Not directly related to Perl, but you might want to take a look at the Tierra project. It's pretty much moribund nowadays, but a few years back (1994-1996) it was a good little example of digital evolution simulation and how one might go about it. The source code is fully available (all in C if I recall correctly). Probably a little dated now, but still worth a look, I think.

Have fun,

Tim

PS. I note that there are a few other resources of potential interest listed on that web site. I've not checked them out though...