F.D., J.C., G.D. and C.Z. thank L. Puymerail. We thank T. Sutikna and W. Saptomo (Pusat Penelitian Arkeologi Nasional); X.-J. Wu and W. Liu (IVPP); J. de Vos (Naturalis); N. Giang Hai, N. Kim Thuy, N. Lan Cuong and N. Thi Mai Huong (Institute of Archaeology); N. Viet (Center for Southeast Asian Prehistory); A. Kijngam and R. Thosarat (Thai Fine Arts Department); the National Research Council of Thailand; G. Garcia-Pack, I. Tattersall and E. Delson (American Museum of Natural History); the Field Museum of Natural History; the Ethiopian Authority for Research and Conservation of the Cultural Heritage; the National Museums of Kenya and Government of Kenya; the Ditsong National Museum of Natural History, the Evolutionary Studies Institute, University of the Witwatersrand; the Centre de Valorisation des Collections scientifiques de l’Université de Poitiers; S. Bahuchet, A. Fort, M. Friess, A. Froment, D. Grimaud-Hervé, L. Huet, V. Laborde and P. Mennecier (MNHN); the Nespos Society (https://www.nespos.org); MorphoSource, Duke University (https://www.morphosource.org/); the Senckenberg Research Institute Frankfurt; the ESRF Paleontological Database (paleo.esrf.eu); P. Fernandez, C. Higham, W. Jungers, Y. Kaifu, R. Kono, H. Matsumura, M. Oxenham, N. Tayles and M. Tocheri for granting access to or sharing information and data on recent and fossil hominins; M. Stoneking and Q. Fu (Max Planck Institute for Evolutionary Anthropology); AST-RX and Imagerie 2D/3D MH-SU platforms (MNHN); G. Champion, A. Giral, A. Gossez, A. Van Heteren, J. Surault and J. Tanedo for discussions or technical assistance; the National Museum of the Philippines and its Directorial staff; colleagues and students from the Archaeological Studies Program (University of the Philippines); the 2011 and 2015 IMQP Erasmus Mundus students; and the Cagayan Provincial Government and the Protected Area Management Board-Peñablanca for authorizing fieldwork at Callao Cave. Funding was provided by the Wenner-Gren Foundation, the Leakey Foundation Research Grant and the University of the Philippines Enhanced Creative Work and Research Grant (ECWRG 2015-1-016). R.G.’s work was partly funded by the Australian Research Council Grant DP110101415. The research of P.J.P. was supported by Australian Research Council grants FT100100527 and DP140100384. The research of G.D. was supported by the Agence Nationale pour la Recherche (ANR ARCHOR-12-CULT-0006), the Omo Group Research Expedition (J.-R. Boisserie), the MEAE, the Université de Poitiers and the Conseil départemental de la Vienne (ACI 2013-2014). The research of J.C. was supported by SYNTHESYS (NL-TAF-1130) and ‘IUSS Ferrara 1391’ grants. Aspects of the research of F.D. were supported by the Labex BCDiv ‘Biological and Cultural Diversities’, Erasmus Mundus IMQP and IDQP, MQPI (MEAE) and PaléoFED.

Reviewer information

Nature thanks Aida Gómez-Robles, William L. Jungers, Yousuke Kaifu and the other anonymous reviewer(s) for their contribution to the peer review of this work.