Molecular Phylogeny of Conjugating Green Algae (Zygnemophyceae, Streptophyta) Inferred from SSU rDNA Sequence Comparisons

Abstract Nuclear-encoded SSU rDNA sequences have been obtained from 64 strains of conjugating green algae (Zygnemophyceae, Streptophyta, Viridiplantae). Molecular phylogenetic analyses of 90 SSU rDNA sequences of Viridiplantae (inciuding 78 from the Zygnemophyceae) were performed using complex evolutionary models and maximum likelihood, distance, and maximum parsimony methods. The significance of the results was tested by bootstrap analyses, deletion of long-branch taxa, relative rate tests, and Kishino–Hasegawa tests with user-defined trees. All results support the monophyly of the class Zygnemophyceae and of the order Desmidiales. The second order, Zygnematales, forms a series of early-branching clades in paraphyletic succession, with the two traditional families Mesotaeniaceae and Zygnemataceae not recovered as lineages. Instead, a long-branch Spirogyra/Sirogonium clade and the later-diverging Netrium and Roya clades represent independent clades. Within the order Desmidiales, the families Gonatozygaceae and Closteriaceae are monophyletic, whereas the Peniaceae (represented only by Penium margaritaceum) and the Desmidiaceae represent a single weakly supported lineage. Within the Desmidiaceae short internal branches and varying rates of sequence evolution among taxa reduce the phylogenetic resolution significantly. The SSU rDNA-based phylogeny is largely congruent with a published analysis of the rbcL phylogeny of the Zygnemophyceae (McCourt et al. 2000) and is also in general agreement with classification schemes based on cell wall ultrastructure. The extended taxon sampling at the subgenus level provides solid evidence that many genera in the Zygnemophyceae are not monophyletic and that the genus concept in the group needs to be revised.     

Molecular Phylogeny and Coevolution

Abstract Recent advances in molecular phylogenetic estimation in diverse organisms have improved our understanding of coevolution. From the phylogenies of interacting organisms, we can interpret the evolution of adaptive characters, and the history of interaction. Molecular approaches are generally more informative than these based solely on phenotypic characters. Molecular genetic method can be applied to organisms that have only simple morphological features and can be used for comparisons at any taxonomic level. Estimation of divergence time is also possible but still difficult because evolutionary rates of macromolecules are not always constant and suitable fossil records are often not available for calibrating rates of change. Here I review recent progress in the application of molecular techniques to the interpretation of coevolutionary relationships.     

Naturalists, Molecular Biologists, and the Challenges of Molecular Evolution

Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era. This revised version was published online in July 2006 with corrections to the Cover Date.     

新编分子进化实验一组A

提供一组新编分子进化实验。通过该实验使学生了解重建分子进化树的基本过程,获得使用不同建树方法、建树材料和建树参数对建树结果影响的正确认识。本实验同时具有开放性和研究性特点,符合实验教学改革的方向和要求。Abstract: This paper presents a group of new experiments on molecular evolution. It allows students to get acquaint with the basic process of the reconstruction of phylogenetic tree using DNA or protein sequences, and to acquire the correct viewpoint how to affect the result of reconstruction when different tree-building methods, materials and parameters were used. This group of experiments are also characteristic of the opening and exploring, which accords with the direction and demand of experimental teaching reform.     

Molecular Phylogenies and Evolution of crt Genes in Algae

ABSTRACT

The carotenoids constitute the most widespread class of pigments in nature. Most previous work has concentrated on the identification and characterization of their chemical physical properties and bioavailability. In recent years, significant amounts of research have been conducted in an attempt to analyze the genes and the molecular regulation of the genes involved in the biosynthesis of carotenoids. However, it is important not to lose sight of the early evolution of carotenoid biosynthesis. One of the major obstacles in understanding the evolution of the respective enzymes and their patterns of selection is a lack of a well-supported phylogenic analysis. In the present research, a major long-term objective was to provide a clearer picture of the evolutionary history of genes, together with an evaluation of the patterns of selection in algae. These phylogenies will be important in studies characterizing the evolution of algae. The gene sequences of the enzymes involved in the major steps of the carotenoid biosynthetic pathway in algae (cyanobacteria, rhofophyta, chlorophyta) have been analyzed. Phylogenetic relationships among protein-coding DNA sequences were reconstructed by neighbor-joining (NJ) analysis for the respective carotenoid biosynthetic pathway genes (crt) in algae. The analysis also contains an estimation of the rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d_N), synonymous nucleotide substitution per synonymous site (d_S), and the ratio of nonsynonmous (d_N/d_S) for the test of selection patterns. The phylogenetic trees show that the taxa of some genera have a closer evolutionary relationship with other genera in some gene sequences, which suggests a common ancient origin and that lateral gene transfer has occurred among unrelated genera. The d_N values of crt genes in the early pathway are relatively low, while those of the following steps are slightly higher, while the d_N values of crt genes in chlorophyta are higher than those in cyanobacteria. Most of the d_N/d_S values exceed 1. The phylogenetic analysis revealed that lateral gene transfer may have taken place across algal genomes and the d_N values suggest that most of the early crt genes are well conserved compared to the later crt genes. Furthermore, d_N values also revealed that the crt genes of chlorophyta are more evolutionary than cyanobacteria. The amino acids' changes are mostly adaptive evolution under the influence of positive diversity selection.     

Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate,Stephanosphaera pluvialis (Volvocales,Chlorophyceae), among Unicellular Algae

The genus Balticola comprises a group of unicellular green flagellate algae and is composed of four species formerly classified in the genus Haematococcus. Balticola is closely related to a colonial green flagellate, Stephanosphaera pluvialis. Although the phylogeny among these genera was previously investigated based on two nuclear gene sequences, the phylogenetic sister of S. pluvialis has yet to be determined. In the present study, the species diversity of Balticola and Stephanosphaera was investigated using 18S rRNA gene sequences, and phylogenetic analyses of combined nuclear and chloroplast gene sequences were performed to understand the evolutionary origin of coloniality in Stephanosphaera. The divergence times of four colonial volvocalean flagellates from their respective unicellular sisters were also estimated. Six Balticola genotypes and a single Stephanosphaera genotype were recognized, and one Balticola genotype was resolved as the sister of S. pluvialis, showing that Balticola is a nonmonophyletic genus. The divergence time of Stephanosphaera from its nearest Balticola relative was estimated to be 4–63 million years ago, and these genera represent the most recently diverged pair of unicellular and colonial flagellates among the Volvocales.     

DNA在鸟类分子系统发育研究中的应用

鸟类分子系统发育研究中常用的DNA技术有DNA杂交、RFLP和DNA序列分析等。DNA杂交技术曾在鸟类中有过大规模的应用,并由此诞生了一套新的鸟类分类系统。在鸟类的RFLP分析中,用的最多的靶序列是线粒体DNA。DNA序列分析技术被认为是进行分子系统发育研究最有效、最可靠的方法。在DNA序列分析中,线粒体基因应用最广泛,但由于其自身的一些不足,近年来,不少学者把目光投向了核基因,将线粒体基因和核基因结合起来进行系统发育研究。目前在鸟类分子系统发育中,应用较多的核基因是scnDNA,其内含子可以用于中等阶元水平的系统研究,而外显子主要用于高等阶元的系统研究。除了分子标记自身的问题之外,鸟类分子系统发育研究中还存在着方法上的问题,包括分子标记的选择,样本数量以及数据处理等。今后鸟类分子系统发育研究应该更加注重方法的标准化。     

Prasinophyceae (Green Algae) from the Lower Proterozoic of the Kola Peninsula

Eukaryotic organisms discovered from the earliest Lower Proterozoic phosphorites (2.04 Ga) of the Kola Peninsula are described. These are fossil forms Pechengia melezhiki gen. et sp. nov., which are tentatively assigned to green algae of the class Prasinophyceae.     

Molecular Phylogeny of Nycticebus Inferred from Mitochondrial Genes

Researchers are still discussing the classification of Nycticebus. We established a molecular phylogeny covering all recognized taxa in Nycticebus to provide information for further evaluation. We sequenced partial D-loop (ca. 390 bp) and cytochrome b genes (425 bp) from 22 specimens. We separated most of the major groups except for some mixing of Nycticebus. coucang coucang and N. bengalensis. Nycticebus pygmaeus diverged earlier from the ancestral stock than the other taxa. Nycticebus coucang menagensis was well discriminated from N. c. coucang. It may be possible to explain the mixing of Nycticebus coucang coucang and N. bengalensis by the hybridization between the 2 groups in the field. Although our data did not provide direct evidence for or against the new proposal that Nycticebus coucang javanicus be raised to the rank of a distinct species (N. javanicus), we have good evidence for regarding N. c. menagensis as a species.Jing-Hua Chen and Deng Pan made equal contributions to the work.     

Phylogeny, Evolution and Historical Zoogeography of Ticks: A Review of Recent Progress

There has been much progress in our understanding of the phylogeny and evolution of ticks, particularly hard ticks, in the past 5 years. Indeed, a consensus about the phylogeny of the hard ticks has emerged. Our current working hypothesis for the phylogeny of ticks is quite different to the working hypothesis of 5 years ago. So that the classification reflects our knowledge of ticks, several changes to the nomenclature of ticks are imminent. One subfamily, the Hyalomminae, will probably be sunk, yet another, the Bothriocrotoninae n. subfamily, will be created. Bothriocrotoninae n. subfamily, and Bothriocroton n. genus, are being created to house an early-diverging (‘basal’) lineage of endemic Australian ticks that used to be in the genus Aponomma (ticks of reptiles). There has been progress in our understanding of the subfamily Rhipicephalinae. The genus Rhipicephalus is almost certainly paraphyletic with respect to the genus Boophilus. Thus, the genus Boophilus will probably become a subgenus of Rhipicephalus. This change to the nomenclature, unlike other options, will keep the name Boophilus in common usage. Rhipicephalus (Boophilus) microplus may still called B. microplus, and Rhipicephalus (Boophilus) annulatus may still be called B. annulatus, but the nomenclature will have been changed to reflect our knowledge of the phylogeny and evolution of these ticks. New insights into the historical zoogeography of ticks will also be presented. This revised version was published online in July 2006 with corrections to the Cover Date.     

period基因的Thr—Gly区段在果蝇和部分双翅目昆虫中的分子进化特征

以亲缘关系极近的近缘种类群、中等距离的远缘种类群为对象,分析生物钟基因period的Thr-Gly区段的分子进化特征,发现Thr-Gly区段在果蝇和部分双翅目昆虫中未曾经历性选择和其他定向的正选择。Thr-Gly区段在果蝇nasuta亚群中的分子进化速率为10.4×10     

遗传密码子进化的阶段性

密码子的起源与进化可划分为4个阶段,即：前密码子期,tRNA形成期,原密码子与有序肽同步起源期,以及密码子进化期。不同的观点,大都能在不同时期找到自己的位置,从而是互补的。在此基础上,首次将主要理论的主旨整合为一个进化过程的理论框架,基本上协调了持续了近半个世纪的确定论和偶然论之争,并且解释了密码子设定的多态性的由来。     

蝗总科部分种类16S rDNA的分子系统发育关系

将自测的我国直翅目蝗总科8科8个种和从互联网GenBank中检索到相关物种的线粒体基因组：16S rDNA序列片段进行同源性比较,计算核苷酸使用频率,并构建分子系统树。在获得的480bp的序列中。A T约占70．7％,G C为29．3％,颠换取代(transversion)的速率大于或接近转换取代(transition)的速率,其中188个核苷酸位点存在变异。研究结果表明：在直翅目蝗总科有差异的188bp中,属内种间的碱基序列差异仅为1．5％,科内属间为3．5％～3．6％,科间差异为4．8％～15．8％,亚目间差异达到15．2％～25．6％。分子系统树表明：科内的属和属内的种均优先聚在一起;蝗总科8科的起源关系为：锥头蝗科→瘤锥蝗科→癞蝗科→斑翅蝗科→剑角蝗科→网翅蝗科和槌角蝗科→斑腿蝗科;锥头蝗科与瘤锥蝗科关系较近,是蝗总科内最原始的类群;槌角蝗科和网翅蝗科互为姐妹群,与最进化的斑腿蝗科关系较近;蚤蝼科为独立的一支,最先分出,似为一个亚目,与现用的分类系统有明显差别;哈螽科(螽嘶总科)和蟋蟀科聚在一起为剑瓣亚目(Ensifera),蚱科和蝗总科的8科组成短瓣亚目(Caehfera),同现用的分类系统。     

漆树科植物漆酚的多样性及演化关系研究

漆酚是漆树科植物独有的化学成分,具有良好的抗氧化、抗肿瘤、抗病毒等生物活性,极具药物和工业生产开发价值。该研究通过对国内外有关漆树科各类群有关漆酚数据的搜集和整理,开展漆树科漆酚的多样性与分布情况的综合统计;同时在利用核基因ETS和叶绿体基因rps16和trnL-F重建漆树科系统发育树的基础上,探讨漆酚在漆树科及各属间的起源和演化关系。结果表明:(1)漆树科漆酚具有较高的多样性,在其苯环和-R链上都有很大的变异。(2)发现漆酚仅存在于Anacardioideae亚科中,是该亚科的一个重要界定特征。(3)基于漆酚苯环结构和-R链特征的祖先性状重建分析表明,漆树科的漆酚是由邻苯二酚向间苯二酚演化,而漆酚-R链的十五烃(烯)基则是向十七烃(烯)基平行演化。     

Phylogeny and Speciation of Felids

The phylogeny of the Felidae is reconstructed using a total evidence approach combining sequences from 12S rRNA, 16S rRNA, NADH-5, and cytochrome b genes with morphological and karyological characters. The 1504-character data set generated two equally parsimonious trees (CI = 0.413, 1795 steps) of which a strict consensus revealed one polytomy in the placement of the bay cat group. The tree supports several traditional groupings such as the genera Panthera and Lynx and the ocelot group of small South American felids, and it provides additional resolution of relationships within and among the major felid lineages. Combining phylogenetic, distributional, and ecological data indicates that vicariant speciation has played a relatively minor role in the diversification of the felids (approximately 26% of events), while sympatric speciation has been more important than expected on theoretical grounds (approximately 51.8% of events), although postspeciation dispersal may have blurred the boundaries between sympatric, parapatric, and peripheral isolate modes. An examination of ecological changes on the felid tree shows repeated patterns of resource partitioning in time (activity patterns), space (preferred habitat type), and food (as measured by body size) among closely related species. The rapid diversification of the cats thus appears to have been associated more with ecological than with geological separation.     

Phylogeny, evolution, and taxonomy of vannellid amoebae

We sequenced 18S rRNA genes from 21 vannellid amoebae (Amoebozoa; Vannellidae), including nearly all available type cultures, and performed a comprehensive phylogenetic analysis for 57 Vannellidae sequences. The results show that species of Vannella and Platyamoeba are completely mixed and do not form distinct clades. Several very closely related species pairs exist, each with a Vannella and a Platyamoeba species differing in only a few nucleotides. Therefore, presence (Vannella) or absence (Platyamoeba) of glycostyles in the cell surface coat is an invalid generic distinction; the genera must be merged. As Vannella has priority, we formally transferred Platyamoeba species into Vannella, except for the non-vannellid P. stenopodia, here renamed Stenamoeba stenopodia gen. n. comb. n. and transferred to the family Thecamoebidae. Our trees show that Vannella glycostyles were probably easily and repeatedly evolutionarily lost. We have established a new genus Ripella, with distinct morphology and sequence signatures for Vannella platypodia and morphologically similar species that form a clearly separate clade, very distant from other Vannellidae. Vannellids form four well-separated single-genus clades: Vannella sensu stricto, Ripella, Clydonella, and Lingulamoeba. Species of the revised genus Vannella comprise four closely related, well-supported subclades: one marine and three freshwater. Here, we provide an illustrated checklist for all 40 known Vannellidae species.     

犬科的线粒体细胞色素b DNA序列及其分子系统学研究

通过对犬科的赤狐、蓝狐、貉和狼４种的线粒体细胞色素ｂ约３７２ｂｐＤＮＡ片段序列分析,结合ＧｅｎＢａｎｋ中狗、西门豺和非洲野犬３种的该区段ＤＮＡ序列的比较,共发现１１３个核苷酸位点存在变异（约３０％）。ＮＪ法构建的分子系统树显示,非洲野犬最先从犬科动物中分化出来;犬属的我狼、狗和西门豺等３种为系统树上独立的一支,且其分歧的时间较赤狐、蓝狐和貉早;赤狐和蓝狐具有较近的亲缘关系。上述结果与形态的观点基本