Distortion of genealogical properties when the sample is very large

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

Volumn 111, Issue 6, 2014, Pages 2385-2390

  Bhaskar, Anand ^a   Clark, Andrew G ^b   Song, Yun S ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENEALOGY AND HERALDRY; HUMANS; MODELS, THEORETICAL;

EID: 84893828278     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1322709111     Document Type: Article

References (32)

1. Takahata N (1993) Allelic genealogy and human evolution. Mol Biol Evol 10(1):2-22.
2. Erlich HA, Bergström TF, Stoneking M, Gyllensten U (1996) HLA sequence polymorphism and the origin of humans. Science 274(5292):1552-1554.
3. 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.
4. Harpending HC, et al. (1998) Genetic traces of ancient demography. Proc Natl Acad Sci USA 95(4):1961-1967.
5. Coventry A, et al. (2010) Deep resequencing reveals excess rare recent variants consistent with explosive population growth. Nat Commun 1:131.
6. 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.
7. Tennessen JA, et al. (2012) Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337(6090):64-69.
8. Fu W, et al. (2013) Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493(7431):216-220, and correction (2013) 495(7440): 270.
9. Keinan A, Clark AG (2012) Recent explosive human population growth has resulted in an excess of rare genetic variants. Science 336(6082):740-743.
10. Ptak SE, Przeworski M (2002) Evidence for population growth in humans is confounded by fine-scale population structure. Trends Genet 18(11):559-563.
11. Städler T, Haubold B, Merino C, Stephan W, Pfaffelhuber P (2009) The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics 182(1):205-216.
12. Kingman JFC (1982) The coalescent. Stochastic Process Appl 13(3):235-248.
13. Kingman JFC (1982) Exchangeability and the evolution of large populations. Exchangeability in Probability and Statistics, eds Koch G, Spizzichino F (North-Holland Publishing Company, Amsterdam), pp 97-112.
14. Kingman JFC (1982) On the genealogy of large populations. J Appl Probab 19:27-43.
15. Gravel S, et al. (2011) Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci USA 108(29):11983-11988.
16. 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.
17. 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-1073.
18. Polanski A, Kimmel M (2003) New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth. Genetics 165(1):427-436.
19. Fisher RA (1930) The distribution of gene ratios for rare mutations. Proc R Soc Edinb 50:205-220.
20. Wakeley J, Takahashi T (2003) Gene genealogies when the sample size exceeds the effective size of the population. Mol Biol Evol 20(2):208-213.
21. 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.
22. Lukic S, Hey J, Chen K (2011) Non-equilibrium allele frequency spectra via spectral methods. Theor Popul Biol 79(4):203-219.
23. Lukic S, Hey J (2012) Demographic inference using spectral methods on SNP data, with an analysis of the human out-of-Africa expansion. Genetics 192(2):619-639.
24. Schaffner SF, et al. (2005) Calibrating a coalescent simulation of human genome sequence variation. Genome Res 15(11):1576-1583.
25. Fu Y-X (2006) Exact coalescent for the Wright-Fisher model. Theor Popul Biol 69(4): 385-394.
26. Wakeley J, King L, Low BS, Ramachandran S (2012) Gene genealogies within a fixed pedigree, and the robustness of Kingman's coalescent. Genetics 190(4):1433-1445.
27. Möhle M, Sagitov S (2001) A classification of coalescent processes for haploid exchangeable population models. Ann Probab 29(4):1547-1562.
28. Möhle M, Sagitov S (2003) Coalescent patterns in diploid exchangeable population models. J Math Biol 47(4):337-352.
29. Bhaskar A, Song YS (2009) Multi-locus match probability in a finite population: A fundamental difference between the Moran and Wright-Fisher models. Bioinformatics 25(12):i187-i195.
30. Low B, Clarke A (1991) Family patterns in nineteenth-century Sweden: Impact of occupational status and landownership. J Fam Hist 16(2):117-138.
31. Moreau C, et al. (2011) Deep human genealogies reveal a selective advantage to be on an expanding wave front. Science 334(6059):1148-1150.
32. Davies JL, Simancík F, Lyngsø R, Mailund T, Hein J (2007) On recombination-induced multiple and simultaneous coalescent events. Genetics 177(4):2151-2160.