Q1.3. How do the frequencies of allele S in the Breeding Pens compare to the frequency of allele S among ferrets in the field population?
They are exactly the same as the field population's frequency.
They are nearly the same as the field population's frequency (within 10%).
They vary, and some are fairly different from the field population's frequency.
Q1.4. How did the frequencies of allele S in the pens come to be different from the frequency in the field?
Just by chance, I happened to grab a different collection of genotypes for each pen.
In some pens, selection favors allele S; in other pens selection favors allele C.
When I selected ferrets to move, I adjusted my choices so that the allele frequencies would be different in each pen.