Hi
By molecular clock, it is referred to the alterations that take place in the small sequences of DNA and which with the passage of time cause organisms to evolve from one to many.
In actual, the main cause of evolution in living organisms is the changes in DNA sequence of organisms, called mutations. Mutations serve as molecular clocks and today, scientists use these mutations to track back changes that took place in the organism over the course of time and to find the appropriate ancestor of organisms.
If we talk specifically about silent mutations, they are mutations that donot depict a great changing in the phenotype of organism or cause physiological abnormalities like diseases. They stay without causing any effect or harm to organisms.
However, these silent mutations if transferred to offspring during reproduction can have a substantial affect after many generation when this mutation will manifest itself. It is because this mutation can affect in combination over some other gene and cause significant effect on organism. This effect can be either harmful or dangerous. Here the organism who will be better able to adapt this mutation will survive as per the principle of natural selection and these selected organism with the passage of time can develop into entirely new specie.
This is how it works mutations work as molecular clocks and can be used to trace the ancestry of organisms.
Hope it help!