The abundance of deleterious polymorphisms in humans

Genetics

Volumn 190, Issue 4, 2012, Pages 1579-1583

  Subramanian, Sankar ^a  

^a GRIFFITH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

AFRICAN AMERICAN; AMINO ACID SUBSTITUTION; ARTICLE; ASIAN; EUROPEAN AMERICAN; GENE FREQUENCY; GENE MUTATION; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; NONHUMAN; NONSYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISM; PHYLOGENETIC TREE ROOT; POPULATION GENETIC STRUCTURE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE; SYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISM;

ADAPTATION, BIOLOGICAL; AMINO ACID SUBSTITUTION; ETHNIC GROUPS; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; TIME FACTORS;

EID: 84859589236     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.111.137893     Document Type: Article

References (35)

1. Adzhubei, I. A., S. Schmidt, L. Peshkin, V. E. Ramensky, A. Gerasimova et al., 2010 A method and server for predicting damaging missense mutations. Nat. Methods 7: 248-249.
2. Ballard, J. W., and M. Kreitman, 1994 Unraveling selection in the mitochondrial genome of Drosophila. Genetics 138: 757-772.
3. Boyko, A. R., S. H. Williamson, A. R. Indap, J. D. Degenhardt, R. D. Hernandez et al., 2008 Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 4: e1000083.
4. Bustamante, C. D., A. Fledel-Alon, S. Williamson, R. Nielsen, M. T. Hubisz et al., 2005 Natural selection on protein-coding genes in the human genome. Nature 437: 1153-1157.
5. Cargill, M., D. Altshuler, J. Ireland, P. Sklar, K. Ardlie et al., 1999 Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22: 231-238.
6. Cirulli, E. T., and D. B. Goldstein, 2010 Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat. Rev. Genet. 11: 415-425.
7. Excoffier, L., 1990 Evolution of human mitochondrial DNA: evidence for departure from a pure neutral model of populations at equilibrium. J. Mol. Evol. 30: 125-139.
8. Eyre-Walker, A., M. Woolfit, and T. Phelps, 2006 The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics 173: 891-900.
9. Hasegawa, M., Y. Cao, and Z. Yang, 1998 Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/ synonymous rate ratio is much higher within species than between species. Mol. Biol. Evol. 15: 1499-1505.
10. Holmes, E. C., 2003 Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. J. Virol. 77: 11296-11298.
11. Hughes, A. L., B. Packer, R. Welch, A. W. Bergen, S. J. Chanock et al., 2003 Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc. Natl. Acad. Sci. USA 100: 15754-15757.
12. Hughes, A. L., B. Packer, R. Welch, A. W. Bergen, S. J. Chanock et al., 2005 Effects of natural selection on interpopulation divergence at polymorphic sites in human protein-coding loci. Genetics 170: 1181-1187.
13. Kimura, M., 1983 The Neutral Theory of Molecular Evolution, Cambridge University Press, Cambridge, UK.
14. Kimura, M., and T. Ohta, 1971 Protein polymorphism as a phase of molecular evolution. Nature 229: 467-469.
15. Kivisild, T., P. Shen, D. P. Wall, B. Do, R. Sung et al., 2006 The role of selection in the evolution of human mitochondrial genomes. Genetics 172: 373-387.
16. Kryazhimskiy, S., and J. B. Plotkin, 2008 The population genetics of dN/dS. PLoS Genet. 4: e1000304.
17. Li, H., and R. Durbin, 2011 Inference of human population history from individual whole-genome sequences. Nature 475: 493-496.
18. Lohmueller, K. E., A. R. Indap, S. Schmidt, A. R. Boyko, R. D. Hernandez et al., 2008 Proportionally more deleterious genetic variation in European than in African populations. Nature 451: 994-997.
19. Marth, G. T., E. Czabarka, J. Murvai, and S. T. Sherry, 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.
20. McDonald, J. H., and M. Kreitman, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
21. Merriwether, D.A., A. G. Clark, S. W. Ballinger, T. G. Schurr, H. Soodyall et al., 1991 The structure of human mitochondrial DNA variation. J. Mol. Evol. 33: 543-555.
22. Nachman, M. W., S. N. Boyer, and C. F. Aquadro, 1994 Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice. Proc. Natl. Acad. Sci. USA 91: 6364-6368.
23. Nachman, M. W., W. M. Brown, M. Stoneking, and C. F. Aquadro, 1996 Nonneutral mitochondrial DNA variation in humans and chimpanzees. Genetics 142: 953-963.
24. Ohta, T., 1973 Slightly deleterious mutant substitutions in evolution. Nature 246: 96-98.
25. Peterson, G. I., and J. Masel, 2009 Quantitative prediction of molecular clock and ka/ks at short timescales. Mol. Biol. Evol. 26: 2595-2603.
26. Rand, D. M., and L. M. Kann, 1996 Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol. Biol. Evol. 13: 735-748.
27. Rand, D. M., M. Dorfsman, and L. M. Kann, 1994 Neutral and non-neutral evolution of Drosophila mitochondrial DNA. Genetics 138: 741-756.
28. Rocha, E. P., J. M. Smith, L. D. Hurst, M. T. Holden, J. E. Cooper et al., 2006 Comparisons of dN/dS are time dependent for closely related bacterial genomes. J. Theor. Biol. 239: 226-235.
29. Ruiz-Pesini, E., D. Mishmar, M. Brandon, V. Procaccio, and D. C. Wallace, 2004 Effects of purifying and adaptive selection on regional variation in human mtDNA. Science 303: 223-226.
30. Subramanian, S., 2009 Temporal trails of natural selection in human mitogenomes. Mol. Biol. Evol. 26: 715-717.
31. Tajima, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
32. Tishkoff, S. A., F. A. Reed, F. R. Friedlaender, C. Ehret, A. Ranciaro et al., 2009 The genetic structure and history of Africans and African Americans. Science 324: 1035-1044.
33. Watterson, G. A., 1978 The homozygosity test of neutrality. Genetics 88: 405-417.
34. Whittam, T. S., A. G. Clark, M. Stoneking, R. L. Cann, and A. C. Wilson, 1986 Allelic variation in human mitochondrial genes based on patterns of restriction site polymorphism. Proc. Natl. Acad. Sci. USA 83: 9611-9615.
35. Wong, G. K., Z. Yang, D. A. Passey, M. Kibukawa, M. Paddock et al., 2003 A population threshold for functional polymorphisms. Genome Res. 13: 1873-1879.