Optimal ancient DNA yields from the inner ear part of the human petrous bone
Open accessAbstract
The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.
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The inner ear region of the petrous bone can yield up to ~100 times more endogenous DNA than other skeletal elements.
“First, we sampled from the inner ear region of the petrous bone3,4 that can yield up to ~100 times more endogenous DNA than other skeletal elements4.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [4]
The Discussion reports substantially higher endogenous DNA yields from petrous samples than from a metatarsal bone of the same individual, supporting the comparison with another skeletal element. But the reported difference is 267- to 410-fold, not an upper limit of approximately 100-fold; the paper also notes that this comparison rests on a single non-petrous bone. (LLM, conf=0.85)
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- Authors
- Pinhasi, R., Fernandes, D., Sirak, K., Novak, M., Connell, S., Alpaslan-Roodenberg, S., Gerritsen, F., Moiseyev, V., Gromov, A., Raczky, P., Anders, A., Pietrusewsky, M., Rollefson, G., Jovanovic, M., Trinhhoang, H., Bar-Oz, G., Oxenham, M., Matsumura, H., & Hofreiter, M.
- Affiliations
- University College Dublin (IE)
- Emory University (US)
- Netherlands Institute in Turkey (TR)
- Russian Academy of Sciences (RU)
- Eötvös Loránd University (HU)
- University of Hawaiʻi at Mānoa (US)
- Whitman College (US)
- Australian National University (AU)
- Sapporo Medical University (JP)
- University of Potsdam (DE)
- Corresponding author
- Pinhasi, Ron
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-06-18
- Volume
- 10
- Issue
- 6
- Pages
- e0129102
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC4472748
- OpenAlex
- W632382092
- Cited by
- 487
- References
- 37
- Citations by year
- 2026: 47 · 2025: 54 · 2024: 49 · 2023: 54 · 2022: 36 · 2021: 56 · 2020: 53 · 2019: 55 · 2018: 33 · 2017: 24 · 2016: 20 · 2015: 5
- FWCI
- 18.68
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- VU Research Portal (publishedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- ELTE Digital Institutional Repository (EDIT) (Eötvös Loránd University) (submittedVersion, other-oa)
- Figshare (submittedVersion, cc-by)
- publish.UP (University of Potsdam) (submittedVersion)
- publish.UP (University of Potsdam) (submittedVersion, cc-by)
- ANU Open Research (Australian National University) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Universität Potsdam (cc-by)
- Funders
- FP7 Ideas: European Research Council (310763, 263441)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Arts and Humanities › Archeology › Paleopathology and ancient diseases
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Keywords
- ancient DNA, petrous bone, inner ear, otic capsule, trabecular bone, cortical bone, hot environment, archaeological samples, shotgun sequencing
- MeSH terms
- Archaeology, DNA, DNA Damage, Fossils, Humans, Ear, Inner, Petrous Bone, Sequence Analysis, DNA
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