Within a decade, various consortia under the Earth BioGenome umbrella aim to sequence 1.5M eukaryotes. All these genomes are connected through life’s common origin, yet owing to conceptual and computational limitations, they are only studied piecemeal in practice. In this talk, I will show how reconstructing ancestral genomes is key to harnessing this treasure trove of information—opening up interesting algorithmic and analytical opportunities, and new biological insights on a broad range of questions, including how to incorporate predicted structure information to increase the accuracy of our evolutionary reconstructions.