Ancient nuclear and mitochondrial DNA sequences from 5 Sima de los Huesos hominin specimens. Sima de les Huesos nuclear DNA

Recently, a mitochondrial genome sequence was reconstructed from a ~430 kyr old hominin femur (femur XIII) from the Sima de los Huesos (SH) in the Atapuerca Mountains, Spain. Surprisingly, it is more closely related to the mitochondrial (mt) DNA of Denisovans, an enigmatic archaic hominin group in Asia, than to Neanderthals in Europe and western Asia. We have now determined additional DNA sequences from this femur as well as from four additional SH individuals. An mtDNA recovered from one of the latter specimens shares the previously described relationship to Denisovan mtDNAs. In contrast, nuclear DNA sequences recovered from two specimens show that the Sima de los Huesos hominins were related to early Neanderthal ancestors. Nuclear sequences deposited here include those used in phylogenetic analyses (mapped sequences >=35bp, map quality 30, filtered for evidence of deamination). In addition to the sequences analyzed in the paper, we also provide sequences with weaker evidence of deamination, i.e. sequences with a C to T difference to the reference genome within the first 3 or last 3 positions.