VI.1.3 The existence of mutation bias and reparation drive causes the same mutation to occur independently and repeatedly in different organisms, complicating the use of molecular traits in phylogenetic studies.
At the present time, molecular-taxonomic techniques represent one of the most important instruments used in phylogenetic studies (see IX). The most universal technique probably consists in sequencing of segments of a certain gene in various species of organisms and constructing phylogenetic trees of these species on the basis of similarity of the nucleotide sequences obtained. The methods of construction of the phylogenetic tree differ substantially, but they are all based on the idea that the degree of similarity of the sequences of the genes of two species reflects their phylogenetic relatedness. The similarity of two sequences reflects the number of mutually identical positions in the nucleotide strand. Homoplasy, i.e. the occurrence of identical traits, in this case the same mutation in a certain position on the DNA strand, in mutually unrelated organisms constitutes a substantial complication in the use of molecular-taxonomic techniques in phylogenetic studies. The opposite of homoplasy is evolutionary homology, i.e. sharing of a single trait by various species through inheritance from a single ancestor. Most the techniques employed automatically assume that the same mutation can be formed even in two unrelated species purely by chance and is capable of more or less eliminating the effect of these homoplasies (see XXIV.1.6). However, if certain mutations are formed not by accident but through mutation bias or reparation drive, the intensity of the false signal (number of homoplasies) can be greater than the intensity of the real phylogenetic signal (number of homologies) and the method can then yield erroneous results. The positions of species in the framework of the obtained phylogenetic tree then need not reflect the degree of their phylogenetic relatedness, but rather the degree of similarity of the mutation biases and reparation drives active in the given species. At the present time, there are, of course, techniques that assist in minimizing the effect of homoplasies caused by the action of evolutionary drives (and selection).