Hierarchical boosting: A machine-learning framework to detect and classify hard selective sweeps in human populations

Bioinformatics

Volumn 31, Issue 24, 2015, Pages 3946-3952

  Pybus, Marc ^a   Luisi, Pierre ^a,b   Dall'Olio, Giovanni Marco ^a,c   Uzkudun, Manu ^a   Laayouni, Hafid ^a,d   Bertranpetit, Jaume ^a   Engelken, Johannes ^a  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b STANFORD UNIVERSITY   (United States)

^c KING'S COLLEGE LONDON   (United Kingdom)

^d UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DEMOGRAPHY; GENETIC POLYMORPHISM; GENETIC SELECTION; GENOMICS; HUMAN; MACHINE LEARNING; POPULATION GENETICS; PROCEDURES;

DEMOGRAPHY; GENETICS, POPULATION; GENOMICS; HUMANS; MACHINE LEARNING; POLYMORPHISM, GENETIC; SELECTION, GENETIC;

EID: 84950272772     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv493     Document Type: Article

References (47)

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. Ayodo, G. et al. (2007) Combining evidence of natural selection with association analysis increases power to detect malaria-resistance variants. Am. J. Hum. Genet., 81, 234-242.
3. Beaumont, M.A. and Balding, D.J. (2004) Identifying adaptive genetic divergence among populations from genome scans. Mol. Ecol., 13, 969-980.
4. Bersaglieri, T. et al. (2004) Genetic signatures of strong recent positive selection at the lactase gene. Am. J. Hum. Genet., 74, 1111-1120.
5. Biswas, S. and Akey, J.M. (2006) Genomic insights into positive selection. Trends Genet., 22, 437-446.
6. Braverman, J.M. et al. (1995) The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics, 140, 783-796.
7. Bühlmann, P. and Hothorn, T. (2008) Rejoinder: boosting algorithms: regularization, prediction and model fitting. Stat. Sci., 22, 477-505.
8. Chen, H. et al. (2010) Population differentiation as a test for selective sweeps. Genome Res., 20, 393-402.
9. Coop, G. et al. (2009) The role of geography in human adaptation. PLoS Genet., 5, 1000500.
10. Fagny, M. et al. (2014) Exploring the occurrence of classic selective sweeps in humans using whole-genome sequencing datasets. Mol. Biol. Evol., 31, 1850-1868.
11. Fay, J.C. and Wu, C.I. (2000) Hitchhiking under positive Darwinian selection. Genetics, 155, 1405-1413.
12. Fu, Y.X. and Li, W.H. (1993) Statistical tests of neutrality of mutations. Genetics, 133, 693-709.
13. Granka, J.M. et al. (2012) Limited evidence for classic selective sweeps in African populations. Genetics, 192, 1049-1064.
14. Grossman, S.R. et al. (2010) A composite of multiple signals distinguishes causal variants in regions of positive selection. Science, 327, 883-886.
15. Grossman, S.R. et al. (2013) Identifying recent adaptations in large-scale genomic data. Cell, 152, 703-713.
16. Hamblin, M.T. and Di Rienzo, A. (2000) Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am. J. Hum. Genet., 66, 1669-1679.
17. Hofer, T. et al. (2009) Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection. Ann. Hum. Genet., 73, 95-108.
18. Hothorn, T. et al. (2010) Model-based Boosting 2.0. J. Mach. Learn. Res., 11, 2109-2113.
19. Kelley, J.L. et al. (2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Res., 16, 980-989.
20. Kent, W.J. et al. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
21. Lin, K. et al. (2011) Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics. Genetics, 187, 229-244.
22. Lohmueller, K.E. et al. (2011) Detecting directional selection in the presence of recent admixture in African-Americans. Genetics, 187, 823-835.
23. Maynard-Smith, J. and Haigh, J. (1974) The hitch-hiking effect of a favourable gene. Genet. Res., 23, 23-35.
24. Messer, P.W. and Petrov, D.A. (2013) Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol. Evol., 28, 659-669.
25. Nielsen, R. et al. (2005) Genomic scans for selective sweeps using SNP data. Genome Res., 15, 1566-1575.
26. Pavlidis, P. et al. (2010) Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics, 185, 907-922.
27. Pickrell, J.K. et al. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Res., 19, 826-837.
28. Pybus, M. et al. (2014) 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Res., 42, 1-7.
29. Raney, B.J. et al. (2014) Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics, 30, 1003-1005.
30. Ronen, R. et al. (2013) Learning natural selection from the site frequency spectrum. Genetics, 195, 181-193.
31. Sabeti, P. et al. (2002a) CD40L association with protection from severe malaria. Genes Immun., 3, 286-291.
32. Sabeti, P.C. et al. (2002b) Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832-837.
33. Sabeti, P.C. et al. (2006) Positive natural selection in the human lineage. Science, 312, 1614-1620.
34. Schaffner, S.F. et al. (2005) Calibrating a coalescent simulation of human genome sequence variation. Genome Res., 15, 1576-1583.
35. Stephan, W. et al. (2006) The hitchhiking effect on linkage disequilibrium between linked neutral loci. Genetics, 172, 2647-2663.
36. Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
37. Teshima, K.M. et al. (2006) How reliable are empirical genomic scans for selective sweeps? Genome Res., 16, 702-712.
38. The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1 092 human genomes. Nature, 491, 56-65.
39. Tishkoff, S. et al. (2001) Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science, 293, 455-462.
40. Tishkoff, S. et al. (2007) Convergent adaptation of human lactase persistence in Africa and Europe. Nat. Genet., 39, 31-40.
41. Vallender, E.J. and Lahn, B.T. (2004) Positive selection on the human genome. Hum. Mol. Genet., 13, 245-254.
42. Vitti, J.J. et al. (2013) Detecting natural selection in genomic data. Annu. Rev. Genet., 47, 97-120.
43. Voight, B.F. et al. (2006) A map of recent positive selection in the human genome. PLoS Biol., 4, e72.
44. Weir, B. and Cockerham, C. (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
45. Wilson, B. et al. (2014) Soft selective sweeps in complex demographic scenarios. Genetics, 198, 669-684.
46. Zeng, K. et al. (2006) Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics, 174, 1431-1439.
47. Zeng, K. et al. (2007) Compound tests for the detection of hitchhiking under positive selection. Mol. Biol. Evol., 24, 1898-1908.