A method of classifying organisms employing evolutionary hypotheses as the basis for classification. It uses recency of common ancestry as the criterion for grouping species together, rather than data on apparent similarity between species.
Cladistics is a branch of biology that determines the evolutionary relationships between organisms based on derived similarities. Cladistic analysis forms the basis for most modern systems of biological classification, which seek to group organisms by evolutionary relationships. In contrast, phenetics groups organisms based on their overall similarity, while approaches that are more traditional tend to rely on key characters (morphology).
As the end result of a cladistic analysis, treelike relationship-diagrams called "cladograms" are drawn up to show different hypotheses of relationships.
In a cladogram, all organisms lie at the leaves, and each inner node is ideally binary (two-way). The two taxa on either side of a split are called sister taxa or sister groups. Each subtree, whether it contains one item or a hundred thousand items, is called a clade. A natural group has all the organisms contained in any one clade that share a unique ancestor (one which they do not share with any other organisms on the diagram) for that clade. These identifying characteristics of a clade are called synapomorphies (shared, derived characters).
Willi Hennig (1913-1976) is widely regarded as the founder of cladistics.
Definitions
A character state (see below) that is present in both the outgroups (the nearest relatives of the group, that are not part of the group itself) and in the ancestors is called a plesiomorphy (meaning "close form", also called ancestral state). A character state that occurs only in later descendants is called an apomorphy (meaning "separate form", also called the "derived" state) for that group. It is not uncommon to informally refer to a collective set of plesiomorphies as a ground plan for the clade or clades they refer to.
Several more terms are defined for the description of cladograms and the positions of items within them. 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.
A clade or species located within another clade can be described as nested within that clade.
Cladistic methods
A cladistic analysis is applied to a certain set of information.
The researcher decides which character states were present before the last common ancestor of the species group (plesiomorphies) and which were present in the last common ancestor (synapomorphies) by considering one or more outgroups. An outgroup is an organism that is considered not to be part of the group in question, but is closely related to the group.
Next, different possible cladograms are drawn up and evaluated.
Many cladograms are possible for any given set of taxa, but one is chosen based on the principle of parsimony: the most compact arrangement, that is, with the fewest character state changes (synapomorphies), is the hypothesis of relationship we tentatively accept (see Occam's razor for more on the principle of parsimony).
As DNA sequencing has become cheaper and easier, molecular systematics has become a more and more popular way to reconstruct phylogenies.
Ideally, morphological, molecular and possibly other (behavioral etc.) phylogenies should be combined: none of the methods is "superior", but all have different intrinsic sources of error. For example, character convergence (homoplasy) is much more common in morphological data than in molecular sequence data, but character reversions are more common in the latter (see long branch attraction).
Cladistics does not assume any particular theory of evolution, only the background knowledge of descent with modification.
Cladistic classification
A recent trend in biology since the 1960s, called cladism or cladistic taxonomy, requires taxa to be clades. In contrast, other taxonomists insist that groups reflect phylogenies and often make use of cladistic techniques, but allow both monophyletic and paraphyletic groups as taxa.
A monophyletic group is a clade, comprising an ancestral form and all of its descendants, and so forming one (and only one) evolutionary group. A paraphyletic group is similar, but excludes some of the descendants that have undergone significant changes.
A group with members from separate evolutionary lines is called polyphyletic. Evolutionary taxonomists consider polyphyletic groups to be errors in classification, often occurring because convergence or other homoplasy was misinterpreted as homology.
Following Hennig, cladists argue that paraphyly is as harmful as polyphyly. The idea is that monophyletic groups can be defined objectively, in terms of common ancestors or the presence of synapomorphies. In contrast, paraphyletic and polyphyletic groups are both defined based on key characters, and the decision of which characters are of taxonomic import is inherently subjective. Many argue that they lead to "gradistic" thinking, where groups advance from "lowly" grades to "advanced" grades, which can in turn lead to teleology.
Going further, some cladists argue that ranks for groups above species are too subjective to present any meaningful information, and so argue that they should be abandoned. A quasi-stable state will result in phylogenies, which may be all but unmappable onto the Linnaean hierarchy, whereas a punctuation event that balances a taxon out of its ecological equilibrium is likely to lead to a split between clades that occurs in comparatively short time and thus lends itself readily for classification according to the Linnaean system.
Other evolutionary systematists argue that all taxa are inherently subjective, even when they reflect evolutionary relationships, since living things form an essentially continuous tree. They also argue that paraphyletic taxa provide information about significant changes in organisms' morphology, ecology, or life history – in short, that both taxa and clades are valuable but distinct notions, with separate purposes. As an unscientific rule of thumb, if a distinct lineage that renders the containing clade paraphyletic has undergone marked adaptive radiation and collected many synapomorphies - especially ones that are radical and/or unprecedented -, the paraphyly is usually not considered a sufficient argument to prevent recognition of the lineage as distinct under the Linnaean system (but it is by definition sufficient in phylogenetic nomenclature).
A formal code of phylogenetic nomenclature, the PhyloCode, is currently under development for cladistic taxonomy. In several instances (see for example Hesperornithes) it has been employed to clarify uncertainties in Linnaean systematics so that in combination they yield a taxonomy that is unambiguously placing the group in the evolutionary tree in a way that is consistent with current knowledge.
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