ALBERT

Beschreibung: We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30x) 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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617501/" 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/PMC3617501/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meyer, Matthias -- Kircher, Martin -- Gansauge, Marie-Theres -- Li, Heng -- Racimo, Fernando -- Mallick, Swapan -- Schraiber, Joshua G -- Jay, Flora -- Prufer, Kay -- de Filippo, Cesare -- Sudmant, Peter H -- Alkan, Can -- Fu, Qiaomei -- Do, Ron -- Rohland, Nadin -- Tandon, Arti -- Siebauer, Michael -- Green, Richard E -- Bryc, Katarzyna -- Briggs, Adrian W -- Stenzel, Udo -- Dabney, Jesse -- Shendure, Jay -- Kitzman, Jacob -- Hammer, Michael F -- Shunkov, Michael V -- Derevianko, Anatoli P -- Patterson, Nick -- Andres, Aida M -- Eichler, Evan E -- Slatkin, Montgomery -- Reich, David -- Kelso, Janet -- Paabo, Svante -- GM100233/GM/NIGMS NIH HHS/ -- R01 GM040282/GM/NIGMS NIH HHS/ -- R01 GM100233/GM/NIGMS NIH HHS/ -- R01-GM40282/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Oct 12;338(6104):222-6. doi: 10.1126/science.1224344. Epub 2012 Aug 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. mmeyer@eva.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936568" target="_blank"〉PubMed〈/a〉

Beschreibung: In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568308/" 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/PMC4568308/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sudmant, Peter H -- Mallick, Swapan -- Nelson, Bradley J -- Hormozdiari, Fereydoun -- Krumm, Niklas -- Huddleston, John -- Coe, Bradley P -- Baker, Carl -- Nordenfelt, Susanne -- Bamshad, Michael -- Jorde, Lynn B -- Posukh, Olga L -- Sahakyan, Hovhannes -- Watkins, W Scott -- Yepiskoposyan, Levon -- Abdullah, M Syafiq -- Bravi, Claudio M -- Capelli, Cristian -- Hervig, Tor -- Wee, Joseph T S -- Tyler-Smith, Chris -- van Driem, George -- Romero, Irene Gallego -- Jha, Aashish R -- Karachanak-Yankova, Sena -- Toncheva, Draga -- Comas, David -- Henn, Brenna -- Kivisild, Toomas -- Ruiz-Linares, Andres -- Sajantila, Antti -- Metspalu, Ene -- Parik, Juri -- Villems, Richard -- Starikovskaya, Elena B -- Ayodo, George -- Beall, Cynthia M -- Di Rienzo, Anna -- Hammer, Michael F -- Khusainova, Rita -- Khusnutdinova, Elza -- Klitz, William -- Winkler, Cheryl -- Labuda, Damian -- Metspalu, Mait -- Tishkoff, Sarah A -- Dryomov, Stanislav -- Sukernik, Rem -- Patterson, Nick -- Reich, David -- Eichler, Evan E -- 098051/Wellcome Trust/United Kingdom -- 1R01DK104339-01/DK/NIDDK NIH HHS/ -- 1R01GM113657-01/GM/NIGMS NIH HHS/ -- 261213/European Research Council/International -- 2R01HG002385/HG/NHGRI NIH HHS/ -- 5DP1ES022577 05/DP/NCCDPHP CDC HHS/ -- HHSN26120080001E/PHS HHS/ -- P30 ES013508/ES/NIEHS NIH HHS/ -- R01 DK104339/DK/NIDDK NIH HHS/ -- R01 GM113657/GM/NIGMS NIH HHS/ -- R01 HG002385/HG/NHGRI NIH HHS/ -- T32 GM007266/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2015 Sep 11;349(6253):aab3761. doi: 10.1126/science.aab3761. Epub 2015 Aug 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. ; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. ; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. ; Department of Pediatrics, University of Washington, Seattle, WA 98119, USA. ; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA. ; Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Novosibirsk State University, Novosibirsk 630090, Russia. ; Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia. ; Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA. ; Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia. ; Raja Isteri Pengiran Anak Saleha (RIPAS) Hospital, Bandar Seri Begawan, Brunei Darussalam. ; Laboratorio de Genetica Molecular Poblacional, Instituto Multidisciplinario de Biologia Celular (IMBICE), Centro Cientifico y Tecnologico-Consejo Nacional de Investigaciones Cientificas y Tecnicas (CCT-CONICET) and Comision de Investigaciones Cientificas de la Provincia de Buenos Aires (CICPBA), La Plata B1906APO, Argentina. ; Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. ; Department of Clinical Science, University of Bergen, Bergen 5021, Norway. ; National Cancer Centre Singapore, Singapore. ; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. ; Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland. ; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. ; Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria. ; Institut de Biologia Evolutiva [Consejo Superior de Investigaciones Cientificas-Universitat Pompeu Fabra (CSIC-UPF)], Departament de Ciencies Experimentals i de la Salut, UPF, Barcelona 08003, Spain. ; Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA. ; Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK. ; Department of Genetics, Evolution and Environment, University College London, WC1E 6BT, UK. ; University of Helsinki, Department of Forensic Medicine, Helsinki 00014, Finland. ; Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. University of Tartu, Department of Evolutionary Biology, Tartu 5101, Estonia. ; Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. ; Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. ; Center for Global Health and Child Development, Kisumu 40100, Kenya. ; Department of Anthropology, Case Western Reserve University, Cleveland, OH 44106-7125, USA. ; Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA. ; Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia. ; Integrative Biology, University of California, Berkeley, CA 94720-3140, USA. ; Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Incorporated, Frederick National Laboratory, Frederick, MD 21702, USA. ; Centre Hospitalier Universitaire (CHU) Sainte-Justine, Departement de Pediatrie, Universite de Montreal, QC H3T 1C5, Canada. ; Departments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. ; Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. ; Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Altai State University, Barnaul 656000, Russia. ; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. ; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. eee@gs.washington.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26249230" target="_blank"〉PubMed〈/a〉

Beschreibung: 〈p〉We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non-Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.〈/p〉

Beschreibung: The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

Beschreibung: Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from 18 Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100 to 1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants.

Beschreibung: 〈p〉By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.〈/p〉