Transformation Series as an Ideographic Character Concept

An ideographic concept of character is indispensable to phylogenetic inference. Hennig proposed that characters be conceptualized as “transformation series”, a proposal that is firmly grounded in evolutionary theory and consistent with the method of inferring transformation events as evidence of phylogenetic propinquity. Nevertheless, that concept is usually overlooked or rejected in favor of others based on similarity. Here we explicate Hennig's definition of character as an ideographic concept in the science of phylogenetic systematics. As transformation series, characters are historical individuals akin to species and clades. As such, the related concept of homology refers to a historical identity relation and is not equivalent to or synonymous with synapomorphy. The distinction between primary and secondary homology is dismissed on the grounds that it conflates the concept of homology with the discovery operations used to detect instances of that concept. Although concern for character dependence is generally valid, it is often misplaced, focusing on functional or developmental correlation (both of which are irrelevant in phylogenetic systematics but may be valid in other fields) instead of the historical/transformational independence relevant to phylogenetic inference. As an ideographic science concerned with concrete objects and events (i.e. individuals), intensionally and extensionally defined properties are inconsistent with the individuation of characters for phylogenetic analysis, the utility of properties being limited to communicating results and facilitating future rounds of testing.     

The Gegenbaur Transformation: a paradigm change in comparative biology

The leading experts in the development of phylogenetic systematics, Walter Zimmermann and Willi Hennig, formulated their research program in opposition to (neo-) idealistic morphology as expounded by authors such as Wilhelm Troll and Adolf Naef. Idealistic morphology was synonymous with systematic morphology for Naef, who wanted it to be strictly kept separate and independent of phylogenetics. Naef conceded, however, that the natural system researched by systematic morphology is to be causally explained by the theory of descent with modification. Naef went on to compile a dictionary that would regulate the translation of the language of systematic morphology into the language of phylogenetics. The switch from idealistic morphology to phylogenetic morphology is paradigmatically exemplified in the two editions (1859, 1870) of Carl Gegenbaur's Grundzüge der vergleichenden Anatomie. This paper traces the development of phylogenetic systematics from Gegenbaur through the work of Adolf Naef to Walter Zimmermann and Willi Hennig. Hennig added to Naef's systematic morphology the dimension of time, which required an ontological replacement: Naef's natural system, a nested hierarchy of intensionally defined sets subject to the membership relation, was replaced by Hennig's phylogenetic system, an enkaptic hierarchy subject to the part-to-whole relation.     

Distinguishing between convergence and parallelism is central to comparative biology: a reply to Williams and Ebach

The definitions of character similarity, homology, homoplasy, heterology, parallelism and convergence are clarified in the framework of current phylogenetic methodology. They are all associated with definite patterns of character change and can consequently be tested by phylogeny building. Their crucial significance in comparative biology is illustrated using demonstrative examples. © The Willi Hennig Society 2006.     

An application of dynamic homology to morphological characters: direct optimization of setae sequences and phylogeny of the family Odontellidae (Poduromorpha, Collembola)

The concept of character and the definition of the attribute are two major theoretical issues of phylogenetics. Lately, great progress has been made in the conceptual development of attributes as historical individuals undergoing series of transformations. While operational application of this ideographic concept of character has been possible since the publication of the direct optimization algorithm and POY software, it has been restricted to molecular characters only. The present paper proposes the first application of direct optimization to morphological characters, in the case study of the phylogeny of Odontellidae. This new homology regime is compared to the traditional homology scheme. The theoretical and operational limitations of the application of direct optimization to morphological characters are discussed. Some thoughts on the basics of its generalization to all morphological characters analyzed in a dynamic homology phylogenetic framework are given.
© The Willi Hennig Society 2009;.     

Willi Hennig’s dichotomization of nature

Two formal assumptions implied in Willi Hennig’s “phylogenetic systematics” were repeatedly criticized for not being biologically grounded. The first is that speciation is always dichotomous; the second is that the stem‐species always goes extinct when its lineage splits into two daughter species. This paper traces the theoretical roots of Hennig’s “principle of dichotomy”. While often considered merely a methodological principle, Hennig’s realist perspective required him to ground the “principle of dichotomy” ontologically in speciation. As a methodological principle, the adherence to a strictly dichotomously structured phylogenetic system allowed Hennig to be unequivocal in character analysis and precise in the rendition of phylogenetic relationships. The ontological grounding of the “principle of dichotomy” in speciation remains controversial, however. This has implications for the application of techniques of phylogeny reconstruction to populations of bisexually reproducing organisms (phylogeography). Beyond that, the “principle of dichotomy” has triggered an intensive debate with respect to phylogeny reconstruction at the prokaryote level. © The Willi Hennig Society 2010.     

The repugnant and the mature in phylogenetic inference: atemporal similarity and historical identity

The significance of “being similar” in the inference of species relationships is refuted once again (see also Hennig, 1966, Phylogenetic Systematics, Univ. of Illinois Press, Urbana, IL). Without merit is Rieppel and Kearney's (Biol. J. Linn. Soc., 2002, 75, 59–82) claim that submitting the relational property of topological similarity, their preferred definition of character, to falsifying tests of similarity benefits that kind of inference. Such a priori uses of similarity, in character analysis, are consistent with observational theory, where a character is defined intensionally in terms of immutable properties. However, the induced hypotheses that follow from this theory, not the deductive test that Rieppel and Kearney wanted, remain controversial, because their predictability is a consequence of circular reasoning, and their projectabality fails empirically from incongruent observation reports. Further, a category mistake is made when the abstract, similarity‐defined, group of organisms is reified, as a part of history. In addition, Rieppel and Kearney failed to provide a special theory for similarity, which renders similarity scientifically repugnant (Quine, 1969, Ontological Relativity and Other Essays, Columbia Univ. Press, New York). A return to Hennig's (1966) evolutionary concept of evidence, as transformation series, is urged, and from which a testable character hypothesis can be formulated. There is no one operation for determining character states in this system—it can be anything that leads to the testable hypothesis of synapomorphy, as an historical identity relation. Character compatibility and conjunction, but not similarity, provide a priori tests in phylogenetic character analysis. In turn, the phylogenetic system of inference leads to explanations of homology, as historical identities, which exemplifies the goal of achieving a mature state of historical knowledge (not of Quine, 1969). Such maturity obtains from attempts to falsify hypotheses of species relationships with severely tested evidence, not from induction of “the” observation statement that Rieppel and Kearney sought to justify their true belief in a hypothesis of relationships.     

Convergence and parallelism: is a new life ahead of old concepts?

In comparative biology, character observations initially separate similar and dissimilar characters. Only similar characters are considered for phylogeny reconstruction; their homology is attested in a two‐step process, firstly a priori of phylogeny reconstruction by accurate similarity statements, and secondly a posteriori of phylogeny analysis by congruence with other characters. Any pattern of non‐homology is then a homoplasy, commonly, but vaguely, associated with “convergence”. In this logical scheme, there is no way to analyze characters which look similar, but cannot meet usual criteria for homology statements, i.e., false similarity detected a priori of phylogenetic analysis, even though such characters may represent evolutionarily significant patterns of character transformations. Because phylogenies are not only patterns of taxa relationships but also references for evolutionary studies, we propose to redefine the traditional concepts of parallelism and convergence to associate patterns of non‐homology with explicit theoretical contexts: homoplasy is restricted to non‐similarity detected a posteriori of phylogeny analysis and related to parallelism; non‐similarity detected a priori of phylogenetic analysis and necessarily described by different characters would then correspond to a convergence event s. str. We propose to characterize these characters as heterologous (heterology). Heterology and homoplasy correspond to different non‐similarity patterns and processes; they are also associated with different patterns of taxa relationships: homoplasy can occur only in non‐sister group taxa; no such limit exists for heterology. The usefulness of these terms and concepts is illustrated with patterns of acoustic evolution in ensiferan insects. © The Willi Hennig Society 2005.     

A formula for maximum possible steps in multistate characters: isolating matrix parameter effects on measures of evolutionary convergence

To identify a biological signal in the distribution of homoplasy, it is first necessary to isolate non-biological factors affecting its measurement. The number of states per character in a phylogenetic data matrix may indicate evolutionary flexibility and, consequently, the likelihood of recurrent evolution. However, we show here that the number of states per character limits the maximum number of steps that may be inferred using parsimony. A formula is provided for the maximum number of steps that may be taken by a character with a given number of states and taxa. We show that as more character states are included the maximum proportion of steps that can be attributed to homoplasy falls, and the greatest amount of homoplasy measurable with the consistency index declines.
© The Willi Hennig Society 2009.     

Othenio Abel (1875–1946) and “the phylogeny of the parts”1

The reconstruction of the evolutionary history of animal phyla was an integral part of Othenio Abel’s paleobiology (paleozoology). Abel took issue with those phylogeneticists who, following the lead of Haeckel, would draw up phylogenetic trees on the basis of transformation series of singular characters considered to be of particular importance. Abel highlighted Louis Dollo’s principle of the chevauchement des spécialisations (crossing of specializations), which transformed phylogenetics from a search for ancestor–descendant sequences to research into relative degrees of relationships. This replacement resolved the conflict, much discussed at the time, between the continuity of ancestor–descendant lineages and the discontinuity inherent in the natural (phylogenetic) system. Walter Zimmermann refined Abel’s methodology, which he called character‐phylogenetics (Merkmalsphylogenie), an approach that was eventually adopted by Willi Hennig.     

Mapping characters on a tree with or without the outgroups

A character of special interest in evolutionary studies is usually optimized on a phylogenetic tree, with or without the outgroups employed in that analysis. Both practices are never justified and look like arbitrary choices. Focusing on one example, we draw the conclusion that authors retain or remove outgroups depending on the way these outgroups sample the diversity of states of the character(s) of special interest. The topology without outgroups is often used by authors when different outgroup taxa non‐exhaustively sample the different states of the character of interest outside of the ingroup. This can make the analysis incoherent, because its different steps are not based on the same data matrix (outgroups are removed in the last step). It can provide several incoherent and possibly different patterns for a same character of interest, one issuing from the first step of phylogeny construction and the other resulting from the a posteriori optimization on the truncated topology. Phylogenetic analyses should be designed to minimize this problem, selecting outgroup and ingroup taxa whose diversity of character states is needed for reconstructing the evolutionary history of the character of interest. © The Willi Hennig Society 2004.     

From types to individuals: Hennig’s ontology and the development of phylogenetic systematics

Contemporary phylogenetic systematics was framed, in part, as a response to a resurgent idealistic morphology in the German‐speaking world in the first half of the 20th century. There were also conceptual and methodological challenges from Anglo‐American researchers who were sceptical about whether a phylogenetic approach to systematics could be made to work. This paper describes these challenges as a way of providing context for some ontological innovations made first by Walter Zimmermann and then by Willi Hennig. The principal argument of this paper is that what has become known as the individuality thesis played a much more important role in the conceptual foundations of Hennig’s version of phylogenetic systematics than has been widely appreciated. Understanding Hennig’s ontology illuminates his responses to objections to phylogenetic systematics from both sides of the Atlantic and sheds substantial light on the extinction part of the dichotomy rule. Although many have taken Hennig’s claim that parent species go extinct at speciation to be an arbitrary and biologically unrealistic rule, extinction of the parent follows directly from the way Hennig understands species and how they are individuated. © The Willi Hennig Society 2011.     

Homology and errors

A recent review of the homology concept in cladistics is critiqued in light of the historical literature. Homology as a notion relevant to the recognition of clades remains equivalent to synapomorphy. Some symplesiomorphies are “homologies” inasmuch as they represent synapomorphies of more inclusive taxa; others are complementary character states that do not imply any shared evolutionary history among the taxa that exhibit the state. Undirected character‐state change (as characters optimized on an unrooted tree) is a necessary but not sufficient test of homology, because the addition of a root may alter parsimonious reconstructions. Primary and secondary homology are defended as realistic representations of discovery procedures in comparative biology, recognizable even in Direct Optimization. The epistemological relationship between homology as evidence and common ancestry as explanation is again emphasized. An alternative definition of homology is proposed. © The Willi Hennig Society 2012.     

Hennigs theorem und die strategie des stammesgeschichtlichen rekonstruierens die agnathen-gnathostomen-beziehung als beispiel

The heavily disputed methodology for the formulation of cladograms advocated by Hennig is subjected to a strict test as far as theoretical consistency and applicability are concerned. It can be convincingly shown that Hennig’s theorem contains indispensible postulates as it requires the establishment of plesiomorphic and apomorphic situations in the process of reconstructing the phylogenetic connections between existing fossil or recent organisms. Hennig’s view that fossil remains cannot by themselves disclose the phylogenetic interrelationships of the organisms and require an assessement of the characters is supported by the model for the evolution of the jaw apparatus in lower vertebrates. The model that is based on the main tenets of an approach for reconstructing phylogenetic transformations provides the key for the evolutionary position of fossil fish groups. In contrast to the logical and theoretical clarity Hennig’s approach does not offer any conclusive arguments as how to discriminate plesiomorphic and apomorphic character states and by which means mono-phyly of an animal group can be ascertained. The shortcomings of Hennig’s methodology are overcome and rectified in the constructivistic approach to phylogeny advocated herein. Furthermore the indispensible aspects of Hennig’s methodology are incorporated in a more general concept of phylogenetic reconstruction which was repeatedly corroborated by attempts to trace the transformation series of several fossil and recent groups of organisms.     

Abstracts of the 23rd Annual Meeting of the Willi Hennig Society. "Phylogenetics and Evolutionary Biology"

The 23rd annual meeting of the Willi Hennig Society took place in Paris with the support of Muséum national d'Histoire naturelle and CNRS (Centre National de la recherche Scientifique), from the 18th to the 23rd of July 2004. Ninety four participants from 16 countries presented 67 talks and 11 posters. The symposia comprised both methodological contributions and strong analyses of case studies, focusing on hot topics in systematics, methodological advances in phylogenetic analysis, epistemology, phylogenetic analysis of behavioral and ecological traits, phylogeny and coevolution of microbial symbioses, taxon and character sampling, biogeography, and the evolution of arthropods. The student participation was very high with 30 student talks (45%) distributed among all symposia, showing the same healthy trend seen in previous meetings. The present abstracts show how much systematics and phylogenetics are scientifically growing and contribute significantly to all research fields of evolutionary biology in the framework of comparative biology.
The Student Awards Committee (Cyrille D'Haese, Diana Lipscomb, John Wenzel) nominated the following winners: Johannes Bergsten, the Hennig Prize ($1000) for "Antagonistic coevolution between the sexes in diving-beetles (Coleoptera: Dytiscidae); phylogeny and experiments in reciprocal illumination", Mahé Ben Hamed, the Brundin Prize ($500) for "Reconstructing the history of Chinese through lexicon. Cladistics, distances and trees" and Lara Lopardo, the Rosen Prize ($250) for the poster "Chilean Anapids and Their Webs, a Phylogenetic Approach (Araneae, Anapidae)".
© The Willi Hennig Society 2004.     

Is ACCTRAN better than DELTRAN?

When parsimony ancestral character reconstruction is ambiguous, it is often resolved in favour of the more complex character state. Hence, secondary loss (secondary “absence”) of a complex feature is favoured over parallel gains of that feature as this preserves the stronger hypothesis of homology. We believe that such asymmetry in character state complexity is important information for understanding character evolution in general. However, we here point out an inappropriate link that is commonly made between this approach and the accelerated transformation (ACCTRAN) algorithm. In ACCTRAN, changes are assigned along branches of a phylogenetic tree as close to the root as possible. This has been taken to imply that ACCTRAN will minimize hypotheses of parallel origins of complex traits and thus that ACCTRAN is philosophically better justified than the alternatives, such as delayed transformation (DELTRAN), where changes are assigned along branches as close to the tips as possible. We provide simple examples to show that such views are mistaken and that neither ACCTRAN nor DELTRAN consistently minimize parallel gain of complex traits. We therefore do not see theoretical grounds for favouring the popular ACCTRAN algorithm. © The Willi Hennig Society 2008.     

Realism in systematics through biogeographical consilience

There is an overlooked gap between any phylogenetic hypothesis and the natural world shaped by historical evolutionary processes, since the main concern during phylogenetic analyses is solely the search for congruence among characters under a defined criterion. Given a scientific realistic view, however, phylogenetic hypotheses are scientific theories that try to depict the historical series of cladogenetic events among biological entities. In this sense, the challenge is to establish a form of measuring the degree of truthfulness of our phylogenetic hypotheses. Here, we advocate the use of consilient biogeographical hypotheses to recognize the biological meaning of a phylogenetic inference apart from its instrumentalist value. Our proposal is based on the assumption that robust biogeographical hypotheses allows us to be close to the real evolutionary history of taxa. © The Willi Hennig Society 2011.     

The role of wood anatomy in phylogeny reconstruction of Ericales

The systematic significance of wood anatomical characters within Ericales is evaluated using separate and combined parsimony analyses including 23 wood characters and 3945 informative molecular characters. Analyses of wood features alone result in poorly resolved and conflicting topologies. However, when pedomorphic character states are coded as inapplicable, the combined bootstrap topology results in an increase of resolution and support at most deeper nodes compared with the molecular analyses. This suggests that phylogenetic information from the limited number of morphological characters is not completely swamped by an overwhelming amount of molecular data. Based on the morphology of vessels and fibers, and the distribution of axial parenchyma, two major wood types can be distinguished within Ericales: (i) a “primitive” type, nearly identical to the wood structure in the more basal outgroup Cornales, which is likely to have persisted in one major clade, and (ii) a “derived” type that must have evolved in at least two separate evolutionary lines. The occurrence of the first type is strongly correlated with shrubs to small trees growing in cold temperate or tropical montane regions, while the second type is common in tall trees of tropical lowlands. This favors the inclusion of ecologically adaptive features in phylogeny reconstruction. © The Willi Hennig Society 2006.