Test of selection for gene variants with in a species

Question

[JstRoRR]

I have 8 gene variants from an insect species. Among these variants some are susceptible to a treatment and some are resistant. The variants are complete coding cDNA sequenced from 8 field strains. Considerable genetic variation was observed at the nucleotide level with a total of 114 polymorphic sites identified of which 28 were non-synonymous, these resolved to a total of eight unique amino acid coding variants. To examine if selection is acting on any of the identified variants we carried out pair wise comparisons of the rate of non-synonymous substitutions per site with the rate of synonymous substitutions per site (ω or Ka/Ks) between the susceptible variant and each field variant. Profound differences were observed between ω values obtained from variant A (ω =0.64) and variant B (ω=0.7) and all other field variants (ω=0.02-0.08). I have used KaKs calculator to estimate Ka/Ks values. I understand the Ks/Ks is not over 1 but still there is a significant difference between resistant and susceptible variants.

My question is, is there a test which we can perform to check which sites are under positive selection?? Like a quantitative analysis based on the count of non-synonymous substitutions (which is higher in resistant variants variant A and variant B)

Many thanks.

Answer 1

[Emily]

Usually you use a Hardy-Weinburg equilibrium to identify if a variant is under selection. In a randomly mating population where the variant is not under selection the following should be true:

p^2 + 2pq + q^2 = 1

Where p is the frequency of allele 1 and q is the frequency of allele 2.

[JstRoRR]

Hi Emily, thanks for your comment. Don't you think sample size would be an issue here, as we just have 8 variants. I have read about McDonald–Kreitman test, can that be of any use here?