Recent progress in polymorphism-based population genetic inference

Journal of Heredity

Volumn 103, Issue 2, 2012, Pages 287-296

  Crisci, Jessica L ^a   Poh, Yu Ping ^a   Bean, Angela ^a   Simkin, Alfred ^a   Jensen, Jeffrey D ^a,b  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b EPFL   (Switzerland)

Author keywords

Bayesian statistics; demography; likelihood estimation; positive selection

Indexed keywords

GENE FREQUENCY; GENE SEQUENCE; GENETIC POLYMORPHISM; HAPLOTYPE; POPULATION SIZE; PRIORITY JOURNAL; REVIEW; SELECTIVE SWEEP;

ANIMALS; DEMOGRAPHY; DROSOPHILA; GENETICS, POPULATION; GENOME; HAPLOTYPES; MODELS, GENETIC; POLYMORPHISM, GENETIC; SELECTION, GENETIC; SPECIES SPECIFICITY;

EID: 84857546653     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esr128     Document Type: Review

References (61)

1. Adams AM, Hudson RR. 2004. Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms. Genetics. 168(3):1699-1712. (Pubitemid 40007380)
2. Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature. 437(7062):1149-1152. (Pubitemid 41509351)
3. Andolfatto P. 2007. Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res. 17(12):1755-1762. (Pubitemid 351359999)
4. Andolfatto P. 2008. Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA. Genetics. 180(3):1767-1771.
5. Bazin E, Dawson KJ, Beaumont M.A. 2010. Likelihood-free inference of population structure and local adaptation in a Bayesian hierarchical model. Genetics. 185(2):587-602.
6. Beaumont MA, Zhang W, Balding DJ. 2002. Approximate Bayesian computation in population genetics. Genetics. 162(4):2025-2035. (Pubitemid 36114682)
7. Becquet C, Przeworski M. 2007. A new approach to estimate parameters of speciation models with application to apes. Genome Res. 17(10):1505-1519. (Pubitemid 47529435)
8. Begun DJ, Aquadro CF. 1992. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature. 356(9):519-520.
9. Braverman JM, Hudson RR, Kaplan NL, Langley CH, Stephan W. 1995. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics. 140(2):783-796.
10. Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA. 2005. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res. 15(11):1553-1565. (Pubitemid 41545009)
11. Chen H, Patterson N, Reich D. 2010. Population differentiation as a test for selective sweeps. Genome Res. 20(3):393-402.
12. Enard D, Depaulis F, Roest Crollius H. 2010. Human and non-human primate genomes share hotspots of positive selection. PLoS Genet. 6(2):e1000840.
13. Eyre-Walker A, Keightley PD. 2009. Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Mol Biol Evol. 26(9):2097-2108.
14. Fay JC, Wu CI. 2000. Hitchhiking under positive Darwinian selection. Genetics. 155(3):1405-1413. (Pubitemid 30463447)
15. Grossman SR, Shylakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, et al. 2010. A composite of multiple signals distinguishes causal variants in regions of positive selection. Science. 327(5967):883-886.
16. Gutenkunst R, Hernandez RD, Williamson S, Bustamante CD. 2009. Inferring the joint desmographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5(10):e1000695.
17. Hastings WK. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika. 57(1):97-109.
18. Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, Sella G, Przeworski M. 2011. Classic selective sweeps were rare in recent human evolution. Science. 331(6019):920-924.
19. Hey J. 2010. Isolation with migration models for more than two populations. Mol Biol Evol. 27(4):905-920.
20. Hey J, Nielsen R. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics. 167(2):747-760. (Pubitemid 38931862)
21. Jensen JD, Kim YH, DuMont VB, Aquadro CF, Bustamante CD. 2005. Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics. 170(3):1401-1410. (Pubitemid 41105491)
22. Jensen JD, Thornton KR, Andolfatto P. 2008. An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. PLoS Genet. 4(9):e1000198. Public Library of Science.
23. Jensen JD, Thornton KR, Bustamante CD, Aquadro CF. 2007. On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. Genetics. 176(4):2371.
24. Jones DA, Wakeley J. 2008. The influence of gene conversion on linkage disequilibrium around a selective sweep. Genetics. 180(2):1251-1259.
25. Kaplan NL, Hudson RR, Langley C.H. 1989. The "hitchhiking effect" revisited. Genetics. 123(4):887-899.
26. Kelly JK. 1997. A test of neutrality based on interlocus associations. Genetics. 146(3):1197-1206. (Pubitemid 27291000)
27. Kim Y. 2006. Allele frequency distribution under recurrent selective sweeps. Genetics. 172(3):1967-1978.
28. Kim YH, Nielsen R. 2004. Linkage disequilibrium as a signature of selective sweeps. Genetics. 167(3):1513.
29. Kim YH, Stephan W. 2002. Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics. 160(2):765-777. (Pubitemid 34194545)
30. Kimura M. 1955. Solution of a process of random genetic drift with a continuous model. Proc Natl Acad Sci USA. 41(3):144-150.
31. Li H, Stephan W. 2006. Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet. 2(10):e166.
32. Lin K, Li H, Schlötterer C, Futschik A. 2011. Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics. Genetics. 187(1):229-244.
33. Loewe L, Charlesworth B, Bartolomé C,Nöel V. 2006. Estimating selection on nonsynonymous mutations. Genetics. 172(2):1079-1092. (Pubitemid 43345440)
34. Macpherson JM, Sella G, Davis JC, Petrov DA. 2007. Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics. 177(4):2083-2099. (Pubitemid 350276990)
35. Maynard Smith JM, Haigh J. 1974. The hitch-hiking effect of a favourable gene. Genet Res. 23(1):23-35.
36. McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 351(6328):652-654. (Pubitemid 21896661)
37. McVean G. 2007. The structure of linkage disequilibrium around a selective sweep. Genetics. 175(3):1395-1406. (Pubitemid 46798239)
38. McVean GA, Charlesworth B. 2000. The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics. 155(2):929-944. (Pubitemid 30397140)
39. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. 1953. Equation of state calculations by fast computing machines. J Chem Phys. 21(6):1087-1092.
40. Nielsen R. 2005. Molecular signatures of natural selection. Annu Rev Genet. 39:197-218. (Pubitemid 43011113)
41. Nielsen R, Wakeley J. 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics. 158(2):885-896. (Pubitemid 32552323)
42. Nielsen R, Williamson S, Kim YH, Hubisz MJ, Clark AG, Bustamante CD. 2005. Genomic scans for selective sweeps using SNP data. Genome Res. 15(11):1566-1575. (Pubitemid 41545010)
43. Parsch J, Zhang Z, Baines JF. 2009. The influence of demography and weak selection on the McDonald-Kreitman test: an empirical study in Drosophila. Mol Biol Evol. 26(3):691-698.
44. Pavlidis P, Jensen JD, Stephan W. 2010. Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics. 185(3):907-922.
45. 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. (Pubitemid 37204085)
46. Przeworski M. 2002. The signature of positive selection at randomly chosen loci. Genetics. 160(3):1179.
47. Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, et al. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature. 419(6909):832-837. (Pubitemid 35238568)
48. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, et al. 2007. Genome-wide detection and characterization of positive selection in human populations. Nature. 449(7164):913-918. (Pubitemid 47598625)
49. Sella G, Petrov DA, Przeworski M, Andolfatto P. 2009. Pervasive natural selection in the Drosophila genome? PLoS Genet. 5(6):e1000495.
50. Stephan W, Song YS, Langley C.H. 2006. The hitchhiking effect on linkage disequilibrium between linked neutral loci. Genetics. 172(4):2647-2663.
51. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123(3):585-595. (Pubitemid 19274682)
52. Thornton K, Andolfatto P. 2006. Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics. 172(3):1607-1619.
53. Thornton KR. 2009. Automating approximate Bayesian computation by local linear regression. BMC Genet. 10:35.
54. Thornton KR, Jensen JD, Becquet C, Andolfatto P. 2007. Progress and prospects in mapping recent selection in the genome. Heredity. 98(6):340-348. (Pubitemid 46801773)
55. Voight BF, Kudaravalli S, Wen X, Pritchard JK. 2006. A map of recent positive selection in the human genome. PLoS Biol. 4(3):e72.
56. Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 7(2):256-276.
57. Wegmann D, Leuenberger C, Excoffier L. 2009. Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood. Genetics. 182(4):1207-1218.
58. Wiehe TH, Stephan W. 1993. Analysis of a genetic hitchhiking model, and its application to DNA polymorphism data from Drosophila melanogaster. Mol Biol Evol. 10(4):842-854. (Pubitemid 23204799)
59. Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, Bustamante CD. 2005. Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Natl Acad Sci USA. 102(22):7882-7887. (Pubitemid 40781032)
60. Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, Nielsen R. 2007. Localizing recent adaptive evolution in the human genome. PLoS Genet. 3(6):e90.
61. Wooding S, Rogers A. 2002. The matrix coalescent and an application to human single-nucleotide polymorphisms. Genetics. 161(4):1641-1650. (Pubitemid 35014764)