How to identify (as opposed to define) a homoplasy: Examples from fossil and living great apes

There is much debate on the definitions of homoplasy and homology, and on how to spot them among character states used in a phylogenetic analysis. Many advocate what I call a processual approach, in which information on genetics, development, function, or other criteria help a priori in identifying two character states as homologous or homoplastic. I argue that the processes represented by these criteria are insufficiently known for most organisms and most characters to be reliably used to identify homoplasies and homologies. Instead, while not foolproof, phylogeny should be the ultimate test for homology. Character states are assumed to be homologous a priori because this is falsifiable and because their initial inclusion in the character-state analysis is based on the assumption that they may be phylogenetically informative. If they fall out as symplesiomorphies or synapomorphies in a phylogenetic analysis, their status as homologies remains unfalsified. If they fall out as homoplasies, having evolved independently in more than one clade, their status as homologous is falsified, and a homoplasy is identified. The character-state transformation series, functional morphology, finer levels of morphological comparison, and the distribution and correlation of characters all help to explain the presence of homoplasies in a given phylogeny. Explaining these homoplasies, and not ignoring them as noise, should be as much a goal of phylogenetic analysis as the production of a phylogeny. Examples from the fossil record of Miocene hominoids are given to illustrate the advantages of a process-informs-pattern-recognition-after-the-fact approach to understanding the evolution of character states. (c) 2007 Elsevier Ltd. All rights reserved.