Mutations can occur anywhere in the chromosome. However, the structural organization of chromosomes must remain intact. In the heads any symbol can change into another (function or terminal); in the tails terminals can only change into terminals. This way, the structural organization of chromosomes is maintained, and all the new individuals produced by mutation are structurally correct programs.

Typically, a mutation rate (p_m) equivalent to two point mutations per chromosome is used. Consider the following 3-genic chromosome:

012345678012345678012345678
-+-+abaaa/bb/ababb*Q*+aaaba

Suppose a mutation changed the element in position 0 in gene 1 to “Q”; the element in position 3 in gene 2 to “Q”; and the element in position 1 in gene 3 to “b”, obtaining:

012345678012345678012345678
Q+-+abaaa/bbQababb*b*+aaaba

Note that if a function is mutated into a terminal or vice versa, or a function of one argument is mutated into a function of two arguments or vice versa, the ET is modified drastically. Note also that the mutation on gene 2 is an example of a neutral mutation, as it occurred in the noncoding region of the gene.

It is worth noticing that in GEP there are no constraints neither in the kind of mutation nor the number of mutations in a chromosome: in all cases the newly created individuals are syntactically correct programs.

In nature, a point mutation in the sequence of a gene can slightly change the structure of the protein or not change it at all, as neutral mutations are fairly frequent (e.g., mutations in introns, mutations that result in the same amino acid due to the redundancy of the genetic code, etc.). Here, although neutral mutations exist (e.g., mutations in the noncoding regions), a mutation in the coding sequence of a gene has a much more profound effect: it usually drastically reshapes the ET.