I have three population to compare their allele frequency. Based on the previous AFLP fingerprint, we know B is derived from A. A and B are closer to each other compared to C, but B shows different phenotype from A and C.
We did RNAseq on those three populations and identified the differential expression genes in each pairwise comparison. After that, I tried to do some SNPs analysis among three races, assuming the mutation may happen on protein coding region which not necessarily results in differential expression. So when identifying the SNPs, I removed all the differential expression genes in each pairwise comparisons and focused on SNP changes from those non differential expressed gene only. Surprisingly, the allele frequency changes (see distribution image https://www.dropbox.com/s/z793h29xja9x21f/Untitled-9.png?dl=0) are more dramatic between B and A than between A and C, which is controvert to our AFLP experiment.
I am a naive on SNP analysis. Does allele frequency changes among different population tell you how distant those populations are? How should I explain the discrepancy between AFLP results and allele frequency change result?