We consider the following DNA sequences of a gene found in t

We consider the following DNA sequences of a gene found in two hypothetical species:

ACT CCG GTG CCC GTT ACA

AGT ACG GTT CCA CTT AGA

Note that codons have been chosen such that every single mutation at 1st or 2nd position is nonsynonymous, and every single mutation at 3rd position is synonymous.

How many synonymous sites are there in each sequence? How many nonsynonymous sites?

b) How many synonymous substitutions are there between these two sequences? How many nonsynonymous substitutions?

Use the results you obtained in a) and b) to calculate dS (number of synonymous substitutions per synonymous site) and dN (number of nonsynonymous substitutions per nonsynonymous site).

Solution

1.

ACT CCG GTG CCC GTT ACA

AGT ACG GTT CCA CTT AGA

The underlined sequences are nonsynonymous sites while other sites are synonymous.

2. There are 4 nonsynonymous substitutions and 2 synonymous substitutions.

3.

dS would be 2/2

dN would be 4/4