An Assessment of Cumulative Classification

We present a method for building systematics when new knowledge is continuously accumulated. The resulting classification is self-correcting and improves itself by sorting new items as they are added to the material and studied. The formulation is based on Bayesian predictive probability distributions. A new item that has not yet been classified is assigned to the class that has maximal posterior probability or is made to form a group of its own. Such a cumulative classification depends on the order in which the items are classified. The introduction of an already classified training set considerably improves the repeatability of the method. As a case study we applied the method to a large data set for the Enterobacteriaceae. The resulting classifications corresponded well to the general structure of the prevailing taxonomy of Enterobacteriaceae.     

Confronting Uncertainty in Life Cycle Assessment Used for Decision Support

The aim of this article is to help confront uncertainty in life cycle assessments (LCAs) used for decision support. LCAs offer a quantitative approach to assess environmental effects of products, technologies, and services and are conducted by an LCA practitioner or analyst (AN) to support the decision maker (DM) in making the best possible choice for the environment. At present, some DMs do not trust the LCA to be a reliable decision‐support tool—often because DMs consider the uncertainty of an LCA to be too large. The standard evaluation of uncertainty in LCAs is an ex‐post approach that can be described as a variance simulation based on individual data points used in an LCA. This article develops and proposes a taxonomy for LCAs based on extensive research in the LCA, management, and economic literature. This taxonomy can be used ex ante to support planning and communication between an AN and DM regarding which type of LCA study to employ for the decision context at hand. This taxonomy enables the derivation of an LCA classification matrix to clearly identify and communicate the type of a given LCA. By relating the LCA classification matrix to statistical principles, we can also rank the different types of LCA on an expected inherent uncertainty scale that can be used to confront and address potential uncertainty. However, this article does not attempt to offer a quantitative approach for assessing uncertainty in LCAs used for decision support.     

Causes,kinds and forms

Realist philosophies of science posit a dialectical relation between theoretical, explanatory knowledge and practical, including taxonomic knowledge. This paper examines the dialectic between the theory of descent and empirical, Linnaean taxonomy which is based on a logic of traditional classes. It considers the arguments of David Hull to the effect that many of the practical problems of empirical classification can be resolved by means of an ontology based upon the theory of descent in which species taxa are regarded as individuals rather than as classes or natural kinds.Contra Hull, it is argued that this view is, at best, only partially consistent with taxonomic practice and that it cannot sustain experimental practice which presupposes that species taxa be regarded as natural kinds. An outline is given of a possible alternative dialectic between a field theory of morphogenesis and a rational systematics involving a logic of relations.     

Classification of the genus Humicola traaen I. preliminary reports and investigations

In this first paper several strains ofHumicola are studied, someone perhaps being new species in the artificial sense. An account of their morphological characteristics and their variability is given. Finally the taxonomy of all the genusHumicola and the opportunity to introduce new species differing in morphological characters only are discussed. The Aa. suggest to introduce also in theHyphomycetes new methods of classification not only based on the morphology, but mostly on the physiology, biochemistry and genetics.     

《伯杰氏鉴定细菌学手册》和“伯杰氏国际系统微生物学学会”历史回顾、发展现状及未来展望

2023年是《伯杰氏鉴定细菌学手册》出版一百周年。《伯杰氏鉴定细菌学手册》的诞生，旨在建立起原核微生物分类的明确标准，开启对原核微生物分类学探索的使命。随着生物学、物理学、化学、分子生物学、生物信息学及其相关研究技术的发展及学科交叉，微生物分类学逐渐发展为以系统发育和多相分类为基础、研究微生物物种进化与生物学特性和物种间相关性的学科，因此新发现的微生物物种及其生物学特征信息增加迅猛，该手册在2015年改名为《伯杰氏古菌与细菌系统学手册》，并采用了电子版，使得更新快捷，为原核微生物系统分类学领域注入新的生机和活力。《伯杰氏鉴定细菌学手册》是微生物系统分类学的经典之作，为微生物学者提供微生物物种分类信息的同时，也在引领该领域的学者探索更为广阔的微生物世界。“伯杰氏国际系统微生物学学会”于2009年成立，旨在促进国际微生物领域的学术交流，推动原核微生物系统分类学的发展。本综述全面回顾了《伯杰氏鉴定细菌学手册》和“伯杰氏国际系统微生物学学会”的发展历史及最新进展，并对其未来发展方向进行了展望。     

New methods for the analysis of binarized BIOLOG GN data of Vibrio species: minimization of stochastic complexity and cumulative classification

We apply minimization of stochastic complexity and the closely related method of cumulative classification to analyse the extensively studied BIOLOG GN data of Vibrio spp. Minimization of stochastic complexity provides an objective tool of bacterial taxonomy as it produces classifications that are optimal from the point of view of information theory. We compare the outcome of our results with previously published classifications of the same data set. Our results both confirm earlier detected relationships between species and discover new ones.     

Revised classification of the Cyanidiophyceae based on plastid genome data with descriptions of the Cavernulicolales ord. nov. and Galdieriales ord. nov. (Rhodophyta)

The Cyanidiophyceae, an extremophilic red algal class, is distributed worldwide in extreme environments. Species grow either in acidic hot environments or in dim light conditions (e.g., “cave Cyanidium”). The taxonomy and classification systems are currently based on morphological, eco-physiological, and molecular phylogenetic characters; however, previous phylogenetic results showed hidden diversity of the Cyanidiophyceae and suggested a revision of the classification system. To clarify phylogenetic relationships within this red algal class, we employ a phylogenomic approach based on 15 plastomes (10 new) and 15 mitogenomes (seven new). Our phylogenies show consistent relationships among four lineages (Galdieria, “cave Cyanidium”, Cyanidium, and Cyanidioschyzon lineages). Each lineage is distinguished by organellar genome characteristics. The “cave Cyanidium” lineage is a distinct clade that diverged after the Galdieria clade but within a larger monophyletic clade that included the Cyanidium and Cyanidioschyzon lineages. Because the “cave Cyanidium” lineage is a mesophilic lineage that differs substantially from the other three thermoacidophilic lineages, we describe it as a new order (Cavernulicolales). Based on this evidence, we reclassified the Cyanidiophyceae into four orders: Cyanidiales, Cyanidioschyzonales, Cavernulicolales ord. nov., and Galdieriales ord. nov. The genetic distance among these four orders is comparable to, or greater than, the distances found between other red algal orders and subclasses. Three new genera (Cavernulicola, Gronococcus, Sciadococcus), five new species (Galdieria javensis, Galdieria phlegrea, Galdieria yellowstonensis, Gronococcus sybilensis, Sciadococcus taiwanensis), and a new nomenclatural combination (Cavernulicola chilensis) are proposed.     

Fallacies and false premises—a critical assessment of the arguments for the recognition of paraphyletic taxa in botany

One of the central controversies in contemporary taxonomy and systematics revolves around whether to accept or to reject paraphyletic taxa. The present review is the result of a survey of the ongoing discussion in botany over the past ca. 15 years, and attempts to systematically and critically assess all individual arguments presented for the formal recognition of paraphyletic groups in the classification of life. Where arguments are found to be without merit, rebuttals are presented in the hope of excluding them from further discussion, which can then concentrate on those that have merit. Where arguments are found to be sound, their implications and possible solutions are discussed. The controversy around paraphyletic taxa can be broken down into three questions: whether their rejection or acceptance would lead to a classification better reflecting patterns of biological diversity and evolutionary history; whether their rejection or acceptance would lead to a more practical, useful and predictive classification; and whether their rejection is compatible with ranked and binary Linnaean taxonomy. All available arguments for paraphyletic taxa relating to the first question are demonstrated to be based on various logical fallacies or false premises, especially misunderstandings of the principles of phylogenetic systematics. The issue of usefulness is harder to resolve, as different classifications serve different needs. It is presumably unavoidable but also preferable that phylogenetic and non‐phylogenetic ways of classifying species continue to coexist, serving different needs. Finally, an insistence on monophyletic taxa is found to be incompatible with binary taxonomy under a set of very specific circumstances and assumptions whose presence and accuracy are not universally accepted. © The Willi Hennig Society 2011.     

Reconceptualizing synergism and antagonism among multiple stressors

The potential for complex synergistic or antagonistic interactions between multiple stressors presents one of the largest uncertainties when predicting ecological change but, despite common use of the terms in the scientific literature, a consensus on their operational definition is still lacking. The identification of synergism or antagonism is generally straightforward when stressors operate in the same direction, but if individual stressor effects oppose each other, the definition of synergism is paradoxical because what is synergistic to one stressor's effect direction is antagonistic to the others. In their highly cited meta‐analysis, Crain et al. (Ecology Letters, 11, 2008: 1304) assumed in situations with opposing individual effects that synergy only occurs when the cumulative effect is more negative than the additive sum of the opposing individual effects. We argue against this and propose a new systematic classification based on an additive effects model that combines the magnitude and response direction of the cumulative effect and the interaction effect. A new class of “mitigating synergism” is identified, where cumulative effects are reversed and enhanced. We applied our directional classification to the dataset compiled by Crain et al. (Ecology Letters, 11, 2008: 1304) to determine the prevalence of synergistic, antagonistic, and additive interactions. Compared to their original analysis, we report differences in the representation of interaction classes by interaction type and we document examples of mitigating synergism, highlighting the importance of incorporating individual stressor effect directions in the determination of synergisms and antagonisms. This is particularly pertinent given a general bias in ecology toward investigating and reporting adverse multiple stressor effects (double negative). We emphasize the need for reconsideration by the ecological community of the interpretation of synergism and antagonism in situations where individual stressor effects oppose each other or where cumulative effects are reversed and enhanced.     

Inference in morphological taxonomy using collinear data and small sample sizes: Monogenean sclerites (Platyhelminthes) as a case study

Vignon, M. (2011) Inference in morphological taxonomy using collinear data and small sample sizes: Monogenean sclerites (Platyhelminthes) as a case study. —Zoologica Scripta, 40, 306–316. Taxonomists and evolutionary biologists frequently use a combination of morphological measurements to distinguish between species and investigate local adaptation. However, the entire set of characters often displays various degrees of collinearity. This paper discusses the effect of using collinear data in morphological taxonomy and ways to handle multicollinearity in a classification context, with special consideration for small sample size. In addition, I propose a robust and easy‐to‐use combination of dimension reduction using partial least squares (PLS) with traditional discriminant methods for morphological data. To do this, I investigated morphological variation patterns among four monogenean populations from the Pacific Ocean using the correlated morphological features of the sclerotized attachment organ. The new approach yielded better prediction results (lower classification error rates) than the traditional dimension reduction method based on principle component analysis (PCA) and is also much more robust for small sample size. This emphasizes that PLS may be more efficient than PCA in dealing with correlated data and extracting the most relevant morphological differences among groups.     

Integrative insect taxonomy based on morphology,mitochondrial DNA,and hyperspectral reflectance profiling

Integrative taxonomy is considered a reliable taxonomic approach of closely related and cryptic species by integrating different sources of taxonomic data (genetic, ecological, and morphological characters). In order to infer the boundaries of seven species of the evacanthine leafhopper genus Bundera Distant, 1908 (Hemiptera: Cicadellidae), an integrated analysis based on morphology, mitochondrial DNA, and hyperspectral reflectance profiling (37 spectral bands from 411–870 nm) was conducted. Despite their morphological similarities, the genetic distances of the cytochrome c oxidase subunit I (COI) gene among the tested species are relatively large (5.8–17.3%). The species‐specific divergence of five morphologically similar species (Bundera pellucida and Bundera spp. 1–4) was revealed in mitochondrial DNA data and reflectance profiling. A key to identifying males is provided, and their morphological characters are described. Average reflectance profiles from the dorsal side of specimens were classified based on linear discriminant analysis. Cross‐validation of reflectance‐based classification revealed that the seven species could be distinguished with 91.3% classification accuracy. This study verified the feasibility of using hyperspectral imaging data in insect classification, and our work provides a good example of using integrative taxonomy in studies of closely related and cryptic species. © 2015 The Linnean Society of London     

MORPHOLOGY OF DNA CONTAINING STRUCTURES (NUCLEOIDS) AS A PROSPECTIVE CHARACTER IN CYANOPHYTE TAXONOMY1

DNA containing structures (nucleoids) were visualized by 4′, 6-diamidino-2-phenylindole (DAPI) fluorescent staining in two groups of cyanophytes (59 filamentous oscillatorialean species and 12 coccal Synechococcus-like organisms) to test the possibility of using nucleoid morphology in cyanophyte taxonomy. The morphology of nucleoids (size, shape, and structure) in oscillatorialean species is specific for individual families. The morphology of the nucleoid in Synechococcus-like species agrees from the proposed separation of the genus Cyanothece from Synechococcus. A much different nucleoid morphology in three species of Cyanothece suggests that these species should be separated into a new genus. On the basis of other characters, the species could be returned to the genus Cyanobacterium. My results indicate that the morphology of nucleoids is a valuable character in the classification of the cyanophytes examined; thus, it is a prospective feature that could be used in the taxonomy of other groups of cyanophytes. Additionally, DAPI staining is not a complicated procedure. The new character is easy to see in samples taken from nature, both living and preserved.     

New perspectives in hemiascomycetous yeast taxonomy

DNA sequencing has revolutionized yeast taxonomy. Although initially rDNA sequences proved to be universal and convenient for assigning phylogenetic relationships, it was eventually supplanted by multigene analysis, which provided more discriminating and robust results. This led to a new classification of the major yeast clades, which is still used as a reference today. More recently, the availability of a large number of complete genome sequences has given a new perspective on the molecular taxonomy of yeasts by providing a high number of genes to compare. It also highlighted an unexpected aspect of yeast genome evolution: the existence of interspecific hybrids outside of the industrial Saccharomyces clade. Together with the loss of heterozygosity in interspecific hybrids and a reduced sexuality leading to clonal propagation, this observation obliges us to reexamine the present concept of species. In parallel, the ongoing challenge is to find a universal molecular marker, to improve fast authentication and, if possible, phylogeny of yeasts. The future of yeast taxonomy will involve the sequencing of more genomes, thorough analysis of populations to obtain a good representation of the biodiversity and integration of these data into dedicated databases.     

Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)

Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.     

Advances in the study of the systematics of Actinidia Lindley

Actinidia (Actinidiaceae) is of economic importance for its edible fruits. Traditional taxonomy divided the genus into four sections, Leiocarpae Dunn, Maculatae Dunn, Strigosae Li, and Stellatae Li. However, phylogenetic studies based on morphology and molecular markers have posed challenges to the four-section scheme. It appears that the natural classification of the genus points to the existence of two groups, one comprising Leiocarpae, and the other Maculatae, Strigosae, and Stellatae. Single- or low-copy genes would probably be useful in untangling the perplexity and the reticulate evolution of the genus. However, any phylogenetic studies must be firmly based on sound taxonomy and identification. Population sampling throughout the distribution range of the taxa should be carried out in order to study the variation pattern of the morphology and, ultimately, to clarify the confusion existing in some taxa. A combination of morphometrics and molecular data is highly desirable for resolving the uncertainty in Actinidia taxonomy.     

The annual cycle ofVibrio Parahaemolyticus in chesapeake bay

An ecological study ofVibrio parahaemolyticus was carried out from December 1970 to December 1971 in the Rhode River of Chesapeake Bay. The annual cycle of the organism was elucidated and factors restricting its distribution in the estuary were described, including the association of the organism with zooplankton. Numerical taxonomy was employed for identification and classification ofV. parahaemolyticus and related organisms on the basis of substrate utilization tests. From characteristics recorded forV. parahaemolyticus, it is concluded to be an estuarine organism.     

Taxonomy of phytopathogenic viruses identified in the Russian far east

The work is devoted to a problem of study of the taxonomy phytopathogenic viruses of Far East. The performance to genera, species and strain of viruses identified in Far East region is briefly given. A genus Potyvirus in more detail is described, as the greatest number identified on Far East phytoviruses is included into structure of this genus. In the given article the classification phythopathogenic of Russian Far East is represented, for which basis the classification of viruses of the message of International Committee on the taxonomy of viruses (1995) is taken.