The molecular clock is a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged.
The biomolecular data used for such calculations are usually nucleotide sequences for DNA or amino acid sequences for proteins.
Even with more sophisticated relaxed-clock analyses, nodes that are distant from fossil calibrations will have a very high uncertainty in dating.
However, endosymbiosis events and gene duplications provide some additional information that has never been exploited in dating; namely, that certain nodes on a gene tree must represent the same events, and thus must have the same or very similar dates, even if the exact date is uncertain.
This use of molecular clocks is based on the assumptions that substitution rates for homologous genes or sites are fairly constant through time and across taxa.
Violation of these conditions can lead to erroneous inferences and result in estimates that are off by orders of magnitude.
In this study, we examine the consistency of substitution rates among a set of conserved genes in diverse bacterial lineages, and address the questions regarding the validity of molecular dating.
The use of nucleotide and amino acid sequences allows improved understanding of the timing of evolutionary events of life on earth.
Molecular estimates of divergence times are, however, controversial and are generally much more ancient than suggested by the fossil record.