Hi Percy,
I think your bacteria challenge is a bit too fuzzy, partially because the delineation of bacterial species is fuzzy.
Is the idea to just let the bacteria diverge or to overcome a specific environmental challenge? Are the human experimenters trying to make their bacteria appear to be naturally evolved? There are certainly many genetic manipulations that would be pretty substantially suggestive of intervention provided the cultures were kept in controlled sterile environments, i.e. introduction of exogenous genetic material such as plasmids. Is the idea that the experimenters just do some small in-del or singe base substitution mutations? You probably need a lot of that sort of mutation to generate something divergent enough to be considered a new species, even in bacteria. Are the experimenters trying to make their changes look random? Do you mean species just in terms of a strain or population rather than as in a biological species?
As it stands I can see a number of scenarios such as you suggest where the manipulated genotype would be readily identifiable depending on exactly what the experimenters did.
TTFN,
WK
Edited by Wounded King, : changed subtitle