Conservation of animal genome structure is the exception not the rule

Species from diverse animal lineages, including molluscs, hemichordates, and chordates, have retained groups of orthologous genes on the same chromosomes for over half a billion years since the last common ancestor of bilaterians. Though there are notable exceptions, it has been proposed that the conservation of chromosome-scale gene linkages is the norm among animals. Here, by examining interchromosomal rearrangements in 64 chromosome-level genomes across 15 bilaterian phyla and at least 52 classes, we show that cases of genome structure conservation are exceptionally rare. Large-scale genome restructuring events correlate with increased rates of protein sequence evolution and may represent a previously underappreciated contributor to adaptation and animal diversity.