Neutral genomic regions refine models of recent rapidhuman population growth

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 2, 2014, Pages 757-762

  Gazave, Elodie ^a   Ma, Li ^a,d   Chang, Diana ^a   Coventry, Alex ^a   Gao, Feng ^a   Muzny, Donna ^b   Boerwinkle, Eric ^b   Gibbs, Richard A ^b   Sing, Charles F ^c   Clark, Andrew G ^a   Keinan, Alon ^a  

^a Department of Molecular Biology and Genetics   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^d UNIVERSITY OF MARYLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE FREQUENCY; GENE LOCUS; GENE SEQUENCE; GENOME; HUMAN; POPULATION GROWTH; POPULATION SIZE; POPULATION STRUCTURE; PRIORITY JOURNAL;

BASE SEQUENCE; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC VARIATION; GENETICS, POPULATION; HUMANS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; POPULATION GROWTH; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA; UNITED STATES;

EID: 84892579470     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1310398110     Document Type: Article

References (49)

1. Cohen JE (1996) How Many People Can the Earth Support? (W. W. Norton & Company, New York), 1st Ed.
2. Roberts L (2011) 9 billion? Science 333(6042):540-543.
3. Haub C (1995) How many people have ever lived on earth? Popul Today 23(2):4-5.
4. Keinan A, Clark AG (2012) Recent explosive human population growth has resulted in an excess of rare genetic variants. Science 336(6082):740-743.
5. Hartl D, Clark A (2007) Principles of Population Genetics (Sinauer, Sunderland, MA).
6. Erlich HA, Bergström TF, Stoneking M, Gyllensten U (1996) HLA sequence polymorphism and the origin of humans. Science 274(5292):1552b-1554b.
7. Garrigan D, Hammer MF (2006) Reconstructing human origins in the genomic era. Nat Rev Genet 7(9):669-680.
8. Harding RM, et al. (1997) Archaic African and Asian lineages in the genetic ancestry of modern humans. Am J Hum Genet 60(4):772-789.
9. Keinan A, Mullikin JC, Patterson N, Reich D (2007) Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans. Nat Genet 39(10):1251-1255.
10. Takahata N (1993) Allelic genealogy and human evolution. Mol Biol Evol 10(1):2-22.
11. Yu N, et al. (2001) Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol Biol Evol 18(2):214-222.
12. Tenesa A, et al. (2007) Recent human effective population size estimated from linkage disequilibrium. Genome Res 17(4):520-526.
13. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD (2009) Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet 5(10):e1000695.
14. Gravel S, et al.; 1000 Genomes Project (2011) Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci USA 108(29):11983-11988.
15. Schaffner SF, et al. (2005) Calibrating a coalescent simulation of human genome sequence variation. Genome Res 15(11):1576-1583.
16. Melé M, et al.; Genographic Consortium (2012) Recombination gives a new insight in the effective population size and the history of the old world human populations. Mol Biol Evol 29(1):25-30.
17. Nelson MR, et al. (2012) An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 337(6090):100-104.
18. Coventry A, et al. (2010) Deep resequencing reveals excess rare recent variants consistent with explosive population growth. Nat Commun 1:131.
19. Tennessen JA, et al.; Broad GO; Seattle GO; NHLBI Exome Sequencing Project (2012) Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337(6090):64-69.
20. Kiezun A, et al. (2012) Exome sequencing and the genetic basis of complex traits. Nat Genet 44(6):623-630.
21. Gazave E, Chang D, Clark AG, Keinan A (2013) Population growth inflates the perindividual number of deleterious mutations and reduces their mean effect. Genetics 195(3):969-978.
22. Chamary JV, Hurst LD (2005) Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol 6(9):R75.
23. Chamary JV, Parmley JL, Hurst LD (2006) Hearing silence: Non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7(2):98-108.
24. Fu W, et al.; NHLBI Exome Sequencing Project (2013) Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493(7431):216-220.
25. Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L (2008) Natural selection has driven population differentiation in modern humans. Nat Genet 40(3):340-345.
26. Waldman YY, Tuller T, Keinan A, Ruppin E (2011) Selection for translation efficiency on synonymous polymorphisms in recent human evolution. Genome Biol Evol 3:749-761.
27. Novembre J, et al. (2008) Genes mirror geography within Europe. Nature 456(7218): 98-101.
28. Humphreys K, et al. (2011) The genetic structure of the Swedish population. PLoS ONE 6(8):e22547.
29. Price AL, et al. (2009) The impact of divergence time on the nature of population structure: An example from Iceland. PLoS Genet 5(6):e1000505.
30. Di Gaetano C, et al. (2012) An overview of the genetic structure within the Italian population from genome-wide data. PLoS ONE 7(9):e43759.
31. The ARIC Investigators (1989) The Atherosclerosis Risk in Communities (ARIC) Study: Design and objectives. The ARIC investigators. Am J Epidemiol 129(4):687-702.
32. Nelson MR, et al. (2008) The Population Reference Sample, POPRES: A resource for population, disease, and pharmacological genetics research. Am J Hum Genet 83(3):347-358.
33. McKenna A, et al. (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297-1303.
34. DePristo MA, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5):491-498.
35. Morrison AC, et al.; Cohorts for Heart and Aging Research in Genetic Epidemiology (CHARGE) Consortium (2013) Whole-genome sequence-based analysis of high-density lipoprotein cholesterol. Nat Genet 45(8):899-901.
36. Cooper GM, et al.; NISC Comparative Sequencing Program (2005) Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15(7):901-913.
37. Myers S, Fefferman C, Patterson N (2008) Can one learn history from the allelic spectrum? Theor Popul Biol 73(3):342-348.
38. Betzig L (2012) Means, variances, and ranges in reproductive success: Comparative evidence. Evol Hum Behav 33(4):309-317.
39. Boyko AR, et al. (2008) Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 4(5):e1000083.
40. Yu F, et al. (2009) Detecting natural selection by empirical comparison to random regions of the genome. Hum Mol Genet 18(24):4853-4867.
41. Ayodo G, et al. (2007) Combining evidence of natural selection with association analysis increases power to detect malaria-resistance variants. Am J Hum Genet 81(2):234-242.
42. Altshuler DM, et al.; International HapMap 3 Consortium (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467(7311):52-58.
43. Abecasis GR, et al.; 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56-65.
44. Price AL, et al. (2006) Principal components analysis corrects for stratification in genome- wide association studies. Nat Genet 38(8):904-909.
45. Akey JM (2009) Constructing genomic maps of positive selection in humans: Where do we go from here? Genome Res 19(5):711-722.
46. Arbiza L, Zhong E, Keinan A (2012) NRE: A tool for exploring neutral loci in the human genome. BMC Bioinformatics 13:301.
47. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-1760.
48. Vuong QH (1989) Likelihood ratio tests for model selection and non-nested hypotheses. Econometrica 57(2):307-333.
49. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18(2):337-338.