Part of neutral mutations is usually gradually fixed in the gene pool of a particular biological species through genetic drift. As the frequency of fixation of neutral mutations in time depends only on the mutation rate, of which it is assumed that it is roughly constant during phylogenesis for most organisms, it is possible for biologists to determine the time that has expired from the moment of divergence of two sister groups (taxa) from the common exclusive ancestor on the basis of the number of substitutions that occurred independently in the two lines from the moment of divergence. If we sequence a certain DNA section for two related species and determine the number of neutral mutations in which they differ, on the basis of a mathematical model that takes into account and eliminates the effect of possible repeated mutations in the same position, we can estimate how many fixation events occurred in the two species from the moment when they branched off from the common ancestor. If, in addition, we know the characteristic substitution rate for the given taxon and the given gene, i.e. the average number of mutations fixed for the given species per time interval, then we can calculate the time that has elapsed since the branching off of the relevant phylogenetic lines. Thus, fixation of neutral mutations can act as a molecular clock, permitting more or less exact dating of the individual events in phylogenesis or, to be more exact, the individual splitting events that occurred during the cladogenesis of the studied taxon.
It is obvious that this substitution rate is frequently not known. However, in this case, we can calibrate the molecular clock on the basis of the number of evolutionary changes in which the two studied species differ from a third species for which we know the moment of divergence from the paleontological record (Fig. IX.6). If, for example, we know that the taxon including species A and B branched off from the taxon including species C at time T1 ago and, since that time, species A has collected KAC mutations in the studied gene and species B KBC mutations, where, since the time of splitting off of species A and B, i.e. over time T2, species A and B collected KAB mutations, we can calculate the time expired since divergence of species A and B according to the equation
T2 = (2KABT1) / (KAC + KBC)
If, on the other hand, we know the time that has expired since branching off of species A and B and we are interested in the time that has expired since the splitting off of these species from species C, we can use the equation
T1 =( KAC + KBC) T2 / 2KAB
Contemporary data and the current theory indicate that the rate of molecular evolution can increase substantially at the moment of speciation. Extensive studies performed on the representatives of a series of taxa have shown that the number of speciations can explain about 22% of the nucleotide substitutions in the DNA of two sister lines. In other words, the nucleotide divergence of two species does not depend only on the time that has elapsed since splitting of the two lines from the last common ancestor, but also on the number of speciations that the ancestors of the two species have undergone since that time (Pagel et al. 2006). It is quite possible that acceleration of anagenesis in populations that underwent peripatric speciations (Flegr 2008) leads to fixation of many positive mutations by selection and a great many neutral and weakly detrimental mutations through the mechanism of genetic draft.