Learning natural selection from the site frequency spectrum

Genetics

Volumn 195, Issue 1, 2013, Pages 181-193

  Ronen, Roy ^a   Udpa, Nitin ^a   Halperin, Eran ^b,c   Bafna, Vineet ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

^c INTERNATIONAL COMPUTER SCIENCE INSTITUTE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE DEACETYLASE 4; MANNAN BINDING LECTIN ASSOCIATED SERINE PROTEINASE; NOTCH RECEPTOR; PROLINE; SCAVENGER RECEPTOR; SERINE; SIGNAL PEPTIDE;

ALGORITHM; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; BALANCING SELECTION; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EVOLUTIONARY ADAPTATION; GENE FREQUENCY; GENETIC ANALYSIS; HETEROZYGOTE; HUMAN; HUMAN GENOME; HYPOXIA; LEARNING; NATURAL SELECTION; NONHUMAN; OLFACTORY RECEPTOR; PRIORITY JOURNAL; SELECTIVE SWEEP; SITE FREQUENCY SPECTRUM; SUPPORT VECTOR MACHINE;

NATURAL SELECTION; SITE FREQUENCY SPECTRUM; SUPERVISED LEARNING;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; ANOXIA; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETIC LOCI; HUMANS; MODELS, GENETIC; POLYMORPHISM, GENETIC; POPULATION; RECEPTORS, NOTCH; SELECTION, GENETIC;

EID: 84883794892     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.152587     Document Type: Article

References (51)

1. Abecasis, G. R., D. Altshuler, A. Auton, L. D. Brooks, R. M. Durbin et al., 2010 A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
2. Achaz, G., 2009 Frequency spectrum neutrality tests: one for all and all for one. Genetics 183: 249-258.
3. Alachiotis, N., A. Stamatakis, and P. Pavlidis, 2012 OmegaPlus: a scalable tool for rapid detection of selective sweeps in wholegenome datasets. Bioinformatics 28: 2274-2275.
4. Bersaglieri, T., P. C. Sabeti, N. Patterson, T. Vanderploeg, S. F. Schaffner et al., 2004 Genetic signatures of strong recent positive selection at the lactase gene. Am. J. Hum. Genet. 74: 1111-1120.
5. Boldt, A. B., P. R. Luz, and I. J. Messias-Reason, 2011 MASP2 haplotypes are associated with high risk of cardiomyopathy in chronic Chagas disease. Clin. Immunol. 140: 63-70.
6. Campbell, C. D., J. X. Chong, M. Malig, A. Ko, B. L. Dumont et al., 2012 Estimating the human mutation rate using autozygosity in a founder population. Nat. Genet. 44: 1277-1281.
7. Campbell, R., 2007 Coalescent size vs. coalescent time with strong selection. Bull. Math. Biol. 69: 2249-2259.
8. Chang, C. C., and C. J. Lin, 2011 LIBSVM: a library for support vector machines. ACM Trans. Intell. Syst. Technol. 2: 27:1-27:27.
9. Chen, H., R. E. Green, S. Paabo, and M. Slatkin, 2007 The joint allele-frequency spectrum in closely related species. Genetics 177: 387-398.
10. Chen, H., N. Patterson, and D. Reich, 2010 Population differentiation as a test for selective sweeps. Genome Res. 20: 393-402.
11. Cingolani, P., A. Platts, M. Coon, T. Nguyen, L. Wang et al., 2012 A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6: 80-92.
12. Durrett, R., 2002 Probability Models for DNA Sequence Evolution, Ed. 2. Springer-Verlag, New York.
13. Fagundes, N. J. R., N. Ray, M. Beaumont, S. Neuenschwander, F. M. Salzano et al., 2007 Statistical evaluation of alternative models of human evolution. Proc. Natl. Acad. Sci. USA 104: 17614-17619.
14. Fan, R.-E., K.-W. Chang, C.-J. Hsieh, X.-R. Wang, and C.-J. Lin, 2008 LIBLINEAR: a library for large linear classification. J. Mach. Learn. Res. 9: 1871-1874.
15. Fay, J. C., and C. I. Wu, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
16. Frazer, K. A., D. G. Ballinger, D. R. Cox, D. A. Hinds, L. L. Stuve et al., 2007 A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
17. Fu, Y. X., 1995 Statistical properties of segregating sites. Theor. Popul. Biol. 48: 172-197.
18. Gilad, Y., C. D. Bustamante, D. Lancet, and S. Paabo, 2003 Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am. J. Hum. Genet. 73: 489-501.
19. Graf, A., A. Smola, and S. Borer, 2003 Classification in a normalized feature space using support vector machines. IEEE Trans. Neural Networks 14: 597-605.
20. Gravel, S., B. M. Henn, R. N. Gutenkunst, A. R. Indap, G. T. Marth et al., 2011 Demographic history and rare allele sharing among human populations. Proc. Natl. Acad. Sci. USA 108: 11983-11988.
21. Gutenkunst, R. N., R. D. Hernandez, S. H. Williamson, and C. D. Bustamante, 2009 Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5: e1000695.
22. Holmberg, V., P. Onkamo, E. Lahtela, P. Lahermo, G. Bedu-Addo et al., 2012 Mutations of complement lectin pathway genes MBL2 and MASP2 associated with placental malaria. Malar. J. 11: 61.
23. Hudson, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
24. Hudson, R. R., M. Slatkin, and W. P. Maddison, 1992 Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
25. Kim, Y., and R. Nielsen, 2004 Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513-1524.
26. Kingman, J. F. C., 1982 On the genealogy of large populations. J. Appl. Probab. 19: 27-43.
27. Kumar, P., S. Henikoff, and P. C. Ng, 2009 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 4: 1073-1081.
28. Lin, K., H. Li, C. Schltterer, and A. Futschik, 2011 Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics. Genetics 187: 229-244.
29. Nachman, M. W., and S. L. Crowell, 2000 Estimate of the mutation rate per nucleotide in humans. Genetics 156: 297-304.
30. 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.
31. Nielsen, R., M. J. Hubisz, I. Hellmann, D. Torgerson, A. M. Andres et al., 2009 Darwinian and demographic forces affecting human protein coding genes. Genome Res. 19: 838-849.
32. Pavlidis, P., J. D. Jensen, and W. Stephan, 2010 Searching for footprints of positive selection in whole-genome snp data from nonequilibrium populations. Genetics 185: 907-922.
33. Pedregosa, F., G. Varoquaux, A. Gramfort, V. Michel, B. Thirion et al., 2011 Scikit-learn: machine learning in python. J. Mach. Learn. Res. 12: 2825-2830.
34. 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.
35. Rosanas-Urgell, A., L. Martin-Jaular, J. Ricarte-Filho, M. Ferrer, S. Kalko et al., 2012 Expression of non-TLR pattern recognition receptors in the spleen of BALB/c mice infected with Plasmodium yoelii and Plasmodium chabaudi chabaudi AS. Mem. Inst. Oswaldo Cruz 107: 410-415.
36. 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.
37. Sabeti, P. C., P. Varilly, B. Fry, J. Lohmueller, E. Hostetter et al., 2007 Genome-wide detection and characterization of positive selection in human populations. Nature 449: 913-918.
38. Sawyer, S. A., and D. L. Hartl, 1992 Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
39. Schaffner, S. F., C. Foo, S. Gabriel, D. Reich, M. J. Daly et al., 2005 Calibrating a coalescent simulation of human genome sequence variation. Genome Res. 15: 1576-1583.
40. Shriver, M. D., G. C. Kennedy, E. J. Parra, H. A. Lawson, V. Sonpar et al., 2004 The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Hum. Genomics 1: 274-286.
41. Tajima, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
42. Thiel, S., R. Steffensen, I. J. Christensen, W. K. Ip, Y. L. Lau et al., 2007 Deficiency of mannan-binding lectin associated serine protease-2 due to missense polymorphisms. Genes Immun. 8: 154-163.
43. Thiel, S., M. Kolev, S. Degn, R. Steffensen, A. G. Hansen et al., 2009 Polymorphisms in mannan-binding lectin (MBL)-associated serine protease 2 affect stability, binding to MBL, and enzymatic activity. J. Immunol. 182: 2939-2947.
44. Tulio, S., F. R. Faucz, R. I. Werneck, M. Olandoski, R. B. Alexandre et al., 2011 MASP2 gene polymorphism is associated with susceptibility to hepatitis C virus infection. Hum. Immunol. 72: 912-915.
45. Tung, J., A. Primus, A. J. Bouley, T. F. Severson, S. C. Alberts et al., 2009 Evolution of a malaria resistance gene in wild primates. Nature 460: 388-391.
46. Udpa, N., D. Zhou, G. G. Haddad, and V. Bafna, 2011 Tests of selection in pooled case-control data: an empirical study. Front. Genet. 2: 83.
47. Voight, B. F., A. M. Adams, L. A. Frisse, Y. Qian, R. R. Hudson et al., 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.
48. Watterson, G., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
49. Wu, T. F., C. J. Lin, and R. C. Weng, 2004 Probability estimates for multi-class classification by pairwise coupling. J. Mach. Learn. Res. 5: 975-1005.
50. Zeng, K., Y.-X. Fu, S. Shi, and C.-I. Wu, 2006 Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 174: 1431-1439.
51. Zhou, D., N. Udpa, M. Gersten, D. W. Visk, A. Bashir et al., 2011 Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 108: 2349-2354.