Conservation of bilaterian genome structure is the exception, not the rule.

Species from diverse animal lineages have conserved groups of orthologous genes together on the same chromosome for over half a billion years since the last common ancestor of bilaterians. Although notable exceptions exist, the stability of chromosome-scale gene linkages has been proposed to be the norm among animals. Here we test this hypothesis across species from 52 bilaterian classes representing 15 different phyla. Contrary to expectations, we find that cases of genome structure conservation are rare, taxonomically restricted and unrepresentative of the general state of bilaterian genomes. Genome restructuring correlates with increased rates of protein sequence evolution and may be an underappreciated factor driving animal adaptation and diversification.