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

Cladogenesis can best be studied using traits that can be formed only once during evolution and cannot disappear once they are formed.However, a minimum number of such traits are known.To a substantial degree, some types of data obtained using molecular biological techniques approach this ideal, e.g. obtained by the taxoprint method (XXIV.3.9) or by analysis of SINE-retroelements (XXIV.3.14).If all the evolutionary changes are irreversible, the Camin-Sokal parsimony method can be used for the reconstruction.Very frequently, the relevant analysis can be performed “manually”, without using a computer, where trees formed on the basis of a small number of traits are usually of very good quality, i.e. reliably reflect the actual cladogenesis of the particular line.

            It is also possible that the traits can be formed only once during evolution, but can disappear repeatedly.Many classical traits can fall in this category, for example morphological traits.If the analysis includes only complicated traits whose formation is dependent on a large number of genes, for which there is low probability that they would be formed several times repeatedly in the same form in evolution, Dolly parsimony can be used for the analysis.It once again holds that analysis of this type of trait is relatively simple and that the results obtained are usually quite reliable.s

            If it is necessary to assume reversibility of all evolutionary changes, then Wagner parsimony must be employed in the reconstruction of cladogenesis.This method is used most often for classical and molecular traits, but is more demanding on calculations and thus almost always requires the use of a powerful computer.Simultaneously, the results obtained are not as reliable as for the previous method.The analysis can often yield several (or even a great many) trees, which differ substantially in their topology and but simultaneously only minimally or not at all in the anticipated number of evolutionary changes.

            General parsimonyis most demanding on the calculation; in this method, the relative weights of the individual types of evolutionary changes can be entered on the basis of their probabilities.This method is useful, for example, in processing data obtained by restriction mapping (see XXIV.3.3).If we map restriction sites (sites at which the DNA chain is cut) with a length of six nucleotides; then the loss of a specific restriction site is six times more probable than its formation.A mutation in any of the six nucleotides is sufficient for the loss of the restriction site; only one specific nucleotide of the six must mutate for its formation.For example, if we must choose between two trees, of which the first assumes one independent formation of a restriction site and ten independent losses and the second requires two independent formations and only four independent losses, then, on the basis of Wagner parsimony, we would have to choose the second tree while, on the basis of general parsimony, which assumes that independent loss of a restriction site is six times more probable than its formation, we would have to choose the first tree.General parsimony is even more demanding on computation than Wagner parsimony but simultaneously yields more reliable results.