Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins

Abstract

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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Figure 1: Percentage of derived alleles shared between the SH specimen and the human, Neanderthal and Denisovan genomes.
Figure 2: Sharing of derived alleles with the Altai Neanderthal.

Accession codes

Primary accessions

European Nucleotide Archive

Data deposits

Sequences generated in this study have been deposited in the European Nucleotide Archive under study accession number PRJEB10597.

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Acknowledgements

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).

Author information

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Authors

Contributions

M.M., J.-L.A. and S.P. directed the experimental work and wrote the manuscript. M.M. designed the laboratory experiments, which S.N., A.A. and B.N. performed. M.M., C.d.F., B.V., J.K. and K.P. analysed the data. J.-L.A., I.M., A.G., J.M.B. and E.C. excavated the fossil and provided archaeological expertise.

Corresponding author

Correspondence to Matthias Meyer.

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Competing interests

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.

Extended Data Figure 4 Number of informative positions identified for each branch of the tree.

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).

Extended Data Table 1 Overview of DNA extracts, libraries and shotgun sequences generated in three experiments
Extended Data Table 2 Characteristics of sequences obtained after mtDNA enrichment
Extended Data Table 3 Fraction of derived alleles shared with the human, Neanderthal and Denisovan genomes and combinations thereof
Extended Data Table 4 Derived allele sharing between putatively deaminated DNA fragments of the five SH specimens and all branches of the hominin evolutionary tree
Extended Data Table 5 Overview of the sequencing runs performed

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Supplementary Information

This file contains Supplementary Text, Supplementary Figures 1-2, Supplementary Tables 1-4 and additional references. (PDF 1478 kb)

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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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