Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations

Genetics

Volumn 185, Issue 3, 2010, Pages 907-922

  Pavlidis, Pavlos ^a   Jensen, Jeffrey D ^b   Stephan, Wolfgang ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA FOOTPRINTING; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC LINKAGE; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOME; HUMAN; HYPOTHESIS; MACHINE LEARNING; POPULATION GENETIC PARAMETERS; POPULATION SIZE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL SIGNIFICANCE; ANIMAL; BIOLOGICAL MODEL; COMPUTER PROGRAM; DROSOPHILA MELANOGASTER; GENETICS; METAGENOMICS; THEORETICAL MODEL;

SANDFLY FEVER SICILIAN VIRUS;

ANIMALS; DROSOPHILA MELANOGASTER; GENOME; LINKAGE DISEQUILIBRIUM; METAGENOMICS; MODELS, GENETIC; MODELS, THEORETICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC; SOFTWARE;

EID: 77955759338     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.116459     Document Type: Article

References (64)

1. AKEY, J. M., 2009 Constructing genomic maps of positive selection in humans: Where do we go from here? Genome Res. 19: 711-722.
2. AKEY, J. M., M. A. EBERLE, M. J. RIEDER, C. S. CARLSON, M. D. SHRIVER et al., 2004 Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol. 2: e286.
3. ANDOLFATTO, P., 2007 Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res. 17: 1755-1762.
4. BARTON, N., 1998 The effect of hitch-hiking on neutral genealogies. Genet. Res. 72: 123-133.
5. BEISSWANGER, S., and W. STEPHAN, 2008 Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila. Proc. Natl. Acad. Sci. USA 105: 5447-5452.
6. BRAVERMAN, J. M., R. R. HUDSON, N. L. KAPLAN, C. H. LANGLEY and W. STEPHAN, 1995 The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140: 783-796.
7. CHADEAU-HYAM, M., C. J. HOGGART, P. F. O'REILLY, J. C. WHITTAKER, M. D. IORIO et al., 2008 Fregene: simulation of realistic sequence-level data in populations and ascertained samples. BMC Bioinformatics 9: 364.
8. CHEVIN, L.-M., S. BILLIARD and F. HOSPITAL, 2008 Hitchhiking both ways: effect of two interfering selective sweeps on linked neutral variation. Genetics 180: 301-316.
9. COOP, G., and R. C. GRIFFITHS, 2004 Ancestral inference on gene trees under selection. Theor. Popul. Biol. 66: 219-232.
10. DUDA, R. O., P. E. HART and D. G. STORK, 2000 Pattern Classification, Ed. 2. Wiley-Interscience, Indianapolis.
11. EXCOFFIER, L., A. ESTOUP and J.-M. CORNUET, 2005 Bayesian analysis of an admixture model with mutations and arbitrarily linked markers. Genetics 169: 1727-1738.
12. FAY, J. C., and C. I. Wu, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
13. GLINKA, S., L. OMETTO, S. MOUSSET, W. STEPHAN and D. DE LORENZO, 2003 Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach. Genetics 165: 1269-1278.
14. HAN, J., and M. KAMBER, 2000 Data Mining: Concepts and Techniques, The Morgan Kaufmann Series in Data Management Systems. Morgan Kaufmann, San Francisco.
15. HARR, B., M. KAUER and C. SCHLÖTTERER, 2002 Hitchhiking mapping: a population-based fine-mapping strategy for adaptive mutations in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 99: 12949-12954.
16. HASTIE, T., R. TIBSHIRANI and J. H. FRIEDMAN, 2001 The Elements of Statistical Learning. Springer, New York.
17. HERMISSON, J., and P. S. PENNINGS, 2005 Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169: 2335-2352.
18. HERNANDEZ, R. D., 2008 A flexible forward simulator for populations subject to selection and demography. Bioinformatics 24: 2786-2787.
19. HEY, J., and R. NIELSEN, 2007 Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA 104: 2785-2790.
20. HOGGART, C. J., M. CHADEAU-HYAM, T. G. CLARK, R. LAMPARIELLO, J. C. WHITTAKER et al., 2007 Sequence-level population simulations over large genomic regions. Genetics 177: 1725-1731.
21. HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
22. JENSEN, J. D., Y. KIM, V. BAUER DUMONT, C. F. AQUADRO and C. D. BUSTAMANTE, 2005 Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170: 1401-1410.
23. JENSEN, J. D., K. R. THORNTON, C. D. BUSTAMANTE and C. F. AQUADRO, 2007 On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. Genetics 176: 2371-2379.
24. JENSEN, J. D., K. R. THORNTON and P. ANDOLFATTO, 2008 An approximate Bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. PLoS Genet. 4: e1000198.
25. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 The hitchhiking effect revisited. Genetics 123: 887-899.
26. KELLY, J. K., 1997 A test of neutrality based on interlocus associations. Genetics 146: 1197-1206.
27. KIM, Y., 2006 Allele frequency distribution under recurrent selective sweeps. Genetics 172: 1967-1978.
28. KIM, Y., and R. NIELSEN, 2004 Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513-1524.
29. KIM, Y., and W. STEPHAN, 2000 Joint effects of genetic hitchhiking and background selection on neutral variation. Genetics 155: 1415-1427.
30. KIM, Y., and W. STEPHAN, 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
31. KIM, Y., and W. STEPHAN, 2003 Selective sweeps in the presence of interference among partially linked loci. Genetics 164: 389-398.
32. KIRBY, D. A., and W. STEPHAN, 1996 Multi-locus selection and the structure of variation at the white gene of Drosophila melanogaster. Genetics 144: 635-645.
33. LANGLEY, C. H., and J. F. CROW, 1974 The direction of linkage disequilibrium. Genetics 78: 937-941.
34. LI, H., and W. STEPHAN, 2006 Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet. 2: e166.
35. MACPHERSON, J. M., G. SELLA, J. C. DAVIS and D. A. PETROV, 2007 Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics 177: 2083-2099.
36. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
37. MCVEAN, G., 2007 The structure of linkage disequilibrium around a selective sweep. Genetics 175: 1395-1406.
38. MYERS, S., C. FEFFERMAN and N. PATTERSON, 2008 Can one learn history from the allelic spectrum? Theor. Popul. Biol. 73: 342-348.
39. NAIR, S., D. NASH, D. SUDIMACK, A. JAIDEE, M. BARENDS et al., 2007 Recurrent gene amplification and soft selective sweeps during evolution of multidrug resistance in malaria parasites. Mol. Biol. Evol. 24: 562-573.
40. NIELSEN, R., 2000 Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154: 931-942.
41. NIELSEN, R., S. WILLIAMSON, Y. KIM, M. J. HUBISZ, A. G. CLARK et al., 2005 Genomic scans for selective sweeps using SNP data. Genome Res. 15: 1566-1575.
42. NIELSEN, R., M. J. HUBISZ, I. HELLMANN, D. TORGERSON, A. M. ANDRÉS et al., 2009 Darwinian and demographic forces affecting human protein coding genes. Genome Res. 19: 838-849.
43. ORENGO, D. J., and M. AGUADÉ, 2004 Detecting the footprint of positive selection in a European population of Drosophila melanogaster: multilocus pattern of variation and distance to coding regions. Genetics 167: 1759-1766.
44. ORENGO, D. J., and M. AGUADÉ, 2010 Uncovering the footprint of positive selection on the X chromosome of Drosophila melanogaster. Mol. Biol. Evol. 27: 153-160.
45. PAVLIDIS, P., S. HUTTER and W. STEPHAN, 2008 A population genomic approach to map recent positive selection in model species. Mol. Ecol. 17: 3585-3598.
46. PFAFFELHUBER, P., A. LEHNERT and W. STEPHAN, 2008 Linkage disequilibrium under genetic hitchhiking in finite populations. Genetics 179: 527-537.
47. PICKRELL, J. K., G. COOP, J. NOVEMBRE, S. KUDARAVALLI, J. Z. LI et al., 2009 Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 19: 826-837.
48. PRZEWORSKI, M., 2002 The signature of positive selection at randomly chosen loci. Genetics 160: 1179-1189.
49. RAMOS-ONSINS, S. E., S. OUSSET, T. MITCHELL-OLDS and W. STEPHAN, 2007 Population genetic inference using a fixed number of segregating sites: a reassessment. Genet. Res. 89: 231-244.
50. SABETI, P. C., D. E. REICH, J. M. HIGGINS, H. Z. LEVINE, D. J. RICHTER et al., 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
51. SPENCER, C. C. A., and G. COOP, 2004 SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 20: 3673-3675.
52. STEPHAN, W., 1995 An improved method for estimating the rate of fixation of favorable mutations based on DNA polymorphism data. Mol. Biol. Evol. 12: 959-962.
53. STEPHAN, W., T. H. E. WIEHE and M. W. LENZ, 1992 The effect of strongly selected substitutions on neutral polymorphism: analytical results based on diffusion theory. Theor. Popul. Biol. 41: 237-254.
54. STEPHAN, W., Y. S. SONG and C. H. LANGLEY, 2006 The hitchhiking effect on linkage disequilibrium between linked neutral loci. Genetics 172: 2647-2663.
55. SVETEC, N., P. PAVLIDIS and W. STEPHAN, 2009 Recent strong positive selection on Drosophila melanogaster HDAC6, a gene encoding a stress surveillance factor, as revealed by population genomic analysis. Mol. Biol. Evol. 26: 1549-1556.
56. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
57. TANG, K., K. R. THORNTON and M. STONEKING, 2007 A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol. 5: e171.
58. TESHIMA, K. M., and H. INNAN, 2009 mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection. BMC Bioinformatics 10: 166.
59. THORNTON, K., and P. ANDOLFATTO, 2006 Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
60. THORNTON, K. R., and J. D. JENSEN, 2007 Controlling the false-positive rate in multilocus genome scans for selection. Genetics 175: 737-750.
61. VOIGHT, B. F., S. KUDARAVALLI, X. WEN and J. K. PRITCHARD, 2006 A map of recent positive selection in the human genome. PLoS Biol. 4: e72.
62. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
63. WIEHE, T. H. E., and W. STEPHAN, 1993 Analysis of a genetic hitchhiking model, and its application to DNA polymorphism data from Drosophila melanogaster. Mol. Biol. Evol. 10: 842-854.
64. ZIVKOVIC, D., and T. WIEHE, 2008 Second-ordermoments of segregating sites under variable population size. Genetics 180: 341-357.