Editing Cladistics (section)

== Terminology for character states ==
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The following terms, coined by Hennig, are used to identify shared or distinct character states among groups:<ref name="Patterson 1982">{{harvnb|Patterson|1982|pp=21–74}}</ref><ref name="Patterson 1988">{{Harvnb|Patterson|1988}}</ref><ref name="de Pinna 1991">{{Harvnb|de Pinna|1991}}</ref>
* {{anchor|plesiomorphy}} A '''[[plesiomorphy]]''' ("close form") or '''ancestral state''' is a character state that a taxon has retained from its ancestors. When two or more taxa that are not nested within each other share a plesiomorphy, it is a '''symplesiomorphy''' (from ''syn-'', "together"). Symplesiomorphies do not mean that the taxa that exhibit that character state are necessarily closely related. For example, Reptilia is traditionally characterized by (among other things) being [[Poikilotherm|cold-blooded]] (i.e., not maintaining a constant high body temperature), whereas birds are [[Homeothermy|warm-blooded]]. Since cold-bloodedness is a plesiomorphy, inherited from the common ancestor of traditional reptiles and birds, and thus a symplesiomorphy of turtles, snakes and crocodiles (among others), it does not mean that turtles, snakes and crocodiles form a clade that excludes the birds.
* {{anchor|apomorphy}}{{anchor|synapomorphy}} An '''[[apomorphy]]''' ("separate form") or '''derived state''' is an innovation. It can thus be used to diagnose a clade – or even to help define a clade name in [[phylogenetic nomenclature]]. Features that are derived in individual taxa (a single species or a group that is represented by a single terminal in a given phylogenetic analysis) are called '''autapomorphies''' (from ''auto-'', "self"). Autapomorphies express nothing about relationships among groups; clades are identified (or defined) by '''synapomorphies''' (from ''syn-'', "together"). For example, the possession of [[Digit (anatomy)|digits]] that are [[Homology (biology)|homologous]] with those of ''Homo sapiens'' is a synapomorphy within the vertebrates. The [[tetrapod]]s can be singled out as consisting of the first vertebrate with such digits homologous to those of ''Homo sapiens'' together with all descendants of this vertebrate (an apomorphy-based [[Phylogenetic nomenclature|phylogenetic definition]]).<ref name="LaurinAnderson2004">{{Harvnb|Laurin|Anderson|2004}}</ref> Importantly, snakes and other tetrapods that do not have digits are nonetheless tetrapods: other characters, such as amniotic eggs and diapsid skulls, indicate that they descended from ancestors that possessed digits which are homologous with ours.
* A character state is '''homoplastic''' or "an instance of '''[[homoplasy]]'''" if it is shared by two or more organisms but is absent from their common ancestor or from a later ancestor in the lineage leading to one of the organisms. It is therefore inferred to have evolved by convergence or reversal. Both mammals and birds are able to maintain a high constant body temperature (i.e., they are warm-blooded). However, the accepted cladogram explaining their significant features indicates that their common ancestor is in a group lacking this character state, so the state must have evolved independently in the two clades. Warm-bloodedness is separately a synapomorphy of mammals (or a larger clade) and of birds (or a larger clade), but it is not a synapomorphy of any group including both these clades. Hennig's Auxiliary Principle<ref name="Hennig 1966">{{Harvnb|Hennig|1966}}</ref> states that shared character states should be considered evidence of grouping unless they are contradicted by the weight of other evidence; thus, homoplasy of some feature among members of a group may only be inferred after a phylogenetic hypothesis for that group has been established.

The terms plesiomorphy and apomorphy are relative; their application depends on the position of a group within a tree. For example, when trying to decide whether the tetrapods form a clade, an important question is whether having four limbs is a synapomorphy of the earliest taxa to be included within Tetrapoda: did all the earliest members of the Tetrapoda inherit four limbs from a common ancestor, whereas all other vertebrates did not, or at least not homologously? By contrast, for a group within the tetrapods, such as birds, having four limbs is a plesiomorphy. Using these two terms allows a greater precision in the discussion of homology, in particular allowing clear expression of the hierarchical relationships among different homologous features.

It can be difficult to decide whether a character state is in fact the same and thus can be classified as a synapomorphy, which may identify a monophyletic group, or whether it only appears to be the same and is thus a homoplasy, which cannot identify such a group. There is a danger of circular reasoning: assumptions about the shape of a phylogenetic tree are used to justify decisions about character states, which are then used as evidence for the shape of the tree.<ref>{{Harvnb|James|Pourtless IV|2009|p=25}}: "Synapomorphies are invoked to defend the hypothesis; the hypothesis is invoked to defend the synapomorphies."</ref> [[Phylogenetics]] uses various forms of [[Maximum parsimony (phylogenetics)|parsimony]] to decide such questions; the conclusions reached often depend on the dataset and the methods. Such is the nature of empirical science, and for this reason, most cladists refer to their cladograms as hypotheses of relationship. Cladograms that are supported by a large number and variety of different kinds of characters are viewed as more robust than those based on more limited evidence.<ref>Brower, AVZ and Schuh, RT. 2021.  ''Biological Systematics:  Principles and Applications'' (3rd edn.). Cornell University Press, Ithaca nY</ref>