You find another gene duplication in a natural population. In order to use the molecular clock to find how long ago the gene duplication event happened you count the number of:

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The question asks about using the molecular clock to estimate when a gene duplication event occurred, based on counting specific genetic changes.
Option a: substitutions. While substitutions in general occur over time, this category is too broad; not all substitutions evolve neutrally or at a constant rate, and counting all substitutions across all sites can be biased by selection and mutation rate variability. This makes it a less reliable clock signal.
Option b: synonymous substitutions. These are changes in the DNA sequence that do not alter the amino acid sequence of the encoded protein. Because they are often neutral with respect to fitness, they tend to accumulate at a more clock-like, relatively constant rate, making them good candidates for molecular clock dating of divergence or duplication events.
Option c: indels. Insertions and deletions can disrupt reading frames and often occur in a biased or context-dependent manner. They are less straightforward to model in time and can complicate alignments, reducing their reliability as a constant-rate clock signal.
Option d: non-synonymous substitutions. These alter the amino acid sequence and are frequently subject to purifying or positive selection, causing their rates to vary with time and functional constraints. This makes them a poorer proxy for neutral clock-like dating than synonymous substitutions.
In summary, while substitutions in general contain time information, synonymous substitutions are preferred for molecular clock analyses of duplication events due to their typically neutral, relatively constant rate, in contrast to indels and non-synonymous changes that are more likely to be influenced by selection and alignment issues.

You find another gene duplication in a natural population. In order to use the molecular clock to find how long ago the gene duplication event happened you count the number of:

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