Fig. 1. Stratigraphic sequences in Denisova Cave, showing locations of sediment samples collected for mtDNA analysis and results obtained for ancient hominins.

a, East Chamber, southeast profile. b, East Chamber, northwest profile. c, Main Chamber, southeast profile. d, Phylogenetic tree of mtDNA genomes used as references to distinguish specific hominin lineages, and estimated placement of the Neanderthal mtDNA lineage identified in sample M76 from Main Chamber layer 20. Filled circles in a–c indicate the locations of individual sediment samples, and colours correspond to the hominin mtDNA detected: red (Denisovan), blue (Neanderthal), yellow (ancient modern human), grey (unidentified ancient hominin) and white (no ancient hominins detected). Other symbols denote samples for which mtDNA could be assigned to one of the specific hominin lineages in d (Denisovan, red open triangles; Neanderthal, blue open diamonds, crosses and star). Composite stratigraphic sections (modified from a previous publication⁸) to the left of each profile show modelled start and end ages (in ka) for sedimentary layers (uncertainties at 95.4% probability). Hominin specimen numbers are shown circled in the layer from which each fossil was recovered: Denisovan (red), Neanderthal (blue) and Neanderthal–Denisovan offspring (both colours)⁵. Dashed lines in profiles in a and b indicate areas in which layer assignment is uncertain⁸. Background shading denotes the associated archaeological assemblage: early Middle Palaeolithic (eMP) (dark green), middle Middle Palaeolithic (mMP) (light green), Initial Upper Palaeolithic (IUP) (dark orange) and Upper Palaeolithic (UP) (light orange).