Systematics as science: A response to Cronquist

Our reply to the commentary on cladistics presented by Cronquist (1987) is aimed at four issues:

1. the application of scientific principles in systematics;
2. the recognition that the analysis of pattern is a vital precursor to any consideration of evolutionary process. A priori judgements of evolutionary process are unnecessary for the generation of informative systematic hypotheses which are chosen for their ability to explain the patterns of character distributions rather than for compatibility with any particular preconceived ideas about evolution;
3. that phenetic concepts such as overall similarity, grades, gaps, and degree of divergence, if included in methods of phylogenetic inference, will give erroneous results. Paraphyletic and polyphyletic groups must, consequently, be rejected from systematics since they have no rational empirical basis for recognition;
4. the fact that many of the problems of phylogenetic analysis attributed by Cronquist to cladistics are common to all systematic methods but that these can be dealt with by the application of such principles as parsimony, synapomorphy, and strict monophyly.

     

Das Triplett aus zwei Monophyla und einem Paraphylum als Baustein des phylogenetischen Systems

The triplet consisting of two monophyletic taxa and one paraphyletic taxon as constructive element of the phylogenetic system Evolution has produced very many novelties (apomorphies). Most of them are small and relatively inconstant, these are more or less indicative of the phylogenetic relationships between closely related species. They cannot be the constitutive character of a supraspecific taxon that exists since a long time and comprises many diversified species. Such a taxon of higher rank can only be characterized by an improbable, rare novelty that has developed only once and has been preserved in all descendent species. Two consecutive apomorphies of this persistent type (‘fixed apomorphies’) characterize three supraspecific taxa, the triplet “A”, “B” and “A minus B” (Fig. 1). The group “A minus B” is rejected in Hennig's theory because it is ‘paraphyletic’, but it is not an artefact created by the systematicist. It is an inevitable mathematical consequence of the differentiatison of the group “B” within the group “A”. Being the result of a subtraction, it is necessarily associated with the two monophyletic partners in the triplet, as it is delimited on one side by the synapomorphy of the group “A”, of which it is a part, and on the other side by the autapomorphy of the separate group “B”. Traditional classifications often include paraphyletic groupings that are inconsistent with phylogenetics, e. g. the Reptilia and the Apterygota. The fault in such cases is that these groups are extended beyond the limits of a triplet and cover more than a single interval between consecutive monophyletic taxa. Paraphyletic groups are admitted in the phylogenetic system only for bridging the gaps in our cladistic information. According to HENNIG'S theory, all supraspecific taxa should be arranged two by two as sister-groups originating from one ancestral species and comprising all descendents of that species. The fixed evolutionary novelties which characterize higher supraspecific taxa are, however, rare and scattered. It is highly improbable that they have developed in sister species, therefore the taxa marked by them cannot be sister-groups (except in very rare cases). In HENNIG'S earlier papers, e. g. in his system of Lepidoptera (1953: 46–49), the alleged ‘sister-groups' are, in reality, the groups “B” and “A minus B” of a triplet (see Fig. 2). In his revised concept (1957 and later), two autapomorphic groups which are most closely related in the recent fauna (“B” and “C” in Fig. 3) are called ‘sister-groups’. But these have originated independently from different ancestors in a plesiomorphic complex of extinct species and are more closely related to parts of this complex than to each other. True sister-groups (“Bx” and “Cx” in Fig. 4) would be formed if these related plesiomorphic species were included, but this extension of the ’backward‘ border of the taxon is not justified by synapomorphy (in the terms of logic, it is a ’metabasis‘), and it would make the classification of fossil species impossible, unless these show at least one synapomorphy with either “B” or “C”. In the system of the recent fauna the sister-groups are identical with the autapomorphic groups, because the plesiomorphic species are extinct. The natural system based on synapomorphies and autapomorphies is the triplet-system as outlined in Figure 6. It is not a new type of classification, but its theoretical foundation was missing, and precise instructions were needed for its use in phylogenetics. The information obtained by HENNIG'S method is entirely preserved in this system and can be retrieved from it, and both recent and extinct species can be classified together. The disadvantage of the triplet-system is that it contains twice as many taxa as HENNIG'S classification. This complexity will limit its use in the practice of taxonomy, but it may be simplified by transforming the system into a sequence of paraphyletic taxa terminating in a single monophylum.     

The recognition of ancestors

The recognition of ancestors is problematic using cladistic logic alone because monophyletic groups (clades) are defined by shared derived characters (synapomorphies) which their ancestors must have lacked. Nevertheless, ancestors possess three key attributes. They belong within a larger, paraphyletic group. They will be morphologically most similar to their immediate descendants, and they evolved before any and all of their descendants. Recognition of ancestors requires both morphological and stratigraphic data and, in practice, the task is to reduce the size of the paraphyletic group within which the ancestor must lie. All ancestor‐descendant relationships are phylogenetic hypotheses. Despite the legendary incompleteness of the fossil record, testing the validity of available data is far more difficult for character analysis than for stratigraphy.     

Trilobite monophyly revisited

Fortey's and Whittington's recent refutation of Lauterbach's hypothesis of a paraphyletic Trilobita is supported. However, much of the character evidence raised by Fortey and Whittington to substantiate the monophyly of the Trilobita (including, inter alia, "Olenellinae”; and Agnostoidea) is ambiguous. Of seven proposed synapomorphies, only one (dorsal cuticle calcification) may be maintained at that node after testing within a cladistic framework. The other six characters are either constrained by calcification or define nodes up or down the cladogram. As positioned by Fortey's and Whittington's characters, Agnostoidea could be regarded either as the most primitive trilobites, or as being outside that clade. Lauterbach's support for an “olenelline"‐chelicerate clade is found to include interdependent characters which are reduced here to two testable derived similarities. Only one of these may conform to general criteria indicative of homology, such as detailed similarity and topology. It is, however, rejected on the basis of parsimony. We emphasize that resolution of the chelicerate‐"olenelline"‐trilobite three‐taxon problem must be based on recognition of homologies among each of these taxa. Nectaspida are excluded from Trilobita as defined by cuticle calcification, but as ingroup “Arachnata”; (sensu Lauterbach) they are important for determining character generality in this clade.     

Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently. Herein these shortcomings are addressed by cladistically analyzing 117 phenotypic characters for 49 tunicate species comprising all higher tunicate taxa, and five craniate and cephalochordate outgroup species. In addition, a combined analysis of the phenotypic characters with 18S rDNA-sequence data is performed in 32 OTUs. The analysis of the combined data is congruent with published molecular analyses. Successively up-weighting phenotypic characters indicates that phenotypic data contribute disproportionally more to the resulting phylogenetic hypothesis. The strict consensus tree from the analysis of the phenotypic characters as well as the single most parsimonious tree found in the analysis of the combined dataset recover monophyletic Appendicularia as sister taxon to the remaining tunicate taxa. Thus, both datasets support the hypothesis that the last common ancestor of Tunicata was free-living and that ascidian sessility is a derived trait within Tunicata. “Thaliacea” is found to be paraphyletic with Pyrosomatida as sister taxon to monophyletic Ascidiacea and the relationship between Doliolida and Salpida is unresolved in the analysis of morphological characters; however, the analysis of the combined data reconstructs Thaliacea as monophyletic nested within paraphyletic “Ascidiacea”. Therefore, both datasets differ in the interpretation of the evolution of the complex holoplanktonic life history of thaliacean taxa. According to the phenotypic data, this evolution occurred in the plankton, whereas from the combined dataset a secondary transition into the plankton from a sessile ascidian is inferred. Besides these major differences, both analyses are in accord on many phylogenetic groupings, although both phylogenetic reconstructions invoke a high degree of homoplasy. In conclusion, this study represents the first serious attempt to utilize the potential phylogenetic information present in phenotypic characters to elucidate the inter-relationships of this diverse marine taxon in a consistent cladistic framework.     

Cladistic Analysis of A Problematic Ammonite Group: the Hamitidae (Cretaceous, Albian–turonian) and Proposals for New Cladistic Terms

The Hamitidae are a family of mid–Cretaceous heteromorph ammonites including lineages leading to four other families. Problems are outlined in trying to describe the phylogeny of completely extinct groups such as these heteromorph ammonites using the existing cladistic terminology, which is largely concerned with extant taxa and their ancestors. To solve these problems, two new terms are proposed: †crown groups and †stem groups, which are equivalent to crown and stem groups in terms of the evolutionary history of a clade, but are not defined on the basis of extant taxa. Instead they are defined by the topology of the phylogenetic tree, the †crown group being a clade defined by synapomorphies but which gave rise to no descendants. A †stem group is a branch of a phylogenetic tree which comprises the immediate sister groups of a given †crown group but is not itself a clade. Examples of these terms are described here with reference to the phylogeny of the Hamitidae and their descendants. The Hamitidae are paraphyletic and form †stem groups to a number of †crown groups, namely the Anisoceratidae, Baculitidae, Scaphitidae, and Turrilitidae. The definitions of the genera and subgenera are refined with respect to the type species and the clades within which they occur, and four new genera are described: Eohamites , Helicohamites , Sziveshamites , and Planohamites .     

When phylogenetics met biogeography: Willi Hennig,Lars Brundin and the roots of phylogenetic and cladistic biogeography

Willi Hennig's (Beitr. Ent. 1960, 10, 15) Die Dipteren-Fauna von Neuseeland als systematisches und tiergeographisches Problem applied a phylogenetic approach to examine the distributional patterns exhibited by the Diptera of New Zealand. Hennig showed how phylogenetic trees may be used to infer dispersal, based on the progression and deviation rules, and also discussed the existence of vicariance patterns. The most important author who applied Hennig's phylogenetic biogeography was Lars Brundin, when analysing the phylogenetic relationships of two taxa of Chironomidae (Diptera) and using them to examine the biogeographic relationships of Australia, New Zealand, South America and South Africa. The relevance of Brundin's contribution was noted by several authors, as it began the cladistic or vicariance approach to biogeography, that implies the discovery of vicariance events shared by different monophyletic groups. Both phylogenetic and cladistic biogeography have a place in contemporary biogeography, the former for analysing taxon biogeography and the latter when addressing Earth or biota biogeography. The recent use of the term “phylogenetic biogeography” to refer to a posteriori methods of cladistic biogeography is erroneous and should be avoided.     

Models and reality: Doctrine and practicality in classification

Phenetic classification corresponds to no biological model and lacks a sound philosophical basis. Cladistics (ignoring meaningless “transformed cladistics”) assumes divergent evolution and, usually, that best estimates of phylogeny are obtained by parsimony principles, both questionable assumptions at times. It is better than phenetics since more-or-less testable hypotheses are generated, but pitfalls are many, in data selection and interpretation (as to homology), and in commensurability of units and direction of change. Above all we learn: homoplasy is rife in nature. Much bad cladistics has been done. If it is to reflect phylogeny, classification cannot be artificially stabilized, but is its only aim to express (hypothesized) cladistic patterns? And can it do that with any degree of overall assurance? Biologists are legitimately interested in defining grades as well as clades. Recognition of an unequivocal clade-grade frequently leaves a paraphyletic grade residue that cannot itself be unequivocally resolved. This is a real problem that requires attention in formal taxonomy and in applying cladistics. Primarily morphological cladistics will be increasingly supplanted by molecular (nucleotide-sequence) cladistics. The role of evolutionary taxonomy will change accordingly.     

Incipient speciation in a neotropical Gesneriaceae: <Emphasis Type="Italic">Columnea kucyniakii</Emphasis> is nested within <Emphasis Type="Italic">C. strigosa</Emphasis>

Speciation is an ongoing process. Many recognized species are fully divergent from each other and their ancestors, whereas others are in earlier stages in the diversification process. Such incipient speciation may create patterns when one or a few populations are phenotypically distinct, but lack genomic level coalescence from each other or from their ancestral species. As a result, such progenitor-derivative species pairs are likely to lack reciprocal monophyly or generate paraphyletic ancestral species. Here we examine phylogenetic patterns in the Columnea strigosa (Gesneriaceae) complex to evaluate whether populations that have been named C. kucyniakii are reciprocally monophyletic with C. strigosa, its presumed ancestral species. Molecular phylogenetic results do not support reciprocal monophyly of the two species, implying that incipient speciation is occurring within the C. strigosa complex. We hereby recommend that C. kucyniakii be recognized at the specific rank despite the fact that it creates a paraphyletic C. strigosa. These findings bear importance in taxonomic decisions about paraphyletic taxa and recognizing evolutionary and morphologically distinct lineages.     

PHYLOGENETIC SELECTION OF A RESOURCE: A NEW USE FOR CLADISTICS

A phylogenetic model for the selection of commercial resources using the cladistic method is proposed. The group selected as an example was the marine agarophyte red algal genus Gracilaria Greville. We suggest the use of the cladistic principle of evolutionary transformational series in order to test the quality of agars instead of the assay‐herror traditional method that consumes time and budget. If we asume that the “good quality of agar” in extant taxa is a sinapomorphic character (but not a reliable taxonomic one), then taxa included in the same monophiletic clade in which the species with “good quality of agar” are, has a high evolutionary posibility to share that character. In order to do this we have to incorporate to the set of available specific characters, those of the taxa actually used as a agar source but not present in the area under scope. A complete set of the basic cladistic data required for run the most popular program currently in use (PAUP) are provided. We applied the model to the Mexican Atlantic species and found that, using Gracilaria chilensis and G. cornea as “indicator taxa,” and found Mexican populations of G. crassissima, G. caudata, G. cervicornis and Gracilariopsis lemaneiformis are candidates for a study of yield and agar properties.     

Aphyly: identifying the flotsam and jetsam of systematics

Many taxon names in any classification will be composed of taxa that have yet to be demonstrated as monophyletic, that is, characterized by synapomorphies. Such taxa might be called aphyletic, the flotsam and jetsam in systematics, simply meaning they require taxonomic revision. The term aphyly is, however, the same as, if not identical to, Hennig's “Restkörper” and Bernardi's merophyly. None of these terms gained common usage. We outline Hennig's use of “Restkörper” and Bernardi's use of merophyly and compare it to aphyly. In our view, application of aphyly would avoid the oft made assumption that when a monophyletic group is discovered from within an already known and named taxon, then the species left behind are rendered paraphyletic. By identifying the flotsam and jetsam in systematics, we can focus on taxa in need of attention and avoid making phylogenetic faux pas with respect to their phylogenetic status.     

Mapping cladograms into morphospaces

In cladistic analyses, taxa are grouped hierarchically into clades according to shared apomorphic character states to construct cladograms; cladograms are interpretable as phylogenetic hypotheses. In morphological space analyses, organism forms are represented as points in morphospaces; point proximities in morphospaces represent similarities that might be attributable to phenetic convergence and, consequently, may correspond inaccurately with hypothesized evolutionary relationships. A method for synthesizing phylogenetic results that are interpreted from cladistic analyses with phenetic results that are obtained from morphological space analyses is presented here; in particular, points that represent forms typifying taxa in morphospace are assigned as terminal nodes for appropriate cladograms that are mapped into morphospaces by positioning nonterminal nodes and orienting internodes according to a geometric algorithm. Nonterminal nodes may be interpreted as ancestors in phylogenetic hypotheses and occupy positions that represent particular organism forms in morphospaces. By mapping cladograms into morphospaces, therefore, evolutionary morphologists can reconstruct ancestral morphologies and test historical transformation hypotheses.     

Remarks on the family-level phylogeny of butterflies (Insecta, Lepidoptera, Rhopalocera)

1. Available evidence on butterfly family-level relationships is re-examined according to the principles of phylogenetic (cladistic) systematics. 2. The assumption of a sister-group relationship between the Hesperioidea and Papilionoidea seems a reasonably substantiated working hypothesis. 3. The Papilionoid families Papilionidae, Pieridae and Lycaenidae sensu Ehrlich (1958) are definable as monophyletic entities; of Ehrlich 's two remaining families, Nymphalidae and Libytheidae, the former is paraphyletic in terms of the latter. 4. The interrelationships between the Papilionoid families may be presented as Papilionidae + (Pieridae + [Lycanidae + Nymphalidae]). 5. In a phylogenetic system any given arrangement of taxa is either correct or not: Contrary to the pheneticists' view (Ehrlich and Ehrlich 1967) phylogenetic systematists cannot accept the existence of a multitude of valid classifications.     

Phylogeny of theCyclanthaceae

The affinities ofCyclanthaceae are discussed, and it is concluded that the sister-group to this family is most probablyPandanaceae. A hypothesis of generic relationships inCyclanthaceae, based on cladistic methods, is presented. Bootstrap analysis and Bremer support (decay index) have been used to test the strength of individual clades, and the result is compared with previously made phylogenetic analyses. TheSphaeradenia group (Chorigyne, Stelestylis, Sphaeradenia, andLudovia) is supported as monophyletic and acceptably resolved, while theAsplundia group (remaining genera inCarludovicoideae) may be paraphyletic, with largely uncertain relationships. A formal recognition of these groups is therefore not justified. The probable character evolution inCarludovicoideae is discussed.     

A reappraisal of orders and families within the subclass Chaetothyriomycetidae (Eurotiomycetes,Ascomycota)

The subclass Chaetothyriomycetidae (Eurotiomycetes, Ascomycota) is an assemblage of ecologically diverse species, ranging from mutualistic lichenised fungi to human opportunistic pathogens. Recent contributions from molecular studies have changed our understanding of the composition of this subclass. Among others, ant-associated fungi, deep-sea fungi and bryophilous fungi were also shown to belong to this group of ascomycetes. The delimitation of orders and families within this subclass has not previously been re-assessed using a broad phylogenetic study and the phylogenetic position of some taxa such as the lichenised family Celotheliaceae or the Chaetothyrialean bryophilous fungi is still unclear. In our study, we assemble new and published sequences from 132 taxa and reconstruct phylogenetic relationships using four markers (nuLSU, nuSSU, mtSSU and RPB1). Results highlight several shortfalls in the current classification of this subclass, mainly due to un-assigned paraphyletic taxa. The family Epibryaceae is therefore described to circumscribe a previously un-assigned lineage. Celotheliales ad int. is suggested for the lineage including the lichen genus Celothelium and various plant pathogens. The delimitation of the family Trichomeriaceae is also broadened to include the genus Knufia and some anamorphic taxa. As defined here, Chaetothyriomycetidae includes four orders (Celotheliales ad int., Chaetothyriales, Pyrenulales, and Verrucariales) and ten families (Adelococcaceae, Celotheliaceae, Chaetothyriaceae, Cyphellophoraceae, Epibryaceae fam. nov., Herpotrichiellaceae, Pyrenulaceae, Requienellaceae, Trichomeriaceae, and Verrucariaceae).     

The threefold parallelism of Agassiz and Haeckel,and polarity determination in phylogenetic systematics

A parallel exists between the threefold parallelism of Agassiz and Haeckel and the three valid methods of polarity determination in phylogenetic systematics. The structural gradation among taxa within a linear hierarchy, ontogenetic recapitulation, and geological succession of the threefold parallelism resemble outgroup comparison, the ontogenetic method, and the paleontological method, respectively, which are methods of polarity determination in phylogenetic systematics. The parallel involves expected congruence among similar components of the distribution of character states among organisms. The threefold parallelism is a manifestation of a world view based on linear hierarchies, whereas polarity determination is part of the methodology of phylogenetic systematics which assumes that organisms are grouped into a nested hierarchy. The threefold parallelism facilitated the ranking of previously established taxa into linear hierarchies consisting mostly of paraphyletic groups. In contrast, methods of polarity determination identify apomorphies that determine and diagnose monophyletic taxa (clades) in the nested genealogical hierarchy. Taxa in linear hierarchies are defined by sets of character states, whereas clades are defined by common ancestry. Although the threefold parallelism was ostensibly abandoned with the rejection of Haeckel's biogenetic law, some of its components continue to facilitate the progressive scenarios that are common in evolutionary thought. Although a general view of progression in organismal history may be invalid, the progressive or directional sequence of character state changes that results in the characterization of a particular clade has considerable heuristic value. Agassiz's ostensibly nested hierarchy and other pre-Darwinian classifications do not provide support for the view that the natural system can be discovered without recourse to the principle of common descent.     

Stability of cladistic relationships between Cetacea and higher-level artiodactyl taxa

Over the past 10 years, the phylogenetic relationships among higher-level artiodactyl taxa have been examined with multiple data sets. Many of these data sets suggest that Artiodactyla (even-toed ungulates) is paraphyletic and that Cetacea (whales) represents a highly derived "artiodactyl" subgroup. In this report, phylogenetic relationships between Cetacea and artiodactyls are tested with a combination of 15 published data sets plus new DNA sequence data from two nuclear loci, interphotoreceptor retinoid-binding protein (IRBP) and von Willebrand factor (vWF). The addition of the IRBP and vWF character sets disrupts none of the relationships supported by recent cladistic analyses of the other 15 data sets. Simultaneous analyses support three critical clades: (Cetacea + Hippopotamidae), (Cetacea + Hippopotamidae + Ruminantia), and (Cetacea + Hippopotamidae + Ruminantia + Suina). Perturbations of the combined matrix show that the above clades are stable to a variety of disturbances. A chronicle of phylogenetic results over the past 3 years suggests that cladistic relationships between Cetacea and artiodactyls have been stable to increased taxonomic sampling and to the addition of more than 1,400 informative characters from 15 data sets.     

Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships

The relationships among basal sauropodomorphs are controversial. Results of cladistic analyses vary from a fully paraphyletic assemblage to a monophyletic core‐prosauropod. We apply the comparative cladistics method to three published cladistic analyses of sauropodomorph dinosaurs, in order to identify root causes for differences between phylogenetic results. Except for three taxa (Saturnalia, Thecodontosaurus, and Efraasia) and one clade (Gravisauria), the remaining genera are recovered with conflicting positions. The comparative method is based on indices that allow for the quantification of the degree of similarity in characters and character states among analyses. A comparison of primary data, character selection, and scoring highlights significant discrepancies in data sets. Our results suggest that one character out of two varies from one analysis to the other. These are the root causes for the phylogenetic incongruence observed. The hurdle of the phylogenetic definition of the clade Sauropoda, which has been defined in four different ways, is also treated. We concur with several recent papers following the first node‐based definition of Sauropoda. © 2015 The Linnean Society of London     

A phylogenetic analysis of the Conchostraca and Cladocera (Crustacea, Branchiopoda, Diplostraca)

A computer-assisted cladistic analysis on morphological characters of the Diplostraca (Conchostraca and Cladocera) has been undertaken for the first time. The morphological information has been obtained from literature and transformed into 56 suitable characters. The analysis included 47 ingroup taxa, comprising five conchostracan taxa (four families of the Spinicaudata and the Laevicaudata) and 42 genera of the Cladocera. A detailed character discussion is presented which will be a useful working base for future phylogenetic studies on the group. A number of systematic groups were, with differing degrees of certainty, supported in all 218 equally short trees. These are the Diplostraca, Cladocera, Gymnomera (Onychopoda and Haplopoda), Onychopoda, Podonidae, Cercopagididae, Anomopoda, Daphniidae, Moininae, Scapholeberinae, Chydoridae, Chydorinae and Sididae. The Spinicaudata were only supported on some of the 218 equally short trees while no support was found for the Conchostraca. Two taxa—the Macrothricidae and Aloninae—were relatively strongly indicated to be paraphyletic. A suggested classificatory hierarchy, without indication of absolute rank, is presented.     

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.