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

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National Science Review 2022年第5期9卷 129-141页

作者： qipian chen Hao Yang Xiao Feng Qingjian chen Suhua Shi Chung-Ⅰ Wu Ziwen He State Key Laboratory of Biocontrol Guangdong Key Laboratory of Plant Resources School of Life SciencesSouthern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Sun Yat-sen University

There has been a large literature in the last two decades affirming adaptive DNA sequence evolution between *** 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 ***,we apply these two tests concurrently to genomic data of Drosophila and *** our surprise,the> 100 genes identified by the two tests do not overlap beyond random *** 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 *** rule out methodological reasons for the *** particular,extensive simulations fail to find scenarios whereby positive selection can only be detected by either MK or PAML,but not *** 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 ***,in a broad survey of primates,birds,Drosophila and Arabidopsis,we found that negative selection rarely stays constant for long in *** a consequence,the variation in negative selection is often misconstrued as a signal of positive *** conclusion,MK,PAML and any method that examines genomic sequence evolution has to explicitly address the variation in negative selection before estimating positive *** 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 *** now,the large literature on positive selection between species has to await reassessment.

关键词： molecular evolution neutral theory natural selection

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Extensive gene flow in secondary sympatry after allopatric speciation

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National Science Review 2022年第12期9卷 24-36页

作者： Xinfeng Wang Ziwen He Zixiao Guo Ming Yang Shaohua Xu qipian chen Shao Shao Sen Li Cairong Zhong Norman C.Duke Suhua Shi State Key Laboratory of Biocontrol Guangdong Key Laboratory of Plant Resources School of Life SciencesSouthern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Sun Yat-sen University Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering School of Life Sciences Fudan University Department of Laboratory Medicine& Pathology University of Washington Hainan Academy of Forestry (Hainan Academy of Mangrove) Centre for Tropical Water and Aquatic Ecosystem Research James Cook University

In the conventional view,species are separate gene pools delineated by reproductive isolation(RI).In an alternative view,species may also be delineated by a small set of ’speciation genes’ without full RI,a view that has gained broad acceptance.A recent survey,however,suggested that the extensive literature on’speciation with gene flow’ is mostly(if not all) about exchanges in the early stages of *** is no definitive evidence that the observed gene flow actually happened after speciation is ***,we wish to know whether ’good species’(defined by the ’secondary sympatry’ test) do continue to exchange genes and,importantly,under what conditions such exchanges can be *** novo whole-genome assembly and re-sequencing of individuals across the range of two closely related mangrove species(Rhizophora mucronata and R. stylosa) reveal the genomes to be well delineated in *** became sympatric in northeastern Australia but remain distinct ***,their genomes harbor～4000-10 000 introgression blocks averaging only about 3-4 *** fine-grained introgressions indicate continual gene flow long after speciation as non-introgressable ’genomic islets,’～1.4 Kb in size,often harbor diverging genes of flower or gamete *** fine-grained introgression in secondary sympatry may help settle the debate about sympatric ***-allopatric *** conclusion,true’good species’ may often continue to exchange genes but the opportunity for detection is highly constrained.

关键词： mangroves population genomics speciation introgression species hybridization

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The population genomics of the mangrove species Sonneratia alba cast light on the genome shaping from isolation and migration

The population genomics of the mangrove species Sonneratia a...

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中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： qipian chen Ziwen He Suhua Shi State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources Sun Yat-sen University

How genomic composition is shaped by isolation,gene flow and selection? We sought for answers by re-sequencing 33 genomes of Sonneratia alba,which is a widespread mangrove species in the Indo-West Pacific（IWP） *** results of comparative genomic analyses indicated low genetic diversity within populations and strong sequence divergence among populations from four major oceanic regions,*** South China Sea,the East Indian Ocean,northwestern Australia and eastern *** observed population structure was shaped by the geographic isolation due to the emergence of merged shelves（Sunda and Sahul shelves） during the Pleistocene glacial ***,as the admixture in the Kukup population indicated,during the interglacial periods,the rising sea level and opening of the Strait of Malacca also permitted genetic exchange between the East Indian Ocean and South China *** contrasts of population structure pattern among genomic loci revealed by genome scanning may provide insight into how isolation and migration shaped the divergence patterns at the genomic ***,the identified highly divergent genes between the two Hainan populations（Sanya and Wenchang） were under strong positive selection as the MK test *** of partial such genes in the Sanya population were further found to be introduced from Indian Ocean via gene flow through the Strait of Malacca,which may be a case of adaptive gene *** study provides clues that interregional genetic exchanges in mangroves facilitate re-use of standing genetic variation to establish in new habitats.

关键词： isolation genome resequencing mangroves migration Sonneratia alba Pleistocene glaciations

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盘龙七片治疗膝骨性关节炎的疗效分析

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中外医疗 2009年第32期28卷 7-9页

作者：肖立军邓德礼陈文贵徐晖广东番禺人民医院骨二科广东广州511400

目的评价盘龙七片治疗膝骨性关节炎的疗效。方法2005年10月至2009年1月我科收治144例膝关节骨性关节炎患者随机分为盘龙七治疗组和双氯芬酸钠对照组。治疗组予以口服盘龙七片,1次3片,每日3次;对照组予以口服双氯芬酸,25mg,1次1粒,每日3... 详细信息

目的评价盘龙七片治疗膝骨性关节炎的疗效。方法2005年10月至2009年1月我科收治144例膝关节骨性关节炎患者随机分为盘龙七治疗组和双氯芬酸钠对照组。治疗组予以口服盘龙七片,1次3片,每日3次;对照组予以口服双氯芬酸,25mg,1次1粒,每日3次。连续治疗6周。疗程结束后评定其疗效。结果2组治疗前年龄和性别等一般资料及关节压痛、平地行走痛、静息痛、晨僵等积分无显著性差异(P>0.05);治疗后2组在关节压痛、平地行走痛、静息痛、晨僵等症状体征方面均有改善,患者外周血IL-6、TNF水平均明显降低,治疗组疗效优于对照组,且2组疗效有显著性差异(P<0.05)。结论盘龙七片是治疗膝骨性关节炎的有效药物,值得推广应用。

关键词：盘龙七片骨性关节炎膝对照研究

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