Positive Darwinian selection and Codon based Z test

Question

[yasirfeb25]

Dear Altruists, Can anyone explain to me 1. what is meant by "Positive Darwinian selection between two genes when analyzed the substitution pattern? 2. what is meant by "Neutrality" indicated by Codon based Z test ?

Thanks.

[Michael]

What have you tried?

Answer 1

[Dave Carlson]

One way to look for positive selection between two sequences is to examine the abundance of synonymous and non-synonymous substitutions present. Under a scenario of neutral evolution (i.e., where selection on the sequence is weak or non-existent and genetic drift is likely the main evolutionary driver), the rate of synonymous substitutions per synonymous site (often called dS or Ks) and the rate of non-synonymous substitutions per non-synonymous site (often called dN or Ka) are expected to be approximately equal.

However, when positive selection is acting, you may see an excess of non-synonymous substitutions compared to synonymous substitutions, assuming that changes to the protein sequence are being favored by positive selection.

Comparing dN and dS using a model of molecular evolution and looking for statistically significant departures from neutral expectations (i.e., dN = dS) is one very common method of testing for positive selection. Such tests are implemented in a variety of programs, including PAML, HYPHY, MEGA, etc. There is a rather enormous literature on this topic. If you'd like to know more, I'd suggest digging into it or perusing a population genetics/molecular evolution textbook.