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PLoS One. 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.

Author information

1
School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.
2
Department of Anthropology, Emory University, Atlanta, Georgia, United States of America.
3
independent researcher, Santpoort-Noord, The Netherlands.
4
Netherlands Institute in Turkey, Istiklal Caddesi, Nur-i Ziya Sokak 5, Beyoğlu, Istanbul, Turkey.
5
Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Universitetskaya Nab. 3, St. Petersburg, Russia.
6
Eötvös Loránd University University, Faculty of Humanities, Institute of Archaeological Sciences, Múzeum körút 4/b, Budapest, Hungary.
7
Department of Anthropology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America.
8
Whitman College, Walla Walla, Washington, United States of America.
9
Museum of Vojvodina, 21 000 Novi Sad, Ulica Dunavska 35, Serbia.
10
Institute of Archaeology, Hoan Kiem District, Hanoi, Vietnam.
11
Zinman Institute of Archaeology, University of Haifa, Mount Carmel, Israel.
12
School of Archaeology and Anthropology, Australian National University, Canberra, Australia.
13
School of Health Science, Sapporo Medical University, Sapporo, Japan.
14
Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknechtstr. 24-25, 14476 Potsdam Golm, Germany; Department of Biology, University of York, Wentworth Way, Heslington, York, United Kingdom.

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.

PMID:
26086078
PMCID:
PMC4472748
DOI:
10.1371/journal.pone.0129102
[Indexed for MEDLINE]
Free PMC Article

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