On the foundations of biological systematics

Summary The foundations of systematics lie in ontology, not in subjective epistemology. Systems and their elements should be distinguished from classes; only the latter are constructed from similarities. The term classification should be restricted to ordering into classes; ordering according to systematic relations may be called systematization.The theory of organization levels portrays the real world as a hierarchy of open systems, from energy quanta to ecosystems; followingHartmann these systems as extended in time are considered the primary units of reality. Organization levels should be distinguished from levels of differentiation within each organization level.Certain biological systems, such as species, continue to be misinterpreted as classes, particularly by logicians unfamiliar with modern biological theory. Replacement of Aristotelian definitions of species by polytypic definitions achieves nothing, because species are individual systems which can be defined from an ontological viewpoint only as wholes. The dispute whether classes (universals) are real per se or only in individuals is of no scientific importance; irrespective of which view is taken, any ordering of physical objects into classes constitutes an hypothesis about the structure of the real world.The distinction between essential and contingent characters (attributes) is relevant only to classification. There are no universal rules for evaluating characters for purposes of systematization. Character statements do not form separate linear sequences. The search for unit characters in an absolute sense is futile. All real characters are reducible to relations and are in principle measurable, although there are limitations on the extent to which this can be presently achieved.The concept of the sexual (biological) species is fundamental to theories of biosystematics. Sexual species may be defined as lineages consisting at any given time of series of populations between which genetic exchange can occur and delimited in time by two successive processes of speciation. Linnaean nomenclature needs modification; in its traditional form it is appropriate only to non-truncated hierarchies, whereas real phylogenies (lineages of species) form truncated hierarchies. In consequence of the distinction between systematization and classification it is concluded that, while taxa may be classified into age classes or evolutionary grades, their limits as taxa (systematic units) can be no different in either case. Classification into evolutionary grades remains an imprecise endeavour, since no general measure of evolutionary differentiation has been devised.The spatial and temporal extent of ecosystems, the postulated basic units of ecosystematics, remains unclarified. Nevertheless there are grounds for expecting progress in this field as the energetic relations between organisms become better understood. Biotic communities are not abstract classes, but systematic units. Physiognomic classification should not be confused with systematization of plant communities; both approaches contribute to an understanding of vegetational structure.     

Essentialism and typological thinking in biological systematics

In biological literature, essentialism and typological thinking are believed to be incompatible with evolutionary ideas. At present, the same considerations underlay the claims to abandon the Linnaean hierarchy, or the fundamental classificatory structure rooted in essentialism. This paper suggests to reconsider the negative views of Plato's typology and Aristotle's essentialism following the narrow interpretations that have nothing to do with the classification of living beings. Plato's theory of 'ideas' (or 'forms') is the basis of classificatory theory; it provided such concepts as 'species', 'genus', 'essence', 'dichotomous division' but the development of this theory in the framework of moral and esthetic values could not be beneficial to biology. Aristotle's essentialism is more complicated and exists in two forms; one of these, or classificatory essentialism, is a modification of Plato's typology; another one, or organismal essentialism, represents the shift of 'essence' from the world of relations between objects to the realm of particular things, where the concept of essence lost its basic meaning. It is senseless to look for unreal 'type of an organism' ('essence of a thing') but precisely this kind of essentialism is attractive for biologists and philosophers. Organismal essentialism is the underlying basis of so-called 'individuality thesis' that is used as a weapon against classificatory essentialism. The same thesis is associated with an extensional vision of taxa that also explains the criticism of Linnaean hierarchy, while the latter is the intentional structure and the first tool suggested for the rank coordination of many unequal taxa.     

Molecular systematics and biological diversification of Boletales

Historical patterns of morphological evolution and ecology in the Boletales are largely unresolved but appear to involve extensive convergence. We studied phylogenetic relationships of Boletales based on two datasets. The nuc-lsu dataset is broadly sampled and includes roughly 30% of the described species of Boletales and 51 outgroup taxa across the Hymenomycetes. The multigene dataset (nuc-ssu, nuc-lsu, 5.8S, mt-lsu, atp6) sampled 42 key species of Boletales in a framework of 14 representative Hymenomycetes. The Boletales are strongly supported as monophyletic in our analyses on both datasets with parsimony, maximum likelihood and Bayesian approaches. Six major lineages of Boletales that currently are recognized on subordinal level, Boletineae, Paxillineae, Sclerodermatineae, Suillineae, Tapinellineae, Coniophorineae, received varied support. The backbone of the Boletales was moderately resolved in the analyses with the nuc-lsu dataset, but support was strong for most major groups. Nevertheless, most brown-rot producing forms were placed as a paraphyletic grade at the base of the Boletales. Analyses on the multigene dataset confirm sister group relationships among Boletales, Agaricales and Atheliales. Boletineae and Suillineae received the highest support values; Paxillineae and Sclerodermatineae were not consistently resolved as monophyletic groups. The Coniophorineae were not monophyletic in any analyses. The Tapinellineae consisting of morphologically diverse brown-rotting fungi forms the basal group in the Boletales. We performed ancestral state reconstruction with BayesMultiState, which suggested that the ancestor of the Boletales was a resupinate or polyporoid saprotrophic fungus, producing a brown-rot.     

A model of immunological distances in systematics

While immunological distances among taxa have had wide use in systematics, there has been some doubt about their utility because of the observed non-metricity of such distance matrices. A model is presented here relating observed immunological distance to the actual number of antigenic site differences between taxa. This model accounts for the observed departures of these distances from the metric condition of reciprocity and triangle inequality. Based upon the model, two procedures are suggested for the transformation of immunological distances to metric distances appropriate for phylogenetic analysis. The model implies that the usual scaling adjustments applied to the immunological distance matrix are inappropriate; however, the same transformation applied instead to an initial similarity matrix will solve a scaling problem. Non-reciprocity of the distances is shown to remain a problem independent of this initial scaling problem. It is suggested that further transformation of these re-scaled distances may be obtained through an extension of the ADCLUS procedure developed in psychology. This approach suggests a general strategy for a transformation to metric distances, given a particular model of non-metricity for the data.     

A simple solution of the non-stationary heat transport problem in capillarized biological tissue

The temperature distribution in a perfused biological tissue is calculated for an instaneous point source. An approximate solution, which is simple enough to be evaluated by means of a hand calculator, is derived from the exact solution. It is expressed in terms of the deviation from an average temperature distribution. In an example, using realistic parameters for blood flow and thermal properties of tissue, the approximate solution differs at most 2% from the exact one. Supported by Deutsche Forschungsgemeinschaft.     

A principle of maximum topological similarity in molecular systematics

The paper deals with the problem of phylogenetic reconstruction on the basis of comparative analysis of features. Main attention is paid to comparison and classification of the biopolymer sequences. Different approaches to this task are critically reviewed. The novel principle of construction of tree-like classification schemes permitting subsequent evolutionary analysis is proposed. It concentrates on reconstruction of the tree with a topologic structure that is most close to topologic features, imprinted in the source distance matrix. Realization of this approach was made possible by development of the special formalism, enabling evaluation and comparison of topologic features of distance matrices and trees.     

Logic in systematics

Systematic biologists attempt to infer the taxonomic relationship of one species to another based on the available evidence. Phylogenetic systematists demand that these species relationships reflect evolutionary history (they expect their taxa to be monophyletic). Just exactly how this is to be achieved remains a subject of debate. There are many different kinds of evidence, and many different ways of inferring taxonomic relationships (plus evolutionary history) from them. In this paper, we argue that one such way of inferring species relationships, the hypothetico‐deductive method, proves a bad fit with phylogenetic systematics because it requires an excessively strong assumption of the relationship that obtains between hypotheses of descent and the available evidence.