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.     

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.     

Coherence, correspondence, and the renaissance of morphology in phylogenetic systematics

The decline in morphological phylogenies has become a pronounced trend in contemporary systematics due to a disregard for theoretical, methodological, conceptual, and philosophical approaches. The role and meaning of morphology in phylogenetic reconstruction and classification have been undermined by the following: (i) the ambiguous delineation of morphological characters; (ii) the putative “objectivity” of molecular data; (iii) that morphology has not been included in data matrices; (iv) that morphology has been mapped onto molecular cladograms; and (v) a separation of a paradigmatic relationship among morphology, phylogeny, and classification. Historical/philosophical arguments including the synthesis of coherence (coherentism) and correspondence (foundationalism) theories—i.e. “foundherentism” as a theory of epistemic justification—provide support for a renaissance of morphology in phylogenetic systematics. In the language of systematics, coherence theory corresponds to the logical/operational congruence of character states translated into a hierarchical/relational system of homologues and monophyletic groups as natural kinds. Correspondence theory corresponds to the empirical/causal accommodation of homologues and monophyletic groups as natural kinds grounded in the concept of semaphoront, and in developmental biology, genetics, inheritance, ontogenesis, topology, and connectivity. The role and meaning of morphology are also discussed in the context of separate and combined analyses, palaeontology, natural kinds, character concepts, semaphoront, modularity, and taxonomy. Molecular systematics suffers from tension between coherence and correspondence theories, and fails to provide a pragmatic language for predicates in science and in everyday life. Finally, the renaissance of morphology is not only dependent on a scientific/philosophical perspective but also depends on political, economic, social, and educational reforms in contemporary systematics. © The Willi Hennig Society 2009.     

From Haeckel to Hennig: the early development of phylogenetics in German-speaking Europe

An outline of the development of phylogenetic thinking and methodology in German literature published between 1862 and 1942 is presented. Central European biologists and palaeontologists of the first post‐Darwinian generation of biologists holding evolutionary views were directly stimulated by Darwin. Members of the second generation, mostly born after 1850, were largely influenced also by colleagues of the first post‐Darwinian generation, mainly by Haeckel. Among them were O. Abel, V. Franz, R. Hertwig, A. Naef, L. Plate, and R. v. Wettstein. Opinions on the relationship between systematics and phylogeny differed considerably. Many authors admitted that phylogeny must be mirrored in systematics but at the same time shared Haeckel's views on classification, which permitted paraphyletic groupings. Particularly Abel and Naef took systematics several steps further, and many important elements of phylogenetic systematics were developed several decades before Hennig. Naef presented a definition of a phylogenetic group that exactly matches Hennig's definition of monophyly. He also formulated a species concept that was implicitly based on reproductive isolation. This was an important presupposition for viewing speciation as the splitting of a stem species into daughter species. However, many authors of the first half of the 20th century repeated old, but established views on phylogenetics, while others overlooked or misunderstood earlier progressive views thus causing slow development of phylogenetic systematics in Central Europe. Its development almost stopped between 1925 and 1950, because of a widespread shift towards typology and extreme idealistic morphology. During that time very few persons such as W. Zimmermann and W. Hennig assembled elements of phylogenetic systematics and combined them with their own thoughts to create a sound theory and methodology.     

Phylogenetic analyses reveal reliable morphological markers to classify mega‐diversity in Onthophagini dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae)

Based largely on homoplastic characters of external morphology, the current systematics of the tribe Onthophagini and allied dung beetle lineages is unstable, contradictory, and thus inefficient. A number of recently proposed molecular phylogenies conflict strongly with each other and with formal classification, and none of them provides new tools for the improvement of dung beetle systematics. We explored the source of these inconsistencies by performing an independent, morphology‐based phylogenetic analysis of the “Serrophorus complex”, one of the most systematically confusing knots among the onthophagines, that involves 52 species from various genera of Onthophagini and allied tribes. The phylogenetic pattern revealed conflicts with existing classifications and with most of the earlier molecular phylogenies. However, it was largely congruent with the molecular phylogeny (Evolution 2005, 59 , 1060), using the largest gene sampling thus far. All current competing phylogenetic hypotheses were evaluated against each other, and the degree of their biogeographic plausibility was used as an additional evaluative criterion. Of the 91 morphological characters involved in our analyses, traits belonging to the endophallic sclerites of the aedeagus had a very strong phylogenetic signal. Terminology of these endophallic characters was established and their morphology was studied in detail, illustrated, and presented as a tool for further practical use. The enormous variety of shapes of the lamella copulatrix within the Onthophagini and allies present a methodological problem in character coding for phylogenetic analyses. Based on the performance of alternative coding approaches, it is argued that a seemingly less informative absence/presence coding scheme would be a better choice. The phylogenetic structure of the Serrophorus complex has been largely resolved, and some taxonomic changes improving its systematics are recommended.
© The Willi Hennig Society 2011.     

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.     

Adolf Naef (1883–1949), systematic morphology and phylogenetics

Several authors have highlighted methodological similarities between Naef’s systematic morphology and Hennig’s phylogenetic systematics. Whereas this may indicate an influence of Naef on Hennig, the relevant issues – such as the principle of generality in character analysis and the threefold parallelism of classification, ontogeny and the Fossil Record – reach back beyond Naef and Hennig and were widely discussed in the German systematics literature of the late 19th and early 20th Century. The same is true of conceptual issues, such as the discussion of the principle of monophyly, which was first introduced by Haeckel in 1866 ( Rieppel 2011b , J Zool Syst Evol Res 49 :1). In spite of methodological and conceptual agreements, Naef’s systematic morphology differed fundamentally from Hennig’s phylogenetic systematics. Naef emphasized the role of unbiased observation and the immediate acquaintance of the investigator with the phenomena given in nature as the basis of natural science in general, and of his hierarchy of types in particular. From the hierarchy of types, Naef derived through conceptual‐logical analysis the natural system, which above the species level forms a nested hierarchy of intensionally defined classes, denoted by general names. The historical‐causal interpretation of the hierarchy of types in turn offers insight into the hypothetical reality of phylogeny. Hennig in contrast denied the possibility of theory‐free observation, indeed of assumption‐free science in general, and on that basis put metaphysical issues above epistemology. Tying individuality to spatiotemporal location, historicity and causality, Hennig took not only species (as did Naef) but also supraspecific monophyletic taxa as individuals, denoted by proper names. From the species up, the phylogenetic system thus becomes a nested hierarchy of complex wholes of increasing degrees of complexity. Diagnostic characters of species or higher taxa can then no longer define classes (as in Naef’s natural system) but are thought to indirectly indicate the phylogenetic relations on which alone the phylogenetic system is to be based.     

Grundsätze der phylogenetischen Systematik (Eine praxisorientierte Übersicht)

The essential elements of phylogenetic systematics in the sense of Hennig are emphasized: The search for synapomorphies based on a special method of comparative morphology, and the aim of an exclusive use of synapomorphies for kinship proof and the basis of systematics. Special aspects of comparative morphology are: “Directed comparisons” steady reciprocal reflection between comparative morphological result and the system methodical efforts for the realization of distinctive details, comprehensive documentation and functional interpretation. This is equally true for recent and fossil forms. Most suitable for the method (in the sense defined above) are groups with numerous differentiated morphological characters, which can also be preserved in the fossil state. The less this is the case the less is the chance for achieving necessary numbers of well proven synapomorphies. Even so, it is not permitted—for those who want to perform phylogenetic systematics in the sense of Hennig—to use convergences, parallelisms or symplesiomorphies in the sense of “synapomorphies” as phylogenetic arguments for kinship relations. Numerous examples and diagrams demonstrate the methodological proceeding, and differences towards other methods of phylogenetical reconstruction and interpretation. Special attention is paid to direct and indirect conclusions drawn from fossils: Time of origin of characters, stem groups and *groups; predictions concerning the appearance (set of characters) of fossils and simultaneous existence of “neighbour groups” (sister groups, and more distantly related taxa).     

The unfalsifiability of cladograms and its consequences

Popper's falsificationism provides the normative reference system in recent discussions regarding theory and methodology of systematics. According to Popper, the falsifiability of a hypothesis represents a necessary precondition for its corroborability. It is shown that cladograms, independent of “strict”, “methodological” or “sophisticated” falsification, are not falsifiable in principle. No present observation is prohibited by any tree hypothesis and, thus, no Popperian test of cladograms exists. It is shown that the congruence test, which is commonly said to represent a Popperian test of cladograms, instead tests sets of apomorphy hypotheses. Three different strategies that have been proposed to circumvent this problem are discussed and refuted: (1) referring to Popper's convention to renounce ad hoc maneuvers; (2) referring to Popper's treatment of probability hypotheses; and (3) decoupling corroboration from falsification. As a consequence, within a Popperian framework the unfalsifiability of cladograms implies that cladograms cannot explain any present day observation and, thus, represent metaphysical hypotheses. However, Popper's falsificationism has been criticized and questioned by many philosophers before and it seems to be about time that phylogeneticists develop their own philosophy of phylogenetics that meets their specific requirements of a historical science that is not seeking for universal laws and regularities, but instead reconstructing particular historical events. © The Willi Hennig Society 2007.     

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 nature of parsimony and instrumentalism in systematics

This paper traces the historical and philosophical roots of the principle of parsimony, and its incorporation in empiricist philosophy of science. It is argued that phylogeny reconstruction looks back to the empiricist tradition in its application of parsimony. The radical coherentism that motivates the application of parsimony in direct optimization of sequence alignment results in an instrumentalist approach to phylogeny reconstruction. A similarly instrumentalist perspective motivated the 'barcoding' initiative in taxonomy and bioconservation. This is contrasted with a realist conception of systematics.     

Rejecting "the given" in systematics

How morphology and systematics come together through morphological analysis, homology hypotheses and phylogenetic analysis is a topic of continuing debate. Some contemporary approaches reject biological evaluation of morphological characters and fall back on an atheoretical and putatively objective (but, in fact, phenetic) approach that defers to the test of congruence for homology assessment. We note persistent trends toward an uncritical empiricism (where evidence is believed to be immediately “given” in putatively theory‐free observation) and instrumentalism (where hypotheses of primary homology become mere instruments with little or no empirical foundation for choosing among competing phylogenetic hypotheses). We suggest that this situation is partly a consequence of the fact that the test of congruence and the related concept of total evidence have been inappropriately tied to a Popperian philosophy in modern systematics. Total evidence is a classical principle of inductive inference and does not imply a deductive test of homology. The test of congruence by itself is based philosophically on a coherence theory of truth (coherentism in epistemology), which is unconcerned with empirical foundation. We therefore argue that coherence of character statements (congruence of characters) is a necessary, but not a sufficient, condition to support or refute hypotheses of homology or phylogenetic relationship. There should be at least some causal grounding for homology hypotheses beyond mere congruence. Such causal grounding may be achieved, for example, through empirical investigations of comparative anatomy, developmental biology, functional morphology and secondary structure. © The Willi Hennig Society 2006.     

The history of the homology concept and the “Phylogenetisches Symposium”

The homology concept has had a long and varied history, starting out as a geometrical term in ancient Greece. Here we describe briefly how a typological use of homology to designate organs and body parts in the same position anatomically in different organisms was changed by Darwin’s theory of evolution into a phylogenetic concept. We try to indicate the diversity of opinions on how to define and test for homology that has prevailed historically, before the important books by Hennig (1950. Grundzüge einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, Berlin) and Remane (1952. Die Grundlagen des Natürlichen Systems, der Vergleichenden Anatomie und der Phylogenetik. Geest & Portig, Leipzig) brought more rigor into both the debate on homology and into the usage of the term homology among systematists. Homology as a theme has recurred repeatedly throughout the history of the “Phylogenetisches Symposium” and we give a very brief overview of the different aspects of homology that have been discussed at specific symposia over the last 48 years. We also honour the fact that the 2004 symposium was held in Jena by pointing to the roles played by biologists active in Jena, such as Ernst Haeckel and Carl Gegenbaur, in starting the development towards a homology concept concordant with an evolutionary world view. As historians of biology, we emphasize the importance of major treatises on homology and its history that may be little read by systematists active today, and have sometimes also received less attention by historians of biology than they deserve. Prominent among these are the works of Dietrich Starck, who also happened to be both a student, and later a benefactor, of systematics at Jena University.     

Buchbesprechung

Abstract

Universal-Futterwerttabellen von O. Kellner und M. Becker. Neubearbeitet von Prof. Dr. Max Becker. Sonderausgabe des Tabellenteils im Anhang von “Kellner/Becker, Grundzüge der Fütterungslehre, 15. Auflage”. Erschienen im Verlag Paul Parey Hamburg und Westberlin 1971, 77 Seiten Tabellen, Gr. 8°, kartoniert Balacron, DM 6,80. Reviewed by A. Pusouser.     

Stability, sensitivity, science and heurism

We examine recently proposed justifications of sensitivity analysis sensu Wheeler (1995 ), here referred to as weighted‐classes sensitivity analysis (WCSA). We refute Giribet's (2003a) claim that WCSA is the strictest possible test for a given phylogenetic hypothesis. Giribet's (2003a) classification of data exploration methods as evaluating “nodal stability” or “nodal support” is arbitrary, at odds with common usage and actually obscures the relationships between the methods he examined, all of which seek to assess the sensitivity of results to variation in analytical conditions. Stability, whether statistical or taxonomic, is not a goal of phylogenetic science. Statistical stability necessarily involves trial repetition, which is impossible in ideographic sciences like phylogenetics. Taxonomic stability can be nothing more than an unintended by‐product of scientific inquiry, i.e., the repeated failure to refute a hypothesis. Schulmeister's (2003 ) “robust‐choice” defense of WCSA does not succeed in placing non‐arbitrary bounds on parameters, and her interpretation of this approach as simultaneously verificationist and falsificationist is logically inconsistent. WCSA is neither scientific nor heuristic and therefore does not contribute to the advancement of objective knowledge claims. © The Willi Hennig Society 2005.     

Hennig's semaphoront concept and the use of ontogenetic stages in phylogenetic reconstruction

A new practice in systematics, “semaphoront” coding, treats developmental stages as terminals, and it derives from Hennig's concept of the same name. Semaphoront coding has been implemented recently by Lamsdell and Selden (BMC Evol. Biol., 2013, 13:98) and Wolfe and Hegna (Cladistics, 2014, 30:366) in an effort to understand the relationships of fossil taxa of unknown developmental stage. We submit that this approach is antithetical to cladistic practice and constitutes a gross misunderstanding of Hennig's original idea. Here we review the concept of the semaphoront and clarify the role of the semaphoront in phylogenetic systematics. We contend that treating ontogenetic stages as terminals both violates tenets of phylogenetic systematics and oversimplifies the complexity of developmental processes. We advocate Hennig's alternative of including data from as many semaphoronts as possible, but implemented using the superior total evidence framework. Finally, we contend that the application of semaphoront coding to any palaeontological question requires invoking multiple, unjustified assumptions, and ultimately will not yield a possible phylogenetic solution. A total evidence approach can grapple with the placement of fossil developmental stages, if only imperfectly.     

Post-Haeckelian comparative biology — Adolf Naef’s idealistic morphology

Summary The present study describes the conceptual framework of Adolf Naef’s idealistic morphology as presented at the onset of the 20^th century. According to Naef, Haeckel’s and Gegenbaur’s approaches towards a phylogenetic biology were insufficient. He made it clear that Haeckel’s ideas were based on typological morphology. Thus, Haeckel’s views on comparative biology pointed back to pre-Darwinian concepts. Naef’s consequence was not to work out his own evolutionary morphology but to systematize the earlier typological concept. Consequently, he separated comparative morphology from phylogenetic studies. This idea was adopted by Hennig and was even imported into modern cladism.     

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.     

Good characters and homology

This paper is a critical comment on a recent article by Lieberman. 1 We question his opinion that DNA is a better data source for phylogenetic reconstructions than bone and discuss his “problems and potential solutions” regarding the homology concept. We conclude that phylogenetic systematics requires a phylogenetic homology concept, and that Lieberman's “solutions,” though useful terms, should not be designated as homology.