Where did all the different alleles at each gene locus come from? They are the result of mutations that occurred during DNA replication prior to meiosis. The simplest mutation, a point mutation, is a change in one amino acid in a protein, producing a new protein and thus a new allele. The albino plant in the photo is the result of a mutation. Mutant alleles that are harmful to individuals that bear them are reduced to low levels in the population by natural selection. Mutant alleles that are neither harmful nor beneficial, for example eye color variants, may remain in a population.