Those crazy Avida people do it again ...

I don't really have time to write anything on this at the moment as I'm busy with another project, but I will note that American Naturalist is making available an interesting paper that uses the AVIDA system to study ecological specialization in digital organisms.

The transition from generalist to specialist may entail the loss of unused traits or abilities, resulting in narrow niche breadth. Here we examine the process of specialization in digital organisms--self-replicating computer programs that mutate, adapt, and evolve. Digital organisms obtain energy by performing computations with numbers they input from their environment. We examined the evolutionary trajectory of generalist organisms in an ecologically narrow environment, where only a single computation
yielded energy. We determined the extent to which improvements in this one function were associated with losses of other functions, leading to organisms that were highly specialized to perform only one or a few functions. Our results show that as organisms evolved improved performance of the selected function, they often lost the ability to perform other computations, and these losses resulted most often from the accumulation of neutral and deleterious mutations. Beneficial mutations, although relatively rare,
were disproportionately likely to cause losses of function, indicating that antagonistic pleiotropy contributed significantly to niche breadth reductions in this system. Occasionally, unused functions were not lost and even increased in performance. Here we find that understanding how the functions were integrated into the genome was crucial to predictions of their maintenance.

Ref: E.A. Ostrowski et al. (2007) "Ecological Specialization and Adaptive Decay in Digital Organisms" Am. Nat. 169, pp. E1-E20.