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. 2015 Jun 18;10(6):e0129102.
doi: 10.1371/journal.pone.0129102. eCollection 2015.

Optimal Ancient DNA Yields From the Inner Ear Part of the Human Petrous Bone

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Free PMC article

Optimal Ancient DNA Yields From the Inner Ear Part of the Human Petrous Bone

Ron Pinhasi et al. PLoS One. .
Free PMC article

Abstract

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.

Conflict of interest statement

Competing Interests: SAR is a self employed freelance osteologist. There are no patents, products in development or marketed products to declare. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. Medial view of a cut of a left petrous bone.
The main image shows the location of the different areas targeted in this study (parts A, B and C) with different colours. The top box shows the direction of the cut. The lower box shows the area comprising parts B and C in detail and non-coloured. Blue and orange arrows point to areas of B and C, respectively.
Fig 2
Fig 2
(A) Percentage of non-clonal human DNA recovered after shotgun sequencing for parts A, B and C for each of the ten specimens analysed, (B) Percentage of non-clonal human DNA recovered after shotgun sequencing for parts A, B and C for the five specimens analysed from hot, humid and arid parts.
Fig 3
Fig 3
(A) Deamination patterns for each of the cases for bone parts A, B and C, before subsampling, (B) Deamination patterns for each of the cases for bone parts A, B and C, after subsampling.

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Grant support

This research was supported by Ron Pinhasi's European Research Council Starting grant (ERC- 2010-StG 263441);ERC Grant to RP (ADNABIOARC, 263441); MH was supported by ERC grant GeneFlow (310763). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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