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He obtained a master's degree and a doctorate in Biological Sciences at the Universidad Complutense de Madrid, where he is professor in the Paleontology Department of the Faculty of Geological Sciences.
Arsuaga is a visiting professor of the Department of Anthropology at the University College of London and since 1982 he has been a member of the Research Team investigating Pleistocene deposits in the Atapuerca Mountains (Province of Burgos, Spain). He has been a co-director since 1991 with José María Bermúdez de Castro and Eudald Carbonell Roura of the Atapuerca Team, which was awarded the Prince of Asturias Prize in "Scientific and Technical Research" category and the Castilla León Prize in "Social Sciences and Humanities" category, both in 1997.
The finds at Atapuerca have shed new light on the first humans in Europe. This contrasts with the secretive atmosphere surrounding the digs to near Orce, in southern Spain, which has yielded tools indicating human presence that predate the finds at Atapuerca. In 2013, Arsuaga co-authored a paper which reported the finding of the oldest human (H. heidelbergensis) DNA ever, dating back 400,000 years. The mitochondrial DNA that stemmed from a fossil found in a cave in Sima de los Huesos had similarities to mitochondrial genomes previously found in the extinct Denisovans in Siberia.
A member of the Musée de l'Homme from Paris, of the International Association for the Study of Human Paleontology, he is vice-president of the Commission of Human Paleontology and Paleoecology of the International Union for Quaternary Research (INQUA). He has been a lecturer at the universities of London, Cambridge, Zurich, Rome, Arizona, Philadelphia, Berkeley, New York, Tel Aviv, among others.
- Amalur, 2002 (ISBN 84-8460-191-9)
- Atapuerca, un millón de años de historia, 1999 (ISBN 84-7491-629-1)
- El enigma de la esfinge, 2001 (ISBN 84-01-34160-4)
- El collar del neandertal, 1999 (ISBN 8478807934)
- La especie elegida, 1998 with Ignacio Martínez (ISBN 84-7880-909-0)
- El primer viaje de nuestra vida, 2012 (ISBN 978-84-9998180-2)
- Carl Zimmer (4 December 2013) Baffling 400,000-Year-Old Clue to Human Origins New York Times. Retrieved 6 December 2013
- Matthias Meyer; et al. (2014). "A mitochondrial genome sequence of a hominin from Sima de los Huesos" (PDF). Nature. 505 (7483): 403–406. Bibcode:2014Natur.505..403M. doi:10.1038/nature12788. PMID 24305051. S2CID 4456221.
- Atapuerca Website (in Spanish)
- Biography at the Universidad Complutense de Madrid (in Spanish)