A new test for detecting recent positive selection that is free from the confounding impacts of demography

Molecular Biology and Evolution
Hai-Peng Li


It has been a long-standing interest in evolutionary biology to search for the traces of recent positive Darwinian selection in organisms. However, such efforts have been severely hindered by the confounding signatures of demography. As a consequence, neutrality tests often lead to false inference of positive selection because they detect the deviation from the standard neutral model. Here, using the maximum frequency of derived mutations (MFDM) to examine the unbalanceness of the tree of a locus, I propose a statistical test that is analytically free from the confounding effects of varying population size and has a high statistical power (up to 90.5%) to detect recent positive selection. When compared with five well-known neutrality tests for detecting selection (i.e., Tajima's D test, Fu and Li's D test, Fay and Wu's H test, the E test, and the joint DH test), the MFDM test is indeed the only one free from the confounding impacts of bottlenecks and size expansions. Simulations based on wide-range parameters demonstrated that the MFDM test is robust to background selection, population subdivision, and admixture (including hidden population structure). Moreover, when two high-frequency mutations are introduced, the MFDM test is...Continue Reading


Nov 1, 1989·The Journal of Psychology·A S Luchins
Feb 1, 1974·Genetical Research·J M Smith, J Haigh
Oct 1, 1995·Theoretical Population Biology·Y X Fu
Oct 1, 1993·The Journal of Social Psychology·A Stahelski, M E Patch
Nov 7, 2001·The American Journal of Pathology·W C WolfJ Chao
Aug 23, 2002·Nature·Wolfgang EnardSvante Pääbo
Dec 6, 2002·Genome Research·Joshua M AkeyMark D Shriver
Mar 12, 2004·Molecular Ecology·Mark A Beaumont, David J Balding
Jul 29, 2004·Genetics·Yuseob Kim, Rasmus Nielsen
Feb 18, 2005·Genetics·Joachim Hermisson, Pleuni S Pennings
May 25, 2005·Genetics·Jeffrey D JensenCarlos D Bustamante
Oct 28, 2005·Genome Research·Rasmus NielsenCarlos D Bustamante
Feb 24, 2006·PLoS Biology·Benjamin F VoightJonathan K Pritchard
Mar 10, 2006·PLoS Biology·Catriona MacCallum, Emma Hill
Jul 11, 2006·Genome Research·Joanna L KelleyJoshua M Akey
Sep 20, 2006·Nature Reviews. Genetics·Paul Marjoram, Simon Tavaré
Oct 17, 2006·PLoS Genetics·Hai-Peng Li, Wolfgang Stephan
Jul 28, 2007·Molecular Biology and Evolution·Ryan D HernandezCarlos D Bustamante
Feb 28, 2008·Evolution; International Journal of Organic Evolution·Matthew W Hahn
May 13, 2008·Journal of Molecular Evolution·Per SjödinMartin Lascoux


Jun 11, 2011·Molecular Biology and Evolution·Simona FornarinoLluis Quintana-Murci
Oct 30, 2012·Molecular Biology and Evolution·Ryan J Haasl, Bret A Payseur
May 23, 2013·PLoS Computational Biology·Hai-Peng Li, Thomas Wiehe
Jun 21, 2012·Genetics·Pavlos PavlidisWolfgang Stephan
Apr 4, 2014·Molecular Biology and Evolution·Maud FagnyGuillaume Laval
Feb 11, 2016·GigaScience·Nikolaos Alachiotis, Pavlos Pavlidis
Aug 21, 2015·Molecular Ecology·Christian D HuberRasmus Nielsen
Mar 3, 2012·Evolution; International Journal of Organic Evolution·Zhong-Hu LiMartin Lascoux
Apr 25, 2015·Annals of Human Genetics·Min CaoGuang Ning
Apr 3, 2015·Investigative Genetics·Andreas Wollstein, Wolfgang Stephan
Sep 3, 2013·Mathematical Biosciences·Filippo DisantoThomas Wiehe
Nov 11, 2014·Annual Review of Ecology, Evolution, and Systematics·Joseph Lachance, Sarah A Tishkoff
Nov 25, 2016·Journal of Evolutionary Biology·F C Almeida, R DeSalle
Mar 16, 2016·PLoS Genetics·Daniel R Schrider, Andrew D Kern
Mar 24, 2017·Molecular Biology and Evolution·Davide RissoDennis Drayna
May 10, 2017·Molecular Biology and Evolution·Daniel R Schrider, Andrew D Kern
Nov 10, 2017·Nature·Jiang-An YinShi-Qing Cai
Oct 2, 2018·Genes & Genetic Systems·Naoko T FujitoNaoyuki Takahata
Oct 14, 2018·Evolution; International Journal of Organic Evolution·Yongshuai SunJianquan Liu
Apr 14, 2017·Journal of Biological Research·Pavlos Pavlidis, Nikolaos Alachiotis
Nov 8, 2017·Molecular Ecology·Xiaoheng ChengMichael DeGiorgio

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