DNA序列在蕨类分子系统学研究中的应用

在分子系统学研究中,目的基因或者基因片段的选择是最关键的一步,由于进化速率的差异,不同的DNA序列适用于不同分类阶元的系统发育研究.本文综述了目前蕨类分子系统发育研究中常用的DNA序列分析,它们分别来自叶绿体基因组、核基因组和线粒体基因组,着重阐明叶绿体基因在蕨类分子系统学研究中的应用.本文还简要介绍了分子系统学研究中常见的问题及解决方法(如内类群和外类群的选择.适宜DNA片段的选择策略),总结了目前蕨类植物分子系统学研究所取得的进展和研究现状,展望了当今国际蕨类分子系统学的研究趋势.     

植物分子系统学近五年的研究进展概况

本文综述了与分子系统学发展密切相关的4个因素：1.分子生物学方法的不断改进;2.基因组的全序列测定;3.用于分子系统学研究的基因种类不断增加,对这些基因进化规律的认识不断深入;4.化石DNA的研究。本文还阐述了核基因及叶绿体基因在系统学研究中的应用,例举了rbcL、matk、18s rDNA和ITS序列分析在植物系统发育研究中取得的重要成果,同时提出了分子系统学研究中应注意的一些问题。     

DNA序列在苔藓分子系统学研究中的应用

DNA是遗传信息的载体,直接对DNA核苷酸排列顺序的分析和比较是研究苔藓分子系统学的最彻底和最理想的方法。本文综述了DNA序列(叶绿体基因组、核基因组和线粒体基因组)在苔藓分子系统学中的应用,探讨了基因片段的选择策略。并提出只有将分子数据和传统分类学取得的研究成果结合起来,构建最合理的系统树,才能更好地推动苔藓分子系统学的发展。     

串珠藻目分子系统学研究进展

串珠藻目(Batrachospermales)是淡水红藻中最主要的类群。近年来, 应用DNA序列分析探讨串珠藻目的系统发育, 并与传统的形态学和生态学特征相结合, 为串珠藻目系统学研究拓展了新的思路。本文回顾了串珠藻目的建立及其所含类群的研究历史, 归纳了目前在串珠藻目系统发育与进化研究中常用的分子标记方法, 其中包括核基因组的18S rDNA、26S rDNA和ITS序列, 叶绿体基因组的rbcL序列, 线粒体基因组的cox2-3序列, 以及新兴的ISSR技术, 并对各种分子标记的特点及适用范围做了评述。结果表明, ITS序列多适用于种群分化及相近种间遗传分析, ISSR标记适用于种下分类群间及同一种群不同个体间基因多态性分析, cox2-3序列在一定程度上也可用于同一种群不同个体间的基因多态性分析, 而18S rDNA 与rbcL序列既可用于种间关系分析, 又可用于更高水平分析的构建系统树。这些分子标记已被证明在研究串珠藻目系统地理、物种起源和散布机制方面有着广泛的应用前景。同时, 本文对串珠藻目分子系统学研究的最新进展也进行了概述,并对今后的研究方向做了展望。     

串珠藻目分子系统学研究进展

串珠藻目（Batrachospermales）是淡水红藻中最主要的类群。近年来,应用DNA序列分析探讨串珠藻目的系统发育,并与传统的形态学和生态学特征相结合,为串珠藻目系统学研究拓展了新的思路。本文回顾了串珠藻目的建立及其所含类群的研究历史,归纳了目前在串珠藻目系统发育与进化研究中常用的分子标记方法,其中包括核基因组的18SrDNA、26SrDNA和ITS序列,叶绿体基因组的rbcL序列,线粒体基因组的cox9．-3序列,以及新兴的ISSR技术,并对各种分子标记的特点及适用范围做了评述。结果表明,ITS序列多适用于种群分化及相近种间遗传分析,ISSR标记适用于种下分类群间及同一种群不同个体间基因多态性分析,cox2-3序列在一定程度上也可用于同一种群不同个体间的基因多态性分析,而18SrDNA与rbcLFF列既可用于种问关系分析,又可用于更高水平分析的构建系统树。这些分子枥对己已被证明在研究串珠藻目系统地理、物种起源和散布机制方面有着广泛的应用前景。同时,本文对串珠藻目分子系统学研究的最新进展也进行了概述,并对今后的研究方向做了展望。     

核基因在两栖爬行动物分子系统学中的研究进展

从DNA水平探索生物进化的理论、生物类群的演化历史具有重要的意义,应用DNA序列研究生物的系统发育和进化规律成为当前分子系统学研究的热点,与线粒体DNA相比,核基因由于包含有更加丰富的生物学信息,运用核基因序列或将核基因序列与线粒体基因序列相结合研究两栖爬行动物的系统发育,正成为分子系统学领域的新的发展趋势.Rag-1、Rag-2、tyrosinase、rhodopsin、C-mos等核基因已在两栖爬行动物分子系统学中得到了广泛的应用.由于目前的技术手段等诸多因素,限制了更多的核基因用于两栖爬行动物分子系统学研究.为此简要介绍了目前核基因在两栖爬行动物分子系统学方面的研究进展,并分析了核基因序列在分子系统学应用上面临的问题和应用前景.     

DNA序列在悬钩子属植物分子系统学研究中的应用进展

悬钩子属植物种类繁多,类群复杂,而且多为多倍体和杂种。该文就近年来国内外有关DNA序列在悬钩子属植物分子系统学研究中的应用现状和进展进行了综述,并对中国悬钩子属植物系统发育研究进行了展望。研究认为:叶绿体DNA序列多应用非编码区,且多与ITS序列联合分析;核基因组中ITS序列应用最为广泛,主要用于研究悬钩子属空心莓组与木莓组的进化关系、栽培品种间亲缘关系及部分杂种和多倍体的起源等;在该属植物中发现了ITS个体内多态性,但未进行ITS假基因检测,其系统学应用价值需重新评价;低拷贝核基因只有GBSSI和LEAFY有相关应用。同时认为,悬钩子属植物系统学研究中应用的DNA序列及研究类群均较少,缺乏对整个悬钩子属全面而系统的研究。指出应进一步选择具有代表性的样本、筛选合适的DNA片段,并结合形态学、孢粉学和细胞学等手段对中国悬钩子属植物系统关系进行深入研究。     

叶蝉科昆虫分子系统发育的研究进展

从基因组DNA的提取、研究的基因片段、PCR引物选用、扩增条件以及叶蝉科不同阶元的分子系统发育分析等方面,综述叶蝉科(半翅目:叶蝉科)昆虫分子系统发育的研究进展。目前角顶叶蝉类的研究成果相对较多,大叶蝉亚科次之,其余类群的研究较少或无。线粒体基因与核基因序列联合分析以及线粒体全序列分析以及基因序列与形态数据相结合分析,分子鉴定叶蝉与共生菌之间的协同进化的研究,将是叶蝉分子系统学未来发展的主要研究手段。     

基因组时代的放线菌系统分类学及其研究进展

由于放线菌在生物技术、医药卫生和环境治理等领域中的实际重要性,已经成为人们研究得最为深入的微生物类群之一。现代放线菌分类学是建立在对16S rRNA基因保守分子序列的系统发育学分析基础上、综合利用多种微生物信息的多相分类学(polyphasic taxonomy)。随着大规模基因测序技术的飞速发展,已经完成了超过100株放线菌的全基因组序列。近年来发展起来的"基因组系统发育学"有助让人们更加系统地理解放线菌类群的发生、演化,以及不同生境类群之间的相互关系。随着越来越多的以系统发育学为指导的基因组测序研究项目,例如"细菌和古菌基因组百科全书(Genomic Encyclopedia of Bacteria andArchaea,GEBA)计划"的出现,标志着放线菌系统学进入了基因组学研究时代。本文对基因组时代的放线菌系统学方法,以及国内外的相关研究成果进行综述。     

鞘翅目昆虫线粒体基因组研究进展

鞘翅目（Coleoptera）是世界上最具多样性的类群,具有很高的生态和形态多样性,这些多样性吸引了很多进化生物学家和分类学家的关注。随着分子生物学的发展,分子生物学技术广泛应用于鞘翅目系统学的研究,但随着研究的深入,简单的分子片段已经不能满足研究的需求,需要发掘更新的分子标记。近年来,线粒体全基因组已经成为鞘翅目分子系统学研究中很重要的分子标记之一,并广泛地应用于鞘翅目昆虫各个阶元的研究中。本文就鞘翅目线粒体全基因组的概况、研究进展及存在问题进行了总结和讨论。目前,鞘翅目线粒体基因组的研究主要包括物种线粒体基因组组成与结构、分子系统学和分子进化等方面。线粒体基因组在解决系统发育和进化方面表现出了很多的优越性,然而也存在着一些缺点,如序列难获得、基因类型单一、各基因进化速率不同、应用较局限等。     

A Primer to Molecular Phylogenetic Analysis in Plants

Reconstructing a tree of life by inferring evolutionary history is an important focus of evolutionary biology. Phylogenetic reconstructions also provide useful information for a range of scientific disciplines such as botany, zoology, phylogeography, archaeology and biological anthropology. Until the development of protein and DNA sequencing techniques in the 1960s and 1970s, phylogenetic reconstructions were based on fossil records and comparative morphological/physiological analyses. Since then, progress in molecular phylogenetics has compensated for some of the shortcomings of phenotype-based comparisons. Comparisons at the molecular level increase the accuracy of phylogenetic inference because there is no environmental influence on DNA/peptide sequences and evaluation of sequence similarity is not subjective. While the number of morphological/physiological characters that are sufficiently conserved for phylogenetic inference is limited, molecular data provide a large number of datapoints and enable comparisons from diverse taxa. Over the last 20 years, developments in molecular phylogenetics have greatly contributed to our understanding of plant evolutionary relationships. Regions in the plant nuclear and organellar genomes that are optimal for phylogenetic inference have been determined and recent advances in DNA sequencing techniques have enabled comparisons at the whole genome level. Sequences from the nuclear and organellar genomes of thousands of plant species are readily available in public databases, enabling researchers without access to molecular biology tools to investigate phylogenetic relationships by sequence comparisons using the appropriate nucleotide substitution models and tree building algorithms. In the present review, the statistical models and algorithms used to reconstruct phylogenetic trees are introduced and advances in the exploration and utilization of plant genomes for molecular phylogenetic analyses are discussed.     

两栖爬行动物的分子系统发生

介绍了两栖爬行动物分子系统发生研究中选用的分子信息的种类及已发表的蛙类,蟾蜍类,龟类,蜥蜴类和蛇类等的分子系统学研究,这些研究中使用的DNA信息主要为mtDNA序列,也使用了一些核DNA序列。其研究的内容涉及目间,科间等高级阶元的系统发生关系,以及属间,种间以及亚种或种群间的系统发生关系。     

Direct amplification of the entire ITS region from poorly preserved plant material using recombinant PCR

Sequences of the internal transcribed spacers (ITS) of the nuclear ribosomal DNA are important molecular markers in phylogenetic analyses. To obtain sequences from herbarium material in which DNA often is severely degraded, the ITS region has to be amplified in two steps. Two methods that reduce bench time and reagents used are described. (i) Separately amplified preparations of subunits ITS-1 and ITS-2 are combined before purification. The presence of two fragments in the sequencing reaction does not impair the quality of sequences. (ii) Newly designed internal primers amplify partly overlapping regions of the two subunits. A combination of these internal primers with the external primers in one PCR allows the amplification of the entire ITS region even when degraded DNAs are used. This recombinant PCR approach, taking into account the +A bases added by several Taq DNA polymerases, will also be useful with other marker regions used in molecular phylogenetics.     

Using protein structural information in evolutionary inference: transmembrane proteins

We present a model of amino acid sequence evolution based on a hidden Markov model that extends to transmembrane proteins previous methods that incorporate protein structural information into phylogenetics. Our model aims to give a better understanding of processes of molecular evolution and to extract structural information from multiple alignments of transmembrane sequences and use such information to improve phylogenetic analyses. This should be of value in phylogenetic studies of transmembrane proteins: for example, mitochondrial proteins have acquired a special importance in phylogenetics and are mostly transmembrane proteins. The improvement in fit to example data sets of our new model relative to less complex models of amino acid sequence evolution is statistically tested. To further illustrate the potential utility of our method, phylogeny estimation is performed on primate CCR5 receptor sequences, sequences of l and m subunits of the light reaction center in purple bacteria, guinea pig sequences with respect to lagomorph and rodent sequences of calcitonin receptor and K-substance receptor, and cetacean sequences of cytochrome b.     

Parasite histories and novel phylogenetic tools: alternative approaches to inferring parasite evolution from molecular markers

Parasitological research is often contingent on the knowledge of the phylogeny/genealogy of the studied group. Although molecular phylogenetics has proved to be a powerful tool in such investigations, its application in the traditional fashion, based on a tree inference from the primary nucleotide sequences may, in many cases, be insufficient or even improper. These limitations are due to a number of factors, such as a scarcity/ambiguity of phylogenetic information in the sequences, an intricacy of gene relationships at low phylogenetic levels, or a lack of criteria when deciding among several competing coevolutionary scenarios. With respect to the importance of a precise and reliable phylogenetic background in many biological studies, attempts are being made to extend molecular phylogenetics with a variety of new data sources and methodologies. In this review, selected approaches potentially applicable to parasitological research are presented and their advantages as well as drawbacks are discussed. These issues include the usage of idiosyncratic markers (unique features with presumably low probability of homoplasy), such as insertion of mobile elements, gene rearrangements and secondary structure features; the problem of ancestral polymorphism and reticulate relationships at low phylogenetic levels; and the utility of a molecular clock to facilitate discrimination among alternative scenarios in host-parasite coevolution.     

On the value of Elongation factor-1α for reconstructing pterygote insect phylogeny

Pterygota are traditionally divided in two lineages, the “Palaeoptera” and Neoptera. Despite several efforts neither morphology nor molecular systematics have resolved the phylogeny of the pterygote insects. Too few markers have yet been identified for adequately tracking mesozoic-aged divergences. We tested the Elongation factor-1α for its phylogenetic value in pterygote insect systematics. This highly conserved nuclear protein-coding gene has previously been reported to be useful in other groups for phylogenetic analyses at the intraordinal level as well as at the interordinal level. The analyses suggest that EF-1α DNA sequences as well as intron positions provide informative markers for pterygote phylogenetics.     

Molecular clocks, molecular phylogenies and the origin of phyla

Erwin, Douglas H. 1989 07 15: Molecular clocks, molecular phylogenies and the origin of phyla. Lethaia , Vol. 22, pp. 251–257. Oslo. ISSN 0024–1164.
Protein, RNA and DNA sequences have been widely used to construct phylogenies and to calculate divergence times using a molecular clock. Reliance on molecular information is particularly attractive when fossil evidence is missing or equivocal, as in the Cambrian metazoan radiation. I consider the applicability of molecular clocks and phylogenetic analysis of molecular data to the origin of metazoan phyla, and conclude that molecular information is often ambiguous or misleading. Amino acid sequences are of limited use because the redundancy of the genetic code masks patterns of descent, while in a nucleotide sequence only four potential states exist at each site (the four nucleotide bases). In each case, homoplasy may often go undetected. The application of a molecular clock to resolve the timing of the metazoan radiation is unwarranted, while molecular phylogenetic reconstruction should be approached with care. A potentially more useful technique for phylogenetic reconstruction would be the use of patterns of genome structure and organization as characters. * Molecular clock, phylogenetics, metazoan radiation, origin of phyla .     

Familial placement and relations of Rehmannia and Triaenophora (Scrophulariaceae s.l.) inferred from five gene regions

Accurate classification systems based on evolution are imperative for biological investigations. The recent explosion of molecular phylogenetics has resulted in a much improved classification of angiosperms. More than five phylogenetic lineages have been recognized from Scrophulariaceae sensu lato since the family was determined to be polyphyletic; however, questions remain about the genera that have not been assigned to one of the segregate families of Scrophulariaceae s.l. Rehmannia Liboschitz and Triaenophora Solereder are such genera with uncertain familial placement. There also is debate whether Triaenophora should be segregated from Rehmannia. To evaluate the phylogenetic relations between Rehmannia and Triaenophora, to find their closest relatives, and to verify their familial placement, we conducted phylogenetic analyses of the sequences of one nuclear DNA (ITS) region and four chloroplast DNA gene regions (trnL-F, rps16, rbcL, and rps2) individually and combined. The analyses showed that Rehmannia and Triaenophora are each strongly supported as monophyletic and together are sister to Orobanchaceae. This relation was corroborated by phytochemical and morphological data. Based on these data, we suggest that Rehmannia and Triaenophora represent the second nonparasitic branch sister to the remainder of Orobanchaceae (including Lindenbergia).     

Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests

Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the selection of substitution models in phylogenetics from a theoretical, philosophical and practical point of view, and summarize this comparison in table format. We argue that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow for the estimation of phylogenies and model parameters using all available models (model-averaged inference or multimodel inference). We also describe how the relative importance of the different parameters included in substitution models can be depicted. To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus(genus Carabus) ground beetles described by Sota and Vogler (2001).     

Do molecules matter more than morphology? Promises and pitfalls in parasites

Systematics involves resolving both the taxonomy and phylogenetic placement of organisms. We review the advantages and disadvantages of the two kinds of information commonly used for such inferences--morphological and molecular data--as applied to the systematics of metazoan parasites generally, with special attention to the malaria parasites. The problems that potentially confound the use of morphology in parasites include challenges to consistent specimen preservation, plasticity of features depending on hosts or other environmental factors, and morphological convergence. Molecular characters such as DNA sequences present an alternative data source and are particularly useful when not all the parasite's life stages are present or when parasitaemia is low. Nonetheless, molecular data can bring challenges that include troublesome DNA isolation, paralogous gene copies, difficulty in developing molecular markers, and preferential amplification in mixed species infections. Given the differential benefits and shortcomings of both molecular and morphological characters, both should be implemented in parasite taxonomy and phylogenetics.