IX.4.1 When using the molecular clock in phylogenetics, it is necessary to bear in mind that it ticks at a different rate for individual genes, individual taxa and even for the same gene and the same taxon in time
It was long disputed whether the molecular clock “ticks” evenly over the long period of time and whether it ticks at the same rate for the individual genes and the individual taxa.It was found that the answer to all these questions is “no”.However, the determined irregularities are not of a character that would prevent use of the molecular clock method in phylogenetics and systematic biology.Knowledge of the character and source of unevenness in the rate of molecular clocks, on the other hand, frequently assists in choosing the best method for studying the phylogeny of the relevant taxon and the combination of several methods also allows study of further processes, for example demographic phenomena occurring at the level of populations or at the level of higher taxa.It is apparent that, for study of the phylogeny of higher taxa, it is preferable to employ data related to the evolution of a more slowly developing gene while, for study at the level of a genus or even a species, it is preferable to use data related to the evolution of the gene that develops fastest.
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.s