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.     

It is normal for classification approaches to be diverse

It is asserted that the postmodern concept of science, unlike the classical ideal, presumes necessary existence of various classification approaches (schools) in taxonomy, each corresponding to a particular aspect of consideration of the "taxic reality". They are set up by diversity of initial epistemological and ontological backgrounds which fix in a certain way a) fragments of that reality allowable for investigation, and b) allowable methods of exploration of the fragments being fixed. It makes it possible to define a taxonomic school as a unity of the above backgrounds together with consideration aspect delimited by them. Two extreme positions of these backgrounds could be recognized in recent taxonomic thought. One of them follows the scholastic tradition of elaboration of a formal and, hence, universal classificatory method ("new typology", numerical phenetics, pattern cladistics). Another one asserts dependence of classificatory approach on the judgment of the nature of taxic reality (natural philosophy, evolutionary schools of taxonomy). Some arguments are put forward in favor of significant impact of evolutionary thinking onto the theory of modern taxonomy. This impact is manifested by the correspondence principle which makes classificatory algorithms (and hence resulting classifications) depending onto initial assumptions about causes of taxic diversity. It is asserted that criteria of "quality" of both classifications proper and classificatory methods can be correctly formulated within the framework of a particular consideration aspect only. For any group of organisms, several particular classifications are rightful to exist, each corresponding to a particular consideration aspect. These classifications could not be arranged along the "better-worse" scale, as they reflect different fragments of the taxic reality. Their mutual interpretation depends on degree of compatibility of background assumptions and of the tasks being resolved. Extensionally, classifications are compatible as much as they coincide by context and hierarchical structure of included taxa. Intentionally, typological classifications are compatible if included taxa are comparable by their diagnoses, while phylogenetic classifications are compatible if the included taxa are ascribed monophyletic status. A brief consideration is given to the "new phylogenetics" (= "genophyletics") as to a classificatory approach aimed at elaboration of parsimonious phylogenetic hypotheses based on molecular biology data and employing numerical methods of cladistic analysis. This approach is shown to borrows some phenetic ideas and revives scholastic principle of unified classificatory basis. It is supposed that, in a time, biological classification would get escaping from plethora of positivistic ideas (including those being developed by nowaday cladistics) and would assimilate (revive) more actively holistic worldview.     

Some notes on relation between taxon and character in taxonomy (regarding the paper of A.A. Stekol'nikov "A problem of truth...", Zhurnal Obshchei Biologii. 2003.V.64. No 4. P.367-368)

Under brief consideration is the problem of primary or secondary status of the judgments about taxa relative to the judgments about characters in the biological classifications. The following formal definition of taxonomic system (classification) TS is provided: TS = BT[T, C(t), R(t), R(c), R(tc)], where BT is a biological theory constituting content-wise background of the system, T is a set of taxa, C(t) is a set of taxonomic characters, R(t) is a set of relationships among taxa (similarity, kinship, etc.), R(c) is a set of relationships among characters (homology, etc.), and R(tc) is a set of correspondences among taxa and characters. The latter correspondences may be complete or incomplete. At ontological level, there two basical traditions exist in biological systematics regarding R(tc) according to which the biological diversity is patterned either as a set of groups of organisms (taxa) or as a set of their properties (characters). In the first case, taxon is "primary" relative to character (in cladistics); in its opposite, character is "primary" relative to taxon (in scholasticism, classical typology, classical phylogenetics). At epistemological level, incompleteness of the taxon-character correspondence makes classificatory procedure iterative and taxonomic diagnoses context-dependent. The interative nature of classificatory procedure makes the "primary" or "secondary" status of both taxa and characters relative and alternating. This makes it necessary to introduces a kind of uncertainty relation in biological systematics which means impossibility of simultaneous definition of both extensional and intentional parameters of the taxonomic system at each step of classificatory iterations.     

Concepts of taxonomy and concepts of biodiversity: the problem of interaction

There is, or there should be, an interaction between concepts of taxonomy and biodiversity. On the one hand, taxonomy develops some general and particular classificatory paradigms, which own diversity is to be taken into account to understand the nature of variety of natural kinds. On the other hand, analysis of the properties of biodiversity may put forward nontrivial problems for taxonomy that cannot be deduced directly from its own statements. From the point view of taxonomy, it is argued that the current concept of biodiversity based entirely on the species concept is deeply rooted in reductionistic view of nature. It is outdated epistemologically and should be replaced by the modern taxonomic concept of the hierarchical phylogenetic pattern. Operationally, the latter presumes a possibility for each species to be assigned a certain "phylogenetic weight", according to its phylogenetic uniqueness. From the point view of biodiversity, it is argued that the global biodiversity is a three component entity, as it includes, in addition to phylogenetic and ecological hierarchies, a biomorphic hierarchy, as well. This calls for taxonomy to elaborate the general principles of classification of biomorphs.     

HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees

MOTIVATION: Numerous database management systems have been developed for processing various taxonomic data bases on biological classification or phylogenetic information. In this paper, we present an integrated system to deal with interacting classifications and phylogenies concerning particular taxonomic groups. RESULTS: An information-theoretic view (taxon view) has been applied to capture taxonomic concepts as taxonomic data entities. A data model which is suitable for supporting semantically interacting dynamic views of hierarchic classifications and a query method for interacting classifications have been developed. The concept of taxonomic view and the data model can also be expanded to carry phylogenetic information in phylogenetic trees. We have designed a prototype taxonomic database system called HICLAS (HIerarchical CLAssification System) based on the concept of taxon view, and the data models and query methods have been designed and implemented. This system can be effectively used in the taxonomic revisionary process, especially when databases are being constructed by specialists in particular groups, and the system can be used to compare classifications and phylogenetic trees. AVAILABILITY: Freely available at the WWW URL: http://aims.cps.msu.edu/hiclas/ CONTACT: pramanik@cps.msu.edu; lotus@wipm.whcnc.ac.cn     

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     

Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead

Advancing prokaryotic taxonomy constitutes a contemporary academic challenge as well as practical necessity. Genome sequencing has greatly facilitated the evaluation of the current taxonomic system and the development of simpler, more portable and accurate, sequence-based alternatives to substitute for the traditional cumbersome methods. Studies based on the former genome-enabled methods reveal that existing taxonomic designations, including the species level, correspond frequently to a continuum of genetic diversity as opposed to natural groupings (e.g. biological species). Improving such artificial and often ambiguous taxonomic designations, however, will require larger genomic datasets and more carefully designed sampling of natural populations. Only then can the promise for a superior genome-based taxonomy materialize.     

Rationality,Representation, and the Risk Mediating Characteristics of a Karakoram Mountain Farming System

Despite emerging appreciations of contextual knowledge systems, elements of diversity in mountain farming systems are often characterized as irrational and as obstacles to achieving the production goals of 'modernized' agriculture. In this paper, I suggest that these negative representations are produced at least in part as a function of the normalization of a large-scale agriculture as rational. A case-study of a mountain farming system in the Karakoram mountains of northern Pakistan is presented to expose a contextual rationality in relation to risk minimization and to challenge characterizations of this system as 'backward,' unsophisticated and irrational. Specifically I examine the risk mediating characteristics of practices such as field dispersal, delayed planting, intercropping, and polyvarietal planting and conclude that the characteristic feature of this local farming system is a contextually rational diversity. This conflicts with the modernist paradigm of rationality and economic growth subscribed to by a local development agency. Intervention based on ill-informed interpretations of traditional practice have the potential to increase vulnerability of villagers by failing to appreciate the contextual rationality of diversity.     

A cryptic taxon of Galápagos tortoise in conservation peril

As once boldly stated, 'bad taxonomy can kill', highlighting the critical importance of accurate taxonomy for the conservation of endangered taxa. The concept continues to evolve almost 15 years later largely because most legal protections aimed at preserving biological diversity are based on formal taxonomic designations. In this paper we report unrecognized genetic divisions within the giant tortoises of the Galápagos. We found three distinct lineages among populations formerly considered a single taxon on the most populous and accessible island of Santa Cruz; their diagnosability, degree of genetic divergence and phylogenetic placement merit the recognition of at least one new taxon. These results demonstrate the fundamental importance of continuing taxonomic investigations to recognize biological diversity and designate units of conservation, even within long-studied organisms such as Galápagos tortoises, whose evolutionary heritage and contribution to human intellectual history warrant them special attention.     

中国兽类名录(2021版)

中国是全球兽类物种多样性最高的国家之一,掌握我国兽类物种多样性和分类地位是兽类学研究的基础前提,也是科学保护野生种群的前提。为厘清中国兽类的物种数量及分类地位等关键分类学信息,中国动物学会兽类学分会组织国内长期致力于兽类各类群分类的科学研究人员,在总结前人研究的基础上,根据最新的形态学和分子遗传学证据,综合现代兽类分类学家意见,经编委会充分讨论,形成了最新的中国兽类名录,包括我国现阶段兽类12目59科254属686种。该中国兽类名录使用基于系统发生关系的分类系统,并对物种有效性进行了充分慎重的确认和讨论。     

Concepts of species in trypanosomatids

This paper is a commentary on "Species concepts for trypanosomes: from morphological to molecular definitions?" by Wendy Gibson published in this journal [1]. Taxonomy has been traditionally based on expert opinion which is influenced among other factors by the philosophical and educational background of the expert concerned. This has resulted in widely different criteria for species among the trypanosomatids when compared to the actual genetic diversity involved. Gibson's paper presents an example of this within the trypanosome sub-genera. Although attempts have been made to put taxonomy on a more objective basis expert opinion still appears to dominate in the actual classifications in use.     

Species limits in butterflies (Lepidoptera: Nymphalidae): reconciling classical taxonomy with the multispecies coalescent

Species delimitation is at the core of biological sciences. During the last decade, molecular‐based approaches have advanced the field by providing additional sources of evidence to classical, morphology‐based taxonomy. However, taxonomy has not yet fully embraced molecular species delimitation beyond threshold‐based, single‐gene approaches, and taxonomic knowledge is not commonly integrated into multilocus species delimitation models. Here we aim to bridge empirical data (taxonomic and genetic) with recently developed coalescent‐based species delimitation approaches. We use the multispecies coalescent model as implemented in two Bayesian methods (dissect/stacey and bp&p ) to infer species hypotheses. In both cases, we account for phylogenetic uncertainty (by not using any guide tree) and taxonomic uncertainty (by measuring the impact of using a priori taxonomic assignments to specimens). We focus on an entire Neotropical tribe of butterflies, the Haeterini (Nymphalidae: Satyrinae). We contrast divergent taxonomic opinion – splitting, lumping and misclassifying species – in the light of different phenotypic classifications proposed to date. Our results provide a solid background for the recognition of 22 species. The synergistic approach presented here overcomes limitations in both traditional taxonomy (e.g. by recognizing cryptic species) and molecular‐based methods (e.g. by recognizing structured populations, and not raising them to species). Our framework provides a step forward towards standardization and increasing reproducibility of species delimitations.     

An exercise in rational taxonomy

The quest for a rational taxonomy of living forms began in the 17th century. Since the general acceptance of Darwin's theory of descent with modification, however, students of morphology became preoccupied with a systematics based on the genealogy of groups; and the rise of molecular phylogenies in recent years results in a further decline in the science of morphology. Reconstructing phylogenies by itself brings us no closer to the goal of rational taxonomy, which is to uncover the natural order inherent in the forms of living things. It is proposed that the rational taxonomy of forms should be derived from a study of development, much as von Baer had envisaged. To illustrate the method, a set of segmentation abnormalities in Drosophila larvae (previously exposed to either vapour) is considered, which can be individually classified as distinct disturbances in the process responsible for establishing normal segmental pattern. The process consists of a hierarchy of four successive bifurcations dividing the embryo's body first into two parts, then four, eight, and finally 16 subdivisions or segments. This gives rise to a taxonomic map of all possible transformations which contains the "phylogeny" of the actual forms and provides a natural system for classifying them. Attempts to recover the "true" phylogeny by various numerical methods are summarized and their implications for the validity of the basic assumptions of contemporary systematics discussed.     

Classification of organisms and structuralism in biology

Structuralism in biology is the oldest trend oriented to the search for natural "laws of forms" comparable with laws of growth of crystal, was revived at the end of 20th century on the basis of structuralist thought in socio-humanitarian sciences. The development of principal ideas of the linguistic structuralism in some aspects is similar to that of biological systematics, especially concerning the relationships between "system" and "evolution". However, apart from this general similarity, biological structuralism is strongly focused on familiar problems of the origin of diversity in nature. In their striving for the renovation of existing views, biological structuralists oppose the neo-darwinism emphasizing the existence of "law of forms", that are independent on heredity and genetic "determinism". The trend to develop so-called "rational taxonomy" is also characteristic of biological structuralism but this attempt failed being connected neither with Darwin's historicism nor with Plato's typology.     

Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora

Background

Inappropriate taxon definitions may have severe consequences in many areas. For instance, biologically sensible species delimitation of plant pathogens is crucial for measures such as plant protection or biological control and for comparative studies involving model organisms. However, delimiting species is challenging in the case of organisms for which often only molecular data are available, such as prokaryotes, fungi, and many unicellular eukaryotes. Even in the case of organisms with well-established morphological characteristics, molecular taxonomy is often necessary to emend current taxonomic concepts and to analyze DNA sequences directly sampled from the environment. Typically, for this purpose clustering approaches to delineate molecular operational taxonomic units have been applied using arbitrary choices regarding the distance threshold values, and the clustering algorithms.

Methodology

Here, we report on a clustering optimization method to establish a molecular taxonomy of Peronospora based on ITS nrDNA sequences. Peronospora is the largest genus within the downy mildews, which are obligate parasites of higher plants, and includes various economically important pathogens. The method determines the distance function and clustering setting that result in an optimal agreement with selected reference data. Optimization was based on both taxonomy-based and host-based reference information, yielding the same outcome. Resampling and permutation methods indicate that the method is robust regarding taxon sampling and errors in the reference data. Tests with newly obtained ITS sequences demonstrate the use of the re-classified dataset in molecular identification of downy mildews.

Conclusions

A corrected taxonomy is provided for all Peronospora ITS sequences contained in public databases. Clustering optimization appears to be broadly applicable in automated, sequence-based taxonomy. The method connects traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both traditional species concepts and genetic divergence.