., et al. A test of neutral molecular evolution based on nucleotide data. Genetics 116 (1987) 153-159
58. McDonald J.H., and Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351 (1991) 652-654
59. Nielsen R., and Yang Z. Likelihood models for detecting positive selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148 (1998) 929-936
60. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 (1986) 418-426
61. Suzuki Y., and Gojobori T. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16 (1999) 1315-1328
62. Kingman J.F.C. 'The coalescent'. Stochastic Process. Appl. 13 (1982) 235-248
63. Hudson R.R. Testing the constant-rate neutral allele model with protein sequence data. Evolution 37 (1983) 203-217
64. Rosenberg N.A., and Nordborg M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3 (2002) 380-390
65. Wang X., et al. Gene losses during human origins. PLoS Biol. 4 (2006) e52
66. Xue Y., et al. Spread of an inactive form of caspase-12 in humans is due to recent positive selection. Am. J. Hum. Genet. 78 (2006) 659-670
67. Patin E., et al. Deciphering the ancient and complex evolutionary history of human arylamine N-acetyltransferase genes. Am. J. Hum. Genet. 78 (2006) 423-436