A taxonomic wish-list for community ecology

Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet-based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists.     

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.     

Concepts of rational taxonomy

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.     

Taxonomy of Lactobacilli and Bifidobacteria

Genera Lactobacillus and Bifidobacterium include a large number of species and strains exhibiting important properties in an applied context, especially in the area of food and probiotics. An updated list of species belonging to those two genera, their phylogenetic relationships and other relevant taxonomic information are reviewed in this paper. The conventional nature of taxonomy is explained and some basic concepts and terms will be presented for readers not familiar with this important and fast-evolving area, which importance is often underestimated. The analysis of biodiversity and its cataloguing, i.e. taxonomy, constitute the basis for applications and scientific communication: reliable identification and correct naming of bacterial strains are not only primary aims of taxonomic studies, but also fundamental elements in an applied context, for the tracking of probiotic strains and a non fraudulent labelling of fermented milks and pharmaceutical products containing probiotic microorganisms. A number of resources freely available have been listed and their use is suggested for people concerned with different aspects of taxonomy. Some perspectives in taxonomy have been outlined, in particular considering the role of culture independent analyses to reveal the still unknown and uncultured microorganisms. Finally, the impact of the availability of whole-genome sequences in taxonomy is briefly explained: they have already begun to give insights on bacterial evolution, which will surely have implications on taxonomy, even if the analysis of data for lactic acid bacteria is still limited to few species.     

红菇科可食真菌的若干分类问题

红菇科Russulaceae包含大量全球广泛采食的野生食用菌,同时也有一定数目的毒菌。该科特别是红菇属的分类是大型真菌分类的难点。近年来DNA数据大量应用于红菇科的分类,更新了属的界定和概念,发现了大量新物种,为食用菌和毒菌的识别和鉴定带来了可用的名称。然而,DNA证据并不总是与形态证据吻合,这又为食用菌和毒菌的识别和名称的使用带来了困扰和不便。本文针对乳菇属、多汁乳菇属和红菇属中的重要食用菌类群,回顾了近年来的分类研究进展,分析了研究背后的数据实情和存在的分类问题。认为：在食用菌和毒菌的确定上,依靠物种复合群共有的形态特征更具有可操作性;依据DNA序列进行的劈分式分类和依靠少数样品的特征及DNA序列上的少量差异发表新种的做法可能产生不便于使用的后果;在乳菇属和红菇属中,“BLAST相似度低的即为新种”的分类实践存在错误风险;充分结合历史资料和各个类群的特点,确定物种划分的阈值,才能有望解决红菇科真菌的分类问题。     

Classical and non-classical taxonomy: where does the boundary pass?

Rise of non-classical science during XX century had certain influence upon development of biological taxonomy. Scientific pluralism (especially normative naturalism of Laudan), contrary to positivist and early post-positivist treatments, made taxonomy acknowledged scientific discipline of its own right. The present state of some schools of taxonomy makes it possible to consider them as a part of non-classical science and constituting the non-classical taxonomy. The latter is characterized by the following most important features. Ontological substantiation of both classificatory approaches and particular classifications is requested which invalidates such formal approaches as nominalistic and phenetic (numerical) schools. This substantiation takes a form of content-wise background preferably causal models which include certain axioms and presumptions about taxonomic diversity being studied, together with its causes, and thus define initial conditions of classificatory procedures. From this viewoint, phylogenetic classificatory approach is the most developed part of non-classical taxonomy. The entire taxonomic diversity is structured into several aspects of different levels of generality, each being outlined by a particular consideration aspect. The latter makes personal knowledge constituting an irremovable part of any scientific statement about taxonomic diversity, thus opposition of "objectively" and "subjectively" elaborated classifications becomes vague. Interrelation of various species concepts corresponding to its different consideration aspects is described by uncertainty relation principle. Classificatory algorithms are to be compatible with the conditions of a background model to ensure particular classifications obtained by their means are interpretable within the same model: this is provided by the correspondence principle. Classification is considered as a taxonomic hypothesis, i.e. a conjectural judgement about structure of particular fragment of taxonomic diversity considered within given consideration aspect; wich is to be forwarded and tested according to certain rules. Recognition of different aspects of taxonomic diversity makes it "legal" to elaborate several classifications of equal status, each reflecting a particular aspect of a fixed fragment of that diversity. This viewpoint makes classical ideas of the "ultimate" Natural (whatever might be its definition) or the best reference systems futile. In general, any pretension of an approach to be "the best" in reflecting taxonomic divesrity is contr-productive. Instead, elaboration of particular spectra of complementary classifications becomes the main task of non-classical taxonomy which describes in sum the entire taxonomic diversity. So, not opposition but correct mutual interpretation of such classifications and uniting them into the comprehensive picture of taxonomic diversity become focal points of non-classical taxonomy.     

The relevance of metrical, chromosomal and allozyme variation to the systematics of the genus Mus

The contribution of metrical, karyological and biochemical techniques towards taxonomic understanding is considered with respect to (1) the delimitation of species; (2) the classification of species at generic level; and (3) subspecific variation. All these techniques are useful for the discrimination of sibling species, with metrical discriminants especially important in helping to establish the geographical limits of species, being applicable to museum collections and to fossil material. In classification at the generic level multivariate morphometric analysis is of very limited value, but karyology and allozyme studies can make important contributions provided the majority of relevant species are examined. All techniques are relevant to establishing the major aspects of subspecific variation, for which formal subspecific nomenclature is rarely appropriate. Problems of extrapolation from inadequate samples are just as acute when using these techniques as with more traditional taxonomy based on morphology. Clear presentation of results in the form of data matrices and dendrograms is important in facilitating the integration of data into a useful taxonomic system.     

New proposals for naming lower-ranked taxa within the frame of the International Code of Zoological Nomenclature

The recent multiplication of cladistic hypotheses for many zoological groups poses a challenge to zoological nomenclature following the International Code of Zoological Nomenclature: in order to account for these hypotheses, we will need many more ranks than currently allowed in this system, especially in lower taxonomy (around the ranks genus and species). The current Code allows the use of as many ranks as necessary in the family-series of nomina (except above superfamily), but forbids the use of more than a few ranks in the genus and species-series. It is here argued that this limitation has no theoretical background, does not respect the freedom of taxonomic thoughts or actions, and is harmful to zoological taxonomy in two respects at least: (1) it does not allow to express in detail hypothesized cladistic relationships among taxa at lower taxonomic levels (genus and species); (2) it does not allow to point taxonomically to low-level differentiation between populations of the same species, although this would be useful in some cases for conservation biology purposes. It is here proposed to modify the rules of the Code in order to allow use by taxonomists of an indeterminate number of ranks in all nominal-series. Such an 'expanded nomenclatural system' would be highly flexible and likely to be easily adapted to any new finding or hypothesis regarding cladistic relationships between taxa, at genus and species level and below. This system could be useful for phylogeographic analysis and in conservation biology. In zoological nomenclature, whereas robustness of nomina is necessary, the same does not hold for nomenclatural ranks, as the latter are arbitrary and carry no special biological, evolutionary or other information, except concerning the mutual relationships between taxa in the taxonomic hierarchy. Compared to the Phylocode project, the new system is equally unambiguous within the frame of a given taxonomic frame, but it provides more explicit and informative nomina for non-specialist users, and is more economic in terms of number of nomina needed to account for a given hierarchy. These ideas are exemplified by a comparative study of three possible nomenclatures for the taxonomy recently proposed by Hillis and Wilcox (2005) for American frogs traditionally referred to the genus Rana.     

The Species Concept as a Cognitive Tool for Biological Anthropology

Taxonomy is caught between the search for the “perfect” theory and an elusive biological variability. The lack of major advances in issues related to how “species” and other taxonomic categories are defined suggests that perhaps we should avoid excessively rigid formalism in this regard. The risk is a separation between elegant but useless theories and confusing applications of the taxonomic tools. Communication is one of the main functions of taxonomy, and stability one of the main parameters that taxonomy users should be sensitive to. An excess of stability may generate anachronistic consequences while continuous revisions may make the tool of taxonomy scarcely practical. The current tendency pushes toward more and more fragmentation of biologically valid taxa. While taxonomy specialists enjoy such challenges, many taxonomy users feel a bit nervous and discouraged when trying to use a tool that is constantly changing. Debates over taxonomy would seem particularly unrewarding for fields with limited samples and scarce biological diversity, such as palaeoanthropology. In this context, where the information available is rarely sufficient to supply consistent taxonomical evidence, there are frequently excessive efforts to create debate on species separations. The risk is that we maintain the debate on a purely theoretical level, or else we distrust a reliable use of taxonomy. A compromise (and recommended) choice between these two extremes would be to rely on shared and reasonable interpretations of homogeneous evolutionary units, without diving into fine‐grained issues that will remain, however, unresolved. Taxonomy should be a tool, not the goal, of the evolutionary biologist. Our mind needs discrete and recognizable objects to structure our perception of reality. There is no reason to expect that nature works the same way. Am. J. Primatol. 75:10‐15, 2013. © 2012 Wiley Periodicals, Inc.     

Is coarse taxonomy sufficient for detecting macroinvertebrate patterns in floodplain lakes?

Taxonomic sufficiency (TS) — defined as the minimum taxonomic detail required to discern some ecological pattern of interest — has been used extensively in bioassessment and biodiversity studies as a way of avoiding a portion of the time and monetary costs associated with species diagnoses. The taxonomic sufficiency for detecting species-level patterns among floodplain-lake benthic-invertebrate assemblages remains unexplored. We examined cross-taxonomic-level congruence in assemblage-environment relationships among 23 Chinese floodplain lakes. Our objectives were: (1) to compare the correlation between species richness and density and those at coarser taxonomic resolution; (2) to identify whether assemblage-environment relationships depend on taxonomic scale; and (3) to test whether the proportion of between-lake variability accounted for by environmental variables was independent of taxonomic scale. When taxonomic structure was described using sequentially coarser taxonomic aggregations, species-level patterns of richness and abundance were sequentially obscured (i.e., genus-level taxonomy best preserved patterns in species composition, order- and class-level taxonomy poorly represented species composition). Similar environmental variables were important for distinguishing lake species assemblages and genus assemblages; however, different environmental variables were important for describing family-, order-, and class-level assemblage patters. Moreover, environmental variables accounted for a similar amount of biological variability, regardless of taxonomic scale. Our results suggest genus taxonomy as sufficient for rapid assessments of lake diversity. Numerical dominance of the species- and genus-rich Chironomidae, Tubificidae, and Naididae, may account for the marked loss of information that occurs when lake invertebrates are assigned only to their families. In summary, we describe taxonomic sufficiency to detecting patterns of richness and abundance among subtropical lake macroinvertebrate faunas. This study will interest Chinese benthologists concerned with conservation and bioassessment.     

Cosmopolitan versus cryptic meiofaunal polychaete species: an approach to a molecular taxonomy

Polychaete taxonomy is characterised by a high number of apparently cosmopolitan species. Detection of subtle but diagnostic ultrastructural differences and – in recent years – investigations at the molecular level have revealed that many of these "species" are actually complexes of morphologically identical or almost identical cryptic species. To disregard their existence would lead to an underestimation of global meiofauna diversity and undermine the value of many scientific studies. Therefore, we strongly recommend that they be given formal taxonomic recognition, beyond their published presentation as "operational taxonomic units", "types" or by alphabetic or numerical designators. Since there are neither generally accepted practical procedures nor any established consensus regarding the application of genetic data in taxonomy, we here provide examples of, and suggestions for, the treatment of meiofaunal species that are distinguished exclusively by molecular data, e.g. by genetic distance values, cluster analyses, diagnostic (= autapomorphic) DNA fragments from DNA fingerprinting procedures (RAPD) and/or DNA sequence differences (e.g. of ITS 2). Although no holotype material may be available because the molecular procedures require the preparation of entire specimens, practical taxonomic problems can be overcome and the recommendations of the Zoological Code of Nomenclature satisfied, by adopting the following procedures: (1) deposition of band-patterns of an individual obtained with the primers used to find diagnostic markers; (2) deposition of DNA in ethanol of one syntype individual; (3) deposition of fixed specimens (syntypes) from the locus typicus. Electronic Publication     

淫羊藿属分类学研究:进展、问题与展望

淫羊藿是我国特有且传统的重要药用植物,逐渐步入大宗品种行列。物种的准确鉴定是药效保障和用药安全的前提,为促进其资源的合理开发和利用,该文对淫羊藿属分类学研究进行系统梳理,并对其中存在的问题及存疑类群进行阐述。淫羊藿属共发表68种,中国58种(85.3%),其中57种为特有分布,具有显著的资源优势。淫羊藿属中国类群的分类学研究较为特殊,共26种集中发表于1990s,共31种(53.4%)为国外研究者命名,且绝大多数依据少量栽培个体命名。由于缺乏广泛的形态调查和性状变异分析,导致大量类群的形态描述不准确或不全面,后续20个类群被归并或降级。依据栽培个体命名的类群是补充描述和分类修订的重点。花色、根茎类型、花茎叶的数量及着生方式等性状在中国类群中存在广泛变异。经分类修订后,该属目前包括46种、1亚种和2变种。淫羊藿属中国组类群仍处于活跃进化中,其形态变异复杂,种间关系无法得到解决,为该属分类的最大挑战。但种质资源的研究和利用需要建立在清晰的分类学基础上。未来研究应基于居群调查,完善各物种的形态描述;在此基础上,整合形态变异特征、地理分布格局和基因序列特征,检测自然种间杂交事件,从而揭示物种的...     

The conservation imperative and setting plant taxonomic research priorities in South Africa

For more than a decade it has been internationally recognised that efforts should be made to remedy the concern that taxonomy is an endangered discipline in the grips of rapid decline. In acknowledgement of the perceived continuing marginalisation of taxonomy, the Darwin Declaration recognised the need to enhance the taxonomic capacity of members who are party to the CBD, and beyond. South Africa is one of the most biodiversity rich countries globally, and the unique and rich flora of the country brings with it a significant conservation imperative. Although the country, and southern African subregion for that matter, has a strong history of taxonomic endeavour, stretching back for over a century, it also suffers from a lack of human and other resources to adequately address its taxonomic needs. This inevitably calls for a process of priority-setting to ensure the wise use of available funding. As one example, it is shown that 1,009 indigenous South African plant taxa are regarded as Data Deficient for taxonomic reasons, following the completion of a recent comprehensive Red Listing exercise. Although not the only criterion to be considered when prioritising taxonomic research, efforts focused on these groups represent a significant opportunity for taxonomists to align their work with national priorities.     

Machine learning approach for automatic recognition of tomato-pollinating bees based on their buzzing-sounds

Bee-mediated pollination greatly increases the size and weight of tomato fruits. Therefore, distinguishing between the local set of bees–those that are efficient pollinators–is essential to improve the economic returns for farmers. To achieve this, it is important to know the identity of the visiting bees. Nevertheless, the traditional taxonomic identification of bees is not an easy task, requiring the participation of experts and the use of specialized equipment. Due to these limitations, the development and implementation of new technologies for the automatic recognition of bees become relevant. Hence, we aim to verify the capacity of Machine Learning (ML) algorithms in recognizing the taxonomic identity of visiting bees to tomato flowers based on the characteristics of their buzzing sounds. We compared the performance of the ML algorithms combined with the Mel Frequency Cepstral Coefficients (MFCC) and with classifications based solely on the fundamental frequency, leading to a direct comparison between the two approaches. In fact, some classifiers powered by the MFCC–especially the SVM–achieved better performance compared to the randomized and sound frequency-based trials. Moreover, the buzzing sounds produced during sonication were more relevant for the taxonomic recognition of bee species than analysis based on flight sounds alone. On the other hand, the ML classifiers performed better in recognizing bees genera based on flight sounds. Despite that, the maximum accuracy obtained here (73.39% by SVM) is still low compared to ML standards. Further studies analyzing larger recording samples, and applying unsupervised learning systems may yield better classification performance. Therefore, ML techniques could be used to automate the taxonomic recognition of flower-visiting bees of the cultivated tomato and other buzz-pollinated crops. This would be an interesting option for farmers and other professionals who have no experience in bee taxonomy but are interested in improving crop yields by increasing pollination.     

DNA barcoding should accompany taxonomy - the case of Cerebratulus spp (Nemertea)

Many issues in DNA barcoding need to be solved before it can reach its goal to become a general database for species identification. While species delimitations are more or less well established in several taxa, there are still many groups where this is not the case. Without the proper taxonomic background/knowledge and corroboration with other kinds of data, the DNA barcoding approach may fail to identify species accurately. The classification and taxonomy of phylum Nemertea (nemerteans, ribbon worms) are traditionally based on morphology, but are not corroborated by an increasing amount of genetic data when it comes to classification either into species or into higher taxa. The taxonomy of the phylum needs to be improved before the full potential of DNA barcoding can be utilized to make sure that valid Linnean names accompany the barcode sequences. We illustrate the problematic situation in the phylum Nemertea by a case study from the genus Cerebratulus.     

VirusTaxo: Taxonomic classification of viruses from the genome sequence using k-mer enrichment

Classification of viruses into their taxonomic ranks (e.g., order, family, and genus) provides a framework to organize an abundant population of viruses. Next-generation metagenomic sequencing technologies lead to a rapid increase in generating sequencing data of viruses which require bioinformatics tools to analyze the taxonomy. Many metagenomic taxonomy classifiers have been developed to study microbiomes, but it is particularly challenging to assign the taxonomy of diverse virus sequences and there is a growing need for dedicated methods to be developed that are optimized to classify virus sequences into their taxa. For taxonomic classification of viruses from metagenomic sequences, we developed VirusTaxo using diverse (e.g., 402 DNA and 280 RNA) genera of viruses. VirusTaxo has an average accuracy of 93% at genus level prediction in DNA and RNA viruses. VirusTaxo outperformed existing taxonomic classifiers of viruses where it assigned taxonomy of a larger fraction of metagenomic contigs compared to other methods. Benchmarking of VirusTaxo on a collection of SARS-CoV-2 sequencing libraries and metavirome datasets suggests that VirusTaxo can characterize virus taxonomy from highly diverse contigs and provide a reliable decision on the taxonomy of viruses.