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Relaxed molecular clock dating

The molecular clock technique is an important tool in molecular systematics, the use of molecular genetics information to determine the correct scientific classification of organisms or to study variation in selective forces.Knowledge of approximately constant rate of molecular evolution in particular sets of lineages also facilitates establishing the dates of phylogenetic events, including those not documented by fossils, such as the divergence of living taxa and the formation of the phylogenetic tree.

Molecular clock users have developed workaround solutions using a number of statistical approaches including maximum likelihood techniques and later Bayesian modeling.It must be remembered that divergence dates inferred using a molecular clock are based on statistical inference and not on direct evidence.The molecular clock runs into particular challenges at very short and very long timescales. When enough time has passed, many sites have undergone more than one change, but it is impossible to detect more than one.If this is correct, the cytochrome c of all mammals should be equally different from the cytochrome c of all birds.Since fish diverges from the main stem of vertebrate evolution earlier than either birds or mammals, the cytochrome c of both mammals and birds should be equally different from the cytochrome c of fish.To achieve this, the molecular clock must first be calibrated against independent evidence about dates, such as the fossil record.

For viral phylogenetics and ancient DNA studies – two areas of evolutionary biology where it is possible to sample sequences over an evolutionary timescale – the dates of the intermediate samples can be used to more precisely calibrate the molecular clock.

If most changes seen during molecular evolution are neutral, then fixations in a population will accumulate at a clock-rate that is equal to the rate of neutral mutations in an individual.

The molecular clock alone can only say that one time period is twice as long as another: it cannot assign concrete dates.

Together with the work of Emile Zuckerkandl and Linus Pauling, the genetic equidistance result directly led to the formal postulation of the molecular clock hypothesis in the early 1960s.

developed the neutral theory of molecular evolution, which predicted a molecular clock. mutations with no effect on fitness) in a new individual be .

Let there be N individuals, and to keep this calculation simple, let the individuals be haploid (i.e. The probability that this new mutation will become fixed in the population is then 1/N, since each copy of the gene is as good as any other.