Glossary of Phylogenetic Terms

operational taxonomic unit or OTU a noncommittal term used for the objects of study (be they species, populations or individuals)

phylogeny a hypothesis of the relationships of organisms

cladistics a phylogenetic approach which only admits of bifurcations in lineages (no polytomies or reticulate evolution) and has explicit rules for their derivation

clade a (monophyletic) group of organisms related by descent from a common ancestor

dendrogram a graphical representation of a phylogeny

cladogram a cladistic representation of a phylogeny, whereby only the branching order is displayed

phylogram a representation of a phylogeny where evolutionary relatedness is shown by both branching order and a distance measure

monophyletic a clade where all the OTU derive from a single common ancestor, and which includes all the descendents of that ancestor

paraphyletic a taxonomic group which does not include all the descendants of an ancestral taxon

polyphyletic a taxonomic group which derives from >1 ancestral taxon

node a branchpoint in a tree (a presumed ancestral OTU)

branch the segment linking one node with another, or a node with a terminal OTU

ingroup the OTU under analysis

outgroup a group of OTU assumed a priori to lie outside the monophyly of the OTU under analysis; used to give direction to determination of

resolved phylogeny one in which all relationships are represented by bifurcations

polytomy (unresolved) a node which gives rise to >2 descendent taxa

rooted phylogenies phylogeny where by use of an outgroup the last common ancestor of the clade of OTU under consideration can be placed

unrooted phylogenies phylogeny where no outgroup is specificed

characters a variable feature which can assume one out of a number of different states

ordered characters character where the transition between states follows (or is assumed to follow) a particular pattern, limiting the allowed transitions between states

reversible characters characters where the pattern of change is reversible

distances a measure of the difference between two objects

similarities a measure of the resemblance between two objects

homology common ancestry of two genes (characters, genes, positions)

paralogy homology having arisen through gene duplication

orthology "true" homologues (used of genes in a multigene family)

plerology homology of repeated sequences that are subject to concerted evolution

plesiomorphy the ancestral character state

symplesiomorphy a shared ancestral character state

synapomorphy a shared derived character state (in reference to a phyogenetic hypothesis)

apomorphy a derived character state

homoplasy independent derivation of a character state in two lineages