In the presence of population structure: From genomics to candidate genes underlying local adaptation

Ecology and Evolution
Nicholas PriceJesse R Lasky

Abstract

Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequ...Continue Reading

References

Dec 1, 1986·Heredity·N Barton, B O Bengtsson
Aug 1, 1993·Genetics·B CharlesworthD Charlesworth
Jul 30, 2002·Evolution; International Journal of Organic Evolution·Andrew P HendryJ Donald McPhail
Mar 12, 2004·Molecular Ecology·Mark A Beaumont, David J Balding
Apr 8, 2004·PLoS Biology·Pamela F ColosimoDavid M Kingsley
Jul 29, 2004·Genetics·Yuseob Kim, Rasmus Nielsen
Oct 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·Elena MontePeter H Quail
Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler
Oct 28, 2005·Genome Research·Rasmus NielsenCarlos Bustamante
Dec 22, 2005·Molecular Ecology·Erika CrispoAndrew P Hendry
Nov 7, 2007·Genome Research·Webb MillerW James Kent
Mar 29, 2008·Briefings in Bioinformatics·Kazutaka Katoh, Hiroyuki Toh
Dec 24, 2008·PloS One·Roosa Leimu, Markus Fischer
Jan 22, 2009·Evolution; International Journal of Organic Evolution·Saskia Sandring, Jon Agren
Mar 11, 2009·The American Naturalist·Joe Hereford
May 1, 2007·Plant Signaling & Behavior·Narendra Tuteja
Jul 25, 2009·Molecular Biology and Evolution·Jonathan M FlowersMichael D Purugganan
Jun 2, 2010·Current Genomics·R V L JoosenJ J B Keurentjes
Jun 16, 2010·Nature Reviews. Genetics·Alkes L PriceNick Patterson
Aug 28, 2010·Journal of Evolutionary Biology·A Pérez-FigueroaA Caballero
Sep 3, 2010·Plant Physiology·Jayaram BhandariDring N Crowell
Nov 19, 2010·Nature Reviews. Genetics·Joy Bergelson, Fabrice Roux
Feb 1, 2011·Briefings in Bioinformatics·Melissa J HubiszAdam Siepel
Mar 17, 2011·Genetics·Patrice A SaloméDetlef Weigel
Apr 12, 2011·Molecular Ecology·Nicolas BiernePatrice David
May 3, 2011·PLoS Genetics·Angela M HancockAnna Di Rienzo
May 10, 2011·Trends in Genetics : TIG·Jill T AndersonThomas Mitchell-Olds
Jun 15, 2011·The American Naturalist·Ying ZhenMark C Ungerer
Jul 7, 2011·Evolution; International Journal of Organic Evolution·Sam Yeaman, Michael C Whitlock
Aug 19, 2011·Proceedings of the National Academy of Sciences of the United States of America·Cheng ZouShin-Han Shiu
Oct 8, 2011·Science·Angela M HancockJoy Bergelson
Oct 8, 2011·Science·A Fournier-LevelA M Wilczek
Nov 24, 2011·Nucleic Acids Research·David M GoodsteinDaniel S Rokhsar

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Citations

Oct 25, 2020·Molecular Ecology Resources·José Luis Blanco-PastorJean-Paul Sampoux
Jan 26, 2021·PLoS Genetics·Benedict WietersJuliette de Meaux

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Software Mentioned

BAYESCAN
R
Phast suite
GEMMA
MAFFT
LASTZ
PLINK
callSynNonSyn
LFMM
GEA

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