Question

Why might amino acid polymorphisms that sweep through populations under directional selection tend to be rarely sampled as polymorphisms?  

Answer 1

Selection involves gene loci having two alleles and occurs if fitness differs among three genotypes. Directional selection occurs when one phenotype is favored over other, that is, when one of the two alleles is favored such that its frequency increase until it reaches fixation. These are the beneficial alleles that will be fixed. Amino acid polymorphism is a single nucleotide change in codon. The substitutions at 3^rd position in codons mostly do not change the amino acids thus, they are neutral. The 1^st and 2^nd position in codons have selection on amino acid substitutions that causes diversity that is less than neutral case. However, in some cases such as small populations, they may be neutral. Selection does not occur during neutral variations thus, amino acid polymorphisms sweeping through populations under directional selection is rarely sampled as polymorphisms.