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      Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia)

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          Abstract

          Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal–Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.

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          The complete genome sequence of a Neandertal from the Altai Mountains

          We present a high-quality genome sequence of a Neandertal woman from Siberia. We show that her parents were related at the level of half siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neandertal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neandertals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high quality Neandertal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neandertals and Denisovans.
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            The genome of the offspring of a Neandertal mother and a Denisovan father

            Neandertals and Denisovans are extinct groups of hominins that separated from each other more than 390,000 years ago1,2. Here we present the genome of “Denisova 11”, a bone fragment from Denisova Cave (Russia)3, and show that it comes from an individual who had a Neandertal mother and a Denisovan father. The father, whose genome bears traces of Neandertal ancestry, came from a population related to a later Denisovan found in the cave4–6. The mother came from a population more closely related to Neandertals who lived later in Europe2,7 than to an older Neandertal found in Denisova Cave8, suggesting that migrations of Neandertals between eastern and western Eurasia occurred sometime after ~120,000 years ago. The finding of a first-generation Neandertal-Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.
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              Neandertal and Denisovan DNA from Pleistocene sediments.

              Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA, we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples, we detected Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave, we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility of detecting the presence of hominin groups at sites and in areas where no skeletal remains are found.
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                Author and article information

                Contributors
                mike.morley@flinders.edu.au
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                26 September 2019
                26 September 2019
                2019
                : 9
                : 13785
                Affiliations
                [1 ]ISNI 0000 0004 0486 528X, GRID grid.1007.6, Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, , University of Wollongong, ; Wollongong, New South Wales 2522 Australia
                [2 ]ISNI 0000 0004 0367 2697, GRID grid.1014.4, Archaeology, College of Humanities and Social Sciences, , Flinders University, ; Adelaide, South Australia 5042 Australia
                [3 ]ISNI 0000 0001 2190 1447, GRID grid.10392.39, Institut für Naturwissenschaftliche Archäologie, , Eberhard-Karls-Universität Tübingen, ; Rümelinstrasse 23, Tübingen 72070 Germany
                [4 ]ISNI 0000 0001 2192 9124, GRID grid.4886.2, Institute of Archaeology and Ethnography, , Russian Academy of Sciences, ; Siberian Branch, Novosibirsk 630090 Russia
                [5 ]ISNI 0000 0001 2342 9668, GRID grid.14476.30, Lomonosov Moscow State University, ; Moscow, 119991 Russia
                [6 ]ISNI 0000000121896553, GRID grid.4605.7, Novosibirsk State University, ; Novosibirsk, 630090 Russia
                [7 ]ISNI 0000 0004 0486 528X, GRID grid.1007.6, Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, , University of Wollongong, ; Wollongong, New South Wales 2522 Australia
                Author information
                http://orcid.org/0000-0001-7730-9637
                http://orcid.org/0000-0002-0128-4119
                Article
                49930
                10.1038/s41598-019-49930-3
                6763451
                31558742
                e785c161-5f99-48fd-851e-f09c0f45419c
                © 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
                : 27 March 2019
                : 3 September 2019
                Funding
                Funded by: Australian research Council (ARC)
                Categories
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                © The Author(s) 2019

                Uncategorized
                evolution,environmental social sciences
                Uncategorized
                evolution, environmental social sciences

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