All methods of ancestral character state reconstruction make explicit assumptions about the homology of the traits under study. In comparative biology the term 'homology' refers to similarity in form or function arising from common ancestry. In other words, homologous features among organisms can be traced to a single evolutionary origin. In the language of Garstang (1922), a homologous trait is a unique historical change in the developmental program of an evolving lineage. Homologous similarities may be observed in any aspect of the heritable phenotype, from properties of genetic sequences (e.g., base composition and gene order), through aspects of development, including cellular, tissue, and organismal phenotypes, to aspects of behavior that emerge from the organization of the nervous system. Homology in behavioral traits has been examined in a number of taxa, and in a variety of contexts (de Queiroz and Wimberger, 1993; Wimberger and de Queiroz, 1996; Blomberg et al., 2003). Taxa are individual branches of the tree of life, and may include species or groups of species that share a common ancestor (the latter are also referred to as clades or monophyletic groups).
It is important to note that developmental, structural, positional, compositional, and functional features of phenotypes are all useful in proposing hypotheses of homology. Yet by the evolutionary definition employed above, only features that can be traced to a common ancestor in an explicitly phylogenetic context are regarded as homologues. Because phylogenies are the product of comparative analyses using many traits, it is in fact congruence in the phylogenetic distribution of characters that serves as the ultimate criterion for homology. By this criterion homologous characters are said to have passed the test of congruence. In other words, congruence in the phylogenetic distribution of numerous character states is regarded to be the ultimate evidence for homology (Patterson, 1982; see Primate Brain Evolution in Phylogenetic Context, Electric Fish, Electric Organ Discharges, and Electroreception).
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