If we look some examples in nature, it's obvious that changes in phenotype don't happen in a way that previous versions are "erased" in genome. Humans sometimes are born with tails, dolphins get back legs and so on. Atavisms are evidence that the general "blueprint" for a limb, for example, is preserved, and change in form is because of different gene expression / regulation.
There was an article recently about a mutant chick embryo which got a reptile snout after researchers tampered with gene regulation.
There are two main ways that gene expression changes: change in stimuli and mutations. A mutation in a regulatory sequence can change the expression of the genes it regulates. External stimulus can also trigger gene expression cascades that are already present, such as skin damage from UV rays can increase melanin production (i.e. tanning).
It is important to understand the impact that these two types of changes in gene expression have on the process of evolution, and it is best not to confuse them.
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