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A mitochondrial genome sequence of a hominin from Sima de los Huesos

Nature volume 505, pages 403–406 (2014)Cite this article

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Abstract

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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Figure 1
Figure 2: Femur XIII reassembled from three parts after sampling.
Figure 3: Patterns of cytosine deamination in the libraries constructed from the Sima de los Huesos hominin femur.
Figure 4: Bayesian phylogenetic tree of hominin mitochondrial relationships based on the Sima de los Huesos mtDNA sequence determined using the inclusive filtering criteria.

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Accession codes

Accessions

GenBank/EMBL/DDBJ

Data deposits

The Sima de los Huesos mtDNA consensus sequence (based on the inclusive filtering criteria) is deposited in GenBank under accession number KF683087.

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Acknowledgements

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).

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Authors and Affiliations

  1. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany,

    Matthias Meyer, Qiaomei Fu, Ayinuer Aximu-Petri, Isabelle Glocke, Birgit Nickel & Svante Pääbo

  2. Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China

    Qiaomei Fu

  3. Centro de Investigación Sobre la Evolución y Comportamiento Humanos, Universidad Complutense de Madrid–Instituto de Salud Carlos III, 28029 Madrid, Spain,

    Juan-Luis Arsuaga, Ignacio Martínez & Ana Gracia

  4. Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain,

    Juan-Luis Arsuaga

  5. Área de Paleontología, Depto. de Geografía y Geología, Universidad de Alcalá, Alcalá de Henares, 28871 Madrid, Spain,

    Ignacio Martínez & Ana Gracia

  6. Centro Nacional de Investigación sobre la Evolución Humana, Paseo Sierra de Atapuerca, 09002 Burgos, Spain,

    José María Bermúdez de Castro

  7. Institut Català de Paleoecologia Humana i Evolució Social, C/Marcel·lí Domingo s/n (Edifici W3), Campus Sescelades, 43007 Tarragona, Spain,

    Eudald Carbonell

  8. Àrea de Prehistòria, Dept. d’Història i Història de l’Art, Univ. Rovira i Virgili, Fac. de Lletres, Av. Catalunya, 35, 43002 Tarragona, Spain,

    Eudald Carbonell

Authors
  1. Matthias Meyer
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Contributions

M.M. designed the experiments and analysed the data; Q.F. performed phylogenetic analyses; A.A., I.G. and B.N. performed the experiments; J.-L.A., I.M., A.G., J.M.B. and E.C. excavated the fossil and provided expert archaeological and anthropological information; J.-L.A. and S.P. were involved in study design; and M.M., J.-L.A. and S.P. wrote the manuscript.

Corresponding author

Correspondence to Matthias Meyer.

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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.

Extended Data Figure 3 Sequence length distribution of unique sequences.

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.

Extended Data Table 1 Characteristics of all libraries prepared for this study
Full size table
Extended Data Table 2 Results from shallow shotgun sequencing of a subset of libraries
Full size table
Extended Data Table 3 Number of sequences retained in the sample libraries after each step of processing and filtering
Full size table
Extended Data Table 4 Inferred time to the most recent common ancestor (TMRCA) of the modern human, Neanderthal, chimpanzee and bonobo mtDNAs, as well as divergence estimates for human/chimpanzee and bonobo/chimpanzee mtDNA (continuation of Table 1)
Full size table

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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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