We thank S. Anders, M. Sepp, E. Leushkin and members of the Kaessmann group for discussions, M. Sanchez-Delgado and N. Trost for assistance in figure design, and I. Moreira for help in the development of the interactive tool. We acknowledge support by the state of Baden-Württemberg through bwHPC and the German Research Foundation (DFG) through grant INST 35/1134-1 FUGG. This research was supported by grants from the European Research Council (615253, OntoTransEvol) and Swiss National Science Foundation (146474) to H.K., by the Marie Curie FP7-PEOPLE-2012-IIF to M.C.-M. (329902) and by a scholarship for MSc studies by the Alexander S. Onassis Public Benefit Foundation (F ZL 084-1/2015-2016) to I.S.

Peer review information

Nature thanks Camille Berthelot, Igor Ulitsky and the other anonymous reviewer(s) for their contribution to the peer review of this work.