Molecular phylogenetics and the perennial problem of homology Penultimate Draft (Forthcoming in 2016, Journal of Molecular Evolution) S. Andrew Inkpen and W. Ford Doolittle Abstract The concept of homology has a long history, during much of which the issue has been how to reconcile similarity and common descent when these are not coextensive. Although thinking molecular phylogeneticists have learned not to say “percent homology” the problems are deeper than that, and unresolved. 1