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

If the relevant paleontological data are not available or do not permit us to draw unambiguous conclusions and if approaches based on comparison of the ontogeneses of the given forms of the trait similarly fail, we can attempt to differentiate homology and homoplasy on the basis of the maximum parsimony principle. The maximum parsimony principle as employed in phylogenetics states that that the most probable course of cladogenesis is the one that can explain the distribution of the individual forms of traits within the phylogenetic tree through the smallest number of anagenetic changes, i.e. smallest number of transitions from one form of the trait to another. Thus, in looking for the maximally parsimonious tree (Fig. XXIII.5), first all the conceivable trees are created for the studied species, on which the studied species form only the terminal branches, where the form of the trait carried is drawn in next to each species. For all the hypothetical ancestors, i.e. for the inner branches of the tree, the most probable forms of the individual traits are also estimated. The most probable combination of forms of traits for the hypothetical ancestor is then chosen so that the total number of evolutionary changes cable of explaining the distribution of traits in the real studied specie sis as small as possible. If, for example, sister species 1 and 2 carry the trait in form A, then it will be assumed that this form of the trait was also carried by their common ancestor. For each created tree, the number of evolutionary changes in all the traits required to explain the distribution of the individual forms of the traits in the studied species and the tree with the smallest number of necessary changes, i.e. the maximally parsimonious tree, will be considered to be the most probable scheme of cladogenesis for the given phylogenetic line. For a small number of species and small number of traits, the maximally parsimonious tree can be sought for “manually”; however, in the vast majority of cases, a sufficiently powerful computer must be used to solve this task.
            The topology of the resultant tree corresponds to the distribution of most of the traits, i.e. minimizes the overall number of changes in all the traits together, but is usually in contradiction with the distribution of some traits. Traits whose distribution corresponds to the topology are probably homologies. On the other hand, traits whose distribution is contrary to this topology, i.e. traits whose distribution would best suit some other topology, are most probably homoplasies.
            In reconstruction of cladogenesis on the basis of the maximum parsimony principle, we simultaneously form hypotheses about phylogenesis on the basis of hypotheses as to what is a homoplasy and what is a homology and formulate hypotheses on division of traits into homologies and homoplasies on the basis of our hypothesis about the phylogeny of a particular taxon. Thus, there is a danger that, while the created hypotheses will be compatible, both the differentiation of homologies and the reconstruction of phylogenesis will be erroneous. If the obtained phylogram assumes substantially fewer evolutionary changes than the phylograms of other topologies, it is highly probable that it is correct. If the differences between phylograms are not very great in this aspect, it is not possible to rely on the obtained results and it is necessary to obtain new data or use a different method for their processing.