Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene1. One of these sites, the ‘Sima de los Huesos’ (‘pit of bones’), has yielded the world’s largest assemblage of Middle Pleistocene hominin fossils2,3, consisting of at least 28 individuals4 dated to over 300,000 years ago5. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits6,7,8. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans9,10, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.
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We thank J. Dabney, M. Dannemann, C. de Filippo, S. Lippold, K. Prüfer, M. Slatkin, M. Stiller, C. Valdiosera and B. Viola for discussions and comments on the manuscript; G. Renaud and U. Stenzel for help with sequence data processing; B. Höber and A. Weihmann for performing the sequencing runs; M. Gansauge, P. Korlević, R. Rodríguez and I. Ureña for help in the laboratory; M. Schreiber for help with graphics; J. Trueba for providing the fossil image; M. Cruz Ortega for restoration of the fossil and the rest of the members of the Sima de los Huesos excavation team for decades of continuous efforts. Genetics work was funded by the Max Planck Society and its Presidential Innovation Fund. Field work at the Sierra de Atapuerca sites is funded by the Junta de Castilla y León and the Fundación Atapuerca. Research was supported by Spanish Ministerio de Ciencia e Innovación (project CGL2009-12703-C03) and Spanish Ministerio de Economía y Competitividad (project CGL2012-38434-C03).
The authors declare no competing financial interests.
Extended data figures and tables
Extended Data Figure 1 Size distribution of all overlap-merged sequences generated by shotgun sequencing (before mapping).
Extended Data Figure 2 5′ and 3′ C to T substitution frequencies plotted against the number of unique mitochondrial sequences retrieved from each sample library.
Libraries prepared from re-extracted pellets or surface material are highlighted in colour.
The distribution obtained from the Sima de los Huesos cave bear is shown for comparison.
Extended Data Figure 4 Sequence coverage of the mitochondrial genome obtained from sequences with terminal C to T substitutions.
Extended Data Figure 5 Sequence coverage of the mitochondrial genome plotted separately for both capture probe sets used (based on sequences with a C to T substitution at the first or last alignment position).
Extended Data Figure 6 Complete view of the mid-point rooted phylogenetic tree constructed with a Bayesian approach under a GTR + I + Γ model of sequence evolution using the Sima de los Huesos consensus sequence generated with inclusive filters as well as 54 present-day humans, 9 ancient humans, 7 Neanderthals, 2 Denosivans, 22 bonobos and 24 chimpanzees.
The posterior probabilities are provided for the major nodes.
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Meyer, M., Fu, Q., Aximu-Petri, A. et al. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505, 403–406 (2014). https://doi.org/10.1038/nature12788
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