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Cladistics or (phylogenetic systematics) is a branch of biology that determines the evolutionary relationships between living things based on derived similarity. Cladistics differs from phenetics, which groups organisms based on overall similarity, and from more traditional approaches based on "key characters".

Based on a wide variety of information, which includes genetic analysis, biochemical analysis, and analysis of morphology, relationship trees called "cladograms" are drawn up to show different possibilities.

A cladogram showing the relationship between various insect groups using horizontal parallel lines joined by vertical lines. In some cladograms of this type, the length of the horizontal lines indicates the amount of time that has passed since the last common ancestor between two groups or species.

A cladogram showing the relationship between various plant groups using intersecting diagonal lines.

In a cladogram, all organisms lie at the endpoints, and each split is ideally binary (two-way). Each branch, whether it only contains one item or a hundred thousand, is called a clade. A correct cladogram should have all the organisms contained in any one clade share a unique ancestor for that clade, one which they do not share with any other organisms on the diagram. Each clade should be set off by a series of characteristics that appear in its members but not in the other forms it diverged from. These identifying characteristics of a clade are called synapomorphies (shared, derived characters). For instance, hardened front wings are a synapomorphy of beetles, while circinate vernation, or the unrolling of new fronds, is a synapomorphy of ferns.

Cladistic Methods Typically, an analysis begins by collecting information on certain features of all the organisms in question, and then deciding which versions were present in their common ancestor (plesiomorphies) and which have been derived since (apomorphies). Usually this is done by considering some outgroup of organisms we know are not too closely related to any of the organisms in question. Only apomorphies are of any use in characterising cladistic divisions.

Next, different possible cladograms are drawn up and evaluated. Clades are typically drawn so that they can have as many synapomorphies as possible. The idea is that a sufficiently large number of characteristics should be large enough to overwhelm any examples of convergent evolution. In other words, there are many ways in which plants and animals, etc., may evolve features that resemble each other because of environmental conditions. A well-known type of convergent evolution is insect mimicry, in which some insects that are edible come to superficially resemble other insects that aren't edible, and so escape being eaten.

In practice, neutral features like exact ultrastructure, which is a term for extremely fine structure, microscopic or molecular composition of cellular structure, tend to do just that, to provide evidence for real relationships even when the appearance of organisms makes it difficult. When equivalent possibilities turn up, one is usually chosen based on the principle of parsimony: the most compact arrangement is likely the best (a sort of variation of Occam's razor). Another approach, particularly useful in molecular evolution, is maximum likelihood, which selects the optimal cladogram that has the highest likelihood based on a specific probability model of changes.

Cladistics has taken a while to settle in, and there is some questioning over in just what sort of circumstances cladistics is applicable. In particular, apomorphies are not always easy to distinguish and data is often unavailable thanks to a sparsity of available forms or a lack of knowledge of characters, and these may invalidate cladograms. There is also concern that use of widely different data sets, for instance structural versus genetic characteristics, may produce widely different trees. However, by and large cladistics has proven a useful and coherent extension of other methods and has gained general support.

Cladistics does not assume any particular theory of evolution, only the background knowledge of descent with modification. Thus, cladistic methods can be, and has recently been, usefully applied to non-biological systems, including determining language families in historical linguistics and the filiation of manuscripts in textual criticism.

Cladistic Classification A recent trend in biology since the 1960s, called cladism or cladistic taxonomy, is to require taxa (named groups in a taxonomy) to be clades. In other words, cladists argue the classification system should be reformed to eliminate all non-clades (paraphyletic and polyphyletic groups). In fact, some cladists have argued for entirely abandoning the Linnaean system of ranked taxa in favor of clades. A formal code of phylogenetic nomenclature, the Phylocode[1] (http://www.ohiou.edu/phylocode/), is currently under development for a cladistic taxonomy that abandons the Linnaean structure.

A true clade is considered to be monophyletic, or containing one (and only one) complete evolutionary grouping deriving from one common ancestor. When a named group is found to contain more than one evolutionary line, it is termed polyphyletic. For example, the once-recognized group Pachydermata was found to be polyphyletic because an elephant and a rhinoceros were each found to be more closely to non-pachyderms than either to each other. Biologists consider groups that turn out to be polyphyletic to be errors in classification, often occurring because converges or other homoplasy[?] was misinterpreted as homology.

If a named group is found to include some but not all of the descendants of the ancestor on which the group is based, it is termed paraphyletic. Paraphyletic groups are usually created when organisms are groups on the basis of plesiomorphies instead of apomorphies. Classic examples of paraphyly include Pisces (fishes), whose descendants include tetrapods (amphibians, reptiles, birds, and mammals), and Reptilia, whose descendants include birds; however, neither tetrapods nor birds are included in the groups named Pisces and Reptilia, respectively. Most paraphyletics groups, however, were erected at the genus level, because species were grouped on overall similarity prior to a cladistic analysis.

The denial of recognition to paraphyletic groups has been very controversial in biology and remains so among a number of more traditional evolutionary taxonomists[?]. They feel that abandonment of paraphyly leads to loss of information in the classification system about significant changes in organisms' morphology, ecology, or life history. Accordingly, they argue that the notions of clade and taxon should be kept distinct, and that paraphyletic taxa are necessary if every group is going to be broken down completely into subgroups. In fact, evolutionary taxomonists such as Peter Ashlock include paraphyly under the term monophyletic, reserving the term holophyletic for the strict sense of monophyletic.

Cladists counter that "significant changes" recognized by evolutionary taxonomists are often too subjective to be a basis for classification.

See also scientific classification, tree of life, systematics, taxonomy, Willi Hennig

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