Homology evolving

The defining criterion for homology has been common ancestry ever since darwinian evolution replaced fidelity to archetype as the explanation for similarity among traits of organisms. Although, in some cases, an alternative criterion of similarity in developmental control or other underlying traits can be helpful in diagnosing homology, evidence for dissociation among traits at different levels of organization (e.g. genotype and phenotype) and for frequency of reticulate (lateral) evolution accentuate the problems inherent in using similarity as the defining criterion. Growing awareness that character history and organismal lineage history can and do differ puts homology definition and assessment center stage in our understanding of the evolution of genomes.