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As products of evolution, genomes document the history of life in a way that complements the fossil record. Although this genomic record is partially obscured by the accumulation of mutations, we can nevertheless look back across hundreds of millions of years by focusing on genomic features that are conserved or slowly evolving. In this talk we introduce the basic principles of comparative genomics and use them to trace the elusive ancient events that transformed our invertebrate ancestors into early vertebrates. These events, which occurred nearly half a billion years ago, include interspecific hybridization and genome doubling, which are revealed by a kind of symmetry breaking. Analysis of the complex history of vertebrate genomes allows us to fill a gap in the fossil record, and points to an understanding of even more ancient events in the history of animals.