Glossary of Cladistic Terms
Compiled by Mike Crisp
For application to characters, see ordered. As applied to trees, it refers to whether distances measured along the branches of the tree add up to the observed distances (from a matrix of pair-wise distance comparisons among terminals).
Apomorphy (adj. apomorphic or apomorphous)
A relatively derived or advanced or unique character state (cf. autapomorphy, synapomorphy, plesiomorphy, symplesiomorphy).
The possession by an organism of a particular feature, e.g. this tree is rough-barked; that tree is half-barked (contrast: character and character states).
An apomorphy in a terminal taxon; diagnoses the terminal but is uninformative about relationships to other terminals; therefore of no use for cladistic tree-building.
A character type with only two states (usually given as 0, 1), in which a change in either direction is 1 step (cf. ordered, unordered, Dollo, irreversible).
Any heritable attribute of organisms that varies among terminal taxa, and so is useful in phylogenetic reconstruction.
Subdivisions of the variation among terminal taxa.
A monophyletic group (= a branch on a cladogram, diagnosed by at least one synapomorphy).
The evolutionary splitting of lineages, i.e. speciation (cf. phylesis).
A branching diagram (tree) assumed to be an estimate of a phylogeny.
Arranging organisms into named groups (taxa), whether natural or artificial (see systematisation).
Congruence (adj. congruent)
Agreement, as between characters and a tree, or between the topologies (shapes) of two trees, e.g. derived from different data sets, such as molecular and morphological. Some authors like to make separate phylogeny estimates from different data sets, and then test their congruence (cf. total evidence).
A class of methods used to estimate the amount of agreement among incongruent or partially congruent trees. Usually represented as a tree that is less resolved than any of the input trees. (There are also consensus statistics.) A consensus tree is not an hypothesis of evolutionary history, and must not be confused with a phylogenetic tree. Therefore it should not be used to trace evolution of characters, areas (biogeography), and so on. Most commonly used is the strict consensus tree, which shows only those clades that are common to all the input trees. A majority-rule consensus tree shows all clades that are found in > 50% of the input trees.
Consistency index (CI)
A measure of the parsimony fit of a character to a tree, or of the average fit of all characters to a tree. Varies from 1.0 (perfect fit) to a value asymptotically approaching zero (poorest fit). It is inflated by autapomorphies which can only take the value 1.0; thus a totally uninformative data set could return a CI equal to 1.0 (cf. retention index).
See sister groups.
A character type in which numerically upward changes are allowed but each such change can only happen once on a tree. Multiple reverse changes (= losses) are allowed (cf. ordered, unordered, irreversible).
A phylogeny of a gene, which may or may not accurately reflect the phylogeny of the organisms (see orthology).
Homology (adj. homologous)
Similarity due to common evolutionary origin, that is derived from the same ancestral character; thus, equivalent to synapomorphy. Morphologists define homology by common developmental origin, which is quite a different concept, being based on a different process, although empirically the two homologies may be congruent. Non-cladists like to include symplesiomorphy in their concept of homology.
Homoplasy (adj. homoplastic or homoplasious)
Similarity due to independent evolutionary change. This may be convergence (= analogy), parallelism (these are actually the same) or reversal (= loss). Thus, homoplasy is a mistaken hypothesis of homology.
Refers to the part of the data that is actually used by a particular method for building trees (cf. uninformative).
The study group whose phylogeny is reconstructed (cf. outgroup).
A character type in which numerically upward changes are allowed and counted as for ordered characters. Downward changes are not allowed (i.e. counted as an infinite number of steps). (cf. ordered, unordered, Dollo).
An historical sequence of ancestors and descendants.
Monophyly (adj. monophyletic)
On a phylogeny, a monophyletic group has a unique origin in a single ancestral species, and includes the ancestor and all of its descendants. It is recognised by a homologous character state (synapomorphy) in all of its members (cf. paraphyly, polyphyly).
A branch-point on a tree / cladogram.
A character type with > 2 states that follow an evolutionarily plausible sequence, e.g. petals many -> 5 -> 3 -> 0. Changes between adjacent states are counted as one step and changes between non-adjacent states are counted as (1 + no. of skipped states), e.g. from 5 petals to 0 (or vice versa) would be 2 steps (cf. unordered, Dollo, irreversible).
True homology of molecular sequences, i.e. descended in toto from the same ancestral sequence. Orthologous sequences exist in only one copy per organism, and accurately reflect the phylogenetic relationships of species (cf. paralogy, plerology, xenology).
A terminal taxon, preferably the sister-group of the ingroup, that is used to root a cladogram (cf. ingroup). The root is placed between the outgroup(s) and the ingroup. Multiple outgroups may be used.
Paralogous molecular sequences result from gene duplication (independent of organism speciation), exist in multiple copies per organism, and will reconstruct gene phylogeny rather than species phylogeny (cf. orthology).
Paraphyly (adj. paraphyletic)
A paraphyletic group originates from a single common ancestor but does not include all of the descendants of that ancestor (cf. monophyly, polyphyly). Its members share only ancestral character states (symplesiomorphies); they do not uniquely share any synapomorphies.
One of several criteria that may be optimised in building phylogenetic trees, but a philosophically important one due to its simplicity; and the basis of the most-commonly used method of cladistic analysis, at least for morphological data. The central idea of cladistic parsimony analysis is that some trees will fit the character-state data better than other trees. Fit is measured by the number of evolutionary changes implied by the tree. The fewer changes the better, e.g. there is no sense in choosing a phylogeny that has roots, flowers and xylem each evolving twice, if another tree exists on which one evolutionary origin for each of the apomorphic (= derived) states would explain the observed distribution of states across taxa.
Similarity of characters without regard to the distinction between synapomorphy, homoplasy and symplesiomorphy. Phenetic methods are poor at reconstructing phylogeny.
Evolutionary events that modify a taxon without causing speciation (cf. cladogenesis).
The unique historical relationship (resulting from evolution) among terminals, represented as a tree (cf. cladogram).
Partial homology of sequences resulting from an inter-mixture of exons and introns; will only reconstruct a composite gene history (cf. orthology).
A relatively primitive or ancestral character state (cf. apomorphy).
Evolutionary ordering of character states, determined either independently of tree construction (direct method) or from a rooted tree (indirect method).
Polyphyly (adj. polyphyletic)
A polyphyletic group does not include a unique common ancestor, i.e. it has multiple evolutionary origins. This concept is best restricted to groups of hybrid origin, e.g. eukaryotes, allopolyploids; otherwise, the distinction from paraphyly is arbitrary (cf. monophyly, paraphyly).
A branch-point in a tree with more than two branches. A polytomy referred to as "hard" results from absence of data to resolve branching dichotomously, and may be interpreted as multiple speciation. A polytomy referred to as "soft" reflects uncertainty resulting from conflict (incongruence) among two or more fully-resolved equally-parsimonious cladograms.
Retention index (RI)
Similar to the consistency index, but defined so that the highest possible value for any character is 1.0 and the lowest is 0.0; removes bias due to autapomorphies (cf. consistency index).
Reversal (= loss)
Evolutionary reversion from an apomorphic to a plesiomorphic character state (cf. homoplasy).
Sister groups (or taxa)
The branches from a node on a cladogram. In a phylogeny, the descendants of an ancestor are called daughters, while the siblings after a speciation event are called sisters (so a descendant is a daughter relative to its ancestor and a sister relative to its other sibling). Note that if either of the daughters undergoes further speciation then the sister to a particular contemporary taxon may actually be a group of contemporary taxa.
An plesiomorphy shared by two or more terminal taxa, only diagnostic of a paraphyletic group (cf. synapomorphy).
An apomorphy shared by two or more terminal taxa; thus diagnoses a clade or monophyletic group.
The evolutionary splitting of lineages.
Difficult to define rigorously in 2 or 3 lines. Defined very simply in a phylogenetic context, species are the smallest lineages that are mutually exclusive from other lineages. The internal branches of a phylogeny may be viewed as ancestral species. Note, however, that the unit lineages of a gene phylogeny are not species. See also terminal.
Reconstructing natural (i.e. phylogenetic) relationships among organisms (cf. classification).
Taxon (pl. taxa)
A named group of organisms, not necessarily a natural (monophyletic) unit (cf. terminal).
Terminal (terminal taxon)
One of the units whose collective phylogeny is reconstructed; in other words, the undivided tips of a tree. Terminals may be higher taxa, species, populations, individuals, or even genes. There should be some rational basis for accepting the integrity of each terminal (for the purpose of the analysis), e.g. a monophyletic or diagnosable unit. Despite the claims by some authors, terminals do not need to be monophyletic; in fact, many species-level terminals are unavoidably paraphyletic. However, higher taxa used as terminals should be monophyletic.
Reconstructing phylogeny by analysing combined data of different kinds, e.g. morphology and gene sequences. A controversial issue, because gene phylogenies may be incongruent with organismal phylogenies (cf. congruence).
All tree-building methods discard some data, and therefore such data are "uninformative" for building trees. For instance, in parsimony methods only characters whose number of steps can vary on trees are informative; autapomorphic and invariant characters are uninformative (these can be determined by inspection of the data). However, in UPGMA autapomorphic characters are informative. (cf. informative).
A character type with > 2 states that have no plausible evolutionary sequence, e.g. the nucleotides A, C, G and T. A change between any pair of states is counted as 1 step (cf. ordered, Dollo, irreversible).
A polyphyletic relationship among sequences resulting from horizontal gene transfer (cf. orthology).