中国栎属植物花粉形态及其系统学意义

从系统学分类学的角度出发 ,对国产栎属 31个种的花粉进行了光学显微镜和扫描电镜观察。研究结果表明栎属的花粉萌发孔对该属的系统与分类无太大的参考价值 ;但栎属的花粉纹饰有颗粒状、聚颗粒状两种主要类型 ,具有重要的系统学分类学价值。花粉形态的研究结果支持将栎属植物划分为常绿类与落叶类的观点 ;栎属巴东栎组植物的花粉纹饰在种间存在分化 ,花粉形态的研究结果支持将巴东栎组至少划分为两个不同类群的观点 ;在佐以其他证据的情况下 ,栎属植物的花粉纹饰还具有重要的分类学价值     

The taxonomic treatment of agamosperms in the genusLimonium mill. (Plumbaginaceae)

Agamospermous species account for a large proportion of the species ofLimonium. Agamospermy is indicated by uneven polyploidy or aneuploidy, low pollen stainability and by the presence of monomorphic self-incompatible populations. The taxonomic treatment of agamospermous taxa varies from recognition of all of them at the same specific rank or by utilising a range of ranks in the taxonomic hierarchy. The influence of evolutionary hypotheses on taxonomic systems is considered. Molecular data provide a means of measuring the genetical relationships of taxa and establishing groups in a taxonomic hierarchy.     

木原均,(A).洛夫与小麦族(禾本科)的现代遗传学属的概念

分类学是认识生物体的一种工具,对生物体间系统关系的理解,种质资源利用的指南,也是一种交流用的普通语言.因此,分类处理需要反映这些关系的近期认识.在自然界,生物体只有两个绝对的单位:个体与种.一个种是一群个体被不可缺少的生殖关系相互联系成为的一个绝对单位.生殖隔离是种与种间的基本界限,同时也是生物演化过程中形成独立基因库(gene pools)的惟一因素.既然在种以上的分类群没有绝对界线,在种以上的任一分类处理都不可能避免人为性.虽然如此,仍然必须作出某些分类适应它们的描述、利用与(或)研究.这篇文章对小麦族分类群间生物系统关系的划分是基于遗传学的研究.我们分类处理的原则是:(1)反映这些种系统演化现今的理解;(2)便于种质资源的利用;(3)避免与传统处理有不必要的剧烈改变.     

Comments on the taxonomic treatment of Arenaria section Plinthine (Caryophyllaceae)

Comments on the taxonomic treatment of Arenaria section Plinthine (Caryophyllaceae) by D. J.Goyder. Comments are given on the taxonomic treatment of Arenaria section Plinthine presented by D. J.Goyder in a revision of this group recently published in the Botanical Journal of the Linnean Society, 97(1): 9–32.     

Integrating DNA barcode data and taxonomic practice: determination, discovery, and description

DNA barcodes, like traditional sources of taxonomic information, are potentially powerful heuristics in the identification of described species but require mindful analytical interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic treatment is discussed, and it is emphasized that the recursive process of character evaluation is both necessary and best served by understanding the empirical mechanics of the discovery process. These undertakings carry enormous ramifications not only for the translation of DNA sequence data into taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance. This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice.     

The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability

The number of functional traits of a wastewater treatment plant (WWTP) microbial community (i.e. functional richness) is thought to be an important determinant of its overall functional performance, but the ecological factors that determine functional richness remain unclear. The number of taxa within a community (i.e. taxonomic richness) is one ecological factor that might be important. Communities that contain more taxa are more likely to have more functional traits, and a positive association is therefore expected between functional and taxonomic richness. Empirical tests for this positive association among WWTP communities, however, are lacking. We address this knowledge gap by measuring the functional and taxonomic richness of 10 independent WWTP communities. We demonstrate that functional and taxonomic richness are positively associated with each other. We further demonstrate that functional and taxonomic richness are negatively associated with the effluent NH₄‐N and BOD₅ concentrations. This led us to hypothesize that correlated variation in functional and taxonomic richness is likely related to variation in ambient nitrogen and carbon availability. We finally demonstrate that this hypothesis is consistent with the functional and taxonomic attributes of the WWTP communities. Together, our results improve our basic understanding of the ecology and functioning of WWTP communities.     

A Study on the Seed of Lardizabalaceae and Sargentodoxaceae, (1) A SEM Examination of Testa

Testa SEM characters of Lardizabalaceae and Sargentodoxaceae have not been used in former studies of taxonomy and phylogeny. In this work examined by scanning electron microscope (SEM). was the testa surface of 5 genera including 15 species of Lardizabalaceae and Sargentodoxaceae. Sargentodoxaceae is found quite different from Lardizabalaceae in its smooth test. The testa sculpture of Akebia, Holboellia and Stauntonia is basically striate, but that of Sinofranchetia, though striate, is verrucous on striations. Decaisnea is very isolated for its mosaic testa sculpture. The tesa examination confirms the rationality of the taxonomic treatment of Sargentodoxaceae by Stapf, the isolated taxonomic position of Decaisnea and Sinofranchetia in Lardizabalaceae, and the close interrelationship among Akebia, Holboellia, and Stauntonia.     

Integrated taxonomy of the <Emphasis Type="Italic">Asplenium normale</Emphasis> complex (Aspleniaceae) in China and adjacent areas

The Asplenium normale D. Don complex comprises several taxa that are either diploid or tetraploid. The tetraploids are assumed to have originated from diploid ancestors by relatively recent autopolyploidization or allopolyploidization. Some of the diploids are readily recognized morphologically but most of the taxa have until now been placed into a single species. However, phylogenetic studies have challenged this treatment and emphasized the notion that the taxonomic treatment of this complex needs to be revised. An integrative taxonomic approach was employed to delimit species in the complex using cytological, morphological, and DNA sequence data. Initially, we employed a diploid first approach to establish a robust taxonomic framework. Special efforts were made to collect and identify the diploid progenitors of each polyploid lineage identified in the plastid DNA based phylogenetic hypothesis. A total of six distinct diploid species were identified. The distinctive nature of the six diploids is strongly supported by sequence differences in plastid DNA and nuclear loci, as well as by the results of morphometric analysis. Diagnostic morphological characters were identified to distinguish the six diploid species, resulting in their revised taxonomy, which includes two novel species, namely, Asplenium normaloides and A. guangdongense. Further studies to strengthen the taxonomic classification of all of the tetraploid taxa are warranted.     

Using the taxon-specific genes for the taxonomic classification of bacterial genomes

Background

The correct taxonomic assignment of bacterial genomes is a primary and challenging task. With the availability of whole genome sequences, the gene content based approaches appear promising in inferring the bacterial taxonomy. The complete genome sequencing of a bacterial genome often reveals a substantial number of unique genes present only in that genome which can be used for its taxonomic classification.

Results

In this study, we have proposed a comprehensive method which uses the taxon-specific genes for the correct taxonomic assignment of existing and new bacterial genomes. The taxon-specific genes identified at each taxonomic rank have been successfully used for the taxonomic classification of 2,342 genomes present in the NCBI genomes, 36 newly sequenced genomes, and 17 genomes for which the complete taxonomy is not yet known. This approach has been implemented for the development of a tool ‘Microtaxi’ which can be used for the taxonomic assignment of complete bacterial genomes.

Conclusion

The taxon-specific gene based approach provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1542-0) contains supplementary material, which is available to authorized users.     

Application of principal components analyses with constant character number in a study of the Bulbostylis/Fimbristylis (Cyperaceae) complex in Nigeria

Interrelationships between OTUs (operational taxonomic units) were assessed through comparisons based on a constant character number, using principal components analysis. This approach results in a uniform treatment of OTUs, despite variations in the number of definite entries for character states that could validly be made. In addition, the risk of distortion of the ordination scatter as a result of a bimodal frequency distribution of the number of characters available for comparisons is minimized. Appropriately applied, the approach also provides indications of the consistency of the features of the ordinations and reveals where more caution in interpretation is advisable.
The main analysis divided the OTUs into two unequal-sized groups, with a few intermediates; these were concluded to be more closely allied to the large than the small group. The significance of these groupings, in terms of their species contents, is discussed in relation to the method and to recent taxonomic treatments of the Bulbostylis/Fimbristylis complex. Some taxonomic conclusions must be tentative because of the limitations of the sample.     

Taxonomic Precision of Different Hypervariable Regions of 16S rRNA Gene and Annotation Methods for Functional Bacterial Groups in Biological Wastewater Treatment

High throughput sequencing of 16S rRNA gene leads us into a deeper understanding on bacterial diversity for complex environmental samples, but introduces blurring due to the relatively low taxonomic capability of short read. For wastewater treatment plant, only those functional bacterial genera categorized as nutrient remediators, bulk/foaming species, and potential pathogens are significant to biological wastewater treatment and environmental impacts. Precise taxonomic assignment of these bacteria at least at genus level is important for microbial ecological research and routine wastewater treatment monitoring. Therefore, the focus of this study was to evaluate the taxonomic precisions of different ribosomal RNA (rRNA) gene hypervariable regions generated from a mix activated sludge sample. In addition, three commonly used classification methods including RDP Classifier, BLAST-based best-hit annotation, and the lowest common ancestor annotation by MEGAN were evaluated by comparing their consistency. Under an unsupervised way, analysis of consistency among different classification methods suggests there are no hypervariable regions with good taxonomic coverage for all genera. Taxonomic assignment based on certain regions of the 16S rRNA genes, e.g. the V1&V2 regions – provide fairly consistent taxonomic assignment for a relatively wide range of genera. Hence, it is recommended to use these regions for studying functional groups in activated sludge. Moreover, the inconsistency among methods also demonstrated that a specific method might not be suitable for identification of some bacterial genera using certain 16S rRNA gene regions. As a general rule, drawing conclusions based only on one sequencing region and one classification method should be avoided due to the potential false negative results.     

木原均,.洛夫与小麦族(禾本科)的现代遗传学属的概念(英文)

分类学是认识生物体的一种工具,对生物体间系统关系的理解,种质资源利用的指南,也是一种交流用的普通语言。因此,分类处理需要反映这些关系的近期认识。在自然界,生物体只有两个绝对的单位:个体与种。一个种是一群个体被不可缺少的生殖关系相互联系成为的一个绝对单位。生殖隔离是种与种间的基本界限,同时也是生物演化过程中形成独立基因库(gene pools)的惟一因素。既然在种以上的分类群没有绝对界线,在种以上的任一分类处理都不可能避免人为性。虽然如此,仍然必须作出某些分类适应它们的描述、利用与(或)研究。这篇文章对小麦族分类群间生物系统关系的划分是基于遗传学的研究。我们分类处理的原则是:(1)反映这些种系统演化现今的理解;(2)便于种质资源的利用;(3)避免与传统处理有不必要的剧烈改变。     

The web and the structure of taxonomy

An easily accessible taxonomic knowledge base is critically important for all biodiversity-related sciences. At present, taxonomic information is organized and regulated by a system of rules and conventions that date back to the introduction of binomial nomenclature by Linnaeus. The taxonomy of any particular group of organisms comprises the sum information in the taxonomic literature, supported by designated type specimens in major collections. In this article, the way modern means of disseminating information will change the practice of taxonomy, in particular the Internet, is explored. Basic taxonomic information, such as specimen-level data, location of types, and name catalogues are already available, at least for some groups, on the Web. Specialist taxonomic databases, key-construction programs, and other software useful for systematists are also increasingly available. There has also been a move towards Web-publishing of taxonomic hypotheses, though as yet this is not fully permitted by the Codes of Nomenclature. A further and more radical move would be to transfer taxonomy completely to the Web. A possible model of this is discussed, as well as a pilot project, the "CATE" initiative, which seeks to explore the advantages and disadvantages of such a move. It is argued that taxonomy needs to forge better links with its user-communities to maintain its funding base, and that an important part of this is making the products of its research more accessible through the Internet.     

杨属植物分类的研究进展和展望

自林奈建立杨属（Populus）以来,众多的学者对杨属的分类进行了研究,并建立了较多的分类系统。目前的国际杨属分类,总体上还停留在传统形态分类阶段,存在明显的地域和国别特征。尽管各国在主流上都采用“属—组—种”的分类阶元,但在种、亚种、变种的划分上,却存在很大的不同。中国和美国分别是细分派和聚合派的代表,两国的分类系统存在很大分歧,但各有优点和缺点。即使在国内,杨属分类也还有很多需要解决的问题。新兴的分子系统学研究,为杨属的分类修订提供了一些有益参考,但总体贡献不大。国际杨属分类的趋势和终极目标是建立基于系统发生的统一分类系统。这需要基于种群和综合物种概念,融合形态学、生态学、生物地理学、基因组生物信息学和进化生物学等的综合系统分类来实现。     

What governs the functional diversity patterns of fishes in the headwater streams of the humid forest enclaves: environmental conditions,taxonomic diversity or biotic interactions?

The relationship between functional and taxonomic diversity is a major issue in ecology. Biodiversity in aquatic environments is strongly influenced by environmental gradients that act as dispersion and niche barriers. Environmental conditions act as filters to select functional traits, but biotic interactions also play a role in assemblage structure. In headwater streams, the relationship between functional and taxonomic diversity remains unclear. In this study we investigated how environmental conditions, taxonomic diversity and biotic interactions influence the spatial distribution of traits and functional diversity in stream fish species. Standardized sampling of fish species was carried out in 50 m sections of 16 streams located in rainforest enclaves in a semiarid region of Brazil (Caatinga biome). The functional diversity indices displayed different responses to the predictor variables used. Functional richness was mainly influenced by environmental conditions, while functional evenness was mostly determined by taxonomic diversity. On the other hand, functional dispersion was explained by a combination of environmental conditions and taxonomic diversity. The spatial distribution of fish species with the same functional traits was random, indicating that biotic interactions are not a strong predictor in these ecosystems. Channel width, pH and substrate were the most important variables in the spatial distribution of the functional traits of the fish species. Our results suggest that the functional structure of fish assemblages in headwater streams depends mainly on environmental conditions and taxonomic diversity.