The radioactive bee is not getting the radioactive effect. There may be other allele values for other species not correct as well, but I did notice that one.

I think I see the issue in the BeeBranches.java file. The allele setting calls of the branch entries are mostly setting against the defaultTemplate, not the alleles array variable for each branch. This is causing the bee species to get allele values somewhat randomly based on the order they are defined in the beeSpecies file. I wasn't complete sure if you had a reason the doing the branch definitions in that way so I didn't push a fix for it.