[rcapper]

That could be but I'm pretty sure you can't say that with any confidence. You can go from allele freqs to HWE expected genotypes but that's about it... And you can't test departure from HWE without your actual genotypes (like, not the pooled samples).

[AdrianP]

60% of loci between all samples are shared, means out of all loci that are variable in any of my populations, 60% will be found in any other population. When you look at how the allele frequency varies, between the different populations, it slightly varies, meaning if it's 49/51 in one populations, it might be 45/55 in the other and 41/59 in the 3rd and 48/52 in the 4th and so on and so forth. I plotted it, it doesn't vary much. This means intra individual variation, not intra population variation.

So you are right, I can't do anything with HWE. Which makes me wonder, can I actually calculate Fst for this.... What if I treat the entire spore population as 1 individual? I can calculate the variation within the population as if it was within that 1 individual, and then between the 6 populations?

[rcapper]

Not sure that I understand what you mean. So 60% of all of your loci are invariants? Or they're only variant in a single population? If that's true, as in, 4 pops are 100% 'A' and the fifth pop is 75% 'A', then that's actually okay and depending on the magnitude of the difference, that might be what you're even looking for.

It totally depends on your experiment, but you might have to demonstrate that 49/51 is statistically different from 48/52, etc etc. Those sound like the same frequencies to me...

I'm also not sure what you mean by "This means intra individual variation, not intra population variation." Sure, the within-pop freqs could be totally different (ex., 100 AAaa tetraploids in one pop, but 50 AAAA and 50 aaaa in the other) but you really can't tell those two situations apart from the data you have.

Yes, you can still calc Fst -- but if your freqs within each pop are the same as the freqs among each pops then Fst will be around 0 (= no differentiation between pops.)

I don't think treating the pop as one individual makes sense, but if it helps you conceptualize it then I guess go for it...

[AdrianP]

For 60%, the allele frequencies are the same.

However, there are population specific alleles. These should raise the Fst, right?

[clarissaboschi]

I have a doubt about Fst from VCFtools.

I used VCFtools to obtain Fst, but VCFtools generates 2 different Fst: mean and weighted.

Which one is best to consider? In my cases these 2 Fst are very different. I asked the same question in the VCFtools forum and I had no reply. I think the weighted is better but I had very high values in this one.

thanks
Clarissa