Cladistics

Cladistics, from the ancient Greek κλάδος, klados, "branch", is the hierarchical classification of species based on phylogeny or evolutionary ancestry. The term phylogenetics is often used synonymously with cladistics. Cladistics is distinguished from other taxonomic systems because it focuses on the evolutionary relationships of species rather than on morphological similarities, which may be convergent, and because it places heavy emphasis on objective, quantitative analysis.

Cladistics originated in the work of the German entomologist, Willi Hennig, who himself referred to it as phylogenetic systematics; the use of the terms "cladistics" and "clade" was popularized by other researchers. Cladistics originated in the field of biology but in recent years has found application in other disciplines, for example in Textual criticism to determine the relationship between the surviving manuscripts of the Canterbury Tales

Cladistics generates diagrams called cladograms that represent the evolutionary tree of life. DNA and RNA sequencing data are used in many important cladistic efforts. Computer programs are widely used in cladistics, due to the highly complex nature of cladogram generation procedures.

Terminology

• A clade is an ancestor and all of its descendents
• A monophyletic group is a clade
• A paraphyletic group is a monophyletic group that excludes some of the descendants (e.g. reptiles are sauropsids excluding birds). Most cladists discourage the use of paraphyletic groups.
• A polyphyletic group is a group consisting of members from two or more non-overlapping monophyletic groups (e.g. flying animals). Most cladists discourage the use of polyphyletic groups.
• An outgroup is an organism that is considered not to be part of the group in question, but is closely related to the group.
• A plesiomorphy (meaning "close form", also called an ancestral state) is a characteristic that is present in both the outgroups and the ancestors.
• An apomorphy (meaning "separate form", also called a "derived" state) is a characteristic that occurs only in later descendants of a group.

Note:

The adjectives plesiomorphic and apomorphic are used instead of "primitive" and "advanced" to avoid placing value-judgments on the evolution of the character states, since both may be advantageous in different circumstances.

It is not uncommon to refer informally to a collective set of plesiomorphies as a ground plan for the clade or clades they refer to.

• A species or clade is basal to another clade if it holds more plesiomorphic characters than that other clade. Usually a basal group is very species-poor as compared to a more derived group. It is not a requirement that a basal group be extant. For example, palaeodicots are basal to flowering plants.
• A clade or species located within another clade is said to be nested within that clade.

Three definitions of clade

There are three major ways to define a clade for use in a cladistic taxonomy.

• Node-based: the last common ancestor of A and B, and all descendants of that ancestor. Crown groups are a type of node-based clade.

• Branch-based: the first ancestor of A which is not also an ancestor of Z, and all descendants of that ancestor. (This type of definition was originally called "stem-based", but this was changed to avoid confusion with the term "stem group".) Total groups are a type of branch-based clade.

• Apomorphy-based: the first ancestor of A to possess derived trait M homologously (that is, synapomorphically) with that trait in A, and all descendants of that ancestor. The process of identifying and naming groups based on apomorphies is the method that most resemble classical systematics, with the exception that cladistic taxa always denote a clade.

History of cladistics

Hennig's major book, even the 1979 version, does not contain the term cladistics in the index. He referred to his own approach as phylogenetic systematics, as implied by the book's title. A review paper by Dupuis observes that the term clade was introduced in 1958 by Julian Huxley, cladistic by Cain and Harrison in 1960, and cladist (for an adherent of Hennig's school) by Mayr in 1965.

From the time of Hennig's original formulation until the end of the 1980s cladistics remained a minority approach to classification. However in the 1990s it rapidly became the dominant method of classification in evolutionary biology. Cheap but increasingly powerful personal computers made it possible to process large quantities of data about organisms and their characteristics. At about the same time the development of effective polymerase chain reaction techniques made it possible to apply cladistic methods of analysis to biochemical and molecular genetic features of organisms as well as to anatomical ones.

Cladistics as a successor to phenetics

For some decades in the mid to late twentieth century, a commonly used methodology was phenetics ("numerical taxonomy"). This can be seen as a predecessor to some methods of today's cladistics (namely distance matrix methods like neighbor-joining), but made no attempt to resolve phylogeny, only similarities.

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