Molecular clock analysis

Between 1962 and 1965, before Kimura postulated the neutral theory of evolution (Kimura, 1968), Zuckerkandl and Pauling published two fundamental papers on the evolutionary rate of proteins (Zuckerkandl & Pauling, 1962; Zuckerkandl & Pauling, 1965). They noticed that the genetic distance of two sequences coding for the same protein, but isolated from different species, seems to increase linearly with the divergence time of the two species. Since several proteins showed a similar behavior, Zuckerkandl and Pauling hypothesized that the rate of evolution for any given protein is constant over time. This suggestion implies the existence of a sort of molecular clock ticking faster or slower for different genes but at a more or less constant rate for any given gene among different phylogenetic lineages (see Fig. 11.1). The clock hypothesis received an enormous popularity almost immediately for several reasons. If a molecular clock exists and the rate of evolution of a gene can be calculated, then this information can easily be used for dating the unknown divergence time between two species just by comparing their DNA or protein sequences. If, on the other hand, the information about the divergence time between two species (for example, estimated from fossil data) is known, then the rate of molecular evolution of a given gene can be inferred. An additional advantage of assuming a molecular clock is that it can render phylogenetic reconstruction much easier and more accurate (see Chapter 5).