A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes

Background: Genomic rearrangements have been studied since the beginnings of modern genetics and models for such rearrangements have been the subject of many papers over the last 10 years. However, none of the extant models can predict the evolution of genomic organization into circular unichromosomal genomes (as in most prokaryotes) and linear multichromosomal genomes (as in most eukaryotes). Very few of these models support gene duplications and losses—yet these events may be more common in evolutionary history than rearrangements and themselves cause apparent rearrangements. Results: We propose a new evolutionary model that integrates gene duplications and losses with genome rearrangements and that leads to genomes with either one (or a very few) circular chromosome or a collection of linear chromosomes. Moreover, our model predictions fit observations about the evolution of gene family sizes as well as existing predictions about the growth in the number of chromosomes in eukaryotic genomes. Finally, our model is based on the existing inversion/translocation models and inherits their linear-time algorithm for pairwise distance computation.