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In chordate phylogeny, changes in the nervous system, jaws, and appendages transformed meek filter feeders into fearsome predators1. Gene duplication is thought to promote such innovation2. Vertebrate ancestors probably had single copies of genes now found in multiple copies in vertebrates3 and gene maps suggest that this occurred by polyploidization2–7. It has been suggested that one genome duplication event occurred before, and one after the divergence of ray-finned and lobe-finned fishes5. Holland et al., however, have argued that because various vertebrates have several HOX clusters, two rounds of duplication occurred before the origin of jawed fishes3. Such gene-number data, however, do not distinguish between tandem duplications and polyploidization events, nor whether independent duplications occurred in different lineages. To investigate these matters, we mapped 144 zebrafish genes …