While misfolded and short-lived proteins are degraded in proteasomes located in 
the nucleus and cytoplasm, the degradation of organelles and long-lived proteins 
in the lysosome occurs by the process of autophagy. Central and necessary to the 
autophagic process are two conserved ubiquitin-like conjugation machineries. 
These conjugation machineries appear to be specific for autophagy and can 
together with genetic and morphological data be used to trace the natural 
history of autophagy. Here we discuss the origin and evolution of autophagy.