Homology and hierarchies: Problems solved and unresolved

Abstract Homology as a topic in phylogenetic analysis has to do with what is conserved in evolution. The problem of homology in systematics — to find homologues, and in so doing, to identify taxa — is distinct from the problem of identifying what kinds of features tend to be conserved, how and why. The two sets of issues are fundamentally interdependent at the point that one selects the appropriate taxonomic units, identifies the characters one wishes to study, or decides what constitutes a single character. Homology as a phenomenon is a manifestation of replication and of continuity of biological information. Replication occurs at many levels in the biological hierarchy: from the DNA replication that accompanies cell replication, to the replication of gross phenotypic characteristics within individual organisms that results in iterative homologues, to the replication of individuals to form a population that persists (in replication through successive generations) in evolutionary time. In replication, biological information may persist unchanged, or it may be disrupted or transformed. Different patterns of change may be expressed at different levels of the biological hierarchy. Here a concept developed in arguments on levels of selection becomes useful: change at one level of the hierarchy — e.g., genes or gross phenotype — may be screened off from changes at other levels. Understanding the manner in which phenotypic features develop or are replicated, the mechanisms of screening off, and the evolutionary origin and transformation of these mechanisms is a major challenge for understanding the biological basis of homology. The recognition or coding of characters for a phylogenetic analysis calls for decisions on what level of description and how complex a unit character is to be recognized. Here an additional point of comparison within the biological hierarchy — the relationship between organisms and taxa — becomes important. We use characters of organisms to trace phylogenies of taxa; yet because traits can arise and subsequently become fixed in different segments of a population linage, phylogenies of organismal characters can conflict with the phylogeny of the taxa that compairse them. For these reasons, a full understanding of evolutionary changes undergone in lineages will require us to combine phylogenetic analyses with analyses of development, studies of developmental and population genetics, and comparisons of gross phenotype.