Inferring population size changes with sequence and SNP data: Lessons from human bottlenecks

Heredity

Volumn 110, Issue 5, 2013, Pages 409-419

  Gattepaille, L M ^a   Jakobsson, M ^a,b   Blum, M G B ^c  

^a UPPSALA UNIVERSITY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

^c LABORATOIRE TIMC IMAG   (France)

Author keywords

Bottlenecks; Demographic inference; Linkage disequilibrium; Out of Africa; Site frequency spectrum; SNPs

Indexed keywords

DATA ACQUISITION; DISEQUILIBRIUM; EVOLUTIONARY BIOLOGY; GENOME; HUMAN EVOLUTION; LIFE HISTORY; POLYMORPHISM; POPULATION SIZE; RECOMBINATION; RECONSTRUCTION;

BAYES THEOREM; DEMOGRAPHY; GENE LINKAGE DISEQUILIBRIUM; HAPLOTYPE; HOMOZYGOTE; HUMAN; METHODOLOGY; POPULATION DENSITY; POPULATION GENETICS; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

BAYES THEOREM; DATA INTERPRETATION, STATISTICAL; DEMOGRAPHY; GENETICS, POPULATION; HAPLOTYPES; HOMOZYGOTE; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION DENSITY;

SANDFLY FEVER SICILIAN VIRUS;

EID: 84878716362     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2012.120     Document Type: Review

References (80)

1. Achaz G (2009). Frequency spectrum neutrality tests: one for all and all for one. Genetics 183: 249-258.
2. Adams AM, Hudson RR (2004). Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms. Genetics 168: 1699-1712. (Pubitemid 40007380)
3. Atzmon G, Hao L, Pe'er I, Velez C, Pearlman A, Palamara PF et al. (2010). Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry. Am J Hum Genet 86: 850.
4. Auton A, Bryc K, Boyko AR, Lohmueller KE, Novembre J, Reynolds A et al. (2009). Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Res 19: 795-803.
5. Barton NH, Charlesworth B (1984). Genetic revolutions, founder effects, and speciation. Annu Rev Ecol Evol Syst 15: 133-164.
6. Blum MGB, Jakobsson M (2011). Deep divergences of human gene trees and models of human origins. Mol Biol Evol 28: 889-898.
7. Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL et al. (2007). Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 3: e163.
8. Chapman NH, Thompson EA (2003). A model for the length of tracts of identity by descent in finite random mating populations. Theor Popul Biol 64: 141-150. (Pubitemid 38042760)
9. Chikhi L, Sousa V, Luisi P, Goossens B, Beaumont MA (2010). The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics 186: 983-995.
10. De A, Durrett R (2007). Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum. Genetics 176: 969-981. (Pubitemid 46961100)
11. DeGiorgio M, Degnan JH, Rosenberg NA (2011). Coalescence-time distributions in a serial founder model of human evolutionary history. Genetics 189: 579-593.
12. Depaulis F, Mousset S, Veuille M (2003). Power of neutrality tests to detect bottlenecks and hitchhiking. J Mol Evol 57: S190-S200. (Pubitemid 37544008)
13. England PR, Osler GH, Woodworth LM, Montgomery ME, Briscoe DA, Frankham R (2003). Effects of intense versus diffuse population bottlenecks on microsatellite genetic diversity and evolutionary potential. Conserv Genet 4: 595-604. (Pubitemid 37216056)
14. Fagundes NJR, Ray N, Beaumont MA, Neuenschwander S, Salzano FM, Bonatto SL et al. (2007). Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci USA 104: 17614-17619. (Pubitemid 350210884)
15. Fay JC, Wu C-I (1999). A human population bottleneck is not incompatible with the discordance between patterns of mitochondrial vs. nuclear DNA variation. Mol Biol Evol 16: 1003-1006.
16. François O, Blum MGB, Jakobsson M, Rosenberg NA (2008). Demographic history of European populations of Arabidopsis thaliana. PLoS Genet 4: e1000075.
17. Garrigan D, Hammer MF (2006). Reconstructing human origins in the genomic era. Nat Rev Genet 7: 669-680. (Pubitemid 44260003)
18. Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG et al. (2011). Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci USA 108: 11983-11988.
19. Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL et al. (2009). Whole population, genome-wide mapping of hidden relatedness. Genome Res 19: 318-326.
20. Gusev A, Palamara PF, Aponte G, Zhuang Z, Darvasi A, Gregersen P et al. (2012). The architecture of long-range haplotypes shared within and across populations. Mol Biol Evol 29: 473-486.
21. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD (2009). Inferring the joint demographic history of multiple populations from multidimensional SNP data. PLoS Genet 5: e1000695.
22. Haddrill P, Thornton KR, Charlesworth B, Andolfatto P (2005). Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res 15: 790-799. (Pubitemid 41003102)
23. Hayes BJ, Visscher PM, McPartlan HC, Goddard ME (2003). Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res 13: 635-643. (Pubitemid 36511922)
24. Heled J, Drummond AJ (2008). Bayesian inference of population size history from multiple loci. BMC Evol Biol 8: 1-15.
25. Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Kidd JM et al. (2011). Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proc Natl Acad Sci USA 108: 5154-5162.
26. Hill WG (1981). Estimation of effective population size from data on linkage disequilibrium. Genet Res 38: 209-216. (Pubitemid 12173026)
27. Ho SYW, Shapiro B (2011). Skyline-plot methods for estimating demographic history from nucleotide sequences. Mol Ecol Resour 11: 423-434.
28. Howrigan DP, Simonson MA, Keller MC (2011). Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms. BMC Genomics 12: 460.
29. Hudson RR (2002). Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338. (Pubitemid 34183119)
30. Huff CD, Witherspoon DJ, Simonson TS, Xing J, Watkins WS, Zhang Y et al. (2011). Maximum-likelihood estimation of recent shared ancestry (ERSA). Genome Res 21: 768-774.
31. Hutter S, Li H, Beisswanger S, De Lorenzo D, Stephan W (2007). Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosome-wide SNP data. Genetics 177: 469-480. (Pubitemid 47555864)
32. Keightley PD, Halligan DL (2011). Inference of site frequency spectra from highthroughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans. Genetics 188: 931-940.
33. 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: 1251-1255. (Pubitemid 47482683)
34. Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, Wilson JF (2010). Genomic runs of homozygosity record population history and consanguinity. PLoS ONE 5: e13996.
35. Laurent SJY, Werzner A, Excoffier L, Stephan W (2011). Approximate Bayesian Analysis of Drosophila melanogaster polymorphism data reveals a recent colonization of southeast Asia. Mol Biol Evol 28: 2041-2051.
36. Li H, Durbin R (2011). Inference of human population history from individual wholegenome sequences. Nature 475: 493-497.
37. Li HP, Stephan W (2006). Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet 2: 1580-1589. (Pubitemid 44656532)
38. Lohmueller KE, Bustamante CD, Clark AG (2009). Methods for human demographic inference using haplotype patterns from genome-wide SNP data. Genetics 182: 217-231.
39. Lohmueller KE, Bustamante CD, Clark AG (2010). The effect of recent admixture on inference of ancient population history. Genetics 185: 611-622.
40. Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD et al. (2008). Proportionally more deleterious genetic variation in European than in African populations. Nature 451: 994-997. (Pubitemid 351301732)
41. Marth GT, Czabarka E, Murvai J, Sherry ST (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. (Pubitemid 38364726)
42. Maruyama T (1982). Stochastic integrals and their application to population genetics. In: Kimura M (ed) Molecular Evolution, Protein Polymorphism and the Neutral Theory. Springer-Verlag: Berlin, pp 151-166.
43. Maruyama T, Fuerst PA (1984). Population bottlenecks and nonequilibrium models in population genetics. I. Allele numbers when populations evolve from zero variability. Genetics 108: 745-763. (Pubitemid 15208414)
44. McEvoy BP, Powell JE, Goddard ME, Visscher PM (2011). Human population dispersal "Out of Africa" estimated from linkage disequilibrium and allele frequencies of SNPs. Genome Res 21: 821-829.
45. McVean GAT (2002). A genealogical interpretation of linkage disequilibrium. Genetics 162: 987-991. (Pubitemid 35365058)
46. Mondol S, Karanth KU, Ramakrishnan U (2009). Why the Indian subcontinent holds the key to global tiger recovery. PLoS Genet 5: e1000585.
47. Mourier T, Ho SYW, Gilbert MTP, Willerslev E, Orlando L (2012). Statistical guidelines for detecting past population shifts using ancient DNA. Mol Biol Evol 29: 2241-2251.
48. Nachman MW, Crowell SL (2000). Estimate of the mutation rate per nucleotide in humans. Genetics 156: 297-304.
49. Nei M, Maruyama T, Chakraborty R (1975). The bottleneck effect and genetic variability in populations. Evolution 29: 1-10.
50. Nielsen R (2005). Molecular signatures of natural selection. Annu Rev Genet 39: 197-218. (Pubitemid 43011113)
51. Nielsen R, Beaumont MA (2009). Statistical inferences in phylogeography. Mol Ecol 18: 1034-1047.
52. Nielsen R, Hubisz MJ, Clark AG (2004). Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data. Genetics 168: 2373-2382. (Pubitemid 40066369)
53. Ohta T, Kimura M (1971). Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics 68: 571-580.
54. Patin E, Laval G, Barreiro LB, Salas A, Semino O, Santachiara-Benerecetti S et al. (2009). Inferring the demographic history of African farmers and Pygmy hunter-gatherers using a multilocus resequencing data set. PLoS Genet 5: e1000448.
55. Peter BM, Wegmann D, Excoffier L (2010). Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure. Mol Ecol 19: 4648-4660.
56. Polanski A, Kimmel M (2003). New explicit expressions for relative frequencies of singlenucleotide polymorphisms with application to statistical inference on population growth. Genetics 165: 427-436. (Pubitemid 37204085)
57. Pritchard JK, Przeworski M (2001). Linkage disequilibrium in humans: models and data. Am J Hum Genet 69: 1-14. (Pubitemid 32614013)
58. Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW (1999). Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol Biol Evol 16: 1791-1798.
59. Ptak S, Przeworski M (2002). Evidence for population growth in humans is confounded by population structure. Trends Genet 18: 559-563. (Pubitemid 35284648)
60. Pybus OG, Rambaut A, Harvey PH (2000). An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155: 1429-1437. (Pubitemid 30463449)
61. Ramirez-Soriano A, Ramos-Onsins SE, Rozas J, Calafell F, Navarro A (2008). Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination. Genetics 179: 555-567.
62. Ramos-Onsins SE, Rozas J (2002). Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19: 2092-2100. (Pubitemid 35440445)
63. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ et al. (2001). Linkage disequilibrium in the human genome. Nature 411: 199-204. (Pubitemid 32455179)
64. Roux C, Pauwels M, Ruggiero M-V, Charlesworth D, Castric V, Vekemans X (2013). Recent and ancient signature of balancing selection around the S-locus in Arabidopsis halleri and A. lyrata. Mol Biol Evol 30: 435-447.
65. Ruzzante DE, Walde SJ, Gosse JC, Cussac VE, Habit E, Zemlak TS et al. (2008). Climate control on ancestral population dynamics: insight from Patagonian fish phylogeography. Mol Ecol 17: 2234-2244. (Pubitemid 351562804)
66. Sawyer SA, Hartl DL (1992). Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
67. Scally A, Durbin R (2012). Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet 13: 745-753.
68. Schaeffer SW (2002). Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura. Genet Res 80: 163-175. (Pubitemid 36267286)
69. Schaffner S, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D (2005). Calibrating a coalescent simulation of human genome sequence variation. Genome Res 15: 1576-1583. (Pubitemid 41545011)
70. Schaper E, Eriksson A, Rafajlovic M, Sagitov S, Mehlig B (2012). Linkage disequilibrium under recurrent bottlenecks. Genetics 190: 217-229.
71. Sjödin P, Sjöstrand AE, Jakobsson M, Blum MGB (2012). Resequencing data provide no evidence for a human bottleneck in Africa during the penultimate glacial period. Mol Biol Evol 29: 1851-1860.
72. 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: 205-216.
73. Tajima F (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595. (Pubitemid 19274682)
74. Tajima F (1997). Estimation of the amount of DNA polymorphism and statistical tests of the neutral mutation hypothesis based on DNA polymorphism. In: Tavaré S, Donnelly P (eds) 'Progress in Population Genetics and Human Evolution'. Springer: Berlin, pp 149-164.
75. The 1000 Genomes Project Consortium (2010). A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
76. Thornton K (2005). Recombination and the properties of Tajima's D in the context of approximate likelihood calculation. Genetics 171: 2143-2148.
77. Thornton KR, Andolfatto P (2006). Approximate Bayesian Inference reveals evidence for a recent, severe, bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
78. Voight BF, Adams AM, Frisse LA, Qian YD, Hudson RR, Di Rienzo A (2005). Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc Natl Acad Sci USA 102: 18508-18513. (Pubitemid 43011256)
79. Williamson-Natesan EG (2005). Comparison of methods for detecting bottlenecks from microsatellite loci. Conserv Genet 6: 551-562. (Pubitemid 43052235)
80. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD et al. (2005). The effects of artificial selection on the maize genome. Science 308: 1310-1314. (Pubitemid 40746127).