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 method used in molecular biology and evolutionary biology to estimate the time (age) of evolutionary events based on genetic divergence. The time is measured in terms of the genetic differences between two species or within a single species, which accumulate constantly at a relatively constant rate over time. In principle, larger genetic differences indicate longer periods of divergence and vice versa. However, it is important to note that this is a relative time measurement rather than absolute time measurement.

To calibrate the molecular clock to an absolute time clock, one must relate genetic divergence (amino acid or nucleotide differences) to known dates or events in the fossil record or with well-established historical data. By correlating these divergence data with the time information, one can establish a calibration point or points in which the molecular clock can be linked to the actual time elapsed. For example, if we know from the fossil record that two species diverged at a certain point in time, we can look at the molecular differences between them and establish a rate of genetic divergence per unit of time, allowing a calibration of the molecular clock.

Calibrating the molecular clock to an absolute time clock is not without challenges. Some potential problems that might be encountered during the calibration process include: 1. Inaccurate fossil record dates: The fossil record is an essential source of information for calibration but, in some cases, the dates may be uncertain or inaccurate. Errors in dating can have a significant impact on the calibration process. 2. Rate variation across different lineages or molecules: The molecular clock assumes a constant rate of genetic divergence across lineages or molecules, which is not always the case. Certain lineages may have faster or slower rates of molecular evolution, and calibrating the molecular clock based on one lineage or molecule may not apply to another. 3. Insufficient data or calibration points: In some cases, there might be a lack of enough calibration points or gaps in the data that make it difficult to establish a reliable calibration. 4. Mutational saturation: Over very long evolutionary time scales, some sites within a molecule may have experienced multiple substitutions, which can lead to an underestimation of the true divergence time. Considering these potential problems, it is crucial to use multiple independent calibration points and cross-validation with different data sources (e.g., fossil records, biogeographical events, and molecular markers) to increase the confidence and accuracy of calibration.