A common misconception is to envision genomic evolution as a matter of single base substitutions (i.e. an adenine becoming a guanine, etc).

Truth is, most of real genome evolution leaps are created by structural variations, i.e. from whole genome/chromosome duplications to microdeletions/microduplications fostered by the existence of repeated sequences interspersed in the genome (mostly due to [retro-]transposons), which act as hotspots for copy/paste/delete events.

And these repeated sequences aren't equal among time and species.