Frozen Evolution. Or, that’s not the way it is, Mr. Darwin. A Farewell to Selfish Gene.

It is not always easy to decide whether homology or homoplasy is involved for a certain trait.In the vast majority of cases the relevant fossil material is not available so that there is no information on whether the closest common ancestor of certain species exhibited the trait or not.In addition, in order to determine which species was the common ancestor of the studied species, we would need to first reconstruct the cladogenesis of the particular taxon, i.e. to know what traits are homologies and which homoplasies.

            The absence or presence of the given trait in members of the phylogenetic line can be of assistance in differentiating homology and homoplasy, where we are certain that some members broke off from the common phylogenetic line sooner than all other species under study.The optimum approach consists in monitoring the presence of a particular trait in a sister taxon, i.e. the line that was the first to branch off from the closest ancestor of the last common ancestor of all the studied species.If the members of the sister taxon also bear this trait, it is more probable that it was also present in the common ancestor of the compared species, i.e. that homology is involved.Understandably, we cannot always be certain that the taxon is a sister taxon of the studied group.In addition, erroneous designation of a sister taxon can seriously endanger the correctness of further analysis.What is more, a method is frequently employed that is based on the implicit assumption that the same traits are rarely formed independently of one another and thus that the presence of the same trait in two different species most probably means that it was inherited from a common ancestor.This is quite a reasonable assumption and is basically the starting point for the maximum parsimony method (see below) and thus entire traditional cladistics.However, in some specific cases, it may be erroneous and thus misleading.

The means through which the particular trait was established during ontogenesis can be a further guideline.The mechanisms of ontogenesis are evolutionarily relatively stable and simultaneously frequently differ for similar traits formed independently during evolution.However, this is not a completely reliable guideline; in some cases a homological trait can also be formed in two different groups of organisms through different ontogenetic mechanisms and, in contrast, in the case of homoplasy, similar or even, in many respects, identical ontogenetic mechanisms can be in operation.