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Evidence that natural selection is the Primary Cause of the Guanine-cytosine Content Variation in Rice Genes

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Journal of Integrative Plant Biology 2007年第9期49卷 1393-1399页

作者： Xiaoli Shi Xiyin Wang Zhe Li Qihui Zhu Ji Yang Song Ge Jingchu Luo State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany the Chinese Academy of Sciences Beijing 100093 China College of Life Sciences National Laboratory of Plant Genetic Engineering and Protein Engineering Center of Bioinformatics Peking University Beijing 100871 China College of Mathematics Hebei Polytechnic University Tangshan 063009 China Center for Evolutionary Biology School of Life Sciences Fudan University Shanghai 200433 China

Cereal genes are classified into two distinct classes according to the guanine-cytosine （GC） content at the third codon sites （GC3）. natural selection and mutation bias have been proposed to affect the GC content. However, there has been controversy about the cause of GC variation. Here, we characterized the GC content of 1 092 paralogs and other single-copy genes in the duplicated chromosomal regions of the rice genome （ssp. indica） and classified the paralogs into GC3-rich and GC3-poor groups. By referring to out-group sequences from Arabidopsis and maize, we confirmed that the average synonymous substitution rate of the GC3-rich genes is significantly lower than that of the GC3-poor genes. Furthermore, we explored the other possible factors corresponding to the GC variation including the length of coding sequences, the number of exons in each gene, the number of genes in each family, the location of genes on chromosomes and the protein functions. Consequently, we propose that natural selection rather than mutation bias was the primary cause of the GC variation.

关键词： guanine-cytosine content mutation bias natural selection paralogs synonymous substitution rate two gene classes

Do different measures of maternal fitness affect estimation of natural selection on floral traits? A lesson from Linum pubescens (Linaceae)

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Journal of Plant Ecology 2017年第2期10卷 406-413页

作者： Laura Bigio Merav Lebel Yuval Sapir The Botanical Garden Department of Molecular Biology and Ecology of PlantsTel Aviv UniversityRamat AvivTel Aviv 69978Israel Earth Science Institute The Hebrew University of JerusalemGivat RamJerusalem 91904Israel Nature-Parks Authority Science DivisionAm-Veolamo 2Jerusalem 95463Israel

Aims Floral traits in animal-pollinated plants are proposed to be selected by the behavior of pollinators,which create differential ***,fitness estimation is not trivial and there is no agreed or universal measure of *** plants,fitness can be measured in various ways,including the number of fruits or seeds,probability of survival,or growth *** Because each fitness measure can be associated with different pol-linator behavior,estimating pollinator-mediated selection on floral traits can differ among various fitness *** used the annual Mediterranean plant,Linum pubescens,as a model to assess the relative role of various fitness measures in estimating pollinator-mediated selection on floral *** compared four maternal fit-ness measures and estimated their relative advantage in assessing natural selection on floral traits of *** identify whether each trait is under pollinator-mediated selection,we used media-tional *** Findings We found that each floral trait was under natural selection assessed by a different fitness *** color combination of floral tube throat and stamen color was under selection when using seed mass as a fitness measure,and floral diameter was under positive direc-tional selection when the number of seeds or number of fruits was used as a fitness *** on floral color was not mediated by pollinators’visitation rates,while flower diameter showed par-tial pollinator-mediated *** conclude that using several fitness measures gives an insight into the mechanisms underlying phenotypic selection on a floral trait,and facilitates the understand-ing of pollinator-mediated selection.

关键词： fitness flower size fruit-set Linum pubescens natural selection pollinator-mediated selection pollinator visitation rate seed-set seed mass

The Core Mechanism of natural selection: How the natural Cycle of Potassium Resources Affects the Biological Evolution and the Change of Human Society

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natural Science 2022年第10期14卷 434-440页

作者： Jiapei Dai Wuhan Institute for Neuroscience and Neuroengineering South-Central Minzu University Wuhan China

Darwin’s theory of evolution believes that biological evolution is a process of natural selection. This theory has been supported by much evidence, but the internal biological mechanism is not clear. Here, I elaborate on the cycle of potassium resources on the earth and the biological utilization and efficiency, which may be the core mechanism of natural selection and affect the evolution of organisms and the development of human society.

关键词： Potassium Resource Cycle natural selection Darwinian Principles Biological Evolution and Biodiversity The Development of Human Society

Lineage-specific positive selection on ACE2 contributes to the genetic susceptibility of COVID-19

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National Science Review 2022年第9期9卷 155-165页

作者： Yuwen Pan Panhong Liu Fang Wang Peng Wu Fanjun Cheng Xin Jin Shuhua Xu Key Laboratory of Computational Biology Shanghai Institute of Nutrition and Health University of Chinese Academy of Sciences Chinese Academy of Sciences College of Life Sciences University of Chinese Academy of Sciences The Third People’s Hospital of Shenzhen National Clinical Research Center for Infectious Disease The Second Affiliated Hospital of Southern University of Science and Technology Cancer Biology Research Center (Key Laboratory of the Ministry of Education) Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Department of Gynecologic Oncology Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Department of Hematology Union Hospital Tongji Medical College Huazhong University of Science and Technology School of Medicine South China University of Technology Department of Liver Surgery and Transplantation Liver Cancer Institute Zhongshan Hospital Fudan University State Key Laboratory of Genetic Engineering Collaborative Innovation Center of Genetics and Development Center for Evolutionary Biology School of Life Sciences Fudan University Human Phenome Institute Zhangjiang Fudan International Innovation Center and Ministry of Education Key Laboratory of Contemporary Anthropology Fudan University School of Life Science and Technology ShanghaiTech University Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences

The Angiotensin-Converting Enzyme-2(ACE2) gene,located on Xp22.2, attracts a great deal of attention because the protein it encodes is believed to be the functional cellular receptor for the new coronavirus(SARS-CoV-2).However,recent studies are controversial,especially concerning the intrinsic link between ACE2 diversity and COVID-19 ***,we conduct a population genetic study on ACE2 in6354 individuals representing 210 present-day populations and 5 329 individuals of ancient or archaic *** dissected the genetic architecture ofACE2 and identified two major haplogroups(hg) in East Asians,***2-hgl(43%) and ACE2-hg2(53%),while other populations harbor more diverse A ***,there was a significant loss of ACE2 common variations in East Asians in contrast to the X-chromosome-wide and genome-wide ***,association analysis between ACE2-hgs and COVID-19 severity in 1229 Han Chinese individuals with various levels of COVID-19 severity showed a higher risk ofACE2-hgl(odds ratio=1.56,P selection were detected,especially on ACE2-hg2,and were traced back to 100 000 years ago(but rose to a strong level during the Bronze Age,5000～3000 years ago,in East Asians).The selection pressures could have stemmed from multiple sources,but pre-COVID-19 viral epidemics and pandemics might have been potential driving forces,which consequently contributed to the genetic susceptibility to COVID-19 within and between populations.

关键词： ACE2 COVID-19 genetic susceptibility genetic diversity natural selection East Asia

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

Co-operation and Phase Behavior under the Mixed Updating Rules

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Chinese Physics Letters 2015年第11期32卷 173-177页

作者：章雯李耀声许晨 Department of Electronics and Communication Engineering Suzhou Institute of Industrial Technology Suzhou 215104 College of Physics Optoelectronics and Energy Sooehow University Suzhou 215006

We present a model by considering two updating rules when the agents play prisoner＇s dilemma on a square lattice. Agents can update their strategies by referencing one of his neighbors of higher payoffs under the imitation updating rule or directly replaced by one of his neighbors according to the death-birth updating rule. The frequency of co-operation is related to the probability q of occurrence of the imitation updating or the death-birth updating and the game parameter b. The death-birth updating rule favors the co-operation while the imitation updating rule favors the defection on the lattice, although both rules suppress the co-operation in the well-mixed population. Therefore a totally co-operative state may emerge when the death-birth updating is involved in the evolution when b is relatively small. We also obtain a phase diagram on the q-b plane. There are three phases on the plane with two pure phases of a totally co-operative state and a totally defective state and a mixing phase of mixed strategies. Based on the pair approximation, we theoretically analyze the phase behavior and obtain a quantitative agreement with the simulation results.

关键词： COOPERATIVENESS PRISONER'S dilemma game BIOLOGICAL systems natural selection GAME theory in biology

Fluctuation theorem for the mutation process in in vitro evolution

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Chinese Physics B 2010年第4期19卷 11-15页

作者：刘琪汤超欧阳颀 Department of Physics Peking University Center for Theoretical Biology Peking University California Institute for Quantitative Biomedical Research Departments of Biopharmaceutical Sciences and Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCA 94143USA

A proposition based on the fluctuation theorem in thermodynamics is formulated to quantitatively describe molecular evolution processes in biology. Although we cannot give full proof of its generality, we demonstrate via computer simulation its applicability in an example of DNA in vitro evolution. According to this theorem, the evolution process is a series of exponentially rare fluctuations fixed by the force of natural selection

关键词： fluctuation theorem molecular evolution natural selection

High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense

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Integrative Zoology 2015年第5期10卷 465-481页

作者： Wei ZHANG Zhenhua LUO Mian ZHAO Hua WU Institute of Evolution and Ecology International Research Centre of Ecology and EnvironmentSchool of Life SciencesCentral China Normal UniversityWuhanChina

Threatened species typically have a small or declining population size,which make them highly susceptible to loss of genetic diversity through genetic drift and *** diversity determines the evolutionary potential of a species;therefore,maintaining the genetic diversity of threatened species is essential for their *** this study,we assessed the genetic diversity of the adaptive major histocompatibility complex(MHC)genes in an endangered and narrowly distributed amphibian species,Leptobrachium leishanense in Southwest *** compared the genetic variation of MHC class I genes with that observed in neutral markers(5 microsatellite loci and cytochrome b gene)to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this *** found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian *** positive selection was evident in the MHC class I *** higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern,as drift can affect all the genome in a similar way but selection directly targets MHC *** demographic analysis revealed no recent bottleneck events in ***,additional population decline will accelerate the dangerous status for this *** suggest that the conservation management of *** should concentrate on maximizing the retention of genetic diversity through preventing their continuous population *** their living habitats and forbidding illegal hunting are the most important measures for conservation of ***.

关键词： demography process genetic diversity major histocompatibility complex natural selection Leptobrachium leishanense

Complex Mutation and Weak selection together Determined the Codon Usage Bias in Bryophyte Mitochondrial Genomes

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Journal of Integrative Plant Biology 2010年第12期52卷 1100-1108页

作者： Bin Wang Jing Liu Liang Jin Xue-Ying Feng Jian-Qun Chen State Key Laboratory of Pharmaceutical Biotechnology Department of Biology Nanjing University Nanjing 210093 China

Mutation and selection are two major forces causing codon usage biases. How these two forces influence the codon usages in green plant mitochondrial genomes has not been well investigated. In the present study, we surveyed five bryophyte mitochondrial genomes to reveal their codon usage patterns as well as the determining forces. Three interesting findings were made. First, comparing to Chara vulgaris, an algal species sister to all extant land plants, bryophytes have more G, C-ending codon usages in their mitochondrial genes. This is consistent with the generally higher genomic GC content in bryophyte mitochondria, suggesting an increased mutational pressure toward GC. Second, as indicated by Wright＇s Nc-GC3s plot, mutation, not selection, is the major force affecting codon usages of bryophyte mitochondrial genes. However, the real mutational dynamics seem very complex. Context-dependent analysis indicated that nucleotide at the 2nd codon position would slightly affect synonymous codon choices. Finally, in bryophyte mitochondria, tRNA genes would apply a weak selection force to fine-tune the synonymous codon frequencies, as revealed by data of Ser4-Pro-Thr-Val families. In summary, complex mutation and weak selection together determined the codon usages in bryophyte mitochondrial genomes.

关键词： PLANT mutation PLANT genomes BRYOPHYTES MITOCHONDRIA CHARA vulgaris natural selection GENETIC code MITOCHONDRIAL DNA