9.2 Frequency-based signatures

One signature of selection is an allele whose frequency is either smaller or larger than you would expect.

Fig. 2. The allele frequencies of this variant shows large differences between population.

How do we determine the expected AF?

We can compare AFs between populations. On average, neutrally evolving variants should have similar frequencies across populations. We can enrich for potential targets of selection by asking which variants show the biggest population-specific frequency differences.

If a variant shows large AF differences and the populations in question share common ancestry – as all populations do – then the allele frequency must have changed in one population.

We can also supplement this with knowledge about when the populations diverged to determine when and how quickly this AF change must have happened.