Statistical tests for detecting positive selection by utilizing high-frequency variants

Kai ZengChung-I Wu


By comparing the low-, intermediate-, and high-frequency parts of the frequency spectrum, we gain information on the evolutionary forces that influence the pattern of polymorphism in population samples. We emphasize the high-frequency variants on which positive selection and negative (background) selection exhibit different effects. We propose a new estimator of theta (the product of effective population size and neutral mutation rate), thetaL, which is sensitive to the changes in high-frequency variants. The new thetaL allows us to revise Fay and Wu's H-test by normalization. To complement the existing statistics (the H-test and Tajima's D-test), we propose a new test, E, which relies on the difference between thetaL and Watterson's thetaW. We show that this test is most powerful in detecting the recovery phase after the loss of genetic diversity, which includes the postselective sweep phase. The sensitivities of these tests to (or robustness against) background selection and demographic changes are also considered. Overall, D and H in combination can be most effective in detecting positive selection while being insensitive to other perturbations. We thus propose a joint test, referred to as the DH test. Simulations indicate t...Continue Reading


Apr 1, 1975·Theoretical Population Biology·G A Watterson
Jun 20, 1991·Nature·J H McDonald, M Kreitman
Feb 1, 1974·Genetical Research·J M Smith, J Haigh
Oct 1, 1995·Theoretical Population Biology·Y X Fu
May 24, 2001·Molecular Biology and Evolution·L MarkovtsovaS Tavare
May 24, 2001·Molecular Biology and Evolution·J D Wall, Richard R Hudson
Apr 5, 2002·Nature·Carlos D BustamanteDaniel L Hartl
Sep 2, 2003·Theoretical Population Biology·R C Griffiths
Feb 24, 2006·PLoS Biology·Benjamin F VoightJonathan K Pritchard


May 9, 2012·Journal of Molecular Evolution·Mohamed IsmailYousry A El-Kassaby
Jan 27, 2009·Biochemical Genetics·Mikiko SoejimaYoshiro Koda
Jan 24, 2013·European Journal of Human Genetics : EJHG·Laure SégurelEvelyne Heyer
May 27, 2010·Heredity·A OjedaMiguel Pérez-Enciso
Aug 30, 2011·Nature Genetics·Jun CaoDetlef Weigel
Nov 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·William M MuirHans H Cheng
Jun 6, 2012·Proceedings of the National Academy of Sciences of the United States of America·Xiaoxia WangAjit Varki
Feb 23, 2013·Genome Biology and Evolution·Marco GalardiniAlessio Mengoni
Feb 26, 2008·Molecular Biology and Evolution·Jian LuChung-I Wu
Oct 17, 2008·Molecular Biology and Evolution·Weiwei ZhaiMontgomery Slatkin
Aug 15, 2009·Molecular Biology and Evolution·Jason A WilderMeredith E Gansner
Jan 8, 2013·Molecular Biology and Evolution·Zélia FerreiraBelen Hurle
Jun 4, 2010·Proceedings. Biological Sciences·Suo QiuDeborah Charlesworth
Nov 28, 2013·Annual Review of Genetics·Joseph J VittiPardis C Sabeti
Jan 1, 2008·Annual Review of Anthropology·Angela M Hancock, Anna Di Rienzo
Jan 30, 2010·BMC Bioinformatics·Julie HussinDamian Labuda
Jul 13, 2011·BMC Evolutionary Biology·Ferran CasalsJaume Bertranpetit
May 9, 2013·BMC Genetics·Kiyoshi EzawaDan Graur
Aug 24, 2013·PLoS Pathogens·Caitlin S PepperellMarcus W Feldman
Jul 9, 2010·Genetics·Luca FerrettiSebastian E Ramos-Onsins
Jun 5, 2012·Genetics·Luca FerrettiSebastian E Ramos-Onsins
Oct 13, 2009·Yi chuan = Hereditas·Kao Lin, Haipeng Li
Dec 18, 2013·Genome Biology and Evolution·Lex E FlagelTodd J Vision
Apr 18, 2014·Molecular Biology and Evolution·Bastian PfeiferMartin J Lercher
Feb 8, 2007·Proceedings of the National Academy of Sciences of the United States of America·Joshua A ShapiroChung-I Wu
Aug 13, 2014·Genome Biology and Evolution·Ryan J HaaslBret A Payseur
Oct 31, 2014·Genome Biology and Evolution·Richard Jovelin, Asher D Cutter
Oct 29, 2014·Genome Biology and Evolution·Alessandra MozziManuela Sironi
Jul 27, 2010·Molecular Biology and Evolution·Delphine GrivetSantiago C González-Martínez
Jun 11, 2011·Molecular Biology and Evolution·Simona FornarinoLluis Quintana-Murci
Feb 10, 2012·Molecular Biology and Evolution·M Madlen VetterJuliette de Meaux
Oct 19, 2007·Nature Reviews. Genetics·Thomas Mitchell-OldsDavid B Goldstein
Oct 1, 2015·Molecular Biology and Evolution·Patrícia Isabel MarquesSusana Seixas
Apr 21, 2009·Trends in Microbiology·B Jesse ShapiroEric J Alm
Mar 3, 2015·Molecular Ecology·Sara BrancoThomas D Bruns
Oct 10, 2013·Molecular Ecology·Luca FerrettiMiguel Pérez-Enciso
Jun 1, 2012·Molecular Ecology·Pu HuangBarbara Anna Schaal
May 12, 2012·Molecular Ecology·C BurgarellaSantiago C González-Martínez
Nov 13, 2012·Evolutionary Applications·Elena MoscaDavid B Neale
Jul 31, 2010·Molecular Ecology·Andrew J HeidelThomas Mitchell-Olds
Jan 25, 2012·The Plant Journal : for Cell and Molecular Biology·Chao-Li HuangTzen-Yuh Chiang
Feb 12, 2011·Molecular Ecology·David HallPär K Ingvarsson
Nov 17, 2009·Molecular Ecology·K Ryo Takahasi
Oct 30, 2009·Evolution; International Journal of Organic Evolution·John P Wares
Feb 7, 2016·Molecular Ecology·Scott T SmallPeter A Zimmerman
Oct 29, 2015·Genome Biology and Evolution·Jae Young Choi, Charles F Aquadro
Jul 16, 2015·Molecular Biology and Evolution·Walter SanseverinoJosep Maria Casacuberta
Sep 1, 2015·Genome Biology and Evolution·Chiara PontremoliManuela Sironi
Apr 25, 2015·Annals of Human Genetics·Min CaoGuang Ning
Jan 30, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Jacob E CrawfordBrian P Lazzaro
Apr 16, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·P GladieuxT Giraud
Oct 4, 2014·American Journal of Human Genetics·Joseph Lachance, Sarah A Tishkoff
Jun 10, 2014·Theoretical Population Biology·M RafajlovićB Mehlig
Jun 27, 2008·Proceedings of the National Academy of Sciences of the United States of America·Juliette de MeauxUlrike Goebel
Aug 20, 2014·Molecular Biology and Evolution·Minxian WangYungang He
Jul 9, 2016·Genome Biology·Sandra UnterseerChris-Carolin Schön
Jul 6, 2016·Theoretical Population Biology·Ingemar Kaj, Carina F Mugal
Jul 18, 2016·Theoretical Population Biology·Xin-Sheng HuXiaoyang Chen
Nov 11, 2014·Annual Review of Ecology, Evolution, and Systematics·Joseph Lachance, Sarah A Tishkoff
Apr 14, 2017·Journal of Biological Research·Pavlos Pavlidis, Nikolaos Alachiotis
Mar 13, 2018·The New Phytologist·Artem PankinMaria von Korff
Jan 19, 2018·Molecular Biology and Evolution·Yvonne WilliJosh Van Buskirk
Oct 24, 2017·Nucleic Acids Research·Sònia CasillasAntonio Barbadilla
Oct 14, 2017·Molecular Biology and Evolution·Julio RozasAlejandro Sánchez-Gracia
Nov 29, 2017·Journal of Experimental & Clinical Cancer Research : CR·Deyang LiJinliang Xing
Sep 13, 2013·Evolutionary Bioinformatics Online·Daniel Garrigan
Jan 25, 2013·American Journal of Botany·Eva Puerma, Montserrat Aguadé
Oct 2, 2018·Genes & Genetic Systems·Naoko T FujitoNaoyuki Takahata
Oct 7, 2016·G3 : Genes - Genomes - Genetics·Dianne VelascoJeffrey Ross-Ibarra
Jul 7, 2017·Genetics·Luca FerrettiSebastian E Ramos-Onsins
Feb 26, 2016·Scientific Reports·Alessandra MozziManuela Sironi
Nov 8, 2017·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Josep M Comeron
Jun 28, 2020·Molecular Biology and Evolution·Yalin ChengFumin Lei
Nov 7, 2016·Genetics·Angela M EarlyAndrew G Clark
Nov 9, 2018·Frontiers in Genetics·Luca FerrettiSebastian E Ramos-Onsins
Feb 26, 2019·Nature Ecology & Evolution·Patrick MonnahanLevi Yant
Jun 15, 2007·Molecular Biology and Evolution·Kai ZengChung-I Wu
Jun 26, 2007·Human Molecular Genetics·Xiaoxia Wang, Jianzhi Zhang
Jan 1, 2013·G3 : Genes - Genomes - Genetics·Jacob E CrawfordKenneth D Vernick
Oct 14, 2017·Scientific Reports·Christina A EichstaedtToomas Kivisild
Jan 10, 2019·Proceedings of the National Academy of Sciences of the United States of America·Felix HornsStephen R Quake
Apr 22, 2020·Evolution Letters·Marianne DehasqueAndrew D Foote
Jun 19, 2013·Genetics·Roy RonenVineet Bafna
May 9, 2015·Genetics·Jochen BlathMaite Wilke-Berenguer
Nov 8, 2017·Molecular Ecology·Delphine GrivetSantiago C González-Martínez
Oct 15, 2019·Frontiers in Genetics·Shu-Ping TsengChin-Cheng Scotty Yang
Oct 3, 2020·Evolutionary Applications·Nina Marchi, Laurent Excoffier
Nov 8, 2015·G3 : Genes - Genomes - Genetics·Nicolas AlcalaSéverine Vuilleumier
Mar 9, 2017·Genetics·Sònia Casillas, Antonio Barbadilla
Jun 20, 2020·PLoS Genetics·Derek SetterJoachim Hermisson
Oct 6, 2020·Journal of the American Statistical Association·Jack KammYun S Song
Dec 24, 2019·Current Biology : CB·Hannes BecherBrian Charlesworth
Oct 13, 2016·Genetics·Pablo LibradoLudovic Orlando
Oct 7, 2020·Molecular Biology and Evolution·Bret A Payseur, Peicheng Jing
Mar 22, 2021·Molecular Ecology Resources·Ulas IsildakMatteo Fumagalli

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