title: Testing for associations between loci and environmental gradients using latent factor mixed models.
abstract: Adaptation to local environments often occurs through natural selection acting on a large number of loci, each having a weak phenotypic effect. One way to detect these loci is to identify genetic polymorphisms that exhibit high correlation with environmental variables used as proxies for ecological pressures. Here, we propose new algorithms based on population genetics, ecological modeling, and statistical learning techniques to screen genomes for signatures of local adaptation. Implemented in the computer program "latent factor mixed model" (LFMM), these algorithms employ an approach in which population structure is introduced using unobserved variables. These fast and computationally efficient algorithms detect correlations between environmental and genetic variation while simultaneously inferring background levels of population structure. Comparing these new algorithms with related methods provides evidence that LFMM can efficiently estimate random effects due to population history and isolation-by-distance patterns when computing gene-environment correlations, and decrease the number of false-positive associations in genome scans. We then apply these models to plant and human genetic data, identifying several genes with functions related to development that exhibit strong correlations with climatic gradients.
authors.affiliation: TIMC-IMAG UMR 5525, Université Joseph Fourier Grenoble, Centre National de la Recherche Scientifique, Grenoble, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Frichot
authors.forename: Sean D
authors.initials: SD
authors.lastname: Schoville
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bouchard
authors.forename: Olivier
authors.initials: O
authors.lastname: François
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000465:Algorithms; D004463:Ecology; D004777:Environment; D059647:Gene-Environment Interaction; D014644:Genetic Variation; D005828:Genetics, Population; D006801:Humans; D008962:Models, Theoretical; D011110:Polymorphism, Genetic; D012641:Selection, Genetic / Q000235:genetics*
keywords: environmental correlations; genome scans; latent factor models; local adaptation; population structure
references.citation: PLoS Genet. 2008 Feb;4(2):e32
references.pmid: 18282109
references.citation: Mol Biol Evol. 2012 Oct;29(10):3237-48
references.pmid: 22617950
references.citation: BMC Bioinformatics. 2009 Feb 03;10:48
references.pmid: 19192299
references.citation: Science. 2008 Feb 22;319(5866):1100-4
references.pmid: 18292342
references.citation: BMC Bioinformatics. 2011 Jun 18;12:246
references.pmid: 21682921
references.citation: PLoS Genet. 2009 Jun;5(6):e1000519
references.pmid: 19543370
references.citation: Annu Rev Genet. 2005;39:197-218
references.pmid: 16285858
references.citation: PLoS Genet. 2006 Dec;2(12):e190
references.pmid: 17194218
references.citation: Nat Genet. 2006 Aug;38(8):904-9
references.pmid: 16862161
references.citation: Genetics. 2000 Jun;155(2):945-59
references.pmid: 10835412
references.citation: Mol Ecol. 2012 May;21(10):2354-68
references.pmid: 22512785
references.citation: Nat Rev Genet. 2011 Oct 18;12(11):767-80
references.pmid: 22005986
references.citation: PLoS Genet. 2011 Apr;7(4):e1001375
references.pmid: 21533023
references.citation: Br Foreign Med Chir Rev. 1860 Apr;25(50):367-404
references.pmid: 30164232
references.citation: PLoS Genet. 2005 Dec;1(6):e82
references.pmid: 16429165
references.citation: Mol Ecol. 2010 Sep;19(17):3760-72
references.pmid: 20723056
references.citation: Genetics. 1993 Jul;134(3):869-93
references.pmid: 8102342
references.citation: Mol Ecol. 2010 Sep;19(17):3789-805
references.pmid: 20723060
references.citation: Mol Ecol. 2004 Apr;13(4):969-80
references.pmid: 15012769
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D901-7
references.pmid: 21037260
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D261-70
references.pmid: 22135298
references.citation: Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9362-7
references.pmid: 19474294
references.citation: Evolution. 2010 Jul;64(7):2173-8
references.pmid: 20163450
references.citation: Genome Res. 2009 May;19(5):711-22
references.pmid: 19411596
references.citation: J Am Stat Assoc. 2008 Dec 1;103(484):1438-1456
references.pmid: 21218139
references.citation: Nat Genet. 2012 Jun 17;44(7):821-4
references.pmid: 22706312
references.citation: Mol Ecol. 2012 Jun;21(12):2839-46
references.pmid: 22574758
references.citation: Genetics. 2010 Aug;185(4):1411-23
references.pmid: 20516501
references.citation: Nat Rev Genet. 2009 Nov;10(11):745-55
references.pmid: 19823195
references.citation: Mol Ecol. 2010 Jul;19(14):2896-907
references.pmid: 20609082
references.citation: Mol Ecol. 2007 Sep;16(18):3955-69
references.pmid: 17850556
references.citation: Mol Biol Evol. 2009 Sep;26(9):1963-73
references.pmid: 19461114
references.citation: PLoS Genet. 2010 Sep 16;6(9):e1001117
references.pmid: 20862358
references.citation: Monogr Popul Biol. 1977;10:1-246
references.pmid: 409931
references.citation: Curr Biol. 2010 Feb 23;20(4):R208-15
references.pmid: 20178769
references.citation: PLoS Genet. 2012 Jan;8(1):e1002453
references.pmid: 22291602
references.citation: PLoS Genet. 2011 Nov;7(11):e1002355
references.pmid: 22072984
references.citation: Bioinformatics. 2002 Feb;18(2):337-8
references.pmid: 11847089
references.citation: Curr Biol. 2005 Jun 7;15(11):1022-7
references.pmid: 15936272
references.citation: Genome Res. 2006 Aug;16(8):980-9
references.pmid: 16825663
references.citation: Front Genet. 2012 Nov 20;3:254
references.pmid: 23181073
references.citation: J Genet. 1948 Jan;48(3):277-84
references.pmid: 18905075
references.citation: Evolution. 2010 Sep;64(9):2489-509
references.pmid: 20500215
references.citation: Mol Ecol. 2010 Jun;19(11):2301-14
references.pmid: 20465581
references.citation: Mol Ecol. 2005 Mar;14(3):671-88
references.pmid: 15723660
references.citation: Nat Genet. 2006 Feb;38(2):203-8
references.pmid: 16380716