 Pre-Darwinian taxonomy focused on classifying according to the “natural system” where taxa were united into large groups due to their “natural affinities” (Winsor 1976). In an effort to clarify the concept of affinity, Richard Owen used the term “homologue” to refer to “the same organ in different animals under every variety of form and function” (Owen 1843). Put into an evolutionary framework, the natural affinities uniting these groups were regarded as the result of descent with modification from common ancestors and “homology” has since become a central term in comparative biology (Donoghue 1992; Hall 1994). To see how homology relates to phylogenetic inference, as well as to introduce some basic terminology, it will be useful to consider an example phylogeny (Figure 1).