Gene duplication has long been recognized as a major force in genome evolution and more recently as an important source of individual variation. In recent studies we classified all gene duplication events in five mammalian genomes based upon the duplication mechanism. This analysis led to several surprising results. We find that RNA-mediated duplication occurs at a much higher rate, and gives rise to many more duplicated sequences, than DNA-mediated duplication. We show that while the chance of RNA-mediated duplicates becoming functional is much lower than that of their DNA-mediated counterparts, the higher rate of retrotransposition leads to nearly equal numbers of new mammalian genes created by each mechanism. We also find that functional RNA-mediated duplicates are closer to neighboring genes and indel-purified-sequences than non-functional RNA-mediated copies, consistent with cooption of regulatory elements at the site of insertion. Overall new genes derived from DNA and RNA-mediated duplication mechanisms are under similar levels of purifying selective pressure, but have broadly different functions resulting in mammalian protein families evolving by either one mechanism or the other, but rarely both.