Identifying loci under positive selection in complex population histories

Genome Research
Alba Refoyo-MartínezFernando Racimo

Abstract

Detailed modeling of a species' history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method-called graph-aware retrieval of selective sweeps (GRoSS)-has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of di...Continue Reading

References

Dec 16, 1992·Biochimica Et Biophysica Acta·S E PlyteJ R Woodgett
Dec 6, 2002·Genome Research·Joshua M AkeyMark D Shriver
May 15, 2004·Proceedings of the National Academy of Sciences of the United States of America·Makoto OhtsukaTakashi Saito
Oct 28, 2005·Genome Research·Bruce S WeirWilliam G Hill
Oct 28, 2005·Genome Research·Rasmus NielsenCarlos Bustamante
Feb 24, 2006·PLoS Biology·Benjamin F VoightJonathan K Pritchard
Nov 6, 2007·Behavior Genetics·Christophe PampoulieVilhjálmur Thorsteinsson
Apr 25, 2009·Science·UNKNOWN Bovine Genome Sequencing and Analysis ConsortiumFeng-Qi Zhao
Aug 29, 2009·Molecular Biology and Evolution·Aida M AndrésRasmus Nielsen
Jan 21, 2010·Genome Research·Hua ChenDavid Reich
Jun 3, 2010·Genetics·Graham CoopJonathan K Pritchard
Oct 13, 2010·Molecular Biology and Evolution·Jun OhashiNaoyuki Tsuchiya
Feb 16, 2011·Bioinformatics·Heng Li
Sep 11, 2012·Genetics·Nick PattersonDavid Reich
Nov 21, 2012·PLoS Genetics·Joseph K Pickrell, Jonathan K Pritchard
Feb 19, 2013·Cell·Sharon R GrossmanPardis C Sabeti
Apr 25, 2013·Molecular Ecology·Jakob Hemmer-HansenGary R Carvalho
May 28, 2013·Molecular Biology and Evolution·Mark LipsonBonnie Berger
Jul 4, 2013·Genetics·Torsten Günther, Graham Coop
Aug 1, 2013·Development·Weisheng V Chen, Tom Maniatis
Oct 8, 2013·American Journal of Human Genetics·Olivier DelaneauJonathan Marchini
Jan 31, 2014·Science·Benjamin Vernot, Joshua M Akey
Mar 1, 1951·Annals of Eugenics·S WRIGHT
Jun 13, 2014·Genome Biology and Evolution·Hyun-Jeong LeeHeebal Kim
Aug 8, 2014·PLoS Genetics·Jeremy J Berg, Graham Coop
Nov 12, 2014·Proceedings of the National Academy of Sciences of the United States of America·Michael J MontagueWesley C Warren
Nov 26, 2014·BMC Bioinformatics·Thorfinn KorneliussenRasmus Nielsen
Jan 13, 2015·Behavior Genetics·Christophe PampoulieAnna K Daníelsdóttir
Mar 10, 2015·Journal of Cell Science·Shuichi Hayashi, Masatoshi Takeichi
Aug 21, 2015·Molecular Ecology·Christian D HuberRasmus Nielsen
Oct 4, 2015·Nature·UNKNOWN 1000 Genomes Project ConsortiumGonçalo R Abecasis

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Citations

Dec 7, 2019·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Ludovic Orlando
Dec 22, 2019·Journal of Molecular Evolution·Sean G Byars, Konstantinos Voskarides
Apr 22, 2020·Evolution Letters·Marianne DehasqueAndrew D Foote
Jan 14, 2021·Human Molecular Genetics·Yuanqing FengSarah A Tishkoff
May 13, 2020·Trends in Genetics : TIG·Jasmin S ReesAida M Andrés
Apr 6, 2021·Frontiers in Genetics·Fernanda M RezendeRaluca G Mateescu
Apr 1, 2021·Genetics·Sivan YairGraham Coop
Jul 10, 2021·Molecular Biology and Evolution·Ornob AlamMichael D Purugganan
Oct 10, 2021·Molecular Biology and Evolution·Jade Yu ChengRasmus Nielsen

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