DNA分子进化的研究基础和策略

从研究方法和技术手段等方面讨论了分子进化研究上的一些重大问题．阐述了基因的基本结构及DNA分子的进化方式：净化选择、中性进化和分化选择。探讨了利用DNA分子进化数据构建系统树的原理,评价了NJ、UPGMAM、MP和ML4种算法在构建进化树时的合理性与不足,以及进化树可靠性检验的方法,并对未来分子进化生物学的发展加以展望。     

肌动蛋白与真核生物的进化

以肌动蛋白氨基酸取代与真核生物进化年代呈线性关系为依据，收集原生生物界，真菌界，植物界和动物界等四界７４种生物的１２８个肌动蛋白序列，通过对其氨基酸序列同源性进行比较，制作出肌动蛋白的分子进化树，并依此进化树从分子水平对真核生物的进化进行一些探讨，从总体上看，肌动蛋白分子进化树较地地反映了真核生物间的进化关系，为确定某些生物的进化位置及进化关系提供了分子证据。     

细菌基因组进化的分子策略

论述了细菌基因组进化的 4个分子策略 :点突变 ,基因组内重排 ,基因水平转移 ,基因缺失。从经典的达尔文进化论角度探讨了细菌基因组进化与表型进化的关系。     

蝗虫分子系统学研究进展

本文从遗传多样性、近缘种鉴别以及分子进化和系统发育重建 3个方面综述了蝗虫分子系统学的研究进展。     

分子进化与系统树

生物在从低级向高级进化的同时,某些生物大分子也在进化。根据分子生物学资料可以构建同源分子的系统树。本文具体介绍了Fitch和Margoliash提出的系统树构建法,并对20种细胞色素c分子组成的系统树作了扼要说明。     

丝氨酸蛋白酶超家族分子结构进化研究

采用刚体结构比较法进行蛋白质的结构比较,根据结构比较分数构建分子进化树, 研究丝氨酸蛋白酶超家族分子的进化规律。对分子进化树进行了一些初步分析,得到了一些有意义的结果。根据蛋白质的进化,可以比较精确的确定某物种的进化地位,对于物种的分类具有重要意义。通过对超家族分子进化的研究可以了解蛋白质超家族不同蛋白质之间的亲缘关系和蛋白质之间的进化差异,对于蛋白质工程分子设计提供帮助,对蛋白质结构预测具有一定意义     

脊椎动物血浆蛋白质的进化

分子生物学的迅猛发展,使我们有可能从分子水平来探讨生物进化这一经典命题。分子进化遂成为进化生物学中的一个新的研究领域。脊椎动物血浆中有数百种蛋白质,依据其一级结构的类似性可划分为仅仅几个家族。蛋白质的进化主要涉及到基因复制(包括加倍)和外显子改组。对不同种属同一种蛋白质的氨基酸排列顺序的比较,可以给出一些有关蛋白质进化的知识。这方面业已取得的成就极大地推进了进化生物学的发展。     

酶分子体外定向进化的研究方法*

酶分子体外定向进化不仅可大幅度提高酶分子的进化效率,短期内在实验室完成自然状态下需要千百万年的进化过程,还可使酶分子按照人们期望的特定目标进化,因此对酶工程今后的发展非常重要。本对酶分子体外定向进化的研究方法进行了归纳总结。     

血红蛋白与脊椎动物高海拔适应进化

高海拔环境是研究脊椎动物对极端环境适应进化过程的典型范例之一.血红蛋白在脊椎动物呼吸和氧化能量代谢中的核心作用决定了其无论在进化生物学还是高原医学研究领域都有着极其重要的意义.然而,如果不清楚研究对象的系统进化地位和机体本身的适应进化特点,就无法对各个水平的适应进化机制作出全面诠释.因此,对脊椎动物的低氧适应进化研究首先从机体生理需求的差异出发.此外,血红蛋白的功能适应性还表现在物种或种群间的空间分布差异导致不同程度的低氧需求.因此,本文从个体和系统发育水平评述了血红蛋白的分子进化及功能适应研究,深入比较了长期定居和短期移居物种间的适应机制区别,系统分析了鸟类及其他脊椎动物适应高海拔低氧环境的趋同和趋异进化特征.最后通过评价不同研究方法的优缺点,结合功能蛋白和物种进化相似的分子遗传规律,为未来高海拔低氧适应进化及高原医学研究提出一些新的思考.总之,本文支持功能验证在适应性进化相关基因研究中的必要性,强调整合分子、细胞和系统水平确定研究方案的重要性,以及系统发育背景和种群进化历史在研究对象选择中的重要意义.     

微生物酶的分子改性和人工进化的研究进展

运用分子生物学技术对微生物来源的酶进行分子改性和人工进化在过去几年中取得了令人瞩目的进展。本文综述了用于酶分子改性和人工进化的主要分子生物学方法,如易错PCR技术、DNA体外随机拼接技术等及其在酶的分子进化和改性中应用成就。     

First molecular evidence for the existence of a Tardigrada + Arthropoda clade

The complete 18S rDNA gene sequence of Macrobiotus group hufelandi (Tardigrada) was obtained and aligned with 18S rDNA and rRNA gene sequences of 24 metazoans (mainly protostomes). Discrete character (maximum-parsimony) and distance (neighbor-joining) methods were used to infer their phylogeny. The evolution of bootstrap proportions with sequence length (pattern of resolved nodes, PRN) was studied to test the resolution of the nodes in neighbor-joining trees. The results show that arthropods are monophyletic. Tardigrades represent the sister group of arthropods (in parsimony analyses) or they are related with crustaceans (distance analysis and PRN). Arthropoda are divided into two main evolutionary lines, the Hexapoda + Crustacea line (weakly supported), and the Myriapoda + Chelicerata line. The Hexapoda + Crustacea line includes Pentastomida, but the internal resolution is far from clear. The Insecta (Ectognatha) are monophyletic, but no evidence for the monophyly of Hexapoda is found. The Chelicerata are a monophyletic group and the Myriapoda cluster close to Arachnida. Overall, the results obtained represent the first molecular evidence for a Tardigrada + Arthropoda clade. In addition, the congruence between molecular phylogenies of the Arthropoda from other authors and this obtained here indicates the need to review those obtained solely on morphological characters.      

REVIEW Evolution and systematics of the Chelicerata

After approximately 40 years of discussion about the question of whether the Arthropoda are a monophyletic or a paraphyletic group or even a polyphyletic assemblage of unrelated taxa, most morphologists, palaeontologists and molecular taxonomists agree that the Arthropoda are a monophylum. The Euarthropoda are composed of the Arachnomorpha and Mandibulata. Myriapods are usually considered to be mandibulates; however, new molecular data as well as some morphological characters show similarities which the Myriapoda share with the Chelicerata, suggesting that there is no taxon Antennata or Atelocerata. Chelicerata are usually considered to be the sister group of Trilobita or, more correctly, Trilobita branch off from the chelicerate stem line. The first adaptive radiation of the Chelicerata took place in the Cambrian. All extant and some extinct orders were present during the Carboniferous. Two systems are compared. It is suggested that the Chelicerata contain the Pantopoda and Euchelicerata. The Euchelicerata are divided into Xiphosura and terrestrial Arachnida. Scorpiones are considered to be the sister group of all other arachnids, the Lipoctena and these are further divided into the Megoperculata (Uropygi, Amblypygi, and Araneae) and Apulmonata (all other groups). The Acari are tentatively considered to be a monophylum and the sister group of the Ricinulei. However, the Actinotrichida and Anactinotrichida diverged early and therefore have had a long history of independent evolution.     

Phylogenetic position of Nemertea derived from phylogenomic data

Nemertea and Platyhelminthes have traditionally been grouped together because they possess a so-called acoelomate organization, but lateral vessels and rhynchocoel of nemerteans have been regarded as coelomic cavities. Additionally, both taxa show spiral cleavage patterns prompting the placement of Nemertea as sister to coelomate Protostomia, that is, either to Neotrochozoa (Mollusca and Annelida) or to Teloblastica (Neotrochozoa plus Arthropoda). Some workers maintain a sister group relationship of Nemertea and Platyhelminthes as Parenchymia because of an assumed homology of G?tte's and Müller's larvae of polyclad Platyhelminthes and the pilidium larvae of heteronemerteans. So far, molecular data were only able to significantly reject a sister group relationship to Teloblastica. Although phylogenomic data are available for Platyhelminthes, Annelida, Mollusca, and Arthropoda, they are lacking for Nemertea. Herein, we present the first analysis specifically addressing nemertean phylogenetic position using phylogenomic data. More specifically, we collected expressed sequence tag data from Lineus viridis (O.F. Müller, 1774) and combined it with available data to produce a data set of 9,377 amino acid positions from 60 ribosomal proteins. Maximum likelihood analyses and Bayesian inferences place Nemertea in a clade together with Annelida and Mollusca. Furthermore, hypothesis testing significantly rejected a sister group relationship to either Platyhelminthes or Teloblastica. The Coelomata hypothesis, which groups coelomate taxa together to the exclusion of acoelomate and pseudocoelomate taxa, is not congruent with our results. Thus, the supposed acoelomate organization evolved independently in Nemertea and Platyhelminthes. In Nemertea, evolution of acoely is most likely due to a secondary reduction of the coelom as it is found in certain species of Mollusca and Annelida. Though looking very similar, the G?tte's and Müller's larvae of polyclad Platyhelminthes are not homologous to the pilidium larvae of heteronemerteans. Finally, the convergent evolution of segmentation in Annelida and Arthropoda is further substantiated.     

节肢动物内共生细菌研究进展

节肢动物门是动物界最大的门,占整个动物种数的80%,全世界约有120万现存种。节肢动物在生长发育过程中会感染多种微生物,这些微生物会与其形成协同进化和互利共生的关系。内共生细菌是一类广泛分布于节肢动物体内的共生微生物,能够进行垂直传播和水平传播,对宿主的生长发育、生殖代谢、适应性、免疫功能和进化等诸多方面均具有重要的作用。目前,随着现代分子生物学理论和技术的发展,节肢动物内共生细菌相关研究主要集中在对其宿主的生殖调控功能、与其宿主、宿主寄主植物以及其宿主体内微生物和宿主天敌间互作关系等方面。因此,利用内共生细菌对昆虫种群动态的生殖调控功能,阻断热带蚊虫带来的疾病或植物病害的传播并对宿主昆虫进行种群压制或种群替换,可达到防控害虫的目的。本文从节肢动物内共生细菌的传播方式、对其宿主生物学效应以及内共生细菌与其宿主、宿主寄主植物、宿主天敌和宿主体内微生物互作关系等多方面进行概述,并对内共生细菌今后研究方向进行展望,以期为生物进化、物种形成和种群压制提供参考。     

Pax6 and eye development in Arthropoda

The arthropod compound eye is one of the three main types of eyes observed in the animal kingdom. Comparison of the eyes seen in Insecta, Crustacea, Myriapoda and Chelicerata reveals considerable variation in terms of overall cell number, cell positioning, and photoreceptor rhabdomeres, yet, molecular data suggest there may be unexpected similarities. We review here the role of Pax6 in eye development and evolution and the relationship of Pax6 with other retinal determination genes and signaling pathways. We then discuss how the study of changes in Pax6 primary structure, in the gene networks controlled by Pax6 and in the relationship of Pax6 with signaling pathways may contribute to our insight into the relative role of conserved molecular-genetic mechanisms and emergence of evolutionary novelty in shaping the ommatidial eyes seen in the Arthropoda.     

Robust support for tardigrade clades and their ages from three protein-coding nuclear genes

Abstract. Coding sequences (5,334 nt total) from elongation factor-1α, elongation factor-2, and the largest subunit of RNA polymerase II were determined for 6 species of Tardigrada, 2 of Arthropoda, and 2 of Onychophora. Parsimony and likelihood analyses of nucleotides and amino acids yielded strong support for Tardigrada and all internal nodes (i.e., 100% bootstrap support for Tardigrada, Eutardigrada, Parachela, Hypsibiidae, and Macrobiotidae). Results are in agreement with morphology and an earlier molecular study based on analysis of 18S ribosomal sequences. Divergence times have been estimated from amino acid sequence data using an empirical Bayesian statistical approach, which does not assume a strict molecular clock. Divergence time estimates are pre-Vendian for Tardigrada/Arthropoda, Vendian or earlier for Eutardigrada/Heterotardigrada, Silurian to Ordovician for Parachela/Apochela, Permian to Carboniferous for Hypsibiidae and Macrobiotidae, and Mesozoic for Isohypsibius/Thulinia (both within Hypsibiidae) and Macrobiotus/Richtersius (both within Macrobiotidae).     

Old trees, new trees--is there any progress?

The amount of comparative data for phylogenetic analyses is constantly increasing. Data come from different directions such as morphology, molecular genetics, developmental biology and paleontology. With the increasing diversity of data and of analytical tools, the number of competing hypotheses on phylogenetic relationships rises, too. The choice of the phylogenetic tree as a basis for the interpretation of new data is important, because different trees will support different evolutionary interpretations of the data investigated. I argue here that, although many problematic aspects exist, there are several phylogenetic relationships that are supported by the majority of analyses and may be regarded as something like a robust backbone. This accounts, for example, for the monophyly of Metazoa, Bilateria, Deuterostomia, Protostomia (= Gastroneuralia), Gnathifera, Spiralia, Trochozoa and Arthropoda and probably also for the branching order of diploblastic taxa (“Porifera”, Trichoplax adhaerens, Cnidaria and Ctenophora). Along this “backbone”, there are several problematic regions, where either monophyly is questionable and/or where taxa “rotate” in narrow regions of the tree. This is illustrated exemplified by the probable paraphyly of Porifera and the phylogenetic relationships of basal spiralian taxa. Two problems span wider regions of the tree: the position of Arthropoda either as the sister taxon of Annelida (= Articulata) or of Cycloneuralia (= Ecdysozoa) and the position of tentaculate taxa either as sister taxa of Deuterostomia (= Radialia) or within the taxon Spiralia. The backbone makes it possible to develop a basic understanding of the evolution of genes, molecules and structures in metazoan animals.     

A serological investigation on the phylogenetic relationship of arthropod classes

Serological kinship of some representative species of arthropods belonging to Crustacea, Arachnida, Myriapoda and Insecta has been studied. There ist weak serological correspondence between the myriapods and insects. The same is the case between Crustacea and Arachnida, and no correspondence was seen between Myriapoda and Insecta on one hand and Crustacea and Arachnida on the other. The results are discussed in relation to the different previous views on the origin and evolution of Arthropoda.     

Complete mitochondrial DNA sequence of the sea-firefly, Vargula hilgendorfii (Crustacea, Ostracoda) with duplicate control regions

The primary structure of the mitochondrial genome of the bioluminescent crustacean, Vargula hilgendorfii, the sea-firefly (Arthropoda, Crustacea, Ostracoda), has sequenced using the transposon Tn5. The genome (15,923 bp) contains the same 37 genes (two ribosomal RNAs, 22 transfer RNAs, and 13 protein-coding genes) found in other Arthropoda. Interestingly, duplicate control regions (fragments of 778 and 855 bp) and triplicate short repeat sequences (fragments of 49 bp) occur. The AT composition of the protein-coding genes is lower than the published complete mitochondrial genomes within the Arthropoda. For gene arrangement, 13 transfer RNA genes and two protein-coding genes have moved and inserted directly or inversely relative to the typical Arthropoda order.