ABSTRACT
This chapter discusses the criteria used to establish and test homology, as well as their relationship with phylogenetic analysis and use for determining different treatments of characters in a quantitative analysis. Homology stands as a relation of basic similarity, either in intrinsic similarity of the compared features or a similarity in position, connections, and development. Those observations on similarity (i.e. homology) are used as evidence of phylogenetic relationships. The notion that a proper recognition of truly homologous similarities—those that truly characterize natural groups—automatically eliminates the need for quantitative analyses is discussed and rejected. The use of development (=ontogeny) as a means to identify apomorphic features is discussed; ontogeny can provide additional criteria for homology (e.g. further similarities in connections, development, etc.) but cannot provide a criterion to identify “polarity”. Rather, developmental programs can only be studied on trees, exactly like the rest of intrinsic features. The practical use of notions of homology to establish costs of character state transformation is discussed, and practical application in the computer program TNT is described.
