The ultrametric tree (UT) is a commonly used model for evolutionary trees assuming that the rate of evolution is constant (molecular clock hypothesis).
Tests of the molecular clock hypothesis indicate that the variations in the rates of molecular evolution are substantially larger than would be expected according to the neutrality theory.
In the early 1960s, biochemists Linus Pauling and Emile Zuckerkandl proposed the molecular clock hypothesis (MCH): that sequence differences between homologous proteins could be used to calculate the time since two species diverged.
Protein sequencing had great potential for the quantitative study of evolution (through the molecular clock hypothesis), but leading evolutionary biologists questioned the relevance of molecular biology for answering the big questions of evolutionary causation.
Some early experimental evidence [34], [35] supports a "Molecular Clock" hypothesis.
If this hypothesis is rejected, then the molecular clock hypothesis can be rejected for this set of sequences.
The greater the variations, on average, the greater the time since the last clonal evolution cycle ("a molecular clock hypothesis").
In the evolutionary process, the substitution rate of biological molecules (amino acids and nucleotides) is considered stable, which is called the "molecular clock" hypothesis.
Since its proposal in 1965 [28], the molecular clock hypothesis has been one of the most hotly debated subjects in evolutionary biology.
These assumptions typically bear either on rates of molecular evolution (molecular clock hypothesis, local clocks models) or on both rates and times (penalized likelihood, Bayesian methods).
Under the molecular clock hypothesis, irrespective of the substitution model and whether or not the substitution rate varies with the site, the number of mutations inferred for the two ingroup branches should be similar.
