THE QUANTIFICATION OF SOME PLANT-TAXA CIRCUMSCRIPTIONS

Intrataxon variability is estimated by the technique of numerical taxonomy. Taxa which had been determined by orthodox taxonomic methods are subjected to analyses by numerical phenetics. Comparisons are made of the amounts of cohesion among the members of different taxa in the Bromeliaceae at several taxonomic levels by computing the degrees of similarities between members of the same taxon and of different taxa. Results of these comparisons with several taxa reveal that the variability of a taxon in terms of phenetic distance computed with a large number of characters does not necessarily agree with a subjective appraisal of variability. The method facilitated difficult taxonomic determinations and provided an estimate of the relative evolutionary ages of different taxonomic groups.     

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.     

DNA barcodes as a tool in biodiversity research: testing pre-existing taxonomic hypotheses in Delphic Apollo butterflies (Lepidoptera,Papilionidae)

Numerous studies have demonstrated that DNA barcoding is an effective tool for detecting DNA clusters, which can be viewed as operational taxonomic units (OTUs), useful for biodiversity research. Frequently, the OTUs in these studies remained unnamed, not connected with pre-existing taxonomic hypotheses, and thus did not really contribute to feasible estimation of species number and adjustment of species boundaries. For the majority of organisms, taxonomy is very complicated with numerous, often contradictory interpretations of the same characters, which may result in several competing checklists using different specific and subspecific names to describe the same sets of populations. The highly species-rich genus Parnassius (Lepidoptera: Papilionidae) is but one example, such as several mutually exclusive taxonomic systems have been suggested to describe the phenotypic diversity found among its populations. Here we provide an explicit flow chart describing how the DNA barcodes can be combined with the existing knowledge of morphology-based taxonomy and geography (sympatry versus allopatry) of the studied populations in order to support, reject or modify the pre-existing taxonomic hypotheses. We then apply this flow chart to reorganize the taxa within the Parnassius delphius species group, solving long-standing taxonomic problems.     

Coordinating the traditional and modern approaches in the systematics of insects

The problem of coordinating the traditional and modern approaches to systematics is ever-lasting due to the continuous development and enrichment of our knowledge of biodiversity, means of analysis, and concepts. Comparative morphology was and still is the cornerstone of studies of insect taxonomy. It gives the most extensive and diverse information on the organisms studied, particularly when it is supported by the data on embryology and functional morphology as well as by analysis of adaptive significance of morphological characters. The limitations of this approach are often related to the presence of homoplasies, reversions, etc. Comparative paleontology is the only approach providing direct evidence of the historical succession of taxa and their characters. However, this approach is fully applicable only to some groups due to the specific features of their morphology and taphonomy. All the modern approaches (molecular, cytogenetic, etc.) are very informative but also have their own limitations; they should not be contrasted with the traditional approaches and certainly should not replace them. The traditional approaches do not become obsolete; it is only their comparative importance in the set of taxonomic tools that may be reevaluated. No single approach can be considered universal for an unambiguous reconstruction of phylogeny and substantiation of the natural system of taxa. Each approach has its own advantages and limitations, and only combined use of different approaches allows a broader range of the problems to be solved. Different approaches may prevail in the studies of different groups of insects and at different levels of taxonomic hierarchy. The intuition of the taxonomist, which is so often criticized by the followers of “objective” systematics, is based on taxonomic experience and scope of knowledge of a particular taxon. It does not imply a subjective bias, but allows the taxonomist to choose the instruments adequate to a particular case.     

The PhyloCode: a critical discussion of its theoretical foundation

The definition of taxon names as formalized by the PhyloCode is based on Kripke's thesis of "rigid designation" that applies to Millian proper names. Accepting the thesis of "rigid designation" into systematics in turn is based on the thesis that species, and taxa, are individuals. These largely semantic and metaphysical issues are here contrasted with an epistemological approach to taxonomy. It is shown that the thesis of "rigid designation" if deployed in taxonomy introduces a new essentialism into systematics, which is exactly what the PhyloCode was designed to avoid. Rigidly designating names are not supposed to change their meaning, but if the shifting constitution of a clade is thought to cause a shift of meaning of the taxon name, then the taxon name is not a "rigid designator". Phylogenetic nomenclature either fails to preserve the stability of meaning of taxon names that it propagates, or it is rendered inconsistent with its own philosophical background. The alternative explored here is to conceptualize taxa as natural kinds, and to replace the analytic definition of taxon names by their explanatory definition. Such conceptualization of taxa allows taxon names to better track the results of ongoing empirical research. The semantic as well as epistemic gain is that if taxon names are associated with natural kind terms instead of being proper names, the composition of the taxon will naturally determine the meaning of its name.
© The Willi Hennig Society 2006.     

Definitions in phylogenetic taxonomy: critique and rationale

A general rationale for the formulation and placement of taxonomic definitions in phylogenetic taxonomy is proposed, and commonly used terms such as "crown taxon" or "node-based definition" are more precisely defined. In the formulation of phylogenetic definitions, nested reference taxa stabilize taxonomic content. A definitional configuration termed a node-stem triplet also stabilizes the relationship between the trio of taxa at a branchpoint, in the face of local change in phylogenetic relationships or addition/deletion of taxa. Crown-total taxonomies use survivorship as a criterion for placement of node-stem triplets within a taxonomic hierarchy. Diversity, morphology, and tradition also constitute heuristic criteria for placement of node-stem triplets.     

Molecular phylogeny of the Neoplecostominae and Hypoptopomatinae (Siluriformes: Loricariidae) using multiple genes

Phasmids are remarkable mimics of twigs, sticks, and leaves. This extreme adaptation for crypsis can easily lead to the convergent evolution of morphology, making it difficult to establish a taxonomic system of phasmids. Accordingly, there are multiple phylogenetic hypotheses that conflict with each other. Phylogenetic arrangements suggested by molecular data disagree with the morphology-based taxonomy in some instances. We collected 13 phasmatodean species, sequenced their mitochondrial genomes, and recovered their molecular phylogeny. Our analyses did not support the monophyly of Areolatae or Anareolatae, two major infraorders of Phasmatodea. The position of Neohirasea was also quite different from the conventional taxonomic systems, thus challenging the previously assumed monophyly of the subfamily Lonchodinae. The enigmatic taxon, Timema, was shown to be distantly related to other phasmatodeans.     

Investigation of serological determinants from single storage plant proteins

The main storage proteins of the angiosperms provide valuable characters for taxonomic research. By comparing the reactivity of one specific protein in different taxa (mainly Ranunculaceae). determinants or determinant groups can be discriminated. Their number is a function of the number of the reference or anti-systems and of the number of taxa compared. These serological determinants prove a posteriori to be good characters and most useful in taxonomy. Their systematic range extends from one genus to the whole of the angiosperms. The resolving power is best between genera within a family. Using such a single protein system, it is possible to co-ordinate the determinants of the taxa investigated and to map their distribution; this is an advantage over the multi-protein systems commonly used. By serological comparison, it should be possible to establish the homology of the main storage globulins throughout the angiosperms.     

Least-inclusive taxonomic unit: a new taxonomic concept for biology

Phylogenetic taxonomy has been introduced as a replacement for the Linnaean system. It differs from traditional nomenclature in defining taxon names with reference to phylogenetic trees and in not employing ranks for supraspecific taxa. However, 'species' are currently kept distinct. Within a system of phylogenetic taxonomy we believe that taxon names should refer to monophyletic groups only and that species should not be recognized as taxa. To distinguish the smallest identified taxa, we here introduce the least-inclusive taxonomic unit (LITU), which are differentiated from more inclusive taxa by initial lower-case letters. LITUs imply nothing absolute about inclusiveness, only that subdivisions are not presently recognized.     

A botanical critique of cladism

Clade versus grade is an old question in taxonomy, going back as far as Darwin himself. Taxonomists have long believed that both must be taken into account in the formation of a general-purpose system. Recently clade has been elevated to a position of total dominance by a group of taxonomists who take their inspiration from Willi Hennig. Mayr has dubbed this approach cladism, and its exponents cladists. Cladistic theory is being vigorously developed and propounded by Hennig’s disputatious disciples, and much of the present-day theory would scarcely be recognized by the founder. I here address myself to what I consider the core features of present-day cladism. The essential distinctive feature of cladism, and its fatal flaw, is that a group is considered to be monophyletic, and thus taxonomically acceptable, only if it includesall the descendants from the most recent common ancestor. The traditional taxonomic view has been that a group can still be considered monophyletic (and thus taxonomically acceptable) after some of its more divergent branches have been trimmed off. This simple and seemingly innocuous difference has profound consequences to the taxonomic system. In Hennigian classification, organisms are ranked entirely on the basis of recency of common descent, that is, on the basis of the sequence of dichotomies in the inferred phylogeny. Theamount of divergence scarcely enters into the picture. This procedure represents an effort to capture taxonomy for a narrowly limited special purpose, at the expense of the important and necessary function of providing a general-purpose system that can be used by all who are concerned with similarities and differences among organisms. The first corollary of the Hennigian concept of phylogenetic taxonomy is that no existing taxon can be ancestral to any other existing taxon. The descendant must be included in the same taxon as its ancestor. At the level of species this is palpably false. The ancestral species often continues to exist for an indefinite time after giving rise to one or more descendants. At the higher taxonomic levels adherence to the principle often requires excessive lumping or excessive splitting to avoid paraphyletic groups (i.e., groups that do not include all of their own descendants), and it forbids the taxonomic recognition of many conceptually useful groups. Neither the prokaryotes nor the dicotyledons form a cladistically acceptable taxon, since both are paraphyletic. The prokaryotes are putatively ancestral to the eukaryotes, and the dicotyledons are putatively ancestral to the monocotyledons. Many other traditional and readily recognizable taxa would have to be abandoned, without being replaced by conceptually useful groups. Fossils present a special problem, because the whole concept of cladistic classification depends on the absence of taxa at the branch points of the cladogram. Presumably all of these branch points were at some time in the past represented by actual taxa, which under cladistic theory can neither be assigned to one of their descendants nor treated as paraphyletic taxa. The difficulty is mitigated somewhat by the gaps in the known fossil record. Once it is admitted that paraphyletic as well as holophyletic groups are taxonomically acceptable, there is much value in cladistic methodology. Formal outgroup comparison for the establisment of polarity, and the emphasis on synapomorphies in the construction of a cladogram can both be usefully incorporated into taxonomic theory and practice. These require no revolution in taxonomic thought. There are unresolved problems, however, in how to gather and manipulate the data, and how to interpret the cladogram produced by computers. In any complex group, the computer may produce several or many cladograms of equal or nearly equal parsimony. This is particularly true in angiosperms, among which the extensive evolutionary parallelism casts doubt on the importance of parsimony and may lead to the production of hundreds of such cladograms for a single group. Despite the claims of objectivity and repeatability in cladistic taxonomy, the necessity for some subjective decisions remains. The Wagner groundplan-divergence method has most of the advantages of formal cladism without the most important disadvantages. Wagner accepts paraphyletic taxa in principle, and he casts a wider net for data bearing on the polarity of characters. In complex groups consisting of many taxa, however, both methods retain a strong subjective component in the computer manipulation and in the degree of reliance on absolute parsimony.     

Molecules and beyond: assessing the distinctness of the Great Lakes wolf

The dog family, Canidae, is a widely distributed group of species that have evolved and radiated relatively recently into 16 genera and 36 recognized species ( Nowak 1999 ). Specific taxonomic designations for some canid taxa can be unclear due to frequent interspecific hybridization among species in both historical and contemporary times, and our imperfect molecular genetic approaches for determining among a series of hypotheses regarding hybridization and evolution. In this issue of Molecular Ecology , Koblmüller et al . tackle the difficult topic of Great Lakes wolf taxonomy and present data that suggest this taxon is currently genetically distinct despite a long history of human persecution and hybridization with related taxa.     

Incongruence between cladistic and taxonomic systems

Cladistic and taxonomic treatments of the same plant group usually exhibit a mixture of congruences and incongruences. The question arises in the case of the incongruences as to which version is right and which is wrong. Many cladists believe that cladistics is a superior approach and gives the best results. There are several conceptual and methodological differences between cladistics and taxonomy that cause incongruence. One important conceptual difference is the use of different criteria for grouping: order of branching vs. similarity and difference (clades vs. taxa). Another is the policy regarding paraphyletic groups: to ban them in cladistics but ignore the ban in taxonomy. These two differences automatically lead to some incongruences. One approach is not right and the other wrong; each is operating by its own standards. However, when cladists apply the paraphyly rule to a taxonomic system and conclude that it needs revision to eliminate paraphyly, as cladists often do, they are judging the taxonomic system by a wrong standard. Several differences between the two schools in the use and handling of characters can also cause incongruence. First consider phenetic characters. Taxonomy uses a very wide range of these, whereas phenetic cladistics sets restrictions on the selection of characters, which deprive it of potentially useful evidence. Taxonomic systems generally rest on a broader empirical foundation than phenetic cladistic systems. Next, consider molecular cladistics, which is the leader in the use of DNA evidence. Two sources of incongruence between molecular cladistics and taxonomic systems can come into play here. First, the molecular evidence used in cladistics comes mainly from cytoplasmic organelles, whereas taxonomic systems are based on characters that are determined mainly by the chromosomal genome. More generally, the database in a molecular cladogram is, in itself, too narrow to serve as a foundation for an organismic classification. In cases of incongruence, the molecular evidence can be a reliable indicator of taxonomic relationships sometimes, misleading other times, and may afford no clear basis for a systematic decision. In this situation, it is helpful, indeed necessary, to integrate the molecular evidence with the phenetic evidence and bring more characters to bear on the question.     

What's in a (biological) name? The wrath of Lord Rutherford

Names in taxonomy have seven different and important properties, some due to their existence in the context of classifications. Names confer or facilitate individuation, information storage and retrieval, and set theories of relationships, explanatory power, testable predictions, conceptual power, and language. No other way of naming in science is so powerful. And this is possible because taxonomic naming is done with full consideration of the theoretical specification of empirical data (characters) and their correspondence among taxa via homology statements. Since Darwin and Hennig, sets of homologous characters distributed among taxa allow precise hypotheses of a genealogical relationship, and this relationship is reflected in the way naming results in a classification.     

Evolutionary theory and systematics: relationships between process and patterns

The relevance of the Modern Evolutionary Synthesis to the foundations of taxonomy (the construction of groups, both taxa and phyla) is reexamined. The nondimensional biological species concept, and not the multidimensional, taxonomic, species notion which is based on it, represents a culmination of an evolutionary understanding. It demonstrates how established evolutionary mechanisms acting on populations of sexually reproducing organisms provide the testable ontological basis of the species category. We question the ontology and epistemology of the phylogenetic or evolutionary species concept, and find it to be a fundamentally untenable one. We argue that at best, the phylogenetic species is a taxonomic species notion which is not a theoretical concept, and therefore should not serve as foundation for taxonomic theory in general, phylogenetics, and macroevolutionary reconstruction in particular. Although both evolutionary systematists and cladists are phylogeneticists, the reconstruction of the history of life is fundamentally different in these two approaches. We maintain that all method, including taxonomic ones, must fall out of well corroborated theory. In the case of taxonomic methodology the theoretical base must be evolutionary. The axiomatic assumptions that all phena, living and fossil, must be holophyletic taxa (species, and above), resulting from splitting events, and subsequently that evaluation of evolutionary change must be based on a taxic perspective codified by the Hennig ian taxonomic species notion, are not testable premises. We discuss the relationship between some biologically, and therefore taxonomically, significant patterns in nature, and the process dependence of these patterns. Process-free establishment of deductively tested “genealogies” is a contradiction in terms; it is impossible to “recover” phylogenetic patterns without the investment of causal and processual explanations of characters to establish well tested taxonomic properties of these (such as homologies, apomorphies, synapomorphies, or transformation series). Phylogenies of either characters or of taxa are historical-narrative explanations (H-N Es), based on both inductively formulated hypotheses and tested against objective, empirical evidence. We further discuss why construction of a “genealogy”, the alleged framework for “evolutionary reconstruction”, based on a taxic, cladistic outgroup comparison and a posteriori weighting of characters is circular. We define how the procedure called null-group comparison leads to the noncircular testing of the taxonomic properties of characters against which the group phylogenies must be tested. This is the only valid rooting procedure for either character or taxon evolution. While the Hennig -principle is obviously a sound deduction from the theory of descent, cladistic reconstruction of evolutionary history itself lacks a valid methodology for testing transformation hypotheses of both characters and species. We discuss why the paleontological method is part of comparative biology with a critical time dimension ana why we believe that an “ontogenetic method” is not valid. In our view, a merger of exclusive (causal and interactive, but best described as levels of organization) and inclusive (classificatory) hierarchies has not been accomplished by a taxic scheme of evolution advocated by some. Transformational change by its very nature is not classifiable in an inclusive hierarchy, and therefore no classification can fully reflect the causal and interactive chains of events constituting phylogeny, without ignoring and contradicting large areas of corroborated evolutionary theory. Attempts to equate progressive evolutionary change with taxic schemes by Haeckel were fundamentally flawed. His ideas found 19th century expression in a taxic perception of the evolutionary process (“phylogenesis”), a merger of typology, hierarchic and taxic notions of progress, all rooted in an ontogenetic view of phylogeny. The modern schemes of genealogical hierarchies, based on punctuation and a notion of “species” individuality, have yet to demonstrate that they hold promise beyond the Haeckel ian view of progressive evolution.     

Assessing the taxonomic resolution of southern African trapdoor spiders (Araneae: Ctenizidae; Cyrtaucheniidae; Idiopidae) and implications for their conservation

Taxonomic classifications simultaneously represent hypotheses of taxon identity and relationships to taxonomists, and real, unchanging entities to users of taxonomic information. Taxonomic changes, while representing scientific progress, can be a source of frustration for users. A method for assessing confidence in the taxonomy of a group of organisms would assist users of the taxonomy. A method is presented for determining the degree of development of a taxonomy, a concept termed ‘taxonomic resolution’. The method was applied to six groups of southern African mygalomorph trapdoor spiders, namely Stasimopus Simon 1892 (Ctenizidae Thorell 1877), Ancylotrypa Simon 1889 (Cyrtaucheniidae Simon 1889), four genera of Idiopidae Simon 1889 assessed as a single group, Galeosoma Purcell 1903, the families Migidae Simon 1889 and Microstigmatidae Roewer 1942, and the burrowing scorpion genus Opistophthalmus C. L. Koch 1837 (Scorpionidae Latreille 1802). The method was based on the assumption that species delimitation in a group of organisms, the taxonomy of which is based on morphological characters, depends on whether the sample of material examined is adequate for assessing variation in those characters. Five assessment criteria were identified and scored for a group of species using the taxonomic literature. Estimates of the number of species remaining to be discovered and described in each group were also included in the assessment. The results obtained for the trapdoor spiders ranged from 15 to 29%, indicating a potentially significant degree of uncertainty in the taxonomy. Results for Migidae and Microstigmatidae were 51 and 78% respectively, whereas the result for Opistophthalmus was 93%. The applied value of a measure of taxonomic resolution, the limitations of the method, and a strategy for developing a more generally applicable method are discussed.     

昆虫细胞分类学的基本问题及染色体系统发育的重建方法

本文非昆虫细胞遗传学及细胞分类学原理与技术的全面评述;而是从细胞遗传学特征（或称染色体特征）在混虫分类学中的应用入手,重点提出与分析了昆虫细胞分类学中的种类鉴定,研究取材,染色体多态现象,多倍体及核型进化方向等基本问题,并着重总结了目前国际上细胞水平染色体数据的处理方法,即传统法,倒位法,数值法与支序法;最后,作者指出了正确看待细胞分类学重要性的态度。