Published on: December 4, 2025

What is molecular clock?

What is molecular clock?

A molecular clock is a figurative term for a biological technique used to estimate the timeframe in which two or more species diverged from a common ancestor. It relies on the observation that genetic mutations—specifically “neutral” mutations that do not affect an organism’s survival—accumulate in DNA or protein sequences at a relatively steady and predictable rate. 
How the Molecular Clock Works:
  • Neutral Mutations: The clock primarily measures neutral mutations (changes in non-coding regions or silent mutations in proteins), which are not influenced by natural selection and therefore build up at a constant pace over millions of years.
  • Genetic Divergence: By comparing the genomes of two different species, researchers count the number of genetic differences between them. The more differences found, the longer it has been since they shared a common ancestor.
  • Calibration: To turn the number of mutations into an actual date (e.g., millions of years ago), the clock must be calibrated using independent evidence. This typically involves the fossil record or well-documented geological events (like the formation of a mountain range) that are known to have split a population. 
Common Examples of Molecular Clocks:
Different genes and proteins “tick” at different speeds, making them useful for different timeframes:
  • Cytochrome c: A slow-evolving protein used to study distantly related species.
  • Hemoglobin: Evolves at an intermediate rate, suitable for broader mammalian lineages.
  • Mitochondrial DNA (mtDNA): Mutates rapidly, making it an ideal clock for studying relatively recent events, such as the migration of modern humans.
  • Ribosomal RNA (rRNA): Evolves very slowly and is used to map ancient evolutionary branches dating back billions of years. 
Limitations and Challenges:
  • Rate Variability: The “clock” does not always run at a perfect speed. Factors like changing generation times, population sizes, and species-specific metabolic rates can cause the clock to slow down or speed up.
  • Relaxed Clock Models: Modern scientists use “relaxed” molecular clock models to account for these variations rather than assuming one universal, strict rate.
  • Saturation: At very long timescales, the same DNA site may mutate multiple times, making it difficult to detect exactly how many changes have occurred