Ancient Genomes link early farmers from Atapuerca in Spain to modern-day Basques Supplementary Information Torsten Günther*, Cristina Valdiosera*, Helena Malmström, Irene Ureña, Ricardo Rodriguez- Varela, Óddny Sverrisdóttir, Evangelia A. Daskalaki, Pontus Skoglund, Thijessen Naidoo, Emma M. Svensson, José María Bermúdez de Castro, Eudald Carbonell, Michael Dunn, Jan Storå, Eneko Iriarte, Juan Luis Arsuaga, José Miguel Carretero, Anders Götherström, Mattias Jakobsson† *These authors contributed equally †correspondence to:
[email protected] 1 Table of Contents S1. The El Portalón site stratigraphic and cultural sequence..................................................3 S1.1. Early Chalcolithic (Pre-Bell Beaker) funerary context, Bronze Age and disturbed layers from the El Portalón cave.......................................................................................................3 S1.2. Sample provenance and radiocarbon dating.................................................................5 S2. Sample preparation, DNA extraction, library construction and sequencing......................7 S2.1. Bone and teeth DNA extraction.....................................................................................7 S2.2. Sequencing Library Building..........................................................................................7 S3. Sequence processing and alignment...............................................................................8 S3.1. Mitochondrial DNA haplogroups....................................................................................8