Systematics Methodology and Taxonomic Nomenclature

Introduction

In the mid-1800s, paleontologists began organizing dinosaurs according to the Linnaean system of taxonomy, which classifies organisms according to overall physical similarity. The Linnaean system places organisms into a nested hierarchy using categories of increasing specificity, including (in ranked order) domains, kingdoms, phyla, classes, orders, families, genera, and species. From the 1880s to the 1960s, scientists refined the classification of dinosaurs using data from new fossils to enhance and revise the evolutionary tree.

In the mid-twentieth century, a new method of classification called “phylogenetic analysis” was invented in an effort to create a classification scheme that better reflected evolutionary relationships between species. Phylogenetic analysis creates groups called “clades” that reflect the inheritance of traits from ancestors to descendants. Paleontologists began using cladistics to classify dinosaurs in the 1960s, leading to years of debate as paleontologists struggled to modify the existing Linnaean hierarchy using phylogenetic analyses.

In the twenty-first century, paleontologists continue to group organisms according to a mixed system that uses both phylogenetic groups and traditional Linnaean categories. New information from molecular analysis and from a constant influx of new fossils and dinosaur species are slowly integrated into the classification scheme, sometimes drastically altering previous concepts and theories about dinosaur relationships. Among the most striking changes resulting from cladistic methods was the reorganization of the Tree of Life (phylogenetic tree) to classify birds as a subgroup of dinosaurs, a finding that is at odds with traditional taxonomic classification.

Key Terms

Characters: In taxonomy, an identifiable trait of an organism (anatomical, genetic, behavioral, etc.) utilized to determine the organism's relationship to other organisms.

Clade: Group of organisms containing all descendants of a common ancestor, as determined through the presence of synapomorphies (or synapomorphic characters).

Cladistics: Method of phylogenetic analysis that involves grouping organisms according to the presence of synapomorphies between organisms and their closest hypothetical ancestors.

Linnaean Taxonomy: System of classification in which organisms are grouped into nested hierarchies of interrelated groups, starting at the most general level of relatedness and proceeding to the species level.

Morphology: Biological term referring to the shape and structure of an organism.

Phenetics: Study of the degree of relatedness between organisms, based on genetic, molecular, or anatomical characters.

Phylogenetics: The study of evolutionary relationships between organisms.

Synapomorphies: In cladistics, a trait that is shared by two or more organisms and their closest shared ancestor.

Systematics: Branch of science concerned with the evolution and relatedness of living organisms.

Taxon (plural: taxa): In phylogenetics, a group of one or more animals comprising an evolutionary unit.

Taxonomy: Branch of biology dealing with describing, naming, and classifying living organisms.

Key Players

Carl Linnaeus: Swedish naturalist Carl Linnaeus created the first and most influential system for naming and classifying organisms based on overall similarity. Linnaeus first published his findings in a small publication called Systema Naturae in 1735, in which he described a system for grouping all life on earth into a series of categories, named according to a set of characteristics that define the group. Linnaeus published numerous revisions of his classification scheme and influenced generations of scientists who contributed to the field. Linnaean taxonomy, attributed to Linnaeus, is still in use for many groups of animals, though it has been heavily modified through more than two centuries of research and discovery.

Richard Owen: British biologist Richard Owen coined the term “Dinosauria” in 1842, as a name for the large fossil bones discovered by paleontologists that Owen considered ancient members of a single reptile group. Owen also provided the first scientific description of Archaeopteryx (meaning “ancient wing”), a prehistoric animal now considered to be one of the earliest known birds. Paleontologists have since refined the term “Dinosauria” on several occasions in an effort to reflect new research and refinements of evolutionary theory.

Willi Hennig: German entomologist Willi Hennig, in an effort to create a classification system that better reflected evolutionary relationships, developed phylogenetic analysis. In a series of theoretical contributions, beginning with Grundzüge einer Theorie der Phylogenetischen Systematik, (Phylogenetic Systematics) published in 1950, Hennig put forth a system called “cladistics” that groups organisms based on key, shared characteristics inherited from a common ancestor. Paleontologists widely embraced cladistics in the 1970s, when they learned that phylogenetic studies were more effective at recreating relationships among organisms known only from isolated remains.

Jacques Gauthier: In his 1986 doctoral thesis, “Saurischian Monophyly and the Origin of Birds,” paleontologist Jacques Gauthier presented the first comprehensive phylogenetic analysis indicating that birds evolved from a theropod dinosaur ancestor. Additional fossil discoveries in the 1990s and 2000s strengthened Gauthier's thesis, convincing most paleontologists to reclassify birds as members of the Dinosauria. Gauthier is one of a group of paleontologists who has advocated the abandonment of the Linnaean system in favor of using phylogenetic nomenclature, a naming system based on cladistics.

History

Linnaean Taxonomy: In his 1735 text Systema Naturae, anatomist Carl Linnaeus established the scientific basis of taxonomy, the science of classifying living things. The essence of the Linnaean system was to group organisms according to similarities in morphology, which is the structure and anatomy of an organism.

Linnaean taxonomy is a rank-based classification system in which organisms are placed into a series of hierarchical categories, each of which is defined by a certain list of key traits that an organism must possess to be included in the category. Each organism is then designated by a unique scientific name consisting of its genus, followed by the species name.

The Linnaean system, in heavily modified form, persisted into the twenty-first century as one of the cornerstones of taxonomic science. In 1842, paleontologist Richard Owen coined the term “Dinosauria” for the large, reptile-like creatures being uncovered from excavations. The rank Dinosauria is now considered a “superorder” in the taxonomic hierarchy, a rank between the class and order categories.

In 1887, British paleontologist Harry Seeley divided the superorder Dinosauria into two orders: the Saurischia, or “lizard-hipped,” dinosaurs and the Ornithischia, or “bird-hipped” dinosaurs. Over the centuries, the dinosaurs were further divided into a number of suborders, including Theropoda, which contains most of the predatory, bipedal dinosaurs such as Allosaurus and Tyrannosaurus, and the suborder Sauropoda, which contains the large long-necked herbivorous dinosaurs such as Brachiosaurus and Diplodocus.

Evolutionary Classification: In the 1950s, German entomologist Willi Hennig introduced cladistics, a system of classification intended to reflect evolutionary relationships between species. Cladistics is the classification system used in phylogenetics, which is the study of evolutionary relationships among groups of organisms. Cladistics creates “clades” based on the presence of shared, inherited characteristics, called “synapomorphies.”

To create a clade, biologists choose one or more characteristics of interest—for example, the shape of a certain bone or a specific section of the organism's genetic code—and then add species to the clade depending on whether they possess the trait in question. Each clade consists of an ancestor species grouped with all or some of its descendents possessing the same trait or a modified version of the trait.

Cladistics was a major revolution in paleontology—cladistic analysis can be effective using limited data, whereas the Linnaean system is more effective if the taxonomist has access to complete specimens. For example, cladistic analysis can create clades using only isolated fragments of fossils. A single clade can trace the inheritance of a single character; Linnaean taxonomy focuses on creating trees from entire species.

Current Research and Implications

The Origin of Birds: At times, cladistic analysis and traditional taxonomy reach different conclusions. For instance, cladistic analysis indicates that birds should be placed in the same clade as the theropod dinosaurs, meaning that birds are a subgroup of dinosaurs.

In the 1870s, pioneering evolutionary biologist Thomas Henry Huxley theorized that birds and dinosaurs were related, but it was not until the 1980s that the scientific community accepted this hypothesis. Phylogenetic analyses by paleontologists John Ostrom and Jacques Gauthier provided the scientific evidence needed to convince most paleontologists that birds were members of the dinosaur lineage. By contrast, Linnaean taxonomy does not arrive at the same conclusion because of the major morphological differences between the two groups.

During the late 1990s and throughout the 2000s, paleontologists working in China have discovered a number of new dinosaur species closely related to birds. Anchiornishuxleyi, discovered in 2009 and named to honor Huxley, is an example a theropod with close ties to the bird lineage. Given the variety of new fossil species, traditional taxonomic methods also place dinosaurs and birds in the same group.

The PhyloCode: Modern evolutionary biologists use a combination of Linnaean taxonomy and phylogenetics to reconstruct evolutionary history. Some scientists believe that the Linnaean system should be completely abandoned in favor of a system built on cladistic analysis.

The International Society for Phylogenetic Nomenclature (ISPN) is a group of scientists dedicated to promoting a new classification system, called “PhyloCode,” to replace the existing system Linnaean system. The project started in the late 1990s and the ISPN has published several revisions of its classification guidelines. Supporters of PhyloCode believe that the Linnaean system is imprecise, overly complex, and that most, if not all of the current taxonomic groups need to be revised.

If the PhyloCode is accepted, all of the rank-based groups would be replaced. The concept of “species” would be replaced by the term “taxon,” defined as one or more organisms constituting a distinct evolutionary type. To give one example of how PhyloCode would change the current system: Aves (birds) would no longer be considered a class, as they are under the Linnaean system, because cladistic analysis shows that birds should be part of the class Reptilia. Under the PhyloCode, Aves would be reclassified as an “unranked group” that “contains” but does not define the group.

The Linnaean system functions by defining groups and classifying organisms according to whether or not they fit the characteristics that define the group. By contrast, the PhyloCode groups are not ranked or defined but, rather, they are constituted by organisms that fit into a certain clade. The group birds would therefore be “defined” as the clade that contains all descendant species arising from a theropod dinosaur ancestor, rather than being defined by a set of characteristics including feathers, beaks, and so forth.

Although a small number of scientists are currently using PhyloCode in their published works, most scientists continue to use the common Linnaean ranks, informed by discoveries from phylogenetic research. The PhyloCode represents one extreme in the ongoing debate over the best method for organizing the scientific Tree of Life to reflect evolutionary history.

Bibliography

Books

Carpenter, Kenneth, and Phillip J. Currie. Eds. Dinosaur Systematics: Approaches and Perspectives. New York: Cambridge University Press, 1992.

• Comprehensive text covering the methods used to create classification groups within the dinosauria. Sections present information on the history of dinosaur taxonomy with in-depth discussions of genetic research, cladistic analysis, and integrative approaches to systematics.

Fastovsky, David E., and David B. Weishampel. Dinosaurs: A Concise Natural History. New York: Cambridge University Press, 2009.

• Introductory text providing basic information on dinosaur evolution and behavior and the science of paleontology. Contains sections on systematics, dinosaur nomenclature, and the debate over traditional taxonomy and cladistic approaches.

—. Evolution and Extinction of the Dinosaurs. New York: Cambridge University Press, 2005.

• Text presents both introductory and more advanced material covering a variety of subjects related to dinosaur evolution. Each section detailing different dinosaur groups contains information on the systematics of the group. The third chapter contains a brief discussion of the history of dinosaur classification.

Fraser, Nicholas C., and Hans-Dieter Sues. In the Shadow of the Dinosaurs: Early Mesozoic Tetrapods. New York: Cambridge University Press, 1997.

• Comprehensive text focusing on tetrapods (four-footed vertebrate animals) living alongside the dinosaurs during the Mesozoic. Includes a discussion of systematic analysis both as applied to dinosaurs and other groups of Mesozoic creatures.

Gee, Henry. Deep Time: Cladistics, the Revolution in Evolution. New York: HarperCollins, 2008.

• Discussion of the science of cladistics written for general readers. Contains a detailed discussion on the history of cladistics and about the debate regarding the efficacy of cladistics versus traditional forms of taxonomic research. The author presents numerous illustrations, applying cladistic analysis to a variety of animal groups.

Weishampel, David, Peter Dodson, and Halszka Osmolska. Dinosauria. Berkeley: University of California Press, 2004.

• Introduction to the dinosaur groups including behavioral research, evolutionary analysis, and information on taxonomic research. Contains a discussion of cladistic analysis as applied to the dinosaurian as a whole, as well as more specific discussions of systematics research as applied to the major dinosaur groups.

Journals

Dodson, Peter. “Origin of Birds: The Final Solution.” Integrative and Comparative Biology 40 (2000): 504–12.

• Discusses the limitations of the cladistic approach as applied to discerning the evolution of birds from dinosaur ancestors. Author also suggests an approach to taxonomy based on utilizing a combination of techniques to gain a more complete view of evolution.

Additional Works Used

Foer, Dan. “Pushing Phylocode: What If We Decide to Rename Every Living Thing on Earth?” Discover. 28 April 2005. Web. 9 May 2011. http://discovermagazine.com/2005/apr/pushing-phylocode.

Soares, Christine. “What's In a Name?” Scientific American. Web. 9 May 2011. <http://www.scientificamerican.com/article.cfm?id=whats-in-a-name>.