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.     

Karl Beurlen (1901–1985), Nature Mysticism, and Aryan Paleontology

The relatively late acceptance of Darwinism in German biology and paleontology is frequently attributed to a lingering of Lamarckism, a persisting influence of German idealistic Naturphilosophie and Goethean romanticism. These factors are largely held responsible for the vitalism underlying theories of saltational and orthogenetic evolutionary change that characterize the writings of many German paleontologists during the first half of the 20th century. A prominent exponent of that tradition was Karl Beurlen, who is credited with having been the first German paleontologist to present a full-fledged theory of saltational evolution and orthogenetic change. A review of Beurlen’s writings reveals motives and concerns far more complex, however, and firmly rooted in contemporary v?lkisch thought and Aryan Science. Beurlen’s mature theory of evolution can indeed be understood as his own contribution to Aryan Geology and Biology, tainted as it was with National-Socialist ideology. Evolutionary biologists of the time who opposed the theories of Beurlen and like-minded authors, i.e., idealistic morphology, typology, saltational change, orthogenesis and cyclism did so on Darwinian principles, which ultimately prevailed. But at the time when the battle was fought, their adherence to the principle of natural selection was likewise ideologically tainted, namely in terms of racial theory. National-Socialist ideology was unable to forge a unity of evolutionary theory in Germany even amongst those of its proponents who endorsed this ideology.     

Plant Morphology: The Historic Concepts of Wilhelm Troll, Walter Zimmermann and Agnes Arber

Recent molecular systematic and developmental genetic findingshave drawn attention to plant morphology as a discipline dealingwith the phenotypic appearance of plant forms. However, sincedifferent terms and conceptual frameworks have evolved overa period of more than 200 years, it is reasonable to surveythe history of plant morphology; this is the first of two paperswith this aim. The present paper deals with the historic conceptsof Troll, Zimmermann and Arber, which are based on Goethe'smorphology. Included are contrasting views of ‘unity anddiversity’, ‘position and process’, and ‘morphologyand phylogeny’, which, in part, are basic views of currentplant morphology, phylogenetic systematics and developmentalgenetics. Wilhelm Troll established the ‘type concept’and the ‘principle of variable proportions’. Hehas provided the most comprehensive overview of the positionalrelations of plant forms. Agnes Arber started from the universaldynamics of life and attempted to describe all structures asprocesses. She paid attention to ‘repetitive branching’,‘differential growth’, and ‘parallelism’.As a result she has recently been rediscovered by developmentalbotanists. Walter Zimmermann rejected any metaphysical influenceon plant form and instead called for objective procedures. Hewas mainly interested in phylogenetic ‘character transformation’and the ‘reconstruction of genealogical lines’.Guided by the example of flower-like inflorescences, a futurepaper will deal with functional and developmental constraintsinfluencing plant forms. Recent morphological concepts (‘trialectical’,‘continuum’/‘fuzzy’, ‘processmorphology’) will be discussed and related to currentmorphological and developmental genetic research. Copyright2001 Annals of Botany Company Plant form, plant morphology, natural philosophy, homology, phylogeny, Goethe, Troll, Arber, Zimmermann, typology, character transformation, differential growth, complementarity     

The science of plant morphology: definition, history, and role in modern biology

As a scientific discipline, plant morphology is 211 yr old, originated by Goethe in 1790. It is a discipline that has largely been Germanic in practice. Because it took its origins from the study of the natural history of plants and the United States is principally an engineering society, the discipline of plant morphology in its pure form has never been widely practiced in this country. What has been labeled "plant morphology" in the United States has served largely as a handmaiden for systematics, using morphological characteristics to carve up diversity into its systematic subunits. Because the heart of plant morphology as a science is a focus on the convergences rather than the homologies in a phylogenetic sense, the German tradition of plant morphology is a unifying science that focuses on fundamental themes that transcend systematic boundaries. This paper traces the history of the science of plant morphology through the lineage of its principal practitioners: Goethe, Hofmeister, von Goebel, and Troll. It also evaluates the principles of plant morphology by applying them to the phyletically diverse Pteridophytes, showing that contemporary members of that group exhibit levels of shoot organization comparable to that of seed plants and discusses the implications of these findings.     

The influence of German idealistic morphology on the development of C.J. van der Klaauw's epistemology

Notwithstanding the general rise of experimental disciplines in biology in the first decades of our century, in Germany and in the Netherlands the interest in the idealistic morphological tradition flourished, and compensated for a reductionistic causal approach to natural phenomena. This article analyses the influence of the German idealistic morphologists W. Lubosch and A. Meyer on the development of C.J. van der Klaauw's epistemology. It discusses the gradual incorporation of non-causal principles into van der Klaauw's concept of biology. Van der Klaauw's epistemological concept of holistic biology was shaped in a critical confrontation with German idealistic morphology, and his early considerations can be interpreted as a direct impulse towards the development of his theory of functional components. Van der Klaauw's theories, being an alternative to the reductionistic experimental sciences, were among the causes of the fact that in the first half of our century biology in the Netherlands took a course deviating from the development of biology in the Anglo-American countries.     

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.     

Phylogeny and biogeographical history of Trogoniformes, a pantropical bird order

With highly conserved morphology throughout the family, a tropical distribution, and no close living relatives, the trogons (Aves: Trogonidae) pose a difficult problem for systematists. Disjunct tropical distributions are often attributed to Gondwanan vicariance, but the fossil record for trogons is mostly from the Tertiary of Europe. This study examined support for the basal relationships among trogons using a combination of nuclear (RAG-1) and mitochondrial (ND2) DNA sequence data. Although some nodes could not be resolved with significant support, there is strong support for the basal position of three New World genera ( Pharomachrus , Euptilotis , and Priotelus ). This phylogenetic hypothesis differs markedly from previous studies of trogon relationships and taxonomic treatments. Biogeographically, it implies an origin and early vicariance events for the crown clade in the New World. Molecular divergence estimates place all of the basal nodes of the trogon phylogeny in the Oligocene, precluding a Gondwanan origin for modern trogons.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 725–738.     

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.     

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.     

Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support

Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data for 12S, 16S, and intervening tRNA-val genes from 23 species of snakes representing most major snake lineages, including all four genera of New World dwarf boas. We then examined the phylogenetic position of these species by estimating the phylogeny of the basal snakes. Our phylogenetic analysis suggests that New World dwarf boas are not monophyletic. Instead, we find Exiliboa and Ungaliophis to be most closely related to sand boas (Erycinae), boas (Boinae), and advanced snakes (Caenophidea), whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation. Our estimate of snake phylogeny differs significantly in other ways from some previous estimates of snake phylogeny. For instance, pythons do not cluster with boas and sand boas, but instead show a strong relationship with Loxocemus and Xenopeltis. Additionally, uropeltids cluster strongly with Cylindrophis, and together are embedded in what has previously been considered the macrostomatan radiation. These relationships are supported by both bootstrapping (parametric and nonparametric approaches) and Bayesian analysis, although Bayesian support values are consistently higher than those obtained from nonparametric bootstrapping. Simulations show that Bayesian support values represent much better estimates of phylogenetic accuracy than do nonparametric bootstrap support values, at least under the conditions of our study.     

On the difference between mono-, holo-, and paraphyletic groups: a consistent distinction of process and pattern

About 50 years ago, the German entomologist Willi Hennig presented a new approach in biological systematics that he called a phylogenetic systematics. The main difference between his approach and traditional Linnean systematics was that he distinguished two new kinds of groups that he called mono- and paraphyletic groups, and whereof he considered only monophyletic groups to be natural groups. However, almost immediately after publication of his approach in English, some biological systematists commented that his monophyletic groups rather ought to be called holophyletic groups. The comment sparked a heated debate about the definition of the concept 'monophyletic groups', but the debate never reached consensus. In this paper, I claim that the controversy does not concern the definition of the concept monophyletic groups per se , but instead conceptualization of phylogenies (i.e. dichotomously branching processes) in a general sense. I discuss the relation between mono-, holo- and paraphyletic groups, and conclude that Hennig's conceptualization of phylogenies is both inconsistent and empirically wrong, whereas Linné's instead is consistent and correct.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 217–220.     

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.     

Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha)

Research in fungal phylogenetics and systematics progressed rapidly in the past decade due to advances in DNA sequencing technologies and analytical methods. A newfound wealth of sequence data acquired through community-wide initiatives has advanced the process of acquiring a stable phylogenetic classification of many fungal taxa. Financial support from the National Science Foundation Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha) for 5 y enabled more than 100 fungal systematists to assess the taxon sampling, molecular markers and analytical methods necessary to facilitate such a project. Later a second NSF program provided financial support for the Assembling the Fungal Tree of Life (AFTOL) project to accomplish much of the research. Deep Hypha may be viewed as an involved parent of AFTOL with a continuing role as coordinator of likeminded workers. Many questions posed at the beginning of the Deep Hypha project have been addressed, at least in part, although some details remain to be clarified. Many of the main branches of the fungal tree are stable and well supported, often as a result of multigene analyses that involved collaboration of many laboratories. More work is necessary, however, to resolve certain branching events near the base of the tree, as well as to reconstruct relationships in some terminal groups. The phylogenetic classification in this issue of Mycologia is a product of the AFTOL project and many other independent research initiatives, and it is an initial synthesis of a working classification designed to be used for all major publications that require a phylogenetic classification of fungi.     

Review: Taxonomy of Nitella (Charales, Charophyceae) based on comparative morphology of oospores and multiple DNA marker phylogeny using cultured material

The genus Nitella is the largest group in the Charales and has the highest diversity of vegetative and oospore morphologies. In his worldwide monograph on the Charales, R. D. Wood characterized the sections and species of Nitella mainly on the basis of vegetative morphology and treated oospore wall morphology as diagnostic at the infraspecific level. Therefore, many species of Nitella exhibiting distinct external morphology of the oospore wall (EMOW) were reduced to infraspecific rank and only 53 of 204 species previously described were recognized within Nitella . However, recent morphological and molecular phylogenetic studies have demonstrated the phylogenetic validity of using EMOW for diagnosing some species of Nitella . More recently, a scanning electron microscopy (SEM) study of internal morphology of the oospore wall (IMOW) and multiple DNA marker analyses using both nuclear and chloroplast gene sequences were conducted to improve our understanding of the taxonomy of Nitella at the species level, on the basis of cultured material of a large number of species. Multiple DNA marker analyses resolved detailed and robust phylogenetic relationships within the genus and demonstrated the taxonomic and phylogenetic significance of IMOW. In addition, they supported the taxonomic decisions based on differences in oospore morphology, suggesting that an integrated approach, involving both SEM studies of the EMOW and IMOW and multiple DNA marker analyses, is appropriate to address problems at lower taxonomic levels within the genus, as well as to construct a natural taxonomic system for the genus. In this paper, recent morphological and molecular phylogenetic studies are reviewed and recent improvements in taxonomy of Nitella are summarized. Moreover, the evolution of morphological features and phylogenetic relationships within Nitella are discussed, focusing especially on oospore morphology.     

On concept formation in systematics

In his “Grundzüge einer Theorie der phylogenetischen Systematik”, Hennig (1950 ) cited three philosophers: the leading empiricist Rudolf Carnap, the conventionalist Hugo Dingler, and the somewhat more obscure empiricist Theodor Ziehen. David Hull characterized Hennig's “Grundzüge” as one long argument against idealistic morphology. It will here be argued that Hennig attacked idealistic morphology (synonymous with “systematic” morphology) for its mode of concept formation. Building on Carnap and Ziehen, who both looked back on Ernst Cassirer, Hennig argued that the “generic”, “thing” or “class” concept of traditional nomothetic science must be replaced with Cassirer's “relation concept.” According to Hennig, such “emancipation” of systematics from the Aristotelian “species” concept would also allow transcendence from the distinction of idiographic from nomothetic sciences, thus preserving the unity of science. However, the establishment of relations in the construction of a system of order presupposes entities that can be, or are, related. Relations presuppose relata, which in modern systematics are best conceptualized (at least at the supraspecific level) not as Aristotelian classes, nor as individuals as was argued by Hennig and Ziehen, but as tokens of natural kinds. © The Willi Hennig Society 2006.     

A phylogenetic analysis of the land plants

Phylogenetic systematics (cladistics) is a theory of phylogeny reconstruction and classification widely used in zoology. Taxa are grouped hierarchically by the sharing of derived (advanced) characters. The information is expressed in a cladogram, a best estimate of a phylogeny. Plant systematists generally use a phenetic system, grouping taxa on overall similarity which results in many groups being formed, at least in part, on the basis of shared primitive characters.
The methods of phylogenetic systematics are used to create a preliminary cladogram of land plants. The current classification of land plants is criticized for its inclusion of many groups which are not monophyletic.
Objections to the use of phylogenetic systematics in botany, apparent convergences within major groups and frequent hybridization, are shown to be invalid. It is concluded that cladistic analysis presents the best estimate of die natural hierarchy of organisms, and should be adopted by plant systematists in their assessment of plant interrelationships.     

Charles Girard: Relationships and Representation in Nineteenth Century Systematics

Early nineteenth century systematists sought to describe what they called the Natural System or the Natural Classification. In the nineteenth century, there was no agreement about the basis of observed patterns of similarity between organisms. What did these systematists think they were doing, when they named taxa, proposed relationships between taxa, and arranged taxa into representational schemes? In this paper I explicate Charles Frederic Girard’s (1822–1895) theory and method of systematics. A student of Louis Agassiz, and subsequently (1850–1858) a collaborator with Spencer Baird, Girard claimed that natural classificatory methods do not presuppose either a special creationist or an evolutionary theory of the natural world. The natural system, in Girard’s view, comprises three distinct ways in which organisms can be related to each other. Girard analyzed these relationships, and justified his classificatory methodology, by appeal to his embryological and physiological work. Girard offers an explicit theoretical answer to the question, what characters are evidence for natural classificatory hypotheses? I show that the challenge of simultaneously depicting the three distinct types of relationship led Girard to add a third dimension to his classificatory diagrams.     

Styles of scientific reasoning: Adolf Remane (1898–1976) and the German evolutionary synthesis

Adolf Remane is widely considered to have been one of the most influential German zoologists of the 20th Century, yet Ernst Mayr persistently characterized him as an idealistic morphologist, that is, a typologist unable to understand population genetics or indeed Darwinian theory. This stands in sharp contrast to Mayr's praise for Bernhard Rensch as one of the most important German contributors to the Modern Synthesis of evolutionary theory. Remane's style of scientific reasoning is analysed in his writings on microsystematics, ecology, comparative morphology and phylogenetics and found to be highly consistent throughout these varied fields of research, while differing fundamentally from the eminently statistical foundations of both population genetics and natural selection theory that were embraced by Mayr. A comparative analysis of Rensch's understanding of science in general, and biology in particular, shows him to share core values with Remane, both authors rooted in the Mandarin tradition of the German professoriate. Biographical and socio‐political factors appear to have influenced Mayr's contrasting perception of Remane and Rensch, one that would influence later biologists and historians of science.