The rapidly increasing availability of whole-genome sequences has enabled the study of whole-genome evolution. Evolutionary mechanisms based on genome rearrangements have attracted much attention and given rise to many models, somewhat independently, the mechanisms of gene duplication and loss have seen much work. However, the two are not independent and thus require a unified treatment, which remains missing to date. Moreover, existing rearrangement models do not fit the dichotomy between most prokaryotic genomes (one circular chromosome) and most eukaryotic genomes (multiple linear chromosomes).