新世纪的中国昆虫系统学

对未来我国昆虫系统学在能力建设、物种编目、理论研究、技术创新和国际合作等方面提出一系列建议。在昆虫系统学能力建设方面,政府和科学家应该在生物分类学能力评估、基础硬件建设、各级生物标本馆中建立伙伴关系（包括标本采集、标本馆管理、 科学研究、 知识共享和标本与资料交换）等方面重点开展工作。在物种编目方面,我国的昆虫物种编目有赖于各级政府和机构继续关注标本的收集和保藏,继续启动一些考察项目,以满足发现和认识昆虫物种的实际需求。在物种水平上研究以往昆虫系统学家的工作,进行地区性和世界性的昆虫类群的订正更是非常必要的。在理论研究方面,我国昆虫系统应该在下列方面积极探索：物种概念、进化理论、比较生物学理论和高级分类系统研究。在技术创新方面,我国的昆虫系统学家应该在数据库与网络技术应用、图形图像处理技术、专家鉴定系统技术、分类性状分析技术、分子生物学技术、系统发育推断程序、信息统一管理技术和知识传播技术等方面进行深入研究,以满足昆虫系统学的发展需求。在国际合作方面,要进一步推动我国昆虫系统学研究机构加入生物分类学全球战略联盟、加入各种相关国际相关组织,要促进物种信息管理系统的建立与共享,要推动研究项目国际化。     

Against the naming of fungi

The use of molecular bar-coding and consensus on nomenclatural practices has encouraged optimism about the future of fungal taxonomy and systematics. There are, however, profound deficiencies in our understanding of fungal diversity and broader problems with the taxonomic enterprise that deserve greater attention. For 250 years mycologists have tried to reconcile fungal diversity with the Linnean fantasy of a divine order throughout nature that included unambiguous species. This effort has failed and today's taxonomy rests on an unstable philosophical foundation. Rather than persisting with the present endeavour, it may be more fruitful to abandon the notion of fungal species pending further basic research. In the meantime, mycologists should consider tagging collections with digital codes and assigning these operational taxonomic units to higher taxonomic ranks whose objective reality is corroborated by strong phylogenetic evidence.     

葡萄属野生资源分类研究进展

葡萄属野生资源在整个葡萄属(Vitis L.)的系统演化中占有十分重要的地位。葡萄属野生资源分布广泛,种间杂交容易,形态变异较为复杂,造成分类工作难度较大。长期以来,部分野生种的分类一直存在争议。本文从世界葡萄属植物的分类历史出发,对葡萄属野生种分类研究进展进行了综述。传统的分类方法不能够很好地解决不同种之间的亲缘关系,近十几年来,多种分子标记被应用于葡萄属的系统发育研究,并构建了葡萄属系统发育的基本框架。但是,分子系统学研究工作开展的远远不够,而且多数研究仍然受到资源的限制。未来建议加强葡萄属野生资源的收集和保护,并开展更全面的分类学修订工作。同时,充分利用分子系统学的相关技术手段,进一步阐明各野生种的分类地位。     

Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex

Taxonomy has traditionally relied on morphological and ecological traits to interpret and classify biological diversity. Over the last decade, technological advances and conceptual developments in the field of molecular ecology and systematics have eased the generation of genomic data and changed the paradigm of biodiversity analysis. Here we illustrate how traditional taxonomy has led to species designations that are supported neither by high throughput sequencing data nor by the quantitative integration of genomic information with other sources of evidence. Specifically, we focus on Omocestus antigai and Omocestus navasi, two montane grasshoppers from the Pyrenean region that were originally described based on quantitative phenotypic differences and distinct habitat associations (alpine vs. Mediterranean‐montane habitats). To validate current taxonomic designations, test species boundaries, and understand the factors that have contributed to genetic divergence, we obtained phenotypic (geometric morphometrics) and genome‐wide SNP data (ddRADSeq) from populations covering the entire known distribution of the two taxa. Coalescent‐based phylogenetic reconstructions, integrative Bayesian model‐based species delimitation, and landscape genetic analyses revealed that populations assigned to the two taxa show a spatial distribution of genetic variation that do not match with current taxonomic designations and is incompatible with ecological/environmental speciation. Our results support little phenotypic variation among populations and a marked genetic structure that is mostly explained by geographic distances and limited population connectivity across the abrupt landscapes characterizing the study region. Overall, this study highlights the importance of integrative approaches to identify taxonomic units and elucidate the evolutionary history of species.     

Systematics of the grey mullets (Teleostei: Mugiliformes: Mugilidae): molecular phylogenetic evidence challenges two centuries of morphology-based taxonomy

The family Mugilidae comprises mainly coastal marine species that are widely distributed in all tropical, subtropical and temperate seas. Mugilid species are generally considered to be ecologically important and they are a major food resource for human populations in certain parts of the world. The taxonomy and systematics of the Mugilidae are still much debated and based primarily on morphological characters. In this study, we provide the first comprehensive molecular systematic account of the Mugilidae using phylogenetic analyses of nucleotide sequence variation at three mitochondrial loci (16S rRNA, cytochrome oxidase I, and cytochrome b) for 257 individuals from 55 currently recognized species. The study covers all 20 mugilid genera currently recognized as being valid. The family comprises seven major lineages that radiated early on from the ancestor to all current forms. All genera that were represented by two species or more, except Cestraeus, turned out to be paraphyletic or polyphyletic. Thus, the present phylogenetic results generally disagree with the current taxonomy at the genus level and imply that the anatomical characters used for the systematics of the Mugilidae may be poorly informative phylogenetically. The present results should provide a sound basis for a taxonomic revision of the mugilid genera. A proportion of the species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) appear to consist of cryptic species, thus warranting further taxonomic and genetic work at the infra-generic level.     

Taxonomic and geographic bias in the genetic study of helminth parasites

The use of genetic information is now fundamental in parasite taxonomy and systematics, for resolving parasite phylogenies, discovering cryptic species, and elucidating patterns of gene flow among parasite populations. The accumulation of available gene sequences per geographical area or per parasite taxonomic group is likely proportional to species richness, but not without some biases. Certain areas and certain taxonomic groups receive more research effort than others, possibly causing a deficit in the relative number of parasite species being characterized genetically in some areas or taxonomic groups. Here, we use data on the number of parasite records per country or helminth family from the London Natural History Museum host-parasite database, and matching data on the number of gene sequences available from the National Center for Biotechnology Information (NCBI) GenBank database, to determine how available gene sequences scale with species richness across countries or parasitic helminth families. Our quantitative analysis identified countries/regions of the world and helminth families that have received the most effort in genetic research. More importantly, it allowed us to generate lists (based on residuals from the statistical model) of the 20 countries/regions and the 20 helminth families with the largest deficit in available gene sequences relative to their helminth species richness. We propose these lists as useful guides toward future allocation of effort to maximise advances in parasite biodiscovery, systematics and population structure.     

基因序列在蚤蝇科分子系统学研究中的应用

概述基因序列在双翅目蚤蝇科分子系统学研究中的应用。对蚤蝇科已测序的分类单元和基因序列进行了总结,12S rDNA和16S rDNA应用最广泛,涉及蚤蝇科17个属;获得基因序列最多的是Melaloncha属。蚤蝇科分子系统学研究内容为高级阶元系统发育分析、物种鉴定和隐存种发现。今后蚤蝇科分子系统学研究应增加蚤蝇标本的种类与数量,选择标准化基因。     

Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species

Biodiversity studies require species level analyses for the accurate assessment of community structures. However, while specialized taxonomic knowledge is only rarely available for routine identifications, DNA taxonomy and DNA barcoding could provide the taxonomic basis for ecological inferences. In this study, we assessed the community structure of sediment dwelling, morphologically cryptic Chironomus larvae in the Rhine-valley plain/Germany, comparing larval type classification, cytotaxonomy, DNA taxonomy and barcoding. While larval type classification performed poorly, cytotaxonomy and DNA-based methods yielded comparable results: detrended correspondence analysis and permutation analyses indicated that the assemblages are not randomly but competitively structured. However, DNA taxonomy identified an additional species that could not be resolved by the traditional method. We argue that DNA-based identification methods such as DNA barcoding can be a valuable tool to increase accuracy, objectivity and comparability of the taxonomic assessment in biodiversity and community ecology studies.     

Molecular relationships of gammaridean amphipods from Arctic sea ice

The information on the biology and ecology of the Arctic sea ice-associated amphipods (Apherusa glacialis, Gammarus wilkitzkii, Onisimus glacialis, and O. nanseni) has increased, but their molecular taxonomic information still remains undisclosed. In the present study, we investigated long-range DNA sequences spanning 18S to 28S rDNA of these four sea ice-associated amphipods and analyzed their genetic relationships with other amphipod taxa. Variations of rDNA within the individuals of the same species were not detected. Phylogenetic analyses showed that each ice amphipod was separated, forming clusters with other conspecifics. Pairwise comparisons led to similar phylogenetic results, showing that the molecular taxonomy of the ice amphipods was in accordance with morphological systematics. In addition, these findings suggest that all four amphipods have little genetic variation compared with their morphologically defined conspecifics from temperate regions. Based on DNA taxonomy, G. wilkitzkii was supported as a species in good standing, refuting a recent synonymization with Gammarus duebeni. Considerably low genetic divergences of O. glacialis and O. nanseni in 18S, ITS, and 28S rDNA suggest the presence of population distinctions within species.     

生态学的多样性指数:功能与系统发育

生物多样性是生态学的核心问题。传统的多样性指数仅包含物种数和相对多度的信息,这类基于分类学的多样性指数并不能很好地帮助理解群落构建和生态系统功能。不同物种对群落构建和生态系统功能所起到的作用类型和贡献也不完全相同,且物种在生态过程中的作用和贡献往往与性状密切相关,因此功能多样性已经成为反映物种群落构建、干扰以及环境因素对群落影响的重要指标。同时,由于亲缘关系相近的物种往往具有相似的性状,系统发育多样性也可以作为功能多样性的一个替代。功能多样性和系统发育多样性各自具有优缺点,但二者均比分类多样性更能揭示群落和生态系统的构建、维持与功能。     

Application of the methods of molecular systematics to classification and identification of bacteria of the genus Bifidobacterium

The methods of molecular systematics currently used in the classification and identification of bifidobacteria are reviewed. The sequencing of the 16S rRNA gene and some other genes considered to be phylogenetic markers is a universal and effective approach to taxonomic characterization of members of the genus Bifidobacterium and to reliable identification of new isolates. Various techniques of obtaining DNA fingerprints (PFGE, RAPD, rep-PCR) are widely used for solving particular problems in identifying bifidobacteria. Bacteria of the genus Bifidobacterium are important organisms in biotechnology and medicine. The research into molecular systematics of bifidobacteria provides a basis not only for the solution of taxonomic problems, but also for monitoring of individual species in the environment and for more detailed study of the genetics and ecology of this group of microorganisms.     

A phylogenetic perspective on species diversity, β‐diversity and biogeography for the microbial world

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high‐altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β‐diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High‐altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β‐diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β‐diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter‐ and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies.     

Systematics,biological knowledge and environmental conservation

Systematics and taxonomy are essential: they respectively elucidate life's history, and organize and verify biological knowledge. This knowledge is built of interrelated concepts which are ultimately accounted for by biological specimens. Such knowledge is essential to decide how much and what biodiversity survives human onslaughts. The preservation of specimens in natural history collections is the essential part of the process which builds and maintains biological knowledge. These collections and the human expertise essential to interpret specimens are the taxonomic resources which maintain accurate and verifiable concepts of biological entities. Present and future knowledge of the complexities and diversity of the biosphere depends on the integrity of taxonomic resources, vet widespread ignorance and disregard for their fundamental value has created a global crisis. Preservation of specimens in natural history collections is chronically neglected and support to study and manage collections is very insufficient. The knowledge held by experienced taxonomists is not being passed on to younger recruits. Neglect of collections has destroyed countless specimens and threatens millions more. These threats to taxonomic resources not only impinge on systematics but all biology: this tragedy jeopardizes the integrity of biological knowledge. The consequences for environmental conservation and therefore humanity are also of dire severity and the biodiversity crisis adds unprecedented weight to the barely recognized crisis in taxonomy and systematics.Where correspondence should     

Phylogeny, classification and taxonomy of European dragonflies and damselflies (Odonata): a review

Although Europe is the cradle of dragonfly systematics and despite great progress in the last 2 decades, many issues in naming its species and understanding their evolutionary history remain unresolved. Given the public interest, conservation importance and scientific relevance of Odonata, it is time that remaining questions on the species?? status, names and affinities are settled. We review the extensive but fragmentary literature on the phylogeny, classification and taxonomy of European Odonata, providing summary phylogenies for well-studied groups and an ecological, biogeographic and evolutionary context where possible. Priorities for further taxonomic, phylogenetic and biogeographic research are listed and discussed. We predict that within a decade the phylogeny of all European species will be known.     

Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?

Recently, dated phylogenies have been increasingly used for ecological studies on community structure and conservation planning. There is, however, a major impediment to a systematic application of phylogenetic methods in ecology: reliable phylogenies with time-calibrated branch lengths are lacking for a large number of taxonomic groups and this condition is likely to continue for a long time. A solution for this problem consists in using undated phylogenies or taxonomic hierarchies as proxies for dated phylogenies. Nonetheless, little is known on the potential loss of information of these approaches compared to studies using dated phylogenies with time-calibrated branch lengths. The aim of this study is to ask how the use of undated phylogenies and taxonomic hierarchies biases a very simple measure of diversity, the mean pairwise phylogenetic distance between community species, compared to the diversity of dated phylogenies derived from the freely available software Phylomatic. This is illustrated with three sets of data on plant species sampled at different scales. Our results show that: (1) surprisingly, the diversity computed from dated phylogenies derived from Phylomatic is more strongly related to the diversity computed from taxonomic hierarchies than to the diversity computed from undated phylogenies, while (2) less surprisingly, the strength of this relationship increases if we consider only angiosperm species.     

The merging of community ecology and phylogenetic biology

The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.     

腐霉属分类性状评价及其中国的种

本文对腐霉属Pythium Pringsheim的研究历史作了简单的回顾,对该属的分类性状和系统进行了论述和评价,最后对中国已发现的55种腐霉,以检索表的方式进行了分类、检索。     

Phylogeny of colletid bees (Hymenoptera: Colletidae) inferred from four nuclear genes

Colletidae comprise approximately 2500 species of bees primarily distributed in the southern continents (only two colletid genera are widely distributed: Colletes and Hylaeus). Previously published studies have failed to resolve phylogenetic relationships on a worldwide basis and this has been a major barrier to the progress of research regarding systematics and evolution of colletid bees. For this study, data from four nuclear gene loci: elongation factor-1alpha (F2 copy), opsin, wingless, and 28S rRNA were analyzed for 122 species of colletid bees, representing all subfamilies and tribes currently recognized; 22 species belonging to three other bee families were used as outgroups. Bayesian, maximum likelihood, and parsimony methods were employed to investigate the phylogenetic relationships within Colletidae and resulted in highly congruent and well-resolved trees. The phylogenetic results show that Colletidae are monophyletic and that all traditionally recognized subfamilies (except Paracolletinae) are also strongly supported as monophyletic. Our phylogenetic hypothesis provides a framework within which broad questions related to the taxonomy, biogeography, morphology, evolution, and ecology of colletid bees can be addressed.