Developmental homologues: lineages and analysis

Developmental processes present several problems for identifying homologies and analyzing their evolution. Most evolutionary techniques approach homologies from either a taxonomic or a molecular perspective. Approaches that can accommodate many problems of developmental evolution are not well developed. Developmental process and evolutionary lineage complexity lead to a number of largely unappreciated conceptual and analytic problems. Developmental processes can evolve by duplication or diversification. Each process is in a hierarchy of super- and subprocesses. As they evolve, process components may be exchanged with or acquired by those of other processes. Because they do not fit into standard analytic procedures, these situations (including reticulate or reticulate-appearing lineages, partial homologues, iterative features, and the tracing of nontaxonomic and nonmolecular evolutionary lineages) are often ignored or considered illegitimate. Biology's disdain for the dichotomously branching phylogenetic lineages that are the basis of standard analytic approaches is ignored at the risk of making falsely negative homology evaluations. I will present an approach that can accommodate analyses of these situations. The use of nontaxonomic and nonmolecular lineages provides a way to structure comparisons between other entities, as taxonomic lineages structure comparisons among potential homologues. From an informational point of view, any entity (either a structure or process) with an evolutionary history is a potential homologue with a potential evolutionary lineage. Comparing lineages of interacting entities can reveal topological incongruences among them. Methods that identify reticulated taxonomic and molecular lineages should also apply to other lineages. Partial homologues, resulting from reticulated lineages, can be handled in several possible ways. Analytically, such an entity can be treated as a partial homologue, a novel feature, an independent sub-unit, or a unitary feature homologous to the major contributor of its inherited features.