bioRxiv
New Results

Ancient human genomes suggest three ancestral populations for present-day Europeans

Iosif Lazaridis , Nick Patterson , Alissa Mittnik , Gabriel Renaud , Swapan Mallick , Karola Kirsanow , Peter H. Sudmant , Joshua G. Schraiber , Sergi Castellano , Mark Lipson , Bonnie Berger , Christos Economou , Ruth Bollongino , Qiaomei Fu , Kirsten Bos , Susanne Nordenfelt , Heng Li , Cesare de Filippo , Kay Prüfer , Susanna Sawyer , Cosimo Posth , Wolfgang Haak , Fredrik Hallgren , Elin Fornander , Nadin Rohland , Dominique Delsate , Michael Francken , Jean-Michel Guinet , Joachim Wahl , George Ayodo , Hamza A. Babiker , Graciela Baillet , Elena Balanovska , Oleg Balanovsky , Ramiro Barrantes , Gabriel Bedoya , Haim Ben-Ami , Judit Bene , Fouad Berrada , Claudio M. Bravi , Francesca Brisighelli , George B.J. Busby , Francesco Cali , Mikhail Churnosov , David E.C. Cole , Daniel Corach , Larissa Damba , George van Driem , Stanislav Dryomov , Jean-Michel Dugoujon , Sardana A. Fedorova , Irene Gallego Romero , Marina Gubina , Michael Hammer , Brenna Henn , Tor Helvig , Ugur Hodoglugil , Aashish R. Jha , Sena Karachanak-Yankova , Rita Khusainova , Elza Khusnutdinova , Rick Kittles , Toomas Kivisild , William Klitz , Vaidutis Kučinskas , Alena Kushniarevich , Leila Laredj , Sergey Litvinov , Theologos Loukidis , Robert W. Mahley , Béla Melegh , Ene Metspalu , Julio Molina , Joanna Mountain , Klemetti Näkkäläjärvi , Desislava Nesheva , Thomas Nyambo , Ludmila Osipova , Jüri Parik , Fedor Platonov , Olga L. Posukh , Valentino Romano , Francisco Rothhammer , Igor Rudan , Ruslan Ruizbakiev , Hovhannes Sahakyan , Antti Sajantila , Antonio Salas , Elena B. Starikovskaya , Ayele Tarekegn , Draga Toncheva , Shahlo Turdikulova , Ingrida Uktveryte , Olga Utevska , René Vasquez , Mercedes Villena , Mikhail Voevoda , Cheryl Winkler , Levon Yepiskoposyan , Pierre Zalloua , Tatijana Zemunik , Alan Cooper , Cristian Capelli , Mark G. Thomas , Andres Ruiz-Linares , Sarah A. Tishkoff , Lalji Singh , Kumarasamy Thangaraj , Richard Villems , David Comas , Rem Sukernik , Mait Metspalu , Matthias Meyer , Evan E. Eichler , Joachim Burger , Montgomery Slatkin , Svante Pååbo , Janet Kelso , David Reich , Johannes Krause

Abstract

We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 year old hunter-gatherer from Luxembourg, and seven ~8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had ~44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.