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Human Auditory Ossicles as an Alternative Optimal Source of Ancient DNA

Kendra Sirak, View ORCID ProfileDaniel Fernandes, Olivia Cheronet, Eadaoin Harney, Matthew Mah, Swapan Mallick, Nadin Rohland, Nicole Adamski, Nasreen Broomandkhoshbacht, Kimberly Callan, Francesca Candilio, Ann Marie Lawson, Kirsten Mandl, Jonas Oppenheimer, Kristin Stewardson, Fatma Zalzala, Alexandra Anders, Juraj Bartík, Alfredo Coppa, Dashtseveg Tumen, Sándor Évinger, Zdeněk Farkaš, Tamás Hajdu, Jamsranjav Bayarsaikhan, Lauren McIntyre, Vyacheslav Moiseyev, Ildikó Pap, Michael Pietrusewsky, Pál Raczky, Alena Šefčáková, Andrei Soficaru, Tamás Szeniczey, Béla Miklós Szőke, Tumurbaatar Tuvshinjargal, Dennis Van Gerven, Sergey Vasilyev, Lynne Bell, David Reich, Ron Pinhasi
doi: https://doi.org/10.1101/654749
Kendra Sirak
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
2Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
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  • For correspondence: ron.pinhasi@univie.ac.at kendra_sirak@hms.harvard.edu daniel.fernandes@univie.ac.at
Daniel Fernandes
2Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
3Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
4CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
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  • ORCID record for Daniel Fernandes
  • For correspondence: ron.pinhasi@univie.ac.at kendra_sirak@hms.harvard.edu daniel.fernandes@univie.ac.at
Olivia Cheronet
2Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
3Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
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Eadaoin Harney
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
5Dept. of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
6The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA and Jena, D-07745, Germany
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Matthew Mah
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
7Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Swapan Mallick
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
7Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Nadin Rohland
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Nicole Adamski
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Nasreen Broomandkhoshbacht
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Kimberly Callan
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Francesca Candilio
3Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
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Ann Marie Lawson
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Kirsten Mandl
3Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
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Jonas Oppenheimer
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Kristin Stewardson
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Fatma Zalzala
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Alexandra Anders
9Institute of Archaeological Sciences, Eötvös Loránd University, 1088 Budapest, Múzeum körút 4/B, Hungary
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Juraj Bartík
10Slovak National Museum–Archaeological Museum, Žižkova 12, P.O. BOX 13, 810 06 Bratislava 16, Slovak Republi
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Alfredo Coppa
11Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, Italy
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Dashtseveg Tumen
12Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia
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Sándor Évinger
13Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Ludovika tér 2, Hungary
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Zdeněk Farkaš
10Slovak National Museum–Archaeological Museum, Žižkova 12, P.O. BOX 13, 810 06 Bratislava 16, Slovak Republi
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Tamás Hajdu
14Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, Pázmány Péter sétány 1/c. H-1117, Hungary
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Jamsranjav Bayarsaikhan
12Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia
15National Museum of Mongolia, Juulchin Street -1, Ulaanbaatar 210146, Mongolia
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Lauren McIntyre
16Oxford Archaeology, Janus House, Osney Mead, Oxford OX2 0ES, UK
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Vyacheslav Moiseyev
17Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, Univercity Emb. 3, St. Petersburg 199034, Russia
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Ildikó Pap
13Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Ludovika tér 2, Hungary
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Michael Pietrusewsky
18Department of Anthropology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
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Pál Raczky
9Institute of Archaeological Sciences, Eötvös Loránd University, 1088 Budapest, Múzeum körút 4/B, Hungary
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Alena Šefčáková
19Department of Anthropology, Slovak National Museum–Natural History Museum, Vajanského nábr. 2, P.O. BOX 13, 810 06 Bratislava 16, Slovak Republic
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Andrei Soficaru
20“Fr. J. Rainer” Institute of Anthropology, Romanian Academy, Eroii Sanitari 8, P. O. Box 35-13, Romania
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Tamás Szeniczey
14Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, Pázmány Péter sétány 1/c. H-1117, Hungary
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Béla Miklós Szőke
21Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, H-1097, Hungary
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Tumurbaatar Tuvshinjargal
15National Museum of Mongolia, Juulchin Street -1, Ulaanbaatar 210146, Mongolia
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Dennis Van Gerven
22Department of Anthropology, University of Colorado at Boulder, 1350 Pleasant Street, Boulder, CO 80309, USA
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Sergey Vasilyev
23Institute of Ethnology and Anthropology, RAS, 32a Leninsky propsect, Moscow, 119991, Russia
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Lynne Bell
24School of Criminology, Forensic Research Centre, Simon Fraser University, 8888 University Drive, Burnaby,BC, V5A 1S6, Canada
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David Reich
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
7Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Ron Pinhasi
3Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
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  • For correspondence: ron.pinhasi@univie.ac.at kendra_sirak@hms.harvard.edu daniel.fernandes@univie.ac.at
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ABSTRACT

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provide optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of valuable morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluated the efficacy of ossicles as an alternative source of ancient DNA. We demonstrate that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quality, quantity, or authenticity across a range of preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that, when available, they should be selected over the cochlea to reduce damage to skeletal integrity. These results identify a second optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 31, 2019.
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Human Auditory Ossicles as an Alternative Optimal Source of Ancient DNA
Kendra Sirak, Daniel Fernandes, Olivia Cheronet, Eadaoin Harney, Matthew Mah, Swapan Mallick, Nadin Rohland, Nicole Adamski, Nasreen Broomandkhoshbacht, Kimberly Callan, Francesca Candilio, Ann Marie Lawson, Kirsten Mandl, Jonas Oppenheimer, Kristin Stewardson, Fatma Zalzala, Alexandra Anders, Juraj Bartík, Alfredo Coppa, Dashtseveg Tumen, Sándor Évinger, Zdeněk Farkaš, Tamás Hajdu, Jamsranjav Bayarsaikhan, Lauren McIntyre, Vyacheslav Moiseyev, Ildikó Pap, Michael Pietrusewsky, Pál Raczky, Alena Šefčáková, Andrei Soficaru, Tamás Szeniczey, Béla Miklós Szőke, Tumurbaatar Tuvshinjargal, Dennis Van Gerven, Sergey Vasilyev, Lynne Bell, David Reich, Ron Pinhasi
bioRxiv 654749; doi: https://doi.org/10.1101/654749
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Human Auditory Ossicles as an Alternative Optimal Source of Ancient DNA
Kendra Sirak, Daniel Fernandes, Olivia Cheronet, Eadaoin Harney, Matthew Mah, Swapan Mallick, Nadin Rohland, Nicole Adamski, Nasreen Broomandkhoshbacht, Kimberly Callan, Francesca Candilio, Ann Marie Lawson, Kirsten Mandl, Jonas Oppenheimer, Kristin Stewardson, Fatma Zalzala, Alexandra Anders, Juraj Bartík, Alfredo Coppa, Dashtseveg Tumen, Sándor Évinger, Zdeněk Farkaš, Tamás Hajdu, Jamsranjav Bayarsaikhan, Lauren McIntyre, Vyacheslav Moiseyev, Ildikó Pap, Michael Pietrusewsky, Pál Raczky, Alena Šefčáková, Andrei Soficaru, Tamás Szeniczey, Béla Miklós Szőke, Tumurbaatar Tuvshinjargal, Dennis Van Gerven, Sergey Vasilyev, Lynne Bell, David Reich, Ron Pinhasi
bioRxiv 654749; doi: https://doi.org/10.1101/654749

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