Recent reconstructions of evolutionary history are often dependent on assigning divergence in terms of changes in amino acid or nucleotide sequences. For example, a comparison of cytochrome c shows 10 amino acid differences between humans and dogs, 24 differences between humans and moths, and 38 differences between humans and yeast. Such data provide no information as to the absolute times of divergence for humans, dogs, moths, and yeast. How might one calibrate the molecular clock to an absolute time clock? What problems might one encounter in such a calibration?

A molecular clock is a concept in molecular evolution that uses the rate of genetic mutations to estimate the time of divergence between different species. It is based on the idea that genetic mutations progress at a relatively constant rate over time. In this case, we have information about the differences in cytochrome c sequences between humans, dogs, moths, and yeast.

To calibrate the molecular clock to an absolute time clock, we need a point of reference with known divergence time, typically obtained from the fossil record or other geological evidence. Once we have this reference point, we can establish the mutation rate by comparing the molecular differences between species with the known divergence time. This mutation rate can then be applied to other species pairs to estimate the time of their divergence. For example, suppose we have information about the divergence time between two species with 10 amino acid differences in cytochrome c. If this divergence time is known to be 50 million years, we can estimate a mutation rate of 10 differences / 50 million years = 1 difference every 5 million years. We can now use this rate to estimate the divergence time between other species.

There are several potential problems one might encounter when calibrating the molecular clock to an absolute time clock: 1. Inaccurate reference points: The fossil record or other geological evidence used for initial calibration might be incomplete or inaccurate, leading to incorrect mutation rate estimations. 2. Variability in mutation rates: Mutation rates might not be constant over time or across different lineages. This could lead to over- or underestimation of divergence times. 3. Horizontal gene transfer: Some organisms, particularly microbes, may exchange genetic material through horizontal gene transfer, which can complicate the interpretation of molecular clock data. 4. Selection pressure: Positive or negative selection pressure on specific genes might influence mutation rates, affecting the accuracy of the molecular clock. 5. Multiple substitutions: If multiple substitutions occur at the same site, the number of observed differences may not accurately reflect the actual number of mutations that have occurred. This is known as saturation and can lead to underestimation of divergence times. In conclusion, calibrating a molecular clock to an absolute time clock requires obtaining a reliable reference point with known divergence time and estimating the mutation rate based on this data. However, there are several potential problems related to the accuracy of the reference points, variability in mutation rates, horizontal gene transfer, selection pressure, and multiple substitutions that can affect the calibration process and divergence time estimation.