title: Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone.
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.
authors.affiliation: School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.
authors.forename: Ron
authors.initials: R
authors.lastname: Pinhasi
authors.affiliation: School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Fernandes
authors.affiliation: Department of Anthropology, Emory University, Atlanta, Georgia, United States of America.
authors.forename: Kendra
authors.initials: K
authors.lastname: Sirak
authors.affiliation: School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.
authors.forename: Mario
authors.initials: M
authors.lastname: Novak
authors.affiliation: School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.
authors.forename: Sarah
authors.initials: S
authors.lastname: Connell
authors.affiliation: independent researcher, Santpoort-Noord, The Netherlands.
authors.forename: Songül
authors.initials: S
authors.lastname: Alpaslan-Roodenberg
authors.affiliation: Netherlands Institute in Turkey, Istiklal Caddesi, Nur-i Ziya Sokak 5, Beyoğlu, Istanbul, Turkey.
authors.forename: Fokke
authors.initials: F
authors.lastname: Gerritsen
authors.affiliation: Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Universitetskaya Nab. 3, St. Petersburg, Russia.
authors.forename: Vyacheslav
authors.initials: V
authors.lastname: Moiseyev
authors.affiliation: Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Universitetskaya Nab. 3, St. Petersburg, Russia.
authors.forename: Andrey
authors.initials: A
authors.lastname: Gromov
authors.affiliation: Eötvös Loránd University University, Faculty of Humanities, Institute of Archaeological Sciences, Múzeum körút 4/b, Budapest, Hungary.
authors.forename: Pál
authors.initials: P
authors.lastname: Raczky
authors.affiliation: Eötvös Loránd University University, Faculty of Humanities, Institute of Archaeological Sciences, Múzeum körút 4/b, Budapest, Hungary.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Anders
authors.affiliation: Department of Anthropology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Pietrusewsky
authors.affiliation: Whitman College, Walla Walla, Washington, United States of America.
authors.forename: Gary
authors.initials: G
authors.lastname: Rollefson
authors.affiliation: Museum of Vojvodina, 21 000 Novi Sad, Ulica Dunavska 35, Serbia.
authors.forename: Marija
authors.initials: M
authors.lastname: Jovanovic
authors.affiliation: Institute of Archaeology, Hoan Kiem District, Hanoi, Vietnam.
authors.forename: Hiep
authors.initials: H
authors.lastname: Trinhhoang
authors.affiliation: Zinman Institute of Archaeology, University of Haifa, Mount Carmel, Israel.
authors.forename: Guy
authors.initials: G
authors.lastname: Bar-Oz
authors.affiliation: School of Archaeology and Anthropology, Australian National University, Canberra, Australia.
authors.forename: Marc
authors.initials: M
authors.lastname: Oxenham
authors.affiliation: School of Health Science, Sapporo Medical University, Sapporo, Japan.
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Matsumura
authors.affiliation: 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.
authors.forename: Michael
authors.initials: M
authors.lastname: Hofreiter
mesh_terms: D001106:Archaeology; D004247:DNA / Q000302:isolation & purification*; D004249:DNA Damage; D007758:Ear, Inner / Q000737:chemistry*; D005580:Fossils; D006801:Humans; D010579:Petrous Bone / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004247:DNA