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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 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 species has to await reassessment.

关键词： molecular evolution neutral theory natural selection

molecular evolution,virology and spatial distribution of HCV genotypes in Pakistan:A meta-analysis

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Infectious Medicine

Infectious Medicine 2023年第4期2卷 324-333页

作者： Arslan Habib Nadiya Habib Khalid Mahmood Anjum Riffat Iqbal Zeeshan Ashraf Muhammad Usman Taj Muhammad Asim Kanwal Javid Faezeh Idoon Saeid Dashti Cassio Rocha Medeiros Ana Pavla Almeida Diniz Gurgel Henrique Douglas Melo Coutinho Laboratory of molecular Immunology School of Life SciencesFudan UniversityShanghai 200433China Department of Zoology University of GujratGujratPunjab 50700Pakistan Department of Zoology University of Veterinary and Animal SciencesLahore 54000Pakistan Department of Zoology Government College UniversityLahore 54000Pakistan Department of Fisheries and Aquaculture University of Veterinary and Animal SciencesLahore 54000Pakistan Department of Zoology University of NarowalNarowal 51600Pakistan Department of Geography Government College UniversityLahore 54000Pakistan Department of Surgical Technology Ferdows School of Allied Medicine and Public HealthBirjand University of Medical SciencesBirjand 97178Iran Ferdows School of Paramedical and Health Birjand University of Medical SciencesBirjand 97178Iran CECAPE College Juazeiro do Norte 63024-015Brazil Department of Engineering and Environment Federal University of ParaibaJoão Pessoa 58051-900Brazil Laboratory of Microbiology and molecular Biology(LMBM) Department of Biological ChemistryRegional University of CaririCrato 63105-000Brazil

Background:Hepatitis C,caused by the Hepatitis C Virus(HCV),is the second most common form of viral hepatitis.The geographical distribution of HCV genotypes can be quite complex,making it challenging to ascertain the most prevalent genotype in a specific area.Methods:To address this,a review was conducted to determine the prevalence of HCV genotypes across various provinces and as a whole in Pakistan.The scientific literature regarding the prevalence,distribution,genotyping,and epidemiology of HCV was gathered from published articles spanning the years 1996-2020.Results:Genotype 1 accounted for 5.1%of the patients,with its predominant subtype being 1a at 4.38%.The frequencies of its other subtypes,1b and 1c,were observed to be 1.0%and 0.31%respectively.Genotype 2 had a frequency of 2.66%,with the most widely distributed subtype being 2a at 2.11%of the patients.Its other subtypes,2b and 2c,had frequencies of 0.17%and 0.36%respectively.The most prevalent genotype among all isolates was 3(65.35%),with the most frequent subtype being 3a(55.15%),followed by 3b(7.18%).The prevalence of genotypes 4,5,and 6 were scarce in Pakistan,with frequencies of 0.97%,0.08%,and 0.32%respectively.The prevalence of untypeable and mixed genotypes was 21.34%and 3.53%respectively.Estimating genotypes proves to be a productive method in assisting with the duration and selection of antiviral treatment.Different HCV genotypes can exhibit variations in their response to specific antiviral treatments.Different genotypes may have distinct natural histories,including variations in disease progression and severity.Some genotypes may lead to more rapid liver damage,while others progress more slowly.Conclusions:This information can guide screening and testing strategies,helping to identify individuals at higher risk of developing severe complications.Studying the distribution of HCV genotypes in a population can provide valuable insights into the transmission dynamics of the virus.

关键词： Genotypes HCV molecular evolution Pakistan Spatial distribution

molecular evolution and species-specific expansion of the NAP members in plants

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Journal of Integrative Plant Biology 2015年第8期57卷 673-687页

作者： Kai Fan Hao Shen Noreen Bibi Feng Li Shuna Yuan Ming Wang Xuede Wang Institute of Crop Science College of Agriculture and Biotechnology Zhejiang University

he NAP（NAC-Like, Activated by AP3/PI） subfamily is one of the important plant-specific transcription factors, and controls many vital biological processes in plants. In the current study, 197 NAP proteins were identified from 31 vascular plants,but no NAP members were found in eight non-vascular plants.All NAP proteins were phylogenetically classified into two groups（NAP I and NAP II）, and the origin time of the NAP I group might be relatively later than that of the NAP II group.Furthermore, species-specific gene duplications, caused by segmental duplication events, resulted in the expansion of the NAP subfamily after species-divergence. Different groups have different expansion rates, and the NAP group preference was found during the expansion in plants. Moreover, the expansion of NAP proteins may be related to the gain and loss of introns.Besides, functional divergence was limited after the gene duplication. Abscisic acid（ABA） might play an important role in leaf senescence, which is regulated by NAP subfamily. These results could lay an important foundation for expansion and evolutionary analysis of NAP subfamily in plants.

关键词： molecular evolution NAP subfamily plant kingdom species-specific expansion

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molecular evolution of Na^(+) channels in teleost fishes

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Integrative Zoology 2009年第1期4卷 64-74页

作者： Harold H.ZAKON Manda C.JOST Derrick J.ZWICKL Ying LU David M.HILLIS Section of Neurobiology Section of Integrative Biology The University of TexasAustinTXUSA

Voltage-dependent sodium channels are critical for electrical excitability.Invertebrates possess a single sodium channel gene;two rounds of genome duplication early in vertebrates increased the number to four.Since the teleost-tetrapod split,independent gene duplications in each lineage have further increased the number of sodium channel genes to 10 in tetrapods and 8 in teleosts.Here we review how the occurrence of multiple sodium channel paralogs has influenced the evolutionary history of three groups of fishes:pufferfish,gymnotiform and mor-myriform electric fish.Pufferfish(tetraodontidae)produce a neurotoxin,tetrodotoxin,that binds to and blocks the pore of sodium channels.Pufferfish evolved resistance to their own toxins by amino acid substitutions in the pore of their sodium channels.These substitutions had to occur in parallel across multiple paralogs for organismal re-sistance to evolve.Gymnotiform and mormyriform fishes independently evolved electric organs to generate elec-tricity for communication and object localization.Two sodium channel genes are expressed in muscle in most fishes.In both groups of weakly electric fishes,one gene lost its expression in muscle and became compartmen-talized in the evolutionary novel electric organ,which is a muscle derivative.This gene then evolved at elevated rates,whereas the gene that is still expressed in muscle does not show elevated rates of evolution.In the electric organ-expressing gene,amino acid substitutions occur in parts of the channel involved in determining how long the channel will be open or closed.The enhanced rate of sequence evolution of this gene likely underlies the spe-cies-level variations in the electric signal.

关键词： electric fish molecular evolution pufferfish sodium channels tetrodotoxin.

molecular evolution of connective tissue growth factor in Cyprinidae (Teleostei:Cypriniformes)

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Progress in Natural Science:Materials International 2008年第2期18卷 155-160页

作者： Xianghui Kong a,b,Xuzhen Wang a,Xiaoni Gan a,Junbing Li a,Shunping He a,a Institute of Hydrobiology,Chinese Academy of Sciences,Wuhan 430072,China b College of Life Science,Henan Normal University,Xinxiang 453007,China Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China College of Life Science Henan Normal University Xinxiang 453007 China

Connective tissue growth factor (CTGF) plays an important role in regulation of cell growth,differentiation,apoptosis and individual development in animals. The study of sequences variation and molecular evolution of CTGF gene across various species of the cyprinid could be helpful for understanding of speciation and gene divergence in this kind of fish. In this study,19 novel sequences of CTGF gene were obtained from the representative species of the family Cyprinidae using PCR amplification,cloning and sequencing. Phylogenetic relationships of Cyprinidae were reconstructed by neighbor-joining (NJ),maximum parsimony (MP),maximum likelihood (ML) and Bayesian method. Oryzias latipes from the family Cyprinodontidae was assigned to be the outgroup taxon. Leuciscini and Barbini were clustered into the monophyletic lineages,respectively,with the high nodal supports. The estimation of the ratio of non-synonymous to synonymous substitution (dN/dS) for the various branches indicated that there stood the different evolution rates between the Leuciscini and the Barbini. With the ratio of dN/dS of the Leuciscini being lower than that of the Barbini,species within the Barbini were demonstrated to be subjected to the relatively less selection pressure and under the relaxable evolution background. A 6 bp indel (insertion/deletion) was found at the 50 end of CTGF gene of Cyprinidae,and this 6 bp deletion only appeared in the Leuciscini,which is a typical characteristic of the Leuciscini and provides evidence for the monophylogeny of the Leuciscini. For the amino acid sequences of CTGF protein,the most variations and indels were distributed in the signal region and IGFBP region of this protein,implying that these variations were correlated with the regulation of the CTGF gene expression and protein activity.

关键词： Connective tissue growth factor Sequence variation molecular evolution Cyprinidae

molecular evolution and phylogeny of the angiosperm ycf2 gene

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Journal of Systematics and evolution 2010年第4期48卷 240-248页

作者： 1 Jin-Ling HUANG 1Gui-Ling SUN 2Da-Ming ZHANG 1(Department of Biology,East Carolina University,Greenville,NC 27858,USA) 2(State Key Laboratory of Systematic and evolutionary Botany,Institute of Botany,Chinese Academy of Sciences,Beijing 100093,China) (Department of Biology East Carolina University Greenville NC 27858 USA) (State Key Laboratory of Systematic and evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China)

Much of the recent progress in understanding angiosperm phylogeny has been achieved using multigene or plastid genome datasets.However,it is largely unclear what size of dataset is required to achieve sufficient resolution.The ycf2 gene is the largest plastid gene in angiosperms and it was used as part of multigene datasets in several earlier investigations into angiosperm relationships.In this study,we show that the ycf2 gene alone can provide a generally well-supported phylogeny that is consistent with those inferred from the most comprehensive multigene or plastid genome datasets.The phylogenetic signal of the ycf2 gene is likely derived from the combination of its long sequence length and low rate of nucleotide substitution.The ycf2 gene may provide a low-cost alternative to comprehensive multigene or genome datasets for investigating angiosperm relationships.

关键词： angiosperm phylogeny indel multigene dataset molecular evolution

molecular evolution of Visual Opsin Genes during the Behavioral Shifts between Different Photic Environments in Geckos

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Asian Herpetological Research 2021年第3期12卷 280-288页

作者： Yao CAI Yuefen FAN Youxia YUE Peng LI Jie YAN Kaiya ZHOU Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjing 210023JiangsuChina School of Food Science Nanjing Xiaozhuang UniversityNanjing 211171JiangsuChina

Reptiles are the most morphologically and physiologically diverse tetrapods,with the squamates having the most diverse habitats.Lizard is an important model system for understanding the role of visual ecology,phylogeny and behavior on the structure of visual systems.In this study,we compared three opsin genes(RH2,LWS and SWS1)among 49 reptile species to detect positively selected genes as well as amino acid sites.Our results indicated that visual opsin genes have undergone divergent selection pressures in all lizards and RH2 and LWS suffered stronger positive selection than SWS1.Twelve positively selected sites were picked out for RH2 and LWS.Moreover,many diagnostic sites were found between geckos and non-gecko lizards,most of which were located near the positively selected sites and some of them have already been reported to be responsible for significant shifts of the wavelength of maximum absorption(λ_(max)).The results indicated that the gecko lineage accelerated the evolution of these genes to adapt to the dim-light environment or nocturnality as well as the switch between nocturnality and diurnality.

关键词： Gecko diurnality molecular evolution nocturnality opsin gene

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molecular evolution of methanogens based on their metabolic facets

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Frontiers in Biology 2011年第6期6卷 490-503页

作者： P.CHELLAPANDI Department of Bioinformatics Centre for Excellence in School of Life SciencesBharathidasan UniversityTiruchirappalli-620024Tamil NaduIndia

The information provided by completely sequenced genomes of methanogens can yield insights into a deeper molecular understanding of evolutionary mechanisms.This review describes the advantages of using metabolic pathways to clarify evolutionary correlation of methanogens with archaea and prokaryotes.Metabolic trees can be used to highlight similarities in metabolic networks related to the biology of methanogens.Metabolic genes are among the most modular in the cell and their genes are expected to travel laterally,even in recent evolution.Phylogenetic analysis of protein superfamilies provides a perspective on the evolutionary history of some key metabolic modules of methanogens.Phage-related genes from distantly related organisms typically invade methanogens by horizontal gene transfer.Metabolic modules in methanogenesis are phylogenetically aligned in closely related methanogens.Reverse order reactions of methanogenesis are achieved in methylotrophic methanogens using metabolic and structural modules of key enzymes.A significant evolutionary process is thought to couple the utilization of heavy metal ions with energetic metabolism in methanogens.Over 30 of methanogens genomes have been sequenced to date,and a variety of databases are being developed that will provide for genome annotation and phylogenomic analysis of methanogens.Into the context of the evolutionary hypothesis,the integration of metabolomic and proteomic data into large-scale mathematical models holds promise for fostering rational strategies for strain improvement.

关键词： methanogens genomics metabolic module phylogeny protein superfamily molecular evolution

Structural Features and molecular evolution of Bowman-Birk Protease Inhibitors and Their Potential Application

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Acta Biochimica et Biophysica Sinica 2005年第5期37卷 283-292页

作者： Rui-Feng QI~(1.2) Zhan-Wu SONG~1 Cheng-Wu CHI~(2.3). 1 College of Life Science, Northwest Normal University, Lanzhou 730070, China: 2 Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China 3 Institute of Protein Research, Tongji University, Shanghai 200092, China College of Life Science Northwest Normal UniversityLanzhou 730070 China Institute of Biochemistry and Cell Biology Chinese Academy of SciencesShanghai 200031 China Institute of Protein Research Tongji UniversityShanghai 200092 China

The Bowman-Birk inhibitors(BBIs)are well-studied serine protease inhibitors that areabundant in dicotyledonous and monocotyledonous plants.BBIs from dicots usually have a molecular weightof 8k and are double-headed with two reactive sites,whereas those from monocots can be divided into twoclasses,one approximately 8 kDa in size with one reactive site(another reactive site was lost)and the otherapproximately 16 kDa in size with two reactive sites.The reactive site is located at unique exposed surfacesformed by a disulfide-linked β-sheet loop that is highly conserved,rigid and mostly composed of nineresidues.The structural features and molecular evolution of inhibitors are described,focusing on the conserveddisulfide bridges.The sunflower trypsin inhibitor-1(SFTI-1),with 14 amino acid residues,is a recentlydiscovered bicyclic inhibitor,and is the most small and potent naturally occurring Bowman-Birk inhibitor.Recently,BBIs have become a hot topic because of their potential applications.BBIs are now used fordefense against pathogens and insects in transgenic plants,which has advantages over using toxic andpolluting insecticides.BBIs could also be applied in the prevention of cancer,Dengue fever,and inflammatoryand allergic disorders,because of their inhibitory activity with respect to the serine proteases that play apivotal role in the development and pathogenesis of these diseases.The canonical nine-residue loop of BBIs/STFI-1 provides an ideal template for drug design of specific inhibitors to target their respective proteases.

关键词： Bowman-Birk protease inhibitor sunflower trypsin inhibitor-1(SFTI-1) molecular evolution drug design