Systematics

Systematics is the study of the diversity of organisms and the relationships among these organisms. Systematics is a natural outgrowth of the need for humans to characterize and categorize the world around them. It is one of the oldest scientific disciplines, with roots in antiquity and a formal scientific literature reaching back to Aristotle. It is the basic comparative science of biology. Comparative sciences such as systematics and astronomy use the similarities and differences among the things studied in an effort to comprehend them and their behavior. This is in contrast to the experimental sciences, in which the outcomes of controlled experiments are used to acquire understanding.

The products of systematic study are used in many other branches of biology in two major ways. First, a biologist may need some knowledge of the kinds, identities, numbers, distribution of species, and populations within species in order to conduct research. For example, do the specimens studied represent one species or several species? If several, what are their identities? Second, the same biologist may need to know the relationships among these entities in order to fully understand the comparative data she has collected. For example, are the similarities in the ecology of two species the result of convergence in a similar environment (the species are not closely related), or common history (the species are closely related)?

This kind of comparative biology is not restricted to systematics. For example, David

Hillis and colleagues at the University of Texas studied an outbreak of the AIDS virus and showed that the affected individuals were infected from a common source. This conclusion was reached by demonstrating that the AIDS viruses in each patient were all related to a common virus ancestor, and that the source of that ancestor was an infected dentist who deliberately infected the unfortunate individuals. So the uses of systematics can span from the highest level of biological organization, such as the study of the origin of entire continents, to very small levels, such as a study of a small group of AIDS patients. Systemat-ics can be divided into four discrete but overlapping activities: discovery, description, tax-onomic scholarship, and synthesis.

The discovery activity consists of the search for new kinds of organisms. Much of this activity takes the form of field expeditions, in which a variety of special techniques are employed to collect organisms and preserve specimens in a manner that allows for future study. Rare or endangered organisms are usually not collected, but are rather documented with photographs or other means. Preserved specimens are placed in collections, usually at recognized natural history museums or other research institutions where they are made available for study by experts. The community of systematic scholars is truly international, and experts on particular groups of organisms regularly visit these collections or request loans of specimens to study. A considerable amount of discovery activity also takes place in the collections themselves, when experts examine specimens and discover new organisms "hidden" among previously known organisms. This requires careful attention to the care and maintenance of natural history collections, a specialty that systematists are expected to learn in addition to their research skills.

Descriptive activities are centered on doc umenting diversity through scientific publication. One basic activity is the description of newly discovered species. The systematist will describe a newly discovered species by examining collected specimens, characterizing their physical appearance, summarizing variation of individuals within and between populations, documenting the species' geographic range, and comparing the species to other species. Another basic activity is to publish a revision of a particular group. The systematist will attempt to examine specimens of all the species in a genus, family, or other group, study the history of names that have been applied to these specimens, adjust the classification as necessary, describe new species, and redescribe known species. Each species account would be similar to a basic species description. Yet another common activity is to publish a flora or fauna, a work that covers all the plant or animal species for a given region of the world. Such works may contain descriptions much like a revision but be directed toward information about each species within the particular region. Or they may be more informal, as in many field guides whose major purpose is to assist the systematist and layperson in identifying specimens. Another basic activity is the generation of identification keys that allow nonspecialists to identify the specimens they observe or collect without having to take them to specialists. Frequently revisions, floras, faunas, and field guides will contain keys.

Systematists who publish species descriptions, revisions, keys, and other descriptive publications are expected to observe good tax-onomic scholarship. Our present systems of classification and nomenclature date back to the late eighteenth century (see Linnaean Hierarchy), and it is common for the same species or group to have several different names. Three Codes of Nomenclature (plant, animal, and bacterial) have been adopted to ensure that all scientists use only one name for a particular species and for certain other taxa, such as genera and families. One of the main goals of the revision of a group is to sort out this history of names and use only the correct names for the species studied. This requires a thorough familiarity with the appropriate code and the correct application of the Rules of Nomenclature to the names of the group that is being revised. It is important to note that these codes do not demand that research and synthesis be conducted in a particular manner—only that names are used correctly. This ensures that systematists from different countries can communicate clearly.

Synthetic activities use the information gained from discovery and description to form hypotheses concerning the animals and plants studied. Syntheses are found as part of works that are mostly descriptive. The very act of comparing a newly discovered species to other known species is a synthetic activity. The revision of a particular group may be based on synthetic activities such as an analysis of the phylogeny of the group. A flora for a particular region might contain a detailed biogeo-graphic analysis that attempts to account for the origin of the entire flora by studying the relationships of its members to species living in other areas. Synthetic activities require a particular philosophical approach to problemsolving, and it is little wonder that this is the area of systematics in which controversy is rife. What, exactly, do we mean when we state that two species are closely related? What principles do we use to form a biological classification? Even if we acknowledge that evolution has produced a Tree of Life, should we base revisions and classifications on phylogeny? Most of the controversy revolves around the role of phylogeny and the Tree of Life and its relationships with biological classification.

Three dominant approaches to systematics emerged in the second half of the twentieth century. "Phenetics" holds that phylogenies are largely not recoverable and that the best approach is to estimate the overall similarity of species and classify on that basis. Its adherents are called pheneticists. "Phylogenetic Systematics" holds that there is a method for recovering phylogenies that is rigorous and testable and that classifications should be based strictly on the recovered phylogenies. Adherents are called phylogeneticists. "Evolutionary taxonomy" holds that reconstructing phylogenies is an important activity but that classifications should be based on both similarity and genealogical relationships, and adherents of this approach seek to balance the two; they are called evolutionary taxonomists.

Phenetics began as a reaction by its proponents, such as Robert R. Sokal of the United States and R. James Sneath of Great Britain, to what they perceived as a lack of rigor in biological systematics. Systematics seemed to these early pheneticists more an art than a science, with little justification for how system-atists made their decisions. They proposed to replace this "art form" with rigorous procedures for determining the overall similarity of organisms, using mostly measurements and other means of quantification. Computer programs were used to summarize the data and organize them into repeatable (for the same measures) indices of similarity. Species that were more similar were grouped into genera, similar genera into families, and so on.

Evolutionary taxonomy is actually the oldest of the three modern approaches; it grew out of the Evolutionary Synthesis (1920-1950). Its proponents, such as Ernst Mayr, G. G., Simpson, and Julian Huxley, wished to incorporate the rejuvenation of Darwinian evolution into systematics. Thus there was a heavy emphasis on the nature of species, integra tion of population phenomena, and recognition of levels of biological organization in theoretical works. The distinctive features of this approach emerged only with the rise of its competitors, phenetics and phylogenetic sys-tematics. By the late 1970s the differences were apparent. Evolutionary taxonomists adopted methods introduced by the phyloge-neticists for reconstructing phylogenies but advocated a dual approach to classification in which some groups were classified according to strict genealogical relationships and others were classified according to similarity relationships. The adoption of certain theoretical concepts such as a dual concept of relationship and a concept of "minimum mono-phyly" (see below) were the theoretical underpinnings of this approach.

The German entomologist Willi Hennig formalized phylogenetic systematics based on earlier German influences. Hennig adopted what he considered a strictly Darwinian concept of "relationship": genealogical relationship. Species were not necessarily closely related because they are similar, but because they shared a unique common ancestor. They might, indeed, be very similar, but in some cases they might not. For example, crocodiles and birds are not very similar, but they share a common ancestor not shared with lizards and snakes. (Dinosaurs share the same ancestor.) Hennig would classify birds and crocodiles together, and not classify crocodiles with snakes and lizards, because he rejected the pre-Dar-winian concept of "relationship" as "similarity relationship."

One of Hennig's central insights, also adopted by later evolutionary taxonomists, was his conclusion that only certain kinds of homologous similarities were evidence of common ancestry relationships among organisms. This led him to conclude that overall similarity could not possibly unravel evolutionary rela tionships. These special homologies, termed synapomorphies, were the homologies thought to have evolved only in the unique common ancestor of the related organisms and not in earlier ancestors. For example, birds and crocodiles (and probably most dinosaurs) build nests and take care of their young; these characteristics are thought to have arisen in the common ancestor of the group. Thus, these characteristics would be synapomorphic homologies, and they would imply a group composed of crocodiles and birds. In contrast, a body covered with scales is certainly a homologous similarity shared by crocodiles and lizards, but this homology is thought to have evolved in the common ancestor of birds, crocodiles, and lizards and thus does not suggest a unique relationship between crocodiles and lizards that excludes birds. Instead, it implies a larger group composed of all vertebrates ("reptiles," mammals, and birds) descended from an ancestor that had epidermal scales. Thus this homology is not "discarded"; it is simply used at a different level of analysis.

Since evolution was not thought to involve large steps during descent, the number of characteristics that supported any particular common ancestry relationship was necessarily small compared with the total number of homologous similarities shared by any two organisms or species (or genera, and so forth). Thus, to work out a phylogeny of a large group, many characteristics would have to be employed, only a few of which would be applicable for any pair of relationships to be tested. Since Hennig's concept of relationship was strictly genealogical, he insisted that natural groups be strictly monophyletic, groups that arose from single ancestral species and that included the species and all its descendants. These groups are termed monophyletic groups, or clades (hence "cladist" is an alternative label for phylogeneticist).

Phenetics and phylogenetic systematics caught the general attention of the systematic community in the 1960s, and the clash between these newer paradigms and evolutionary taxonomy became the dominant theme of theoretical systematics for some twenty years. Phenetics and phylogenetic sys-tematics were associated with distinctly different empirical methods. Pheneticists produced "dendrograms"—tree graphs linking species by estimates of overall similarity. Phy-logeneticists produced phylogenetic trees— tree graphs linking taxa by common ancestry as shown by synapomorphies. Both pheneti-cists and phylogeneticists rejected overall similarity as a method for discovering phylogenies, but pheneticists abandoned the search for phylogeny, while phylogeneticists continued the search as a necessary step to achieve their concept of "relationship" as genealogical relationship through the discovery of synapo-morphic homologies.

There is no doubt that the pheneticists were at least partly justified; systematics did seemingly lack a rigorous and testable set of methods. But phenetics, after an initial popularity, failed. There were many reasons for the failure, but three stand out. First, the results were rarely repeatable for the same specimens using different systems of measures and different indices of similarity. If the phenetics community could have settled on one method of collecting traits and one method of linking organisms into similarity relationships, they might have developed an internally consistent system. However, that was never accomplished. Second, the similarity measures contained information from both homologous and convergent traits. But evolutionary biologists wanted to know which traits were homologous and which were convergent. Evolutionary biologists needed phylogenetic trees to obtain that information; similarity dendrograms did not provide it. Third, phylogenetic systemat-ics demonstrated that phylogenies were, indeed, recoverable in a rigorous and testable manner. The recovery of historical information did not need to be an art form. Phylogenies (or, more properly, hypotheses of phylogeny) are much more interesting to evolutionary biologists than similarity measures, even when measures of similarity were organized into dendrograms that look like phylogenies.

Evolutionary taxonomists did not have an explicit method for discovering phylogenetic trees. They adopted the methods of phyloge-netic systematics. In the clash of paradigms, evolutionary taxonomists attempted to reach a middle ground on the issue of classification by adopting a dual concept of relationship. In some cases groups should be classified genealogically, but in other cases they should be classified by similarity. The justification for grouping by similarity grew out of an interpretation of the evolutionary synthesis that levels of organization were significant evolutionary phenomena that denoted so-called adaptive zones. In reality, this amounted to a justification that certain "important" and long-recognized groups should be retained in classifications, even though their continued recognition violated the concept that organisms should be classified strictly on the basis of common ancestry relationships (that is, the concept of strict monophyly).

The position of the evolutionary taxono-mists is best evaluated by a contrasting example of how an evolutionary taxonomist and a phylogeneticist might classify birds. Evolutionary taxonomists recognize Aves (birds) as a class of vertebrates. There is a historical precedence for this, as systematists have long recognized birds as one of the major classes of vertebrates. There was a supposed theoretical justification as well. Birds have departed so strongly from the level of organization repre sented by reptiles that they now occupy an adaptive zone worthy of class recognition. Although this might sound very reasonable, there is a problem. The decision also requires recognition of Class Reptilia, which includes the closest living relatives of birds, dinosaurs, and other archosaurs such as crocodiles and alligators, along with more distantly related organisms such as snakes and lizards. This seemed a reasonable conclusion, because Rep-tilia also is a long-recognized group, but it leads to the conclusion that the common ancestor of birds, dinosaurs, and crocodiles is a reptile. That, then, leads to the idea that Rep-tilia is somehow ancestral to Aves, a shorthand notion that if the ancestor of archosaurs were found it would be classified as a reptile rather than classified in a group that included all of its descendants, dinosaurs, crocodiles, and birds. This concept has been termed minimum monophyly. Aves is classified on the basis of genealogical relationships; Reptilia is classified on the basis of similarity relationships (dinosaurs and crocodiles are similar to lizards and snakes); and the system was justified by appealing to the concept of minimum mono-phyly, which allows groups (Reptilia) to be ancestors of other groups (Aves).

Phylogenetic systematists reacted sharply to the concept of minimum monophyly and grouping by similarity. Their paradigm demanded strict monophyly and grouping by genealogy. Phylogeneticists argued that species are the highest level of biological organization capable of being ancestors, and that Aves should be placed within the group Archosauria along with all other descendants of the ancestor of archosaurs, such as dinosaurs and crocodiles. In other words, Reptilia would disappear from classifications altogether and would be replaced by Archosauria (birds, crocodiles, dinosaurs, and so forth) and Lepidosauria (snakes, lizards, and so forth).

Hennig and his colleagues saw phyloge-netic systematics as the systematic culmination of the Darwinian Revolution, rejecting the pre-evolutionary idea of similarity as the basis for classification and embracing Darwin's idea that classifications that reflect genealogy should be adopted whenever possible. However, they faced several political problems. For one thing, strictly phylogenetic classifications would lead to the abandonment of many familiar groups, such as Reptilia and the ape Family Pongidae. (Chimpanzees and gorillas are more closely related to humans than to gibbons.) And, it would lead to lowering the hierarchical ranks of other groups that are monophyletic, such as classifying Aves as an order of Archosauria rather than one of the classes of vertebrates.

In spite of the political difficulties, and in spite of the fact that popular classifications found in school texts still have not changed, phylogenetic systematics has established itself as the dominant paradigm of systematics. There are several reasons for its success. First, the phylogenetic method of discovering phy-logenies has proven a boon to evolutionary biologists who require information about the genealogies of species to do critical research in evolutionary biology. What is the correlation between geologic history and the history of the origin of species? Are certain modes of speci-ation more common than others? Are newly evolved species more genetically conservative or genetically diverse than older species? One needs a phylogeny to answer all of these questions.

The issue of classification has become clear. As it turns out, the claim by phylogeneticists that species are the highest possible level of biological organization capable of being ancestors is widely accepted. Those who disagree argue that only populations and individual organisms can be ancestors; no one argues that higher taxa, such as genera or classes, can be ancestors. Thus, while most biologists accept speciation as a natural process, there are no recognized natural processes that allow groups of species such as Reptilia to give rise to entire other groups, such as Aves. This conclusion undermines the major assumption underlying the concept of minimum mono-phyly. There is another problem with evolutionary taxonomy. The philosopher David Hull pointed out more than thirty years ago that classifications containing a mix of groups formed on the basis of similarity and genealogy will always be logically inconsistent with the phylogeny as a whole if they contain "similarity groups" such as Reptilia along with "genealogy groups" such as Aves. In spite of the fact that inclusion of such groups as Reptilia seems a good accommodation to the world of practical taxonomy, a classification that included such groups would be illogical relative to the Tree of Life. It seems that if biological classification is to fulfill Darwin's paradigm, it will have to be phylogenetic and adhere to the concept of strict monophyly.

Evolutionary biologists not only need phy-logenies to answer critical evolutionary questions, they also need biological classifications that organize this information in a manner that is logical relative to the phy-logeny itself.

See also: Classification, Biological; Linnaean Hierarchy; Phylogeny

Bibliography

Ax, Peter. 1987. The Phylogenetic System: The Sys-tematization of Organisms on the Basis of Their Phylogenesis. New York: John Wiley; Hennig, Willi. 1966. Phylogenetic Systematics. Urbana: University of Illinois Press (The classic. Not an easy read, but worth it); Mayr, Ernst, and Peter D. Ashlock. 1991. Principles of Systematic Zoology. New York: McGraw-Hill; Ridley, Mark. 1985. Evolution and Classification: The Reformation of Cladism. New York: Long; Sokal, Robert R., and Peter H. A. Sneath. 1963. Numerical Taxonomy. San Francisco: W. H. Freeman; Wiley, Edward O. 1981. Phylogenetics: The Principles and Practice of Phylogenetic Systematics. New York: John Wiley; Wiley, Edward O., et al. 1991. The Compleat Cladist: A Primer of Phylogenetic Systematics. Lawrence, KS: Museum of Natural History, University of Kansas.

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