Polymorphisms Substitutions Synonymous 224 950 Nonsynonymous 65 598 Fay et al. (
ID: 273752 • Letter: P
Question
Polymorphisms
Substitutions
Synonymous
224
950
Nonsynonymous
65
598
Fay et al. (2002) surveyed polymorphism at 45 genes in D. melanogaster and in D. simulans. The segregating sites are classified as either synonymous or nonsynonymous. The sequences of these genes in the two Drosophila species were compared to assess the number of substitutions.
The results are summarized in the following McDonald-Kreitman table. Assume that the number of synonymous sites of these 45 genes is LS = 8,000 and the number of nonsynonymous sites is LNS = 20,000.
(a) Based on ratio of the observed number of non-synonymous and synonymous substitutions alone, and assuming synonymous substitutions are neutral, compute KA/KS.
(b) Using the estimate of KA/KS. from (a), is there evidence this gene may have been under positive selection (i.e. is KA/KS > 1 )?
Polymorphisms
Substitutions
Synonymous
224
950
Nonsynonymous
65
598
Explanation / Answer
Answer
A) KA/ KS= balance between neutral mutation purifying selection and beneficial mutation.
KA= no of non synonymous substitution / non synonymous site
= 598/8000
KS= no of synonymous substitution / no if synonymous sute
= 950/20000
So KA/ KS= 598*20000/8000*950= 1.574
KA/KS >1 implies positive Darwinian selection
B) yes it shows that KA/ KS is grater than 1 so the non synonymous substitution are more compare to synonymous substitution.