A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago1. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals2. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.
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Arsuaga, J. L. et al. Neandertal roots: cranial and chronological evidence from Sima de los Huesos. Science 344, 1358–1363 (2014)
Meyer, M. et al. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505, 403–406 (2014)
Reich, D. et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053–1060 (2010)
Sawyer, S. et al. Nuclear and mitochondrial DNA sequences from two Denisovan individuals. Proc. Natl Acad. Sci. USA 112, 15696–15700 (2015)
Qin, P. & Stoneking, M. Denisovan ancestry in East Eurasian and Native American populations. Mol. Biol. Evol. 32, 2665–2674 (2015)
Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012)
Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014)
Arsuaga, J. L. et al. Postcranial morphology of the middle Pleistocene humans from Sima de los Huesos, Spain. Proc. Natl Acad. Sci. USA 112, 11524–11529 (2015)
Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007)
Krause, J. et al. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464, 894–897 (2010)
Sawyer, S., Krause, J., Guschanski, K., Savolainen, V. & Pääbo, S. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS ONE 7, e34131 (2012)
Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013)
Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010)
Rasmussen, M. et al. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334, 94–98 (2011)
Stringer, C. The status of Homo heidelbergensis (Schoetensack 1908). Evol. Anthropol. 21, 101–107 (2012)
Lycett, S. J. Understanding ancient hominin dispersals using artefactual data: a phylogeographic analysis of Acheulean handaxes. PLoS ONE 4, e7404 (2009)
Lahr, M. M. & Foley, R. A. Towards a theory of modern human origins: Geography, demography, and diversity in recent human evolution. Yb. Phys. Anthropol . 41, 137–176 (1998)
Dennell, R. W., Martinon-Torres, Bermúdez de Castro, J. M. Hominin variability, climatic instability and population demography in Middle Pleistocene Europe. Quat. Sci. Rev. 30, 1511–1524 (2011)
Rink, W. J. et al. New radiometric ages for the BH-1 hominin from Balanica (Serbia): implications for understanding the role of the Balkans in Middle Pleistocene human evolution. PLoS ONE 8, e54608 (2013)
Korlevic´, P. et al. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. Biotechniques 59, 87–93 (2015)
Gansauge, M. T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nature Protocols 8, 737–748 (2013)
Slon, V., Glocke, I., Barkai, R., Gopher, A., Hershkovitz, I. & Meyer, M. Mammalian mitochondrial capture, a tool for rapid screening of DNA preservation in faunal and undiagnostic remains, and its application to Middle Pleistocene specimens from Qesem Cave (Israel). Quat. Int. http://dx.doi.org/10.1016/j.quaint.2015.03.039 (2015)
Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012)
Dabney, J. & Meyer, M. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques 52, 87–94 (2012)
Maricic, T., Whitten, M. & Pääbo, S. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS ONE 5, e14004 (2010)
Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. USA 110, 2223–2227 (2013)
Renaud, G., Kircher, M., Stenzel, U. & Kelso, J. freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers. Bioinformatics 29, 1208–1209 (2013)
Renaud, G., Stenzel, U. & Kelso, J. leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res. 42, e141 (2014)
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009)
Green, R. E. et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134, 416–426 (2008)
Briggs, A. W. et al. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 325, 318–321 (2009)
Gansauge, M. T. & Meyer, M. Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Res. 24, 1543–1549 (2014)
Skoglund, P. et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc. Natl Acad. Sci. USA 111, 2229–2234 (2014)
Horai, S. et al. Man’s place in Hominoidea revealed by mitochondrial DNA genealogy. J. Mol. Evol. 35, 32–43 (1992)
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013)
Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014)
We thank B. Höber and A. Weihmann for help with sequencing the libraries, G. Renaud for processing the raw sequence data, S. Castellano and U. Stenzel for discussions and comments on the manuscript. Genetics work was funded by the Max Planck Society and its Presidential Innovation Fund. Field work at the Sierra de Atapuerca sites was funded by the Junta de Castilla y Leon, the Fundacion Atapuerca, the Spanish Ministerio de Ciencia e Innovacion (project CGL2009-12703-C03) and the Spanish Ministerio de Economia y Competitividad (project CGL2012-38434-C03).
The authors declare no competing financial interests.
Extended data figures and tables
Extended Data Figure 1 Sharing of derived alleles at diagnostic positions separating the hominin groups in the mitochondrial tree.
The chimpanzee was used as outgroup to determine the ancestral state, which is shared with all individuals in the tree except those belonging to the labelled branch. Provided are the number of diagnostic sites available for this analysis (top left panel) as well as the number of sequences supporting the derived state, their percentage (in brackets) and the total number of observations. Numbers above the branch include all sequences whereas bold numbers below the branch are limited to sequences showing evidence of cytosine deamination. Published data from library A2021 of femur XIII were included in this analysis for comparison.
Extended Data Figure 2 Frequency of C to T substitutions at the beginning and end of nuclear sequence alignments.
Solid lines denote all sequences and dashed lines only those sequences carrying a C to T substitution at the opposing end.
Extended Data Figure 3 Sex determination based on the number of sequences aligning to chromosome X and the autosomes.
Ninety-five per cent binomial confidence intervals are provided as well as the expected ratios of X to (X + autosomal) sequences for male and female samples. The analysis was performed with and without enrichment of endogenous DNA by filtering for the presence of C to T substitutions at terminal alignment positions. Present-day human contamination in the unfiltered sequences appears to have been introduced at least partly by female individuals.
For comparison with the SH sequence data, we show the sharing of derived alleles at these positions using published sequence data from a Neanderthal (Vindija 33.16), a Denisovan individual (Denisova 4) and an early modern human (Ust’Ishim).
Extended Data Figure 5 Derived allele sharing with the Neanderthal- and Denisovan-specific branches in deaminated DNA fragments from all five specimens from SH.
Only sequences with a terminal C to T substitution were used in this analysis. Error bars, 95% confidence intervals. Significance was tested using Fisher’s exact test (two-tailed).
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Meyer, M., Arsuaga, J., de Filippo, C. et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature 531, 504–507 (2016). https://doi.org/10.1038/nature17405
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