Fig. 1: Neanderthal sites and genomic information.

a, Locations of all of the sites with Neanderthal remains (the number of individuals is given in parentheses for sites with multiple individuals) from whom nuclear DNA has been extracted, with a close-up of the Chagyrskaya and Okladnikov caves in the Altai region of southern Siberia. b, Nuclear genomes ranked by the extent of coverage and colour-coded by site (blue, Chagyrskaya from this study; orange, Okladnikov from this study; grey, published previously in refs. ^{1,2,3,4,5,6,7,8}). c, Maximum-likelihood tree for mtDNA sequences from the Neanderthal individuals included in this study in the context of known hominin variation. The reference genome is rCRS and the accession numbers for the present-day humans are East Asian (AF346973), European (AF346981) and African (AF381988). Okladnikov 2 refers to the mtDNA sequence in ref. ⁴¹ (this specimen is listed as Okladnikov 14 in Extended Data Table 1). Data from refs. ^{1,2,3,4,6,30,41,42,43,44,45,46,47,48,49}. d, Maximum-likelihood tree based on consensus calling of 6.9 Mb of the Y chromosome of four Chagyrskaya individuals with coverage of more than onefold, along with previously published Y-chromosome data from three Neanderthals, two Denisovans and four present-day humans. The reference genome is hg19. Data from refs. ^{26,50,51,52,53}. In c and d, the haplogroups are shown for present-day human populations.