Population thinking and tree thinking in systematics

Two new modes of thinking have spread through systematics in the twentieth century. Both have deep historical roots, but they have been widely accepted only during this century. Population thinking overtook the field in the early part of the century, culminating in the full development of population systematics in the 1930s and 1940s, and the subsequent growth of the entire field of population biology. Population thinking rejects the idea that each species has a natural type (as the earlier essentialist view had assumed), and instead sees every species as a varying population of interbreeding individuals. Tree thinking has spread through the field since the 1960s with the development of phylogenetic systematics. Tree thinking recognizes that species are not independent replicates within a class (as earlier group thinkers had tended to see them), but are instead inter-connected parts of an evolutionary tree. It lays emphasis on the explanation of evolutionary events in the context of a tree, rather than on the states exhibited by collections of species, and it sees evolutionary history as a story of divergence rather than a story of development. Just as population thinking gave rise to the new field of population biology, so tree thinking is giving rise to the new field of phylogenetic biology.     

The proximate/ultimate distinction in the multiple careers of Ernst Mayr

Ernst Mayr's distinction between “ultimate” and “proximate” causes is justly considered a major contribution to philosophy of biology. But how did Mayr come to this “philosophical” distinction, and what role did it play in his earlier “scientific” work? I address these issues by dividing Mayr's work into three careers or phases: 1) Mayr the naturalist/researcher, 2) Mayr the representative of and spokesman for evolutionary biology and systematics, and more recently 3) Mayr the historian and philosopher of biology. If we want to understand the role of the proximate/ultimate distinction in Mayr's more recent career as a philosopher and historian, then it helps to consider hisearlier use of the distinction, in the course of his research, and in his promotion of the professions of evolutionary biology and systematics. I believe that this approach would also shed light on some other important “philosophical” positions that Mayr has defended, including the distinction between “essentialism: and “population thinking.”     

Molecular systematics: A synthesis of the common methods and the state of knowledge

The comparative and evolutionary analysis of molecular data has allowed researchers to tackle biological questions that have long remained unresolved. The evolution of DNA and amino acid sequences can now be modeled accurately enough that the information conveyed can be used to reconstruct the past. The methods to infer phylogeny (the pattern of historical relationships among lineages of organisms and/or sequences) range from the simplest, based on parsimony, to more sophisticated and highly parametric ones based on likelihood and Bayesian approaches. In general, molecular systematics provides a powerful statistical framework for hypothesis testing and the estimation of evolutionary processes, including the estimation of divergence times among taxa. The field of molecular systematics has experienced a revolution in recent years, and, although there are still methodological problems and pitfalls, it has become an essential tool for the study of evolutionary patterns and processes at different levels of biological organization. This review aims to present a brief synthesis of the approaches and methodologies that are most widely used in the field of molecular systematics today, as well as indications of future trends and state-of-the-art approaches.     

Ontogeny, systematics, and phylogenetics: Perspectives of future synthesis and a new model of the evolution of bilateria

Ontogeny is considered as a process that allows linking two key components of biological systematics in an objective way: historically independent character attribution and phylogeny. It is proposed to designate the general theory that unifies the ??static?? traditional taxonomy and the dynamic evolutionary process on the basis of ontogenetic transformation of shapes of organisms as the ontogenetic systematics. One of the important practical applications is a new model of the evolution of bilaterian animals, which supposes an ancestral status of clonal asexual reproduction and its multiple reduction in different lines of Bilatera.     

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.     

Evolution,actuality and species concept: a need for a palaeontological tool

Species concept was developed to fit neontological necessities in ordering biological variability. Transversal (horizontal, synchronic) taxonomy shows hierarchical requirements quite different from those involved in longitudinal (vertical, diachronic) classifications. Furthermore, limitations within the species concept itself make it scarcely available in many paleontological contexts. Classical species definitions are often limited by theoretic and logic constraints, that are seldom available to describe practical situations. Morphology is an uncertain source of phylogenetic information, but it is still the main ground of biological comparison for extinct populations. Therefore, efforts in species recognition should be devoted to making taxonomy a useful tool for communication. First, inferences in systematics have to be led upon the available information about characters and processes. If this information is missing or not developed, no detailed conclusions can be supported. Secondly, definitions should be sufficiently elastic and generalised to allow an adaptation to each different case-study. The final target is to synthesise actual evolutionary histories, and not biological potentialities.     

On the Three-Taxon Approach to Parsimony Analysis

The following three basic defects for which three-taxon analysis has been rejected as a method for biological systematics are reviewed: (1) character evolution is a priori assumed to be irreversible; (2) basic statements that are not logically independent are treated as if they are; (3) three-taxon statements that are considered as independent support for a given tree may be mutually exclusive on that tree. It is argued that these criticisms only relate to the particular way the three-taxon approach was originally implemented. Four-taxon analysis, an alternative implementation that circumvents these problems, is derived. Four-taxon analysis is identical to standard parsimony analysis except for an unnatural restriction on the maximum amount of homoplasy that may be concentrated in a single character state. This restriction follows directly from the basic tenet of the three-taxon approach, that character state distributions should be decomposed into basic statements that are, in themselves, still informative with respect to relationships. A reconsideration of what constitutes an elementary relevant statement in systematics leads to a reformulation of standard parsimony as two-taxon analysis and to a rejection of four-taxon analysis as a method for biological systematics.     

On the origin of the typological/population distinction in Ernst Mayr’s changing views of species, 1942–1959

Ernst Mayr’s typological/population distinction is a conceptual thread that runs throughout much of his work in systematics, evolutionary biology, and the history and philosophy of biology. Mayr himself claims that typological thinking originated in the philosophy of Plato and that population thinking was first introduced by Charles Darwin and field naturalists. A more proximate origin of the typological/population thinking, however, is found in Mayr’s own work on species. This paper traces the antecedents of the typological/population distinction by detailing Mayr’s changing views of species between 1942 and 1955. During this period, Mayr struggles to refine the biological species concept in the face of tensions that exist between studying species locally and studying them as geographically distributed collections of variable populations. The typological/population distinction is first formulated in 1955, when Mayr generalizes from the type concept versus the population concept in taxonomy to typological versus population thinking in biology more generally. Mayr’s appeal to the more general distinction between typological and population thinking coincides with the waning status of natural history and evolutionary biology that occurs in the early 1950s and the distinction plays an important role in Mayr’s efforts to legitimate the natural historical sciences.     

Genetic polymorphism of Microbotryum violaceum s. I. isolates collected from different plant species on the territory of Russia

The present-day studies in the field of systematics and phylogeny of microorganisms, fungi, in particular, are characterized by a wide use of new approaches and methods of molecular biology. The use of a diversity of genetic markers permits a distinct differentiation of closely related species into individual evolutionary independent lines. It is shown in this work that all Microbotryum violaceum s. l. isolates studied by us are divided into five evolutionary groups according to the host plant.     

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.     

Genetic polymorphism of <Emphasis Type="Italic">Microbotryum violaceum</Emphasis> s. l. Isolates collected from different plant species on the territory of Russia

The present-day studies in the field of systematics and phylogeny of microorganisms, fungi, in particular, are characterized by a wide use of new approaches and methods of molecular biology. The use of a diversity of genetic markers permits a distinct differentiation of closely related species into individual evolutionarily independent lines. It is shown in this work that all Microbotryum violaceum s. l. isolates studied by us are divided into five evolutionary groups according to the host plant.     

Toward the synthesis of taxonomy,ontogeny, and phylogenetics: A new concept of <Emphasis Type="Italic">Ontogenetic Systematics</Emphasis>

Over the past decade, the morphological paradigm in the traditional field of systematics and evolutionary biology has been challenged and has actually been replaced by the molecular paradigm. In this study, an attempt is made to evaluate the current state of the problem concerning the relationship between the fundamentals of systematics and evolution. It is shown that the interrelatedness of evolution, ontogeny, systematics, and phylogenetics is deeply underestimated in the approaches used in recent research. Instead of considering the above fields of biology as separate categories, as is common in recent studies, the synthetic concept of ontogenetic systematics is proposed, which unifies them into an integrated process.     

Species: Beasts of burden

Ernst Mayr (1904–2005) was the twentieth century's most influential writer to wrestle with the species problem. 1 - 4 The following draws heavily on his work, albeit without presumptuously claiming to mirror his thinking or present any original ideas. As a personal meditation, I am thinking mostly of platyrrhines. Following Mayr, I adhere to what is commonly called the Biological Species Concept (BSC) as a way of thinking about a species in the real‐world biosphere as a taxon. I also hold to the idea that the Linnaean category called species has the same function as other categories: a linguistic tool for organizing and retrieving information about biodiversity while embodying evolutionary hypotheses. In other words, alpha taxonomy, the area of systematics that involves identifying, naming, and classifying species, is not purely an exercise in either biology or inventory because it involves communication as well. The burdensome work of the species category stems partly from tension created by the several purposes associated with the concept: the objective observation and examination of a fundamental biological phenomenon, the collection and interpretation of data in a selective context of relevance, and the intention to deploy scientific decisions as a form of communication within a dynamic but highly structured language system.     

The role of theories in biological systematics

The role of scientific theories in classifying plants and animals is traced from Hennig's phylogenetics and the evolutionary taxonomy of Simpson and Mayr, through numerical phenetics, to present-day cladistics. Hennig limited biological classification to sister groups so that this one relation can be expressed unambiguously in classifications. Simpson and Mayr were willing to sacrifice precision in representation in order to include additional features of evolution in the construction of classifications. In order to make classifications more objective, precise and quantitative, numerical pheneticists limited themselves to representing degrees of phenetic similarity. Finally, present-day cladists can be separated into phylogenetic cladists, who retain much of Hennig's theory of classification, and pattern cladists, who have stripped Hennig's system down to its bare essentials.     

ON THE INDEPENDENCE OF SYSTEMATICS

Abstract— Before the publication of On the Origin of Species the standing patterns of natural history—common plan, homology, ontogenetic parallelism, and the hierarchy of groups — were taken as indications of a biological order that had not yet been understood. Darwin covered all of these in chapter 13 of the Origin , arguing that his theory was the first to provide a reasonable explanation for the existence of such patterns. Since Darwin took these relations to be established by previous biology, and used them as evidence for the explanatory power of his theory, he was clearly of the opinion that they were independent of that theory. Although several modern figures have argued to the contrary, it seems that Darwin was right. The patterns listed above are recoverable from observation without reference to evolutionary theory, which theory may then be applied to provide an account of the processes by which they may have come about. That aspect of systematics concerned with the identification of the empirical patterns evidently constitutes a study prior to and independent of theories of process.     

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.

     

Perspectives Poulton,Wallace and Jordan: How discoveries in Papilio butterflies led to a new species concept 100 years ago

A hundred years ago, in January 1904, E.B. Poulton gave an address entitled ‘What is a species?’ The resulting article, published in the Proceedings of the Entomological Society of London, is perhaps the first paper ever devoted entirely to a discussion of species concepts, and the first to elaborate what became known as the ‘biological species concept’. Poulton argued that species were syngamic (i.e. formed reproductive communities), the individual members of which were united by synepigony (common descent). Poulton's species concept was informed by his knowledge of polymorphic mimicry in Papilio butterflies: male and female forms were members of the same species, in spite of being quite distinct morphologically, because they belonged to syngamic communities. It is almost certainly not a coincidence that Alfred Russel Wallace had just given Poulton a book on mimicry in December 1903. This volume contained key reprints from the 1860s including the first mimicry papers, by Henry Walter Bates, Wallace himself and Roland Trimen. All these papers deal with species concepts and speciation as well as mimicry, and the last two contain the initial discoveries about mimetic polymorphism in Papilio: strongly divergent female morphs must belong to the same species as non‐mimetic males, because they can be observed in copula in nature. Poulton, together with his contemporaries Karl Jordan and Walter Rothschild, who had monographed world Papilionidae, were strongly influential on the evolutionary synthesis 40 years later. Ernst Mayr, in particular, had collected birds and butterflies for Walter Rothschild, and had visited Tring, where Jordan worked, in the 1920s. The recognition of different kinds of reproductive and geographic isolation, the classification of isolating mechanisms, the use of the term sympatry, and the biological species concept all trace back to Poulton's 1904 paper. Poulton's paper, in turn, inherits much from Wallace's 1865 paper on Asian Papilio contained in the very book Wallace gave Poulton a month earlier. Wallace's gift, and Poulton's subsequent New Year address are thus key events in the history of species concepts, systematics and evolutionary biology.