Question

How is the d_n/d_s ratio used when testing whether allele frequency change resulted from selection vs drift?

Answer 1

1. dn/ds ratio is used to detect the protein undergoing the adaptation. This test was originally developed for distantly diverged genetic sequence.

This Ratio is also represented as Ka/Ks Ratio, the of substitution rates at such sites like non-synonymous and synonymous sites.

This ratio is required to estimate the relationship between the neural mutation, beneficial selection, and purifying selection

The frequency of changes resulted from positive selection over the divergent lineages dn/ds>1 which is violated with in populations.

The dn/ds is relatively insentive to the strenght of natural selection, it is anticipated signature of adaptive evolution.

Compared to the case of divergent lineages, the behavior of dN/dS within a population is so radically different that inferences of positive and negative selection based on dN/dS are problematic or, in many cases, impossible.

Whereas dN/dS<1 is a faithful indication of negative selection across divergent lineages, the observation of dN/dS<1 within a population is consistent with either weak negative or strong positive selection.

The intuition behind this result is straightforward: strong positive selection within a population will produce rapid sweeps at selected sites (but not at neutral sites, which are assumed, independent).

As a result, two individuals sampled from such a population are likely to contain the same allele at each selected site, producing a dN/dS value less than unity.

By contrast, selective sweeps along divergent lineages will tend to produce fixed differences between representative individuals sampled from the two independent populations.

Thus, the simple interpretation of dN/dS that applies to divergent lineages does not apply within a population