As I understand, the underlying mechanism of the formation of new genes must first consist of a gene duplication event. This results in one gene constrained to its original function whereas the other gene is removed from the pressure of selection thereby allowing it to drift/be selected for change either to produce a specialised but similar function or a entirely new function. Where often this is followed by exon shuffling. I understand this at a protein level. New kinases for instance or the evolution of haemoglobin.
However, when trying to apply this idea to the macro view of evolution, confusion arrises. Take the evolution of the mammalian ear bones. These originally evolved from the gills of fish, became part of the jaw bones in jawed fish, a way of detecting vibrations in the jaws of reptiles and finally a way of amplifying sound waves in mammals. What is happening, in this case, on a molecuar, DNA level. Are mutations occuring in the genes of the bones? The promoters of these genes? Transcription factors which control the development of the bones? Did gene duplication have to occur in this case? Presumably there was not a organism with two bones, one serving its orginal function, say supporting the gills, and the other serving a new function, which would be as a jaw? Simultaniously?
