A comprehensive analysis comparing linear and generalized linear models in detecting adaptive SNPs.

Molecular Ecology Resources
Lan LuoJun Zhu

Abstract

To understand how organisms adapt to their environment, a gene-environmental association (GEA) analysis is commonly conducted. GEA methods based on mixed models, such as linear latent factor mixed models (LFMM) and LFMM2, have grown in popularity for their robust performance in terms of power and computational speed. However, it is unclear how the assumption of a Gaussian distribution for the response variables influences model performance. In this paper, we develop a generalized linear model (GLM) that allows for non-Gaussian distribution in the genotypic response variables, and treatment of multiallelic nucleotide polymorphisms. Moreover, this multinomial logistic regression model (MLR) is combined with an admixture-based model or principal components analysis to correct for population structure (MLR-ADM and MLR-PC). Using simulations, we evaluate the type 1 error, false discovery rates (FDR), and power to detect selected SNPs, to guide model choice and best practices. With genomic control, MLR-PC and LFMM2 have similar type 1 error, FDRs, and power when analysing biallelic SNPs, while dramatically outperforming models not accounting for population structure. Differences in performance occur under continuous population struct...Continue Reading

References

Jun 12, 1999·American Journal of Human Genetics·J K Pritchard, N A Rosenberg
May 10, 2000·American Journal of Human Genetics·S A BacanuK Roeder
Apr 21, 2001·Biometrics·B Devlin, K Roeder
Apr 17, 2002·Science·Howard M CannL Luca Cavalli-Sforza
Dec 21, 2002·Science·Noah A RosenbergMarcus W Feldman
Dec 16, 2005·Genome Research·Efrosini SetakisDavid J Balding
Dec 30, 2006·PLoS Genetics·Nick PattersonDavid Reich
Oct 14, 2009·Nature Reviews. Genetics·John Novembre, Anna Di Rienzo
Jun 3, 2010·Genetics·Graham CoopJonathan K Pritchard
May 12, 2012·Molecular Ecology·Patrick G Meirmans
Sep 11, 2012·Genetics·Nick PattersonDavid Reich
Apr 2, 2013·Molecular Biology and Evolution·Eric FrichotOlivier François
Nov 28, 2013·Annual Review of Genetics·Joseph J VittiPardis C Sabeti
Feb 6, 2014·Genetics·Eric FrichotOlivier François
Mar 13, 2014·Molecular Ecology·Pierre de VillemereuilOscar E Gaggiotti
Jul 18, 2015·Molecular Ecology·Christian RellstabRolf Holderegger
Oct 4, 2015·Nature·UNKNOWN 1000 Genomes Project ConsortiumGonçalo R Abecasis
Nov 19, 2015·Molecular Ecology·Brenna R ForesterJesse R Lasky
Dec 17, 2015·Molecular Ecology·Olivier FrancoisSean D Schoville
Jan 19, 2019·Molecular Biology and Evolution·Kevin CayeOlivier François

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