title: Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations.
abstract: A major goal of population genomics is to reconstruct the history of natural populations and to infer the neutral and selective scenarios that can explain the present-day polymorphism patterns. However, the separation between neutral and selective hypotheses has proven hard, mainly because both may predict similar patterns in the genome. This study focuses on the development of methods that can be used to distinguish neutral from selective hypotheses in equilibrium and nonequilibrium populations. These methods utilize a combination of statistics on the basis of the site frequency spectrum (SFS) and linkage disequilibrium (LD). We investigate the patterns of genetic variation along recombining chromosomes using a multitude of comparisons between neutral and selective hypotheses, such as selection or neutrality in equilibrium and nonequilibrium populations and recurrent selection models. We perform hypothesis testing using the classical P-value approach, but we also introduce methods from the machine-learning field. We demonstrate that the combination of SFS- and LD-based statistics increases the power to detect recent positive selection in populations that have experienced past demographic changes.
authors.affiliation: Department of Biology II, Ludwig-Maximilians-University Munich, 82152 Planegg, Germany. pavlidis@bio.lmu.de
authors.forename: Pavlos
authors.initials: P
authors.lastname: Pavlidis
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Jensen
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Stephan
mesh_terms: D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics*; D016678:Genome; D015810:Linkage Disequilibrium; D056186:Metagenomics; D008957:Models, Genetic; D008962:Models, Theoretical; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012641:Selection, Genetic; D012984:Software
references.citation: Genome Res. 2005 Nov;15(11):1566-75
references.pmid: 16251466
references.citation: PLoS Biol. 2007 Jul;5(7):e171
references.pmid: 17579516
references.citation: BMC Bioinformatics. 2009 May 30;10:166
references.pmid: 19480708
references.citation: Mol Biol Evol. 2007 Feb;24(2):562-73
references.pmid: 17124182
references.citation: Bioinformatics. 2008 Dec 1;24(23):2786-7
references.pmid: 18842601
references.citation: Mol Biol Evol. 1995 Sep;12(5):959-62
references.pmid: 7476143
references.citation: Genetics. 1974 Nov;78(3):937-41
references.pmid: 4217751
references.citation: Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12949-54
references.pmid: 12351680
references.citation: Genetics. 2008 Sep;180(1):341-57
references.pmid: 18716326
references.citation: Genetics. 2003 May;164(1):389-98
references.pmid: 12750349
references.citation: Theor Popul Biol. 1975 Apr;7(2):256-76
references.pmid: 1145509
references.citation: BMC Bioinformatics. 2008 Sep 08;9:364
references.pmid: 18778480
references.citation: PLoS Biol. 2004 Oct;2(10):e286
references.pmid: 15361935
references.citation: Genetics. 2006 Apr;172(4):2647-63
references.pmid: 16452153
references.citation: Genetics. 2000 Jul;155(3):1405-13
references.pmid: 10880498
references.citation: Genetics. 1997 Jul;146(3):1197-206
references.pmid: 9215920
references.citation: Genome Res. 2009 May;19(5):826-37
references.pmid: 19307593
references.citation: Bioinformatics. 2004 Dec 12;20(18):3673-5
references.pmid: 15271777
references.citation: Mol Biol Evol. 1993 Jul;10(4):842-54
references.pmid: 8355603
references.citation: Genetics. 2007 Nov;177(3):1725-31
references.pmid: 17947444
references.citation: Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2785-90
references.pmid: 17301231
references.citation: Genetics. 2007 Mar;175(3):1395-406
references.pmid: 17194788
references.citation: Mol Biol Evol. 2009 Jul;26(7):1549-56
references.pmid: 19349642
references.citation: Genetics. 2007 Feb;175(2):737-50
references.pmid: 17110489
references.citation: Genetics. 2003 Nov;165(3):1269-78
references.pmid: 14668381
references.citation: Genome Res. 2009 May;19(5):711-22
references.pmid: 19411596
references.citation: PLoS Biol. 2006 Mar;4(3):e72
references.pmid: 16494531
references.citation: Genetics. 2002 Mar;160(3):1179-89
references.pmid: 11901132
references.citation: Genetics. 2006 Mar;172(3):1967-78
references.pmid: 16361239
references.citation: Nature. 2002 Oct 24;419(6909):832-7
references.pmid: 12397357
references.citation: Genetics. 2005 Mar;169(3):1727-38
references.pmid: 15654099
references.citation: Mol Ecol. 2008 Aug;17(16):3585-98
references.pmid: 18627454
references.citation: Genetics. 1995 Jun;140(2):783-96
references.pmid: 7498754
references.citation: Genetics. 2005 Apr;169(4):2335-52
references.pmid: 15716498
references.citation: Genetics. 2002 Feb;160(2):765-77
references.pmid: 11861577
references.citation: Genetics. 2000 Feb;154(2):931-42
references.pmid: 10655242
references.citation: Theor Popul Biol. 2008 May;73(3):342-8
references.pmid: 18321552
references.citation: Genetics. 1996 Oct;144(2):635-45
references.pmid: 8889526
references.citation: Mol Biol Evol. 2010 Jan;27(1):153-60
references.pmid: 19759233
references.citation: PLoS Genet. 2006 Oct 13;2(10):e166
references.pmid: 17040129
references.citation: Genetics. 2008 May;179(1):527-37
references.pmid: 18493069
references.citation: Genetics. 2006 Mar;172(3):1607-19
references.pmid: 16299396
references.citation: Genetics. 2007 Dec;177(4):2083-99
references.pmid: 18073425
references.citation: Theor Popul Biol. 2004 Nov;66(3):219-32
references.pmid: 15465123
references.citation: Genome Res. 2007 Dec;17(12):1755-62
references.pmid: 17989248
references.citation: Genetics. 2004 Jul;167(3):1513-24
references.pmid: 15280259
references.citation: Bioinformatics. 2002 Feb;18(2):337-8
references.pmid: 11847089
references.citation: PLoS Genet. 2008 Sep 19;4(9):e1000198
references.pmid: 18802463
references.citation: Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5447-52
references.pmid: 18381818
references.citation: Genetics. 1989 Dec;123(4):887-99
references.pmid: 2612899
references.citation: Genet Res. 2007 Aug;89(4):231-44
references.pmid: 18208629
references.citation: Genetics. 2005 Jul;170(3):1401-10
references.pmid: 15911584
references.citation: Genetics. 2008 Sep;180(1):301-16
references.pmid: 18716333
references.citation: Genetics. 2004 Aug;167(4):1759-66
references.pmid: 15342514
references.citation: Genet Res. 1974 Feb;23(1):23-35
references.pmid: 4407212
references.citation: Genetics. 2000 Jul;155(3):1415-27
references.pmid: 10880499
references.citation: Genetics. 1989 Nov;123(3):585-95
references.pmid: 2513255
references.citation: Genome Res. 2009 May;19(5):838-49
references.pmid: 19279335
references.citation: Genetics. 2007 Aug;176(4):2371-9
references.pmid: 17565955