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

Bibliographic Data

ID23328187
AuthorsRon Pinhasi (0000-0003-1629-8131, University College Dublin, corresponding author), Daniel M Fernandes (0000-0002-7434-6552, University College Dublin), Kendra A Sirak (0000-0003-2347-3479, Emory University), Kendra Sirak, Mario Novak (0000-0002-4567-8742, University College Dublin), Sarah Connell (0000-0001-9202-5798, University College Dublin), Songül Alpaslan-Roodenberg (0000-0002-1536-2931), F Gerritsen (0000-0002-6665-1928), Vyacheslav Moiseyev (0000-0003-1748-2686, Peter the Great's Museum of Anthropology and Ethnography), A V Gromov (0000-0002-3263-3801, Peter the Great's Museum of Anthropology and Ethnography), Pál Raczky (0000-0001-5556-723X, Eötvös Loránd University), Abram Anders (0000-0001-6652-3902, Eötvös Loránd University), Alexandra Anders, M Pietrusewsky (0000-0002-6886-0950, University of Hawaiʻi at Mānoa), Gary Rollefson, Gary O Rollefson (0000-0002-1083-6675, Whitman College), Marija Jovanović (0000-0002-1783-2888), Hiep Trinhhoang, Trinhhoang Hiep, Guy Bar-Oz (0000-0002-1009-5619, Carmel (Israel)), Marc F Oxenham (0000-0002-5804-2145, Australian National University), Marc Oxenham, H Matsumura (0000-0001-5453-7987, Sapporo Medical University), Michael Hofreiter (0000-0003-0441-4705, University of Potsdam)
EditorsMichael D Petraglia (0000-0001-5434-6793)
Year2015
Volume10
Issue6
Pagese0129102
Publication date2015-06-18
Peer ReviewedYes
Open AccessYes
TypeARTICLE
VenuePLoS ONE (JOURNAL)
Journal identifiersISSN: 1932-6203 • E-ISSN: 1932-6203
PublisherPublic Library of Science (PLoS) (PUBLISHER)
DOI10.1371/journal.pone.0129102
PMID26086078
PMCIDPMC4472748
OpenAlexW632382092
LanguageEN
Citations received108
References cited31

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.

Ancient DNA · Biology · DNA · DNA sequencing · Endogeny · Exogenous DNA · Inner ear · Petrous bone · Shotgun sequencing · Temporal bone · Anatomy · Environmental DNA in Biodiversity Studies · Forensic and Genetic Research · Genetics · Medicine · Molecular Biology Techniques and Applications