Isolating the human cochlea to generate bone powder for ancient DNA analysis

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Abstract

The cortical bone that forms the structure of the cochlea, part of the osseous labyrinth of the inner ear, is now one of the most frequently used skeletal elements in analyses of human ancient DNA. However, there is currently no published, standardized method for its sampling. This protocol describes the preparation of bone powder from the cochlea of fragmented skulls in which the petrous pyramid of the temporal bone is accessible. Using a systematic process of bone removal based on distinct anatomical landmarks and the identification of relevant morphological features, a petrous pyramid is cleaned with a sandblaster, and the cochlea is located, isolated, and reduced to a homogeneous bone powder. All steps are carried out in dedicated ancient DNA facilities, thus reducing the introduction of contamination. This protocol requires an understanding of ancient DNA clean-room procedures and basic knowledge of petrous pyramid anatomy. In 50–65 min, it results in bone powder with endogenous DNA yields that can exceed those from teeth and other bones by up to two orders of magnitude. Compared with drilling methods, this method facilitates a more precise targeting of the cochlea, allows the user to visually inspect the cochlea and remove any residual sediment before the generation of bone powder, and confines the damage to the inner ear region and surface of the petrous portion of fragmentary crania.

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Fig. 1: Step-by-step walkthrough of the isolation and cleaning of the cochlea for a DNA analysis.
Fig. 2: Comparative yields of endogenous ancient DNA obtained from the cochlea alone and from the cochlea plus the surrounding dense bone.

Data availability

The raw sequencing data that support the findings of this study have been deposited in the Sequence Read Archive under accession code SRP058345.

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Acknowledgements

We thank E. Harney, P. Skoglund, and D. Reich for their comments on the manuscript. Support for this project was provided by ERC starting grant ADNABIOARC (263441) to R.P.

Author information

R.P. conceived and developed the concept, and provided supervision. D.F., O.C., and K.S. designed the protocol and contributed expertise. R.P., D.F., O.C., and K.S. contributed equally to the writing and editing of the manuscript.

Correspondence to Ron Pinhasi.

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The authors declare no competing interests.

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Related links

Key references using this protocol

Pinhasi, R. et al. PLoS One 10, e0129102 (2015): https://doi.org/10.1371/journal.pone.0129102

Skoglund, P. et al. Nature 538, 510–513 (2016): https://doi.org/10.1038/nature19844

Lazaridis, J. et al. Nature 536, 419–424 (2016): https://doi.org/10.1038/nature19310

Mathieson, I. et al. Nature 528, 499–503 (2015): https://doi.org/10.1038/nature16152

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Pinhasi, R., Fernandes, D.M., Sirak, K. et al. Isolating the human cochlea to generate bone powder for ancient DNA analysis. Nat Protoc 14, 1194–1205 (2019) doi:10.1038/s41596-019-0137-7

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