不产氧光合细菌的分类学进展

不产氧光合细菌(APB)一直是研究生命起源与进化、光合作用和固氮机理的良好模式生物.近年来,APB资源研究发展迅速,不断发现新的物种、模式种及特殊功能物种,不断提出新的分类单元,APB分类系统发生了较大变化,同时引起了一定混乱.本文对不产氧光合细菌定义、分类系统和分类指征最新进展进行了系统述评,对分类系统中存在的问题和发展趋势也进行了评述.     

木原均,Á.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。     

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。     

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.     

中专生物学“生物的类群”一章的教学

教学目的一、通过学生自学,使他们对生物的类群有初步的了解. 二、通过参观实物、标本和挂图等,对生物界的主要类群的主要特征有较深刻的印象,使学生了解生物界分类的基本知识.为学习“生物进化”打下基础. 教学内容 (一)拟出自学思考题. 1.生物分类系统的阶梯(等级)是如何确定的?分为哪几个等级? 2.什么叫物种?种的学名是怎么组成的?生物的分类有什么意义? 3.区别下列各类群: (1)原核生物与真核生物 (2)无脊椎动物和脊椎动物 (3)病毒和细菌 (4)种和品种     

脱泛蛋白酶及其功能

脱泛蛋白酶(DUB)是催化脱泛蛋白化的一种酶,在生物体内普遍存在,具有重要作用。对脱泛蛋白酶的分类、结构特点、作用和生物功能进行了综述。     

基于Web的中国昆虫科级鉴别分类系统InsectID的设计与开发

详细介绍了国内首个昆虫科级鉴别分类网络系统InsectID(见http://insectx.3322.org)的设计思路、各组成部分的结构与功能,讨论了开发过程中分类检索表的转化与再现、系统分类树与特征解释机制的实现等关键问题。该系统具有分类单元全面、信息可靠、鉴定简单、扩充性强、更新便捷等诸多优点,是昆虫分类研究与教学的有力工具,也适用于其他生物分类系统的构建。     

KEGG数据库在生物合成研究中的应用

KEGG(Kyoto Encyclopedia of Genes and Genomes)提供了一个操作平台,即以基因组信息(GENES)和化学物质信息(LIGAND)为构建模块,通过代谢网络(PATHWAY)将基因组和生物系统联系起来,然后根据功能等级进行归纳分类(BRITE)。KEGG还为各种组学研究提供相关软件,用于代谢途径重建、遗传分析和化合物比对。作为一个综合数据库,KEGG不仅指导生物燃料、药物和新材料等生物基化学品的合成,而且致力于研究日趋严重的环境问题。系统介绍了KEGG数据库的结构、功能及其相关工具的最新进展,并展望在生物合成中的应用前景。     

Halkieria系统进化及其化石分类学研究进展

Halkieria是寒武纪一类躯体上披有骨质鳞片的疑难后生动物,前后各有一个大壳板,两侧对称,其钙质骨片在软躯体上排列形成几条规律的纵向带。半个世纪以来,学术界对Halkieria生物系统确切位置的讨论以及Halkieriidae不同属种亲缘关系的探索从未停止。本文总结了Halkieria化石在骨片属种分类、古地理和地层分布、生物系统分类学的研究进展,对当前的生物系统分类归纳出以下几种观点:1) Halkieria为腕足动物的祖先,并与托莫特壳类有一定的亲缘关系;2)Halkieria与Wiwaxia等骨片化石具有单源性,组成一种新的分类单元Halwaxiidae,属于软体动物干群或腕足动物和环节动物的干群;3)Halkieria为软体动物有刺亚门干群,与无板纲、多板纲更为亲近; 4) Halkieria为环节动物的祖先。目前,虽然多数人根据Halkieria与现生多板纲的骨片排列一致将Halkieria归属软体动物有刺亚门的干群,但近年来世界各地新化石材料的陆续发现及壳体发育研究使得Halkieria的系统分类位置出现新的争议。通过对化石分类学的系统厘定和生物分类研究进展的总结梳理,...     

淡水浮游植物功能类群分类法的提出、发展及应用

浮游植物分类方法是揭示浮游植物群落演替规律、开展淡水生态研究的工作基础和重要工具.林氏分类法和分子鉴定法在生态学应用上存在的不足促进了浮游植物功能类群分类法的发展.功能类群分类法是一种以浮游植物个体生态学为依据的生态分类法.本文概述了浮游植物功能类群(functional group,FG)、生态功能类群(morpho-functional group,MFG)和形态功能类群(morphology-based functional group,MBFG)等浮游植物分类方法的理论基础和分类依据,分析比较了这3种分类方法的优势与不足,认为FG是目前应用于水生生态学研究和水环境生物评价中相对适用的浮游植物分类方法.介绍了功能类群分类法在国内外淡水浮游植物生态学研究中的应用现状,简述了以FG为基础提出的Q指数法和Q-R指数法两种水质评价法的评价标准及存在的不足.
     

Using the relationship between taxonomic and functional diversity to assess functional redundancy in streams of an altered tropical watershed

The relationship between taxonomic and functional diversity indices has been used to better describe and understand the structure of biological communities. Functional diversity is expected to have an asymptotic relationship with species richness because at some point, the addition of new species will increase some of the already established functional groups (functional redundancy). However, the asymptotic relationship may not be reached in intermediately disturbed systems once many intolerant species that would have played a redundant role or even represented some functional groups have been lost. This study aimed to address such a relationship (taxonomic and functional indices) and to evaluate the functional redundancy in intermediately disturbed streams in the Atlantic Rainforest domain. We expected a positive linear relationship between taxonomic and functional diversity; however, we did not expect to find an asymptotic relationship between richness and functional diversity because of the loss of many intolerant species caused by anthropogenic uses. The taxonomic diversity indices were Species Richness (SR) and Simpson’s Diversity (SD), while the functional diversity indices were the Functional Richness (FRic) and Functional Dispersion (FDisp). The two taxonomic and two functional diversity indices showed a significant positive relationship that never reached an asymptote, suggesting low functional redundancy in the fish communities. Our results indicate that care is needed in the management of the studied streams because assemblies with low functional redundancy are more susceptible to loss of functions in the case of species loss.     

Invasive species removal increases species and phylogenetic diversity of wetland plant communities

Plant invasions result in biodiversity losses and altered ecological functions, though quantifying loss of multiple ecosystem functions presents a research challenge. Plant phylogenetic diversity correlates with a range of ecosystem functions and can be used as a proxy for ecosystem multifunctionality. Laurentian Great Lakes coastal wetlands are ideal systems for testing invasive species management effects because they support diverse biological communities, provide numerous ecosystem services, and are increasingly dominated by invasive macrophytes. Invasive cattails are among the most widespread and abundant of these taxa. We conducted a three‐year study in two Great Lakes wetlands, testing the effects of a gradient of cattail removal intensities (mowing, harvest, complete biomass removal) within two vegetation zones (emergent marsh and wet meadow) on plant taxonomic and phylogenetic diversity. To evaluate native plant recovery potential, we paired this with a seed bank emergence study that quantified diversity metrics in each zone under experimentally manipulated hydroperiods. Pretreatment, we found that wetland zones had distinct plant community composition. Wet meadow seed banks had greater taxonomic and phylogenetic diversity than emergent marsh seed banks, and high‐water treatments tended to inhibit diversity by reducing germination. Aboveground harvesting of cattails and their litter increased phylogenetic diversity and species richness in both zones, more than doubling richness compared to unmanipulated controls. In the wet meadow, harvesting shifted the community toward an early successional state, favoring seed bank germination from early seral species, whereas emergent marsh complete removal treatments shifted the community toward an aquatic condition, favoring floating‐leaved plants. Removing cattails and their litter increased taxonomic and phylogenetic diversity across water levels, a key environmental gradient, thereby potentially increasing the multifunctionality of these ecosystems. Killing invasive wetland macrophytes but leaving their biomass in situ does not address their underlying mechanism of dominance and is less effective than more intensive treatments that also remove their litter.     

Is polychaete family-level sufficient to assess impact on tropical estuarine gradients?

Regular, robust monitoring programs set up to assess the environmental conditions of aquatic systems often target different biological groups. And, of these, macroinvertebrate communities and particularly the class Polychaeta are frequently used. Identifying these organisms takes time, money and specialized expertise to ensure correct identification to the lowest possible taxonomic level. Identification errors can lead to an erroneous assessment. The concept of taxonomic sufficiency has been proposed both to minimize errors and to save time and money. This study tested the usefulness of this concept in tropical estuaries in northeast Brazil. We selected two transitional systems with different degrees of human impact due to different land uses and different conservation systems: the Mamanguape estuary, which is in an environmental conservation unit for sustainable use, and the highly impacted, urban Paraíba do Norte estuary. The results clearly showed that nutrient concentrations were markedly higher in the Paraíba do Norte estuary in the dry season and that the composition of the polychaete assemblages differed between the two estuaries as well as along the spatial gradient of each estuary. The use of either genus or family level led to equivalent representation in each system in terms of taxon richness and both the Margalef and Shannon-Wiener diversity indices. Both taxonomic levels described similar changes in the polychaete assemblage along the estuarine gradients. Based on our findings, the use of a coarser taxonomic level (i.e., family) is a good option when the aim is to implement a monitoring program in tropical estuaries with the polychaete assemblages as one of the target groups. This time-efficient taxonomic resolution can help improve sampling designs and allow long-term monitoring studies without losing much vital information.     

Benthic macroinvertebrate biodiversity improved with irrigation ponds linked to a rice paddy field

Traditionally, many irrigation ponds supplied water to paddy fields, but most of these ponds have disappeared through improvements in irrigation systems. The aim of this study was to assess the ecological functions (especially biodiversity conservation) of irrigation ponds by using benthic macroinvertebrates that inhabit paddy fields. This study was conducted in Hwaseong‐si, Yesan‐gun, Hongseong‐gun, Uljin‐gun and Damyang‐gun, Korea. Benthic macroinvertebrates were collected using a quadrat sampler from August to September for three years (2010–2012) in paddy fields with and without an irrigation pond. In the comparisons between two paddy field types (paddy fields with and without an irrigation pond) for species richness and densities of benthic macroinvertebrates, the species richness and densities were higher in the paddy fields with a pond than in the paddy fields without a pond (P < 0.001). Biodiversity enhancement effect degree (BEED) of the irrigation pond showed positive values in all survey regions. There were no significant differences among the survey regions. BEED showed positive values in all taxonomic groups (excluding Crustacea) and were not significantly different among taxonomic groups. The BEED values for non‐insects, passive dispersers, were relatively higher than for insects, active dispersers. The results indicate that BEED is related to the dispersal abilities of each taxonomic group and an irrigation pond increases biodiversity in a paddy field in all regions. Therefore, the irrigation pond is one method that can be immediately applied in paddy fields in order to improve the biodiversity of agricultural ecosystems.     

Incongruence between cladistic and taxonomic systems

Cladistic and taxonomic treatments of the same plant group usually exhibit a mixture of congruences and incongruences. The question arises in the case of the incongruences as to which version is right and which is wrong. Many cladists believe that cladistics is a superior approach and gives the best results. There are several conceptual and methodological differences between cladistics and taxonomy that cause incongruence. One important conceptual difference is the use of different criteria for grouping: order of branching vs. similarity and difference (clades vs. taxa). Another is the policy regarding paraphyletic groups: to ban them in cladistics but ignore the ban in taxonomy. These two differences automatically lead to some incongruences. One approach is not right and the other wrong; each is operating by its own standards. However, when cladists apply the paraphyly rule to a taxonomic system and conclude that it needs revision to eliminate paraphyly, as cladists often do, they are judging the taxonomic system by a wrong standard. Several differences between the two schools in the use and handling of characters can also cause incongruence. First consider phenetic characters. Taxonomy uses a very wide range of these, whereas phenetic cladistics sets restrictions on the selection of characters, which deprive it of potentially useful evidence. Taxonomic systems generally rest on a broader empirical foundation than phenetic cladistic systems. Next, consider molecular cladistics, which is the leader in the use of DNA evidence. Two sources of incongruence between molecular cladistics and taxonomic systems can come into play here. First, the molecular evidence used in cladistics comes mainly from cytoplasmic organelles, whereas taxonomic systems are based on characters that are determined mainly by the chromosomal genome. More generally, the database in a molecular cladogram is, in itself, too narrow to serve as a foundation for an organismic classification. In cases of incongruence, the molecular evidence can be a reliable indicator of taxonomic relationships sometimes, misleading other times, and may afford no clear basis for a systematic decision. In this situation, it is helpful, indeed necessary, to integrate the molecular evidence with the phenetic evidence and bring more characters to bear on the question.     

雀形目高级阶元分类与起源研究概况

对雀肜目鸟类高级阶元的分类和系统发育的研究进行了简要概述.经典分类与应用分子生物学方法建立的分类系统在高级阶元(总科)有较大差异,但科级的分类基本一致.在雀形目鸟类起源研究方面,古生物学研究结果认为其起源于劳亚古陆;而分子生物学的证据则认为其起源于冈瓦纳古陆.由于化石的证据与"分子钟"的推测年代相差较大,因此对雀形目鸟类的起源还存在争议,但是目前的研究更倾向于"冈瓦纳起源"假说.     

The effect of taxonomic resolution on the assessment of ecological water quality classes

Within the ecological assessment of running waters based on benthic macroinvertebrates different levels of taxonomic resolution (species, genus, family and higher) are in use. Although assessment systems are often developed with detailed data on species level, water managers and other end-users could like to use data on higher taxonomic levels to assess the ecological quality of a water body because of limited human or money resources. The question that arises is, if an assessment system built with species level data is also applicable using data with a higher taxonomic resolution. Within the AQEM project a multimetric assessment system was developed to evaluate the ecological quality classes (from bad (1) to high (5) ecological quality) of different stream types throughout Europe. The present study focuses on the question whether the resulting water quality class changes using the AQEM Assessment Software (AAS) with different taxonomic resolutions and if yes, how large the deviations of ecological quality classes from the original classes are and if the deviations are unidirectional. For analyses data from four Austrian and two Dutch stream types were used. It is demonstrated that the assignment of a site to an ecological quality class may change if different taxonomic levels are used. Deviations in both directions (higher/lower ecological quality class) were observed. In most cases the divergence was only one ecological quality class, but also larger deviations occasionally occurred. The causes of changes in the assessment were investigated by separately looking into the underlying metrics of the multimetric system. Some of the evaluated metrics rely on autecological information on species level and are simply not applicable on higher taxonomic levels. Other metrics worked on higher taxonomic levels as well and showed more or less good distinctions between ecological quality classes. It is concluded that the AQEM Assessment Software is not applicable if data on higher taxonomic levels are used. As the deviations were not unidirectional and ranged from one to three ecological quality classes, it is not possible to include a correction factor for using the software with higher taxonomic resolution data.     

Functional Anatomy: A Taxonomic Proposal

It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.     

Microbiology is the basis of sustainable agriculture: an opinion

Agricultural microbiology is presented as a synthetic research field responsible for knowledge transfer from general microbiology and microbial ecology to the agricultural biotechnologies. The major goal of agricultural microbiology is a comprehensive analysis of symbiotic micro‐organisms (bacteria, fungi) interacting with agriculturally important plants and animals: here we have focussed on plants. In plants, interactions with micro‐organisms are diverse, ranging from two‐partite symbioses (e.g. legume–rhizobia N₂‐fixing nodular symbioses or arbuscular mycorrhiza) to multipartite endophytic and epiphytic (root‐associated, phyllosphere) communities. Two‐partite symbioses provide the clearest models for addressing genetic cooperation between partners, resulting in the formation of super‐organism genetic systems, which are responsible for host productivity. Analysis of these systems has now been extended considerably by using the approaches of metagenomics, which allow the dissection of taxonomic/population structures and the metabolic/ecological functions of microbial communities, which have resulted from the adaptation of free‐living, soil microflora in the endosymbiotic niches. Both beneficial (nutritional, defensive, regulatory) and antagonistic (biocontrol) functions expressed by symbiotic microbes towards their hosts are the potential subjects of effective agronomic use. A fundamental knowledge of the genetics, molecular biology, ecology and evolution of symbiotic interactions could enable the development of microbe‐based sustainable agriculture. This could achieve: (a) an improvement of major adaptive functions and productivity in crop plants by manipulating their microbial cohabitants; (b) partial or even full substitution of ecologically hazardous agrochemicals (mineral fertilizers, pesticides) by microbial preparations; (c) a decrease in the cost and an improvement of the quality of agricultural products.     

几何形态测量法结合Micro CT扫描对两水系花斑裸鲤的形态分析

研究采用现代几何形态测量法并结合Micro CT扫描技术对两水系(黄河上游与柴达木水系格尔木河)花斑裸鲤(Gymnocypris eckloni Herzenstein)的形态进行定量分析, 讨论两水系花斑裸鲤是否存在先前研究未能发现的形态差异。结果显示: 花斑裸鲤的两个地理种群在基于其头部形态轮廓二维坐标的主成分分析和判别分析的结果均聚在一起, 这与之前文献记载的两水系花斑裸鲤的形态学特征相一致, 并且对两水系花斑裸鲤进行的典型变量分析也同样支持这一结果; 对花斑裸鲤两个地理种群背鳍支鳍骨插入椎骨间的相对位置这一形态特征进行卡方检验, 结果表明在骨骼这一更具分类学意义的形态特征上表现出显著性差异。通过对花斑裸鲤两个地理种群的几何形态与Micro CT扫描, 准确定量地分析了两水系花斑裸鲤形态上的异同, 为正确评价两水系花斑裸鲤真实的演化关系奠定了形态学基础。