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1.
With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.  相似文献
2.
Summary Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or transition type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or transversion type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = — (1/2) ln {(1 — 2P — Q) }. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = — (1/2) ln (1 — 2P — Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.Contribution No. 1330 from the National Institute of Genetics, Mishima, 411 Japan  相似文献
3.
Evolutionary trees from DNA sequences: A maximum likelihood approach   总被引:126,自引:0,他引:126  
Summary The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.By acceptance of this article, the publisher and/or recipient acknowledges the U.S. government's right to retain a nonexclusive, royalty-free licence in and to any copyright covering this paperThis report was prepared as an account of work sponsored by the United States Government. Neither the United States nor the United States Department of Energy, nor any of their employees, nor any of their contractors, subcontractors, or their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness or usefulness of any information, apparatus, product or process disclosed, or represents that its use would not infringe privately-owned rights  相似文献
4.
核rDNA的ITS序列在被子植物系统与进化研究中的应用   总被引:88,自引:0,他引:88       下载免费PDF全文
被子植物与其它高等真核生物相似,核rDNA是高度重复的串联序列。由于同步进化的力量,绝 大多数物种中这些重复单位间已发生纯合或接近纯合。核rDNA的内转录间隔区(ITS)包含被5.8S rDNA所分隔的ITS1和ITS2两个片段,ITSl的长度为187~298bp,ITS2为187~252bp,经PCR扩 增后可以方便地对这两个片段进行直接测序或克隆测序。ITS序列变异较快,可以提供较丰富的变异 位点和信息位点,已证实它是研究许多被子植物类群系统与进化的重要分子标记,不仅可用于解决科、 亚科、族、属、组内的系统发育和分类问题,而且可用于重建多倍体复合体的网状进化关系,探讨异源多倍体的起源过程,然而,正是由于ITS序列变异较快,它一般不适于科以上水平的系统发育研究。  相似文献
5.
鱼类线粒体DNA研究新进展   总被引:72,自引:0,他引:72  
郭新红  刘少军  刘巧  刘筠 《遗传学报》2004,31(9):983-1000
线粒体DNA是分子生物学研究中的一个热门领域,已成为鱼类进化生物学和群体遗传学研究的重要分子遗传标记。本文对鱼类线粒体DNA分子生物学的最新研究进展进行了较详细的阐述。重点介绍鱼类线粒体DNA全序列的研究进展、组成及特征,鱼类线粒体DNA非编码区结构研究进展,鱼类线粒体DNA多态性及其主要的检测方法;综述了最近有关鱼类线粒体DNA在鱼类系统学、种间杂交渐渗、种群识别、起源和进化、地理分化等研究中的应用情况。  相似文献
6.
Genome evolution in polyploids   总被引:67,自引:0,他引:67  
Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.  相似文献
7.
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA   总被引:63,自引:0,他引:63  
Summary A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized leastsquares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.3±11.7, 13.3±1.5, 10.9±1.2, 3.7±0.6, and 2.7±0.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a protochimpanzee after the former had developed bipedalism.  相似文献
8.
黄河源区景观格局与生态功能的动态变化   总被引:56,自引:4,他引:52       下载免费PDF全文
王根绪  郭晓寅  程国栋 《生态学报》2002,22(10):1587-1598
利用20世纪70年代、80年代与90年代三期遥感资料,选取有代表性的9个有关度量景观空间结构与景观异质性的定量指标,通过FRAGSTATS计算方法,系统研究了黄河源区景观生态结构与景观格局变化,表明在近30a来,区域景观空间格局趋于破碎化和多样化,其形成与发展的主要内在因素是高寒稀疏化草原草地、黑土化与杂类草草地和沙化草地等景观类型的迅速发展,其景观面积分别增加了384.16%、66.63%和421.09%;选取景观生物生产力、景观土壤养分、景观植被覆盖度等景观功能的表征参数,提出了景观格局动态演变下分析景观功能变化的定量方法及其数学模型。在明确近30a来区域景观格局演变特征的基础上,研究了黄河源区不同时段不同景观类型间生态功能的转移流动特征及其区域生态环境效应,表明:近30a来,黄河源区景观功能变化强烈;区域景观动态演变将形成区域内部景观功能向减退与增强两个方向的变化,两个方向的强度均衡将形成区域整体生态功能的特征。研究区域景观格局的动态变化所引起的区域生态功能演变特征,可充分认识区域生态系统变化的内在因素和演变趋势。  相似文献
9.
从超氧化物歧化酶的分布和结构看其分子进化   总被引:51,自引:0,他引:51       下载免费PDF全文
超氧化物歧化酶(SOD)是一种催化超氧化物阴离子自由基发生歧化反应, 生成氧和过氧化氢的金属酶. 按其结合的金属离子, 区分为Fe-SOD, Mn-SOD和CuZn-SOD三种. Fe-SOD主要存在于原核细胞中;Mn-SOD在原核和真核细胞中都存在;CuZn-SOD主要存在于真核细胞中. Fe, Mn-SOD的一级结构, 空间结构及其性质很相似, 来自一个共同的祖先; CuZn-SOD的结构与前两者相差较大, 是在以后的发展中单独进化的.  相似文献
10.
植物多酚氧化酶的研究进展   总被引:49,自引:1,他引:48  
多酚氧化酶(polyphenol oxidase,PPO)是一类普遍存在于植物、真菌和昆虫质体中,由核基因编码,能与铜相结合的金属蛋白酶.它能分别催化单酚羟基和二羟基酚氧化为O-二酚和O-醌.植物多酚氧化酶是许多果蔬等农产品酶促褐变的主要原因,同时它在植物的光合作用、抗病虫害、生长发育以及花色的形成中起一定作用.本文综述了植物多酚氧化酶在细胞学、分子遗传学及其生产应用等方面的研究进展.  相似文献
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