Two decades of suspect evidence for adaptive molecular evolution——negative selection confounding positive-selection signals  

作　　者：Qipian Chen Hao Yang Xiao Feng Qingjian Chen Suhua Shi Chung-Ⅰ Wu Ziwen He 

机构地区：[1]State Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources,School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai),Sun Yat-sen University,Guangzhou 510275,China

出　　处：《National Science Review》2022年第5期125-137,共13页国家科学评论（英文版）

基　　金：supported by the National Natural Science Foundation of China(31971540 and 31830005);the National Key Research and Development Program of China(2017FY100705);the Guangdong Basic and Applied Basic Research Foundation(2019A1515010752);the Science and Technology Project of Guangzhou(202102020483);the Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(311021006)。

摘　　要：There has been a large literature in the last two decades affirming adaptive DNA sequence evolution between species.The main lines of evidence are from(i)the McDonald-Kreitman(MK)test,which compares divergence and polymorphism data,and(ii)the phylogenetic analysis by maximum likelihood(PAML)test,which analyzes multispecies divergence data.Here,we apply these two tests concurrently to genomic data of Drosophila and Arabidopsis.To our surprise,the>100 genes identified by the two tests do not overlap beyond random expectation.Because the non-concordance could be due to low powers leading to high false negatives,we merge every 20-30 genes into a’supergene’.At the supergene level,the power of detection is large but the calls still do not overlap.We rule out methodological reasons for the non-concordance.In particular,extensive simulations fail to find scenarios whereby positive selection can only be detected by either MK or PAML,but not both.Since molecular evolution is governed by positive and negative selection concurrently,a fundamental assumption for estimating one of these(say,positive selection)is that the other is constant.However,in a broad survey of primates,birds,Drosophila and Arabidopsis,we found that negative selection rarely stays constant for long in evolution.As a consequence,the variation in negative selection is often misconstrued as a signal of positive selection.In conclusion,MK,PAML and any method that examines genomic sequence evolution has to explicitly address the variation in negative selection before estimating positive selection.In a companion study,we propose a possible path forward in two stages—first,by mapping out the changes in negative selection and then using this map to estimate positive selection.For now,the large literature on positive selection between specieshas to await reassessment.

关 键 词：molecular evolution neutral theory natural selection 

分 类 号：Q75[生物学—分子生物学]