In phylogenetics, basal is the direction of the base (or root) of a rooted phylogenetic tree or cladogram. CladeC may be described as basal within a larger clade D if its root is directly linked (adjacent) to the root of D. The terms deep-branching or early-branching are similar in meaning. If C is a basal clade within D that has the lowest taxonomic rank of all basal clades within D, C may be described as the basal taxon of that rank within D. While there must always be two or more equally basal clades sprouting from the root of every cladogram, those clades may differ widely in rank[n 1] and/or species diversity. Greater diversificationmay be associated with more evolutionary innovation, but ancestral characters should not be imputed to the members of a less species-rich basal clade without additional evidence, as there can be no assurance such an assumption is valid.[n 2]
In general, clade A is more basal than clade B if B is a subgroup of the sister group of A. Within large groups, "basal" may be used more loosely to mean 'closer to the root than the great majority of', and in this context terminology such as "very basal" may arise. A 'core clade' is a clade representing all but the basal clade of lowest rank within a larger clade.
A basal group forms a sister group to the rest of the larger clade, such as in the following example:
Non-basal group #1
Non-basal group #2
Non-basal group #3
It is assumed in this example that the terminal branches of the cladogram depict all the extant taxa of a given rank within the clade; otherwise, the diagram could be highly deceptive.
In phylogenetics, the term basal can be correctly applied to clades of organisms, but not to lineages or to individual traits possessed by the organisms—although it may be misused in these ways in technical literature.[n 3] A basal group may or may not represent a good analogy for the last common ancestor of a larger clade. In describing characters, "ancestral" or "plesiomorphic" (but not "basal", see Criticism) are preferred to "primitive", which may carry false connotations of inferiority or a lack of complexity.
The flowering plant family Amborellaceae, restricted to New Caledonia in the southwestern Pacific,[n 4] is a basal clade of extant angiosperms, containing the most basal species, genus, family and order within the group (out of a total of about 250,000 angiosperm species). While the traits of Amborella trichopoda are regarded as providing significant insight into the evolution of flowering plants, they are a mix of plesiomorphic (archaic) and apomorphic (derived) features that have only been sorted out via comparison with other angiosperms and their positions within the phylogenetic tree (the fossil record could potentially also be helpful in this respect, but is absent in this case).
Within the primate family Hominidae (great apes), gorillas (eastern and western) are a sister group to common chimpanzees, bonobos and humans. These five species form a clade, the subfamily Homininae (African apes), of which Gorilla is the basal genus. However, if the analysis is not restricted to genera, the Homo plus Pan clade is also basal. This semantic ambiguity is discussed in the Criticism section.
Subfamilies Homininae and Ponginae are both basal within Hominidae, but given that there are no nonbasal subfamilies in the cladogram it is unlikely the term would be applied to either. In general, a statement to the effect that one group (e.g., orangutans) is basal, or branches off first, within another group (e.g., Hominidae) may not make sense unless the appropriate taxonomic level(s) (genus, in this case) is specified. If that level cannot be specified (i.e., if the clade in question is unranked) a more detailed description of the relevant sister groups may be needed.
In this example, orangutans differ from the other genera in their Eurasian range. This fact plus their basal status provides a hint that the most recent common ancestor of extant great apes may have been Eurasian (see below), a suggestion that is consistent with other evidence.