ALBERT

Description: The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal'ta in south-central Siberia, to an average depth of 1x. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105016/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105016/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raghavan, Maanasa -- Skoglund, Pontus -- Graf, Kelly E -- Metspalu, Mait -- Albrechtsen, Anders -- Moltke, Ida -- Rasmussen, Simon -- Stafford, Thomas W Jr -- Orlando, Ludovic -- Metspalu, Ene -- Karmin, Monika -- Tambets, Kristiina -- Rootsi, Siiri -- Magi, Reedik -- Campos, Paula F -- Balanovska, Elena -- Balanovsky, Oleg -- Khusnutdinova, Elza -- Litvinov, Sergey -- Osipova, Ludmila P -- Fedorova, Sardana A -- Voevoda, Mikhail I -- DeGiorgio, Michael -- Sicheritz-Ponten, Thomas -- Brunak, Soren -- Demeshchenko, Svetlana -- Kivisild, Toomas -- Villems, Richard -- Nielsen, Rasmus -- Jakobsson, Mattias -- Willerslev, Eske -- R01 HG003229/HG/NHGRI NIH HHS/ -- England -- Nature. 2014 Jan 2;505(7481):87-91. doi: 10.1038/nature12736. Epub 2013 Nov 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark [2]. ; 1] Department of Evolutionary Biology, Uppsala University, Norbyvagen 18D, Uppsala 752 36, Sweden [2]. ; Center for the Study of the First Americans, Texas A&M University, TAMU-4352, College Station, Texas 77845-4352, USA. ; 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Integrative Biology, University of California, Berkeley, California 94720, USA [3] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia. ; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark. ; 1] The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark [2] Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA. ; Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark. ; 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark [2] AMS 14C Dating Centre, Department of Physics and Astronomy, University of Aarhus, Ny Munkegade 120, Aarhus DK-8000, Denmark. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia. ; 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia. ; Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia. ; Estonian Genome Center, University of Tartu, Tartu 51010, Estonia. ; Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115479, Russia. ; 1] Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115479, Russia [2] Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Street 3, Moscow 119991, Russia. ; 1] Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Bashkorostan 450054, Russia [2] Biology Department, Bashkir State University, Ufa, Bashkorostan 450074, Russia. ; 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Bashkorostan 450054, Russia. ; The Institute of Cytology and Genetics, Center for Brain Neurobiology and Neurogenetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyeva Avenue, Novosibirsk 630090, Russia. ; Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Russian Academy of Medical Sciences and North-Eastern Federal University, Yakutsk, Sakha (Yakutia) 677010, Russia. ; 1] The Institute of Cytology and Genetics, Center for Brain Neurobiology and Neurogenetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyeva Avenue, Novosibirsk 630090, Russia [2] Institute of Internal Medicine, Siberian Branch of the Russian Academy of Medical Sciences, Borisa Bogatkova 175/1, Novosibirsk 630089, Russia. ; Department of Integrative Biology, University of California, Berkeley, California 94720, USA. ; 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark. ; The State Hermitage Museum, 2, Dvortsovaya Ploshchad, St. Petersberg 190000, Russia. ; 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK. ; 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia [3] Estonian Academy of Sciences, Tallinn 10130, Estonia. ; 1] Department of Evolutionary Biology, Uppsala University, Norbyvagen 18D, Uppsala 752 36, Sweden [2] Science for Life Laboratory, Uppsala University, Norbyvagen 18D, 752 36 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24256729" target="_blank"〉PubMed〈/a〉

Description: Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 (14)C years before present (bp) (13,000 to 12,600 calendar years bp). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 +/- 35 (14)C years bp (approximately 12,707-12,556 calendar years bp) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4x and show that the gene flow from the Siberian Upper Palaeolithic Mal'ta population into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years bp. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rasmussen, Morten -- Anzick, Sarah L -- Waters, Michael R -- Skoglund, Pontus -- DeGiorgio, Michael -- Stafford, Thomas W Jr -- Rasmussen, Simon -- Moltke, Ida -- Albrechtsen, Anders -- Doyle, Shane M -- Poznik, G David -- Gudmundsdottir, Valborg -- Yadav, Rachita -- Malaspinas, Anna-Sapfo -- White, Samuel Stockton 5th -- Allentoft, Morten E -- Cornejo, Omar E -- Tambets, Kristiina -- Eriksson, Anders -- Heintzman, Peter D -- Karmin, Monika -- Korneliussen, Thorfinn Sand -- Meltzer, David J -- Pierre, Tracey L -- Stenderup, Jesper -- Saag, Lauri -- Warmuth, Vera M -- Lopes, Margarida C -- Malhi, Ripan S -- Brunak, Soren -- Sicheritz-Ponten, Thomas -- Barnes, Ian -- Collins, Matthew -- Orlando, Ludovic -- Balloux, Francois -- Manica, Andrea -- Gupta, Ramneek -- Metspalu, Mait -- Bustamante, Carlos D -- Jakobsson, Mattias -- Nielsen, Rasmus -- Willerslev, Eske -- BB/H005854/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H008802/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- P25032/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2014 Feb 13;506(7487):225-9. doi: 10.1038/nature13025.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, DK-1350 Copenhagen K, Denmark [2]. ; 1] Anzick Family, 31 Old Clyde Park Road, Livingston, Montana 59047, USA [2]. ; Center for the Study of the First Americans, Departments of Anthropology and Geography, Texas A&M University, 4352 TAMU, College Station, Texas 77843-4352, USA. ; Department of Evolutionary Biology, Uppsala University, Norbyvagen 18D, 752 36 Uppsala, Sweden. ; 1] Department of Integrative Biology, University of California, Berkeley, 4134 Valley Life Sciences Building, Berkeley, California 94720, USA [2] Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK (I.B.); Department of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, Pennsylvania 16802, USA (M.D.). ; 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, DK-1350 Copenhagen K, Denmark [2] AMS 14C Dating Centre, Department of Physics & Astronomy, University of Aarhus, Ny Munkegade 120, DK-8000 Aarhus C, Denmark. ; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby DK-2800, Denmark. ; 1] The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark [2] Department of Human Genetics, University of Chicago, 920 E. 58th Street, CLSC 4th floor, Chicago, Illinois 60637, USA. ; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark. ; Education Department, Montana State University, Box 5103, Bozeman, Montana 59717, USA. ; Program in Biomedical Informatics and Department of Statistics, Stanford University, Stanford, California 94305, USA. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, DK-1350 Copenhagen K, Denmark. ; Anthropology Department, PhD Program, University of Montana, 4100 Mullan Road, no. 217, Missoula, Montana 59808, USA. ; School of Biological Sciences, Washington State University, PO Box 644236, Eastlick Hall 395, Pullman, Washington 99164, USA. ; Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, Riia 23b, 51010 Tartu, Estonia. ; 1] Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK [2] Integrative Systems Biology Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia. ; School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK. ; Department of Anthropology, Southern Methodist University, Dallas, Texas 75275, USA. ; 1] Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK [2] Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK. ; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK. ; Department of Anthropology and Institute for Genomic Biology, University of Illinois Urbana-Champaign, 209F Davenport Hall, 607 Matthews Avenue, Urbana, Illinois 61801, USA. ; 1] School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK [2] Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK (I.B.); Department of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, Pennsylvania 16802, USA (M.D.). ; BioArCh, Departments of Biology, Archaeology and Chemistry, University of York, Wentworth Way, York YO10 5DD, UK. ; MRC Centre for Outbreak, Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, Imperial College Faculty of Medicine, London W2 1PG, UK. ; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. ; 1] Department of Genetics, School of Medicine, Stanford University, Littlefield Center, Stanford, California 94305, USA [2] Center for Evolutionary and Human Genomics, Stanford University, Littlefield Center, Stanford, California 94305, USA. ; 1] Department of Evolutionary Biology, Uppsala University, Norbyvagen 18D, 752 36 Uppsala, Sweden [2] Science for Life Laboratory, Uppsala University, Norbyvagen 18D, 752 36 Uppsala, Sweden. ; Department of Integrative Biology, University of California, Berkeley, 4134 Valley Life Sciences Building, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24522598" target="_blank"〉PubMed〈/a〉

Description: The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Allentoft, Morten E -- Sikora, Martin -- Sjogren, Karl-Goran -- Rasmussen, Simon -- Rasmussen, Morten -- Stenderup, Jesper -- Damgaard, Peter B -- Schroeder, Hannes -- Ahlstrom, Torbjorn -- Vinner, Lasse -- Malaspinas, Anna-Sapfo -- Margaryan, Ashot -- Higham, Tom -- Chivall, David -- Lynnerup, Niels -- Harvig, Lise -- Baron, Justyna -- Della Casa, Philippe -- Dabrowski, Pawel -- Duffy, Paul R -- Ebel, Alexander V -- Epimakhov, Andrey -- Frei, Karin -- Furmanek, Miroslaw -- Gralak, Tomasz -- Gromov, Andrey -- Gronkiewicz, Stanislaw -- Grupe, Gisela -- Hajdu, Tamas -- Jarysz, Radoslaw -- Khartanovich, Valeri -- Khokhlov, Alexandr -- Kiss, Viktoria -- Kolar, Jan -- Kriiska, Aivar -- Lasak, Irena -- Longhi, Cristina -- McGlynn, George -- Merkevicius, Algimantas -- Merkyte, Inga -- Metspalu, Mait -- Mkrtchyan, Ruzan -- Moiseyev, Vyacheslav -- Paja, Laszlo -- Palfi, Gyorgy -- Pokutta, Dalia -- Pospieszny, Lukasz -- Price, T Douglas -- Saag, Lehti -- Sablin, Mikhail -- Shishlina, Natalia -- Smrcka, Vaclav -- Soenov, Vasilii I -- Szeverenyi, Vajk -- Toth, Gusztav -- Trifanova, Synaru V -- Varul, Liivi -- Vicze, Magdolna -- Yepiskoposyan, Levon -- Zhitenev, Vladislav -- Orlando, Ludovic -- Sicheritz-Ponten, Thomas -- Brunak, Soren -- Nielsen, Rasmus -- Kristiansen, Kristian -- Willerslev, Eske -- England -- Nature. 2015 Jun 11;522(7555):167-72. doi: 10.1038/nature14507.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen K, Denmark. ; Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden. ; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs Lyngby, Denmark. ; 1] Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen K, Denmark [2] Faculty of Archaeology, Leiden University, 2300 Leiden, The Netherlands. ; Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden. ; Oxford Radiocarbon Accelerator Unit, University of Oxford, Oxford OX1 3QY, UK. ; Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, 2100 Copenhagen, Denmark. ; Institute of Archaeology, University of Wroclaw, 50-139 Wroclaw, Poland. ; Archaeological Institute, University of Zurich, CH-8006, Zurich, Switzerland. ; Department of Anatomy, Wroclaw Medical University, 50-368 Wroclaw, Poland. ; Department of Anthropology, University of Toronto, Toronto ONM5S 2S2, Canada. ; Department of Archeology and General History, Gorno-Altaisk State University, 649000 Gorno-Altaisk, Russia. ; Institute of History and Archaeology RAS (South Ural Department), South Ural State University, 454080 Chelyabinsk, Russia. ; Environmental Research and Material Science and Centre for Textile Research, The National Museum of Denmark, 1471 Copenhagen K, Denmark. ; Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St Petersburg, Russia. ; Department of Anthropology, Polish Academy of Sciences, 50-449 Wroclaw, Poland. ; Biocentre of the Ludwig-Maximilian-University Munchen, 82152 Munich, Germany. ; 1] Department of Biological Anthropology, Institute of Biology, Eotvos Lorand University, H-1117 Budapest, Hungary [2] Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary. ; The Archaeological Museum of Wroclaw, 50-077 Wroclaw, Poland. ; Samara State Academy of Social Science and Humanities, 443099 Samara, Russia. ; Institute of Archaeology of the Hungarian Academy of Sciences, Research Center for the Humanities, H-1250 Budapest, Hungary. ; 1] Institute of Archaeology and Museology, Faculty of Arts, Masaryk University, CZ-602 00 Brno, Czech Republic [2] Department of Vegetation Ecology, Institute of Botany of the Czech Academy of Sciences, CZ-602 00 Brno, Czech Republic. ; Department of Archaeology, University of Tartu, 51003 Tartu, Estonia. ; Archaeological Superintendence of Lombardy, 20123 Milano, Italy. ; Department of Archaeology, University of Vilnius, LT-01513 Vilnius, Lithuania. ; The SAXO Institute, University of Copenhagen, 2300 Copenhagen S, Denmark. ; Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, 51010 Tartu, Estonia. ; Department of History, Yerevan State University, 0025 Yerevan, Armenia. ; 1] Hungarian National Museum, H-1083 Budapest, Hungary [2] Department of Biological Anthropology, University of Szeged, H-6726 Szeged, Hungary. ; Department of Biological Anthropology, University of Szeged, H-6726 Szeged, Hungary. ; Institute of Archaeology and Ethnology of the Polish Academy of Sciences, 61-612 Poznan, Poland. ; Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. ; Zoological Institute of the Russian Academy of Sciences, 199034 St Petersburg, Russia. ; Department of Archaeology, State Historical Museum, 109012 Moscow, Russia. ; Institute for History of Medicine and Foreign Languages of the First Faculty of Medicine, Charles University, 121 08 Prague, Czech Republic. ; Research Center for the History and Culture of the Turkic Peoples, Gorno-Altaisk State University, 649000 Gorno-Altaisk, Russia. ; Department of Pre- and Early History, Institute of Archaeological Sciences, Faculty of Humanities, Eotvos Lorand University, H-1088 Budapest, Hungary. ; Matrica Museum, 2440 Szazhalombatta, Hungary. ; Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia. ; Department of Archaeology, Faculty of History, Moscow State University, 119991 Moscow, Russia. ; 1] Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs Lyngby, Denmark [2] Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark. ; Center for Theoretical Evolutionary Genetics, University of California, Berkeley, California 94720-3140, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26062507" target="_blank"〉PubMed〈/a〉