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      The problem with petrous? A consideration of the potential biases in the utilization of pars petrosa for ancient DNA analysis

      research-article
      Author(s): a , b , c , a
      Publication date (Electronic):
      Journal: World Archaeology
      Publisher: Routledge
      Keywords: Ancient DNA, petrous, bias, palaeogenomic data

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          ABSTRACT

          Advances in NGS sequencing technologies, improved laboratory protocols and new bioinformatic workflows have seen huge increases in ancient DNA (aDNA) research on archaeological materials. A large proportion of aDNA work now utilizes the petrous portion of the temporal bone ( pars petrosa), which is recognized as an excellent skeletal element for long-term ancient endogenous (host) DNA survival. This has been significant due to the often low endogenous content of other skeletal elements, meaning that large amounts of sequencing are frequently required to obtain sufficient genetic coverage. However, exclusive sampling of the petrous for aDNA analysis introduces a new set of potential biases into our scientific studies – and these issues are yet to be considered by ancient DNA researchers. This paper aims to outline the possible biases of utilizing petrous bones to undertake aDNA analyses and highlight how these complications may potentially be overcome in future research.

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          A high-coverage genome sequence from an archaic Denisovan individual.

          Matthias Meyer, Martin Kircher, Marie-Theres Gansauge … (2012)
          We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
          Article 0 comments Cited 828 times – based on 0 reviews     Review now
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            Ancient human genomes suggest three ancestral populations for present-day Europeans

            Iosif Lazaridis, Nick Patterson, Nick Patterson … (2015)
            We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.
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              Massive migration from the steppe was a source for Indo-European languages in Europe

              Wolfgang Haak, Iosif Lazaridis, Nick Patterson … (2015)
              We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ∼8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ∼24,000-year-old Siberian. By ∼6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ∼4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ∼75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ∼3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.
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                Author and article information

                Journal
                Journal ID (nlm-ta): World Archaeol
                Journal ID (iso-abbrev): World Archaeol
                Journal ID (publisher-id): RWAR
                Journal ID (publisher-id): rwar20
                Title: World Archaeology
                Publisher: Routledge
                ISSN (Print): 0043-8243
                ISSN (Electronic): 1470-1375
                Publication date Collection: 2019
                Publication date (Electronic): 10 January 2020
                Volume: 51
                Issue: 4 , Ancient DNA Research: Blessing or Curse for Archaeology?
                Pages: 574-585
                Affiliations
                [a ]Department of Earth Sciences, Natural History Museum , London, UK
                [b ]PalaeoBARN, School of Archaeology, University of Oxford , Oxford, UK
                [c ]Ancient Genomics Laboratory, The Francis Crick Institute , London, UK
                Author notes
                CONTACT Sophy Charlton sophy@ 123456palaeo.eu Department of Earth Sciences, Natural History Museum , Cromwell Road, London, SW7 5BD UK
                Author information
                http://orcid.org/0000-0001-7487-2635
                http://orcid.org/0000-0002-8731-818X
                http://orcid.org/0000-0001-8322-6918
                Article
                Publisher ID: 1694062
                DOI: 10.1080/00438243.2019.1694062
                PMC ID: 7195170
                PubMed ID: 32405262
                SO-VID: 7cd4d3d4-6777-4d93-89d4-ef2ef841e610
                Copyright © © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Page count
                References: 71, Pages: 12
                Funding
                Funded by: European Research Council 10.13039/100010663
                Award ID: 617777
                Funded by: Wellcome Trust Investigator Award 10.13039/100004440
                Award ID: 100713/Z/12/Z
                S.C and I.B were supported by the European Research Council [grant ID: 617777]. T.B and I.B were supported by the Wellcome Trust [project no. 100713/Z/12/Z].
                Categories
                Subject: Articles

                Keywords: ancient dna,petrous,bias,palaeogenomic data
                Data availability:
                Keywords: ancient dna, petrous, bias, palaeogenomic data

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