The Impact of Message Mutation on the Fitness of a Genetic Code

The Standard Genetic Code is organized such that similar codons encode similar amino acids. One explanation suggested that the Standard Code is the result of natural selection to reduce the fitness ``load' that derives from the mutation and mistranslation of protein-coding genes. We review the arguments against the mutational load-minimizing hypothesis and argue that they need to be reassessed. We review recent analyses of the organization of the Standard Code and conclude that under cautious interpretation they support the mutational load-minimizing hypothesis. We then present a deterministic asexual model with which we study the mode of selection for load minimization. In this model, individual fitness is determined by a protein phenotype resulting from the translation of a mutable set of protein-coding genes. We show that an equilibrium fitness may be associated with a population with the same genetic code and that genetic codes that assign similar codons to similar amino acids have a higher fitness. We also show that the number of mutant codons in each individual at equilibrium, which determines the strength of selection for load minimization, reflects a long-term evolutionary balance between mutations in messages and selection on proteins, rather than the number of mutations that occur in a single generation, as has been assumed by previous authors. We thereby establish that selection for mutational load minimization acts at the level of an individual in a single generation. We conclude with comments on the shortcomings and advantages of load minimization over other hypotheses for the origin of the Standard Code. Received: 4 April 2001 / Accepted: 22 October 2001     

Physical theory,origin of flight,and a synthesis proposed for birds

Neither flapping and running to take-off nor gliding from heights can be disproved as the assured evolutionary origin of self-powered flight observed in modern vertebrates. Gliding with set wings would utilize available potential energy from gravity but gain little from flapping. Bipedal running, important in avian phylogeny, possibly facilitated the evolution of flight. Based on physical principles, gliding is a better process for the origin of powered flight than the "ground-up" process, which physically is not feasible in space or time (considering air resistance, metabolic energy costs, and mechanical resistance to bipedal running). Proto-avian ancestors of Archaeopteryx and Microraptor probably flapped their sparsely feathered limbs synchronously while descending from leaps or heights, with such "flutter-gliding" presented as a synthesis of the two earlier theories of flight origin (making use of the available potential energy from gravity, involving wing thrusts and flapping, coping with air resistance that slows air speed, but effecting positive fitness value in providing lift and slowing dangerous falls).     

基于叶绿体基因多样性的中国水稻起源进化研究

针对目前亚洲栽培稻起源地和进化途径学说众多、分歧巨大的现状,本研究选择原产中国的98份亚洲栽培稻和125份普通野生稻为材料,对叶绿体中atpA序列、rps16内含子序列、trnP-rpl33间隔区、trnG-trnfM序列、trnT-trnL间隔区序列的五段高突变序列进行测序,利用生物信息学方法进行比对分析,绘制Network网络图,构建系统发育树。结果表明,普通野生稻的Indel和SNP数目均比亚洲栽培稻多,序列多样性丰富;基于单倍型的Network网络图和系统发育树可将所有参试材料归为3个类群,类群I主要为粳稻与普通野生稻,类群II主要为籼稻,类群III主要为普通野生稻,而类群II和类群III亲缘关系较近,提示粳、籼两个亚种可能由偏粳、偏籼的普通野生稻分别进化而来,支持二次起源学说;所有与亚洲栽培稻亲缘关系较近的普通野生稻均来源于华南地区,支持华南地区为我国亚洲栽培稻起源中心的论点。     

中国栽培稻的起源与演化

中国栽培稻起源地主要有4种假说:华南起源说、云南起源说、长江中下游说和长江中游-淮河上游说。对其进行了简要概括,并进行评述:目前没有一种假说能完全符合水稻起源的4个条件,此外有些学者提出水稻的多起源中心;从分子生物学角度综述了栽培稻籼粳分化研究进展,主要有两个起源说:一源论和二次(或多次)起源论,大量研究支持籼稻和粳稻多起源论;从古DNA、水稻落粒性与驯化、植硅石等方面探讨栽培稻起源演化的研究方法。旨在能为水稻的起源演化研究提供有价值的参考。     

世界杨柳科植物的起源,分化和地理分布

全世界杨柳科共有６５０种。分为３属,即钻天柳属、杨属和柳属。花序下垂利于风媒,花序直立利于虫媒。钻天柳属具有利于风媒的雄花序和利于虫媒的雌花序,这是一种进货不完全的现象,是杨柳科中最原始的类群;杨属是杨柳科中适应风媒的分支;柳属是适应虫媒的分支。绝大多数种类分布在北半球温带,是较典型的温带科。其现代分布中分化中心在东亚地区。根据地史资料、化石资料以及杨柳科和其外类群的现代分布情况,我们认为,杨柳科     

橐吾属的起源、演化与地理分布

橐吾属Ligularia Cass．是菊科千里光族款冬亚族的一个大属。在款冬亚族中本属与大吾风草属Farfugium Lindl．亲缘关系最近,但进化程度较高。本属包括6组,11系129种。所有种类均分布在亚洲,仅2种扩散至欧洲。在东亚地区有119种,占该属总种数的96％。高度集中在横断山区的有4组、6系67种,其中61种为特有种,占该属总组数的66％,总系数的54．5％,总种数的52％。这个事实表明了横断山区是该属的多度中心和多样化中心。通过性状分析,伞房组伞房系Sect．Corymbosae,Ser．Calthifoliae叶肾形,具掌状叶脉,头状花序大而少,排列呈伞房状,总苞半球形,被认为是该属的原始类群。原始种齿叶橐吾L. dentata和鹿蹄橐吾L.hodgsonii的分布区从我国四川东部经过湖北、湖南、安徽、福建等省至日本。这个分布格局与近缘属大吴风草属Farfugium一致。 根据共同起源原理,这两个属的祖先极有可能就发生在这一地区。因此我们推测东亚地区从中国四川东部至日本这一地区是本属的发源地,然而根据地质历史和现代分布,作者认为中国中部(包括四川东部)是本属的初始起源地。该属起源后,基本上沿亚洲南缘的山地扩散,少数种类向东北至亚洲东北部。本属起源时间至少不晚于中白垩纪。     

金钱松（属）的细胞分类学研究

我国特有植物金钱松Ｐｓｅｕｄｏｌａｒｉｘａｍａｂｉｌｌｓ的体细胞染色体数目为２ｎ＝４４,不同于ｎ＝１２（Ｍｉｙａｋｅ＆Ｙａｓｕｉ,１９１１）和２ｎ＝２４（Ｄｕｎｉｅｕ－Ｖａｂｒｅ,１９６１）的结果。核型公式为Ｋ（２ｎ）＝４４＝４ｓｍ＋４０ｔ）４ＳＣ）属３Ｂ类型,与Ｋ（ｎ）＝２２＝２ｍ＋２０ｔ（Ｓａｘ＆Ｓａｘ,１９３３）和Ｋ（２ｎ）＝４４＝４ｓｍ＋４０ｔ（Ｈｉｚｕｍｅ１９８８）有差异。染色体相对长度组成为＝４４＝４Ｌ＋１２Ｍ＿２＋２６Ｍ＿１＋２Ｓ。金钦松（属）不仅在染色体数目（２ｎ＝４４）和核型（具２０对端着丝粒染色体）而且它的一些形态、解剖学和植化性状与所有松科其它各属不同。另外,它的一系列形态、解剖、孢粉、生化、植化和古植物学特征显然表明把该属与落叶松属、雪松属一起组成落叶松亚科是不适宜的。因此似乎有理由把金钱松从该亚科分出并建立一个单型的金钱松新亚科。本文还对金钱松（属）核型可能由近缘的铁杉属起源和进化而来作了讨论。     

木兰科的化石记录

通过整理和分析木兰科植物的化石记录发现：不论是植物大化石还是花粉,迄今为止在白垩纪以前地层中尚无可靠的记录,自白垩纪以来,木兰科的许多种广泛发生于北半球,如亚洲,欧洲及北美等地,但非洲和大洋洲至今尚未发现木兰科的化石记录。该科最早的化石记录为中国东北延吉地区早白垩世大拉子组的喙柱始木兰Archimagnolia rostrato-stylose Tao et Zhang. 根据现有化石记录,并结合木兰科现代植物的地理分布,推测：1）木兰科的起源时间不迟于早白垩世Aptian-Albian期;2）木兰科起源地点可能是东亚,后来经过欧洲进入北美,再从北美迁移到达南美洲;3）在地质历史时期,木兰属的出现比鹅掌楸属早,从而支持根据形态学与分子系统学研究得出的木兰属较鹅掌楸属原始的结论。     

Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum

The chloroplast genome has experienced many architectural changes during the evolution of chlorophyte green algae, with the class Chlorophyceae displaying the lowest degree of ancestral traits. We have previously shown that the completely sequenced chloroplast DNAs (cpDNAs) of Chamydomonas reinhardtii (Chlamydomonadales) and Scenedesmus obliquus (Sphaeropleales) are highly scrambled in gene order relative to one another. Here, we report the complete cpDNA sequence of Stigeoclonium helveticum (Chaetophorales), a member of a third chlorophycean lineage. This genome, which encodes 97 genes and contains 21 introns (including four putatively trans-spliced group II introns inserted at novel sites), is remarkably rich in derived features and extremely rearranged relative to its chlorophycean counterparts. At 223,902 bp, Stigeoclonium cpDNA is the largest chloroplast genome sequenced thus far, and in contrast to those of Chlamydomonas and Scenedesmus, features no large inverted repeat. Interestingly, the pattern of gene distribution between the DNA strands and the bias in base composition along each strand suggest that the Stigeoclonium genome replicates bidirectionally from a single origin. Unlike most known trans-spliced group II introns, those of Stigeoclonium exhibit breaks in domains I and II. By placing our comparative genome analyses in a phylogenetic framework, we inferred an evolutionary scenario of the mutational events that led to changes in genome architecture in the Chlorophyceae.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Nucleotide sequence data reported are available in the GenBank database under the accession number DQ630521.