Regarding the number of samples used in the Fst anapysis using PopGenome

Question

[kopelol]

Hi, I'm trying to perform Fst analysis using Popgenome package in R.

I'd like to compare 2 population, but the number of samples of both population is different(Pop1 n=50, Pop2 n=200).

I this case, should I use all samples(50+200=250)? or should I select 50 samples from Pop2 randomly?

One concern is that the number of core genome SNPs called is different between these two datasets(n=250(Pop1 n=50, Pop2 n=200) or n=100(Pop1 n=50, Pop2 n=50)).

Thanks,