Muhd,
Flavobacterial
nylon digestion, where a single thymine deletion allowed the metabolism of nylon.
Also, Barry Hall (Hall, 1982) effectively knocked out the lac operon in
E.coli, only to see a new enzyme, expression control mechanism, & a new transport molecule that facilitates the movement of lactose into the cell evolve. So, not only have beneficial mutations been observed, but the evolution of complex systems too.
Mark