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      Mitochondrial ancestry of medieval individuals carelessly interred in a multiple burial from southeastern Romania

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          Abstract

          The historical province of Dobruja, located in southeastern Romania, has experienced intense human population movement, invasions, and conflictual episodes during the Middle Ages, being an important intersection point between Asia and Europe. The most informative source of maternal population histories is the complete mitochondrial genome of archaeological specimens, but currently, there is insufficient ancient DNA data available for the medieval period in this geographical region to complement the archaeological findings. In this study, we reconstructed, by using Next Generation Sequencing, the entire mitochondrial genomes (mitogenomes) of six medieval individuals neglectfully buried in a multiple burial from Capidava necropolis (Dobruja), some presenting signs of a violent death. Six distinct maternal lineages (H11a1, U4d2, J1c15, U6a1a1, T2b, and N1a3a) with different phylogenetic background were identified, pointing out the heterogeneous genetic aspect of the analyzed medieval group. Using population genetic analysis based on high-resolution mitochondrial data, we inferred the genetic affinities of the available medieval dataset from Capidava to other ancient Eurasian populations. The genetic data were integrated with the archaeological and anthropological information in order to sketch a small, local piece of the mosaic that is the image of medieval European population history.

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          The Genomic History of Southeastern Europe

          Farming was first introduced to Europe in the mid-7th millennium BCE–associated with migrants from Anatolia who settled in the Southeast before spreading throughout Europe. To understand the dynamics of this process, we analyzed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document a West-East cline of ancestry in indigenous hunter-gatherers and–in far-eastern Europe–early stages in the formation of Bronze Age Steppe ancestry. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited hunter-gatherer admixture, but that some groups that remained mixed extensively, without the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West, with intermittent genetic contact with the Steppe up to 2000 years before the migrations that replaced much of northern Europe’s population.
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            The Beaker Phenomenon and the Genomic Transformation of Northwest Europe

            Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200–1800 BCE. The forces propelling its expansion are a matter of long-standing debate, with support for both cultural diffusion and migration. We present new genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 Beaker-associated individuals. We detected limited genetic affinity between Iberian and central European Beaker-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, migration played a key role in the further dissemination of the Beaker Complex, a phenomenon we document most clearly in Britain, where the spread of the Beaker Complex introduced high levels of Steppe-related ancestry and was associated with a replacement of ~90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought Steppe-related ancestry into central and northern Europe 400 years earlier.
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              Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

              DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5′-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments.
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                Author and article information

                Contributors
                rusu.n.ioana@gmail.com
                alessandra.modi@unifi.it
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                30 January 2019
                30 January 2019
                2019
                : 9
                : 961
                Affiliations
                [1 ]ISNI 0000 0004 1937 1397, GRID grid.7399.4, Molecular Biology Center, , Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, ; 400271 Cluj Napoca, Romania
                [2 ]ISNI 0000 0004 1937 1397, GRID grid.7399.4, Department of Molecular Biology and Biotechnology, , Faculty of Biology and Geology, Babeș-Bolyai University, ; 400006 Cluj Napoca, Romania
                [3 ]ISNI 0000 0004 1757 2304, GRID grid.8404.8, Dipartimento di Biologia, , Università di Firenze, ; 50122 Florence, Italy
                [4 ]ISNI 0000 0004 1937 1397, GRID grid.7399.4, Department of Ancient History and Archaeology, , Faculty of History and Philosophy, Babeș-Bolyai University, ; 400084 Cluj Napoca, Romania
                [5 ]ISNI 0000 0004 1937 1397, GRID grid.7399.4, Nanostructured Materials and Bio-Nano-Interfaces Center, , Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, ; 400271 Cluj Napoca, Romania
                [6 ]Department of Research-Development and Projects, Museum of National History and Archeology, 900745 Constanța, Romania
                [7 ]ISNI 0000 0004 1937 1389, GRID grid.418333.e, Institute of Biology Bucharest, , Romanian Academy, ; 060031 Bucharest, Romania
                Author information
                http://orcid.org/0000-0002-6152-8832
                http://orcid.org/0000-0002-2989-2941
                Article
                37760
                10.1038/s41598-018-37760-8
                6353917
                0e7594b6-7999-4250-998f-bb8bae224133
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 12 June 2018
                : 13 December 2018
                Funding
                Funded by: Executive Unit for Financing Higher Education, Research, Development and Innovation (UEFISCDI), PN-II-PT-PCCA-2011-3.1-1153, contract number 229/2013
                Funded by: Department of Excellence fund to Department of Biology University of Florence (2018-2022)
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