Delimitation of the Thoracosphaeraceae (Dinophyceae), including the calcareous dinoflagellates, based on large amounts of ribosomal RNA sequence data

The phylogenetic relationships of the Dinophyceae (Alveolata) are not sufficiently resolved at present. The Thoracosphaeraceae (Peridiniales) are the only group of the Alveolata that include members with calcareous coccoid stages; this trait is considered apomorphic. Although the coccoid stage apparently is not calcareous, Bysmatrum has been assigned to the Thoracosphaeraceae based on thecal morphology. We tested the monophyly of the Thoracosphaeraceae using large sets of ribosomal RNA sequence data of the Alveolata including the Dinophyceae. Phylogenetic analyses were performed using Maximum Likelihood and Bayesian approaches. The Thoracosphaeraceae were monophyletic, but included also a number of non-calcareous dinophytes (such as Pentapharsodinium and Pfiesteria) and even parasites (such as Duboscquodinium and Tintinnophagus). Bysmatrum had an isolated and uncertain phylogenetic position outside the Thoracosphaeraceae. The phylogenetic relationships among calcareous dinophytes appear complex, and the assumption of the single origin of the potential to produce calcareous structures is challenged. The application of concatenated ribosomal RNA sequence data may prove promising for phylogenetic reconstructions of the Dinophyceae in future.     

DISCONTINUOUS MITOCHONDRIAL AND CHLOROPLAST LARGE SUBUNIT RIBOSOMAL RNAs AMONG GREEN ALGAE: PHYLOGENETIC IMPLICATIONS1

To provide insights into the occurrence, evolution, and phylogenetic distribution of discontinuous mitochondrial and chloroplast large subunit ribosomal RNAs (LSU rRNAs) among green algae, we surveyed 12 taxa representing three classes of green algae: the Chlorophyceae, Pleurastrophyceae, and Micromonadophyceae (sensu Mattox and Stewart 1984). We present evidence that discontinuous mitochondrial and chloroplast LSU rRNAs are quite widespread among green algae. Mitochondrial LSU rRNAs appear discontinuous in zoosporic chlorophycean lineages displaying a clockwise or directly opposed configuration in their flagellar apparatus, as well as in chlorococcalean autosporic taxa phylogenetically related to them, but are continuous among zoosporic green algal lineages with a counterclockwise flagellar apparatus configuration, as well as among chlorococcalean autosporic taxa phylogenetically related to them. Chloroplast LSU rRNAs appear discontinuous in all of the lineages investigated. Discontinuous mitochondrial LSU rRNA represents a molecular trait that might have originated at or near the base of Chlorophyceae, whereas discontinuous chloroplast LSU rRNA might have developed very early in the evolutionary history of the green algal group itself. We suggest, therefore, that the presence of discontinuous mitochondrial but not chloroplast LSU rRNA can be used as an additional character in assessing phylogenetic affiliations among green algae.     

毛茛科分子系统发育研究进展

毛茛科(Ranunculaceae)在被子植物的系统演化中占有十分重要的地位,其系统位置和科下演化关系一直备受争议。近20多年的分子系统学研究表明,以往基于形态学的分类系统与分子系统学研究结果存在巨大差异。通过形态学性状界定的绝大多数亚科都没有得到分子系统学支持。此外,通过形态学确定的一些属如升麻属(Cimicifuga)、黄三七属(Souliea)、獐耳细辛属(Hepatica)、白头翁属(Pulsatilla)和水毛茛属(Batrachium)等,根据分子系统学研究均应予以归并。而分子系统学研究也确立了一些类群的属级地位,如露蕊乌头属(Gymnaconitum)等。以中国分布的毛茛科植物为例,通过以往分子系统学研究,共有10个属被归并,2个属新被确立。然而,毛茛科分子系统学研究对于科下许多类群之间的关系目前仍然没有得到很好的解决,如毛茛亚科和翠雀族等类群的系统发育关系仍需要进行深入研究后方能确定。该文对近年来国内外有关毛茛科的分子系统学研究进展进行了综述,并对该科尚存的一些问题和未来的研究方向进行了讨论。     

Relatedness, phylogeny, and evolution of the fungi

Recent advances in fungal systematics are reviewed in relation to our previous studies. The usefulness of the integrated analysis of genotypic (especially 18S rRNA gene sequence comparisons) and phenotypic (especially ultrastructural and chemotaxonomic data) characters has been emphasized for the major groups and selected taxa of the fungi, and the impact to fungal systematics and evolution is discussed. Our noteworthy studies and findings are: 1) polyphyly of the chytridiomycetes and zygomycetes, 2) phylogenetic origin of the entomophthoralean fungi includingBasidiobolus, 3) detection of a major new lineage “Archiascomycetes,” comprisingTaphrina, Protomyces andSaitoella, Schizosaccharomyces, andPneumocystis, within the Ascomycota, and its phylogenetic and evolutionary significance, 4) polyphyletic origins of species in the anamorphic genusGeosmithia, and 5) phylogenetic placement ofMixia osmundae, species correctly and incorrectly assigned to the genusTaphrina, and basidiomyceotus yeasts. The newest 18S rDNA sequence-based neighbor-joining trees of the Ascomycota are demonstrated. “Traditional studies of evolution have amply demonstrated that evolution at the phenotypic level is characterized by adaptation and opportunism, irregularity in pace, and inequality of rates among lineages. In contrast, studies of molecular evolution have revealed quite different features characterized by changes that are conservative in nature, random in pattern (independent of phenotypic characters), and quite regular in pace with equal rates among diverge [sic] lineages for a given protein”. (Kimura, M. 1983. The neutral theory of molecular evolution, pp. 308–309, Cambridge University Press, Cambridge.) Recipient of the 2nd Mycological Society of Japan's Excellent Achievement Award, 1998; the awarding lecture was given at the 42nd Annual Meeting of the Mycological Society of Japan, 16 May, 1998, Kyoto University, Kyoto. This review is based mainly on the publications intended for the Award.     

Molecular biological study on speciation and phylogeny of the order Entomobryomorpha (Collembola: Hexapoda)

In order to elucidate the phylogenetic relationship among groups of the order Entomobryomorpha (Collembola), the sequences on the ITS 1 to ITS 2 fragments of the rRNA gene were analyzed in 11 species of three families. In order to avoid the potential risks and inconsistencies of a single method or data set, the phylogenetic reconstructions were based on three different approaches: methods of maximum parsimony, maximum likelihood and neighbor joining. The inferred phylogenies supported monophyly of the order Entomobryomorpha. The relationships between families were different, but the orders of branching within each family were the same. Entomobryidae and Isotomidae were paraphyletic, whereas Tomoceridae was monophyletic. Tomoceridae was subdivided into two branches; the molecular analysis provided results distinctive enough to separate the two genera by the high bootstrap value. On the other hand, two different populations of putative Homidia koreana appeared to be different species, although their chaetotaxy is identical. A wide coverage of characters, including not only morphological characters but also genetic data such as allozymes and DNA sequences, will give a more accurate picture of the classification and phylogeny of the studied group.     

线粒体DNA序列特点与昆虫系统学研究

昆虫线粒体DNA是昆虫分子系统学研究中应用最为广泛的遗传物质之一。线粒体DNA具有进化速率较核DNA快 ,遗传过程不发生基因重组、倒位、易位等突变 ,并且遵守严格的母系遗传方式等特点。本文概述了mtDNA中的rRNA、tRNA、蛋白编码基因和非编码区的一般属性 ,分析了它们在昆虫分子系统学研究中的应用价值 ,以及应用DNA序列数据来推导分类阶 (单 )元的系统发育关系时 ,基因或DNA片段选择的重要性     

基因序列在金龟总科(Scarabaeoidea)分子系统学研究中的应用

基因序列分析是揭示金龟总科系统发育关系的重要工具。统计了应用于金龟总科中13个科的线粒体和核基因序列,综述了COⅠ、16S rRNA、28S rRNA、18S rRNA等基因序列在金龟总科分子系统学研究的新进展,探讨了不同基因序列在分类鉴定、隐存种发现、系统发育关系重建等方面的作用,对未来研究趋势进行了展望,为进一步阐明金龟总科系统发育机制奠定基础。     

Sequence variations in the large-subunit ribosomal RNA gene of ammonia (foraminifera,protozoa) and their evolutionary implications

An unusually high divergence was observed in the ribosomal RNA genes of a free-living population of foraminifera belonging to the genusAmmonia. The sequences of a large-subunit (LSU) rDNA expansion segment D1 and flanking regions were obtained from 20 specimens namedAmmonia sp. 1 andAmmonia sp. 2. The sequence divergence between the two species averages 14%. Within each species it ranges from 0.2% to 7.1% inAmmonia sp. 1 and from 0.7% to 2.3% inAmmonia sp. 2. We did not find two specimens having identical sequences. Moreover, in opposition to the generally acaepted view, rDNA sequence variations were also found within a single individual. The variations among several rDNA copies in a single specimen ofAmmonia may reach up to 4.9%. Most of the observed variations result from multiplication of CA or TA serial repeats occurring in two particularly variable regions. For single base changes, C-T transitions are most frequently observed. We discuss the evolution of expansion segments and their use for phylogenetic studies. Correspondence to: J. Pawlowski     

菌物分子系统学研究进展

分子生物学技术的发展以及计算机的广泛使用给菌物系统学在分子水平上带来了革命性变化,本文简要回顾了菌物分子系统学研究现状与分析方法,并就目前菌物分子系统学中存在的问题以及该研究的发展方向提出了一些看法。     

Advantages and Disadvantages of Molecular Phylogenetics: A Case Study of Ascaridoid Nematodes

The advantages of nucleotide sequence data for studying phylogeny have been shown to include number of potential characters available for comparison, rate independence between molecular and morphological evolution, and utility of molecular data for modeling patterns of nucleotide substitution. Potential pitfalls have also been revealed and include difficulties of inferring positional homology, incongruence between organismal and gene genealogies, and low likelihood of recovering the correct phylogeny given certain patterns in the timing of speciation events. Statistical methods for comparing phylogenetic hypotheses have been used to assess the reliability of alternative trees for ascaridoid nematodes. Based on partial ribosomal RNA sequences, tree topologies inconsistent with monophyly of the Ascaridinae were significantly worse by maximum likelihood inference. The topology of the maximum parsimony tree based on full-length sequences of 18S rRNA and 300 nucleotides of Cytochrome oxidase II for 13 ascaridoid species was generally consistent with traditional taxonomic expectations at lower ranks, but inconsistent with most proposed arrangements at higher taxonomic levels.