The overfishing altered the allele frequencies of certain genes.

Actually directly altering the genes would have to involve mutation or direct engineering which is a bit more involved.

I think a good way to think about this is with human dwarfism. Many humans with achondroplasia get it through de novo mutation, but some get it by a combination of having two recessive loss of function genes that get transmitted by both parents (often of normal height)

Now imagine a laser beam that went and killed every human above a certain height. Young people would be spared along with adults with dwarfism. Over many generations, previously rare genes for dwarfism would increase in frequency shifting the average height of the population lower and lower.

It is the change in frequency that matters here more than the underlying explanation of what changed the genes.

Overfishing didn't alter their genes. It altered the genepool.