ALBERT

Description: We sequenced the genomes of a approximately 7,000-year-old farmer from Germany and eight approximately 8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had approximately 44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574/" 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/PMC4170574/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lazaridis, Iosif -- Patterson, Nick -- Mittnik, Alissa -- Renaud, Gabriel -- Mallick, Swapan -- Kirsanow, Karola -- Sudmant, Peter H -- Schraiber, Joshua G -- Castellano, Sergi -- Lipson, Mark -- Berger, Bonnie -- Economou, Christos -- Bollongino, Ruth -- Fu, Qiaomei -- Bos, Kirsten I -- Nordenfelt, Susanne -- Li, Heng -- de Filippo, Cesare -- Prufer, Kay -- Sawyer, Susanna -- Posth, Cosimo -- Haak, Wolfgang -- Hallgren, Fredrik -- Fornander, Elin -- Rohland, Nadin -- Delsate, Dominique -- Francken, Michael -- Guinet, Jean-Michel -- Wahl, Joachim -- Ayodo, George -- Babiker, Hamza A -- Bailliet, Graciela -- Balanovska, Elena -- Balanovsky, Oleg -- Barrantes, Ramiro -- Bedoya, Gabriel -- Ben-Ami, Haim -- Bene, Judit -- Berrada, Fouad -- Bravi, Claudio M -- Brisighelli, Francesca -- Busby, George B J -- Cali, Francesco -- Churnosov, Mikhail -- Cole, David E C -- Corach, Daniel -- Damba, Larissa -- van Driem, George -- Dryomov, Stanislav -- Dugoujon, Jean-Michel -- Fedorova, Sardana A -- Gallego Romero, Irene -- Gubina, Marina -- Hammer, Michael -- Henn, Brenna M -- Hervig, Tor -- Hodoglugil, Ugur -- Jha, Aashish R -- Karachanak-Yankova, Sena -- Khusainova, Rita -- Khusnutdinova, Elza -- Kittles, Rick -- Kivisild, Toomas -- Klitz, William -- Kucinskas, Vaidutis -- Kushniarevich, Alena -- Laredj, Leila -- Litvinov, Sergey -- Loukidis, Theologos -- Mahley, Robert W -- Melegh, Bela -- Metspalu, Ene -- Molina, Julio -- Mountain, Joanna -- Nakkalajarvi, Klemetti -- Nesheva, Desislava -- Nyambo, Thomas -- Osipova, Ludmila -- Parik, Juri -- Platonov, Fedor -- Posukh, Olga -- Romano, Valentino -- Rothhammer, Francisco -- Rudan, Igor -- Ruizbakiev, Ruslan -- Sahakyan, Hovhannes -- Sajantila, Antti -- Salas, Antonio -- Starikovskaya, Elena B -- Tarekegn, Ayele -- Toncheva, Draga -- Turdikulova, Shahlo -- Uktveryte, Ingrida -- Utevska, Olga -- Vasquez, Rene -- Villena, Mercedes -- Voevoda, Mikhail -- Winkler, Cheryl A -- Yepiskoposyan, Levon -- Zalloua, Pierre -- Zemunik, Tatijana -- Cooper, Alan -- Capelli, Cristian -- Thomas, Mark G -- Ruiz-Linares, Andres -- Tishkoff, Sarah A -- Singh, Lalji -- Thangaraj, Kumarasamy -- Villems, Richard -- Comas, David -- Sukernik, Rem -- Metspalu, Mait -- Meyer, Matthias -- Eichler, Evan E -- Burger, Joachim -- Slatkin, Montgomery -- Paabo, Svante -- Kelso, Janet -- Reich, David -- Krause, Johannes -- 8DP1ES022577-04/DP/NCCDPHP CDC HHS/ -- GM100233/GM/NIGMS NIH HHS/ -- GM40282/GM/NIGMS NIH HHS/ -- HG002385/HG/NHGRI NIH HHS/ -- HG004120/HG/NHGRI NIH HHS/ -- HHSN26120080001E/PHS HHS/ -- P01 HG004120/HG/NHGRI NIH HHS/ -- R01 GM100233/GM/NIGMS NIH HHS/ -- R01 HG002385/HG/NHGRI NIH HHS/ -- R01 HG006399/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- England -- Nature. 2014 Sep 18;513(7518):409-13. doi: 10.1038/nature13673.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. ; Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. ; Institute for Archaeological Sciences, University of Tubingen, Tubingen 72074, Germany. ; Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. ; Institute of Anthropology, Johannes Gutenberg University Mainz, Mainz D-55128, Germany. ; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. ; 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. [2] Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA. ; Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. ; 1] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. [2] Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. ; Archaeological Research Laboratory, Stockholm University, 114 18, Sweden. ; 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. [3] Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100049, China. ; Australian Centre for Ancient DNA and Environment Institute, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia. ; The Cultural Heritage Foundation, Vasteras 722 12, Sweden. ; 1] National Museum of Natural History, L-2160, Luxembourg. [2] National Center of Archaeological Research, National Museum of History and Art, L-2345, Luxembourg. ; Department of Paleoanthropology, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tubingen, Tubingen D-72070, Germany. ; National Museum of Natural History, L-2160, Luxembourg. ; State Office for Cultural Heritage Management Baden-Wurttemberg, Osteology, Konstanz D-78467, Germany. ; Center for Global Health and Child Development, Kisumu 40100, Kenya. ; 1] Institutes of Evolution, Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK. [2] Biochemistry Department, Faculty of Medicine, Sultan Qaboos University, Alkhod, Muscat 123, Oman. ; Laboratorio de Genetica Molecular Poblacional, Instituto Multidisciplinario de Biologia Celular (IMBICE), CCT-CONICET &CICPBA, La Plata, B1906APO, Argentina. ; Research Centre for Medical Genetics, Moscow 115478, Russia. ; 1] Research Centre for Medical Genetics, Moscow 115478, Russia. [2] Vavilov Institute for General Genetics, Moscow 119991, Russia. ; Escuela de Biologia, Universidad de Costa Rica, San Jose 2060, Costa Rica. ; Institute of Biology, Research group GENMOL, Universidad de Antioquia, Medellin, Colombia. ; Rambam Health Care Campus, Haifa 31096, Israel. ; Department of Medical Genetics and Szentagothai Research Center, University of Pecs, Pecs H-7624, Hungary. ; Al Akhawayn University in Ifrane (AUI), School of Science and Engineering, Ifrane 53000, Morocco. ; Forensic Genetics Laboratory, Institute of Legal Medicine, Universita Cattolica del Sacro Cuore, Rome 00168, Italy. ; 1] Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. [2] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK. ; Laboratorio di Genetica Molecolare, IRCCS Associazione Oasi Maria SS, Troina 94018, Italy. ; Belgorod State University, Belgorod 308015, Russia. ; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada. ; Servicio de Huellas Digitales Geneticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires, 1113 CABA, Argentina. ; Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. ; Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland. ; Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk 630090, Russia. ; Anthropologie Moleculaire et Imagerie de Synthese, CNRS UMR 5288, Universite Paul Sabatier Toulouse III, Toulouse 31000, France. ; North-Eastern Federal University and Yakut Research Center of Complex Medical Problems, Yakutsk 677013, Russia. ; Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA. ; ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA. ; Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA. ; Department of Clinical Science, University of Bergen, Bergen 5021, Norway. ; NextBio, Illumina, Santa Clara, California 95050, USA. ; Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria. ; 1] Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. [2] Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia. ; College of Medicine, University of Arizona, Tucson, Arizona 85724, USA. ; Division of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK. ; Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA. ; Department of Human and Medical Genetics, Vilnius University, Vilnius LT-08661, Lithuania. ; Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia. ; Translational Medicine and Neurogenetics, Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch 67404, France. ; 1] Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. [2] Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia. [3] Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia. ; 1] Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. [2] Amgen, 33 Kazantzaki Str, Ilioupolis 16342, Athens, Greece (T.L.); Banaras Hindu University, Varanasi 221 005, India (L.S.). ; Gladstone Institutes, San Francisco, California 94158, USA. ; Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia. ; Centro de Investigaciones Biomedicas de Guatemala, Ciudad de Guatemala, Guatemala. ; Research Department, 23andMe, Mountain View, California 94043, USA. ; Cultural Anthropology Program, University of Oulu, Oulu 90014, Finland. ; Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam 65001, Tanzania. ; Research Institute of Health, North-Eastern Federal University, Yakutsk 677000, Russia. ; Dipartimento di Fisica e Chimica, Universita di Palermo, Palermo 90128, Italy. ; 1] Instituto de Alta Investigacion, Universidad de Tarapaca, Arica 1000000, Chile. [2] Programa de Genetica Humana ICBM Facultad de Medicina Universidad de Chile, Santiago 8320000, Chile. [3] Centro de Investigaciones del Hombre en el Desierto, Arica 1000000, Chile. ; Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh EH8 9AG, UK. ; 1] Institute of Immunology, Academy of Science, Tashkent 70000, Uzbekistan. [2]. ; 1] Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia. [2] Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia. ; 1] Department of Forensic Medicine, Hjelt Institute, University of Helsinki, Helsinki 00014, Finland. [2] Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA. ; Unidade de Xenetica, Departamento de Anatomia Patoloxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenomica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galcia 15872, Spain. ; Research Fellow, Henry Stewart Group, Russell House, London WC1A 2HN, UK. ; Institute of Bioorganic Chemistry Academy of Sciences Republic of Uzbekistan, Tashkent 100125, Uzbekistan. ; Department of Genetics and Cytology, V. N. Karazin Kharkiv National University, Kharkiv 61077, Ukraine. ; 1] Instituto Boliviano de Biologia de la Altura, Universidad Mayor de San Andres, 591 2 La Paz, Bolivia. [2] UniversidadAutonoma Tomas Frias, Potosi, Bolivia. ; 1] Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. [2] Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk 630089, Russia. [3] Novosibirsk State University, Novosibirsk 630090, Russia. ; Basic Research Laboratory, NCI, NIH, Frederick National Laboratory, Leidos Biomedical, Frederick, Maryland 21702, USA. ; Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia. ; 1] Lebanese American University, School of Medicine, Beirut 13-5053, Lebanon. [2] Harvard School of Public Health, Boston, Massachusetts 02115, USA. ; Department of Medical Biology, University of Split, School of Medicine, Split 21000, Croatia. ; Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. ; Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK. ; Department of Biology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. ; 1] CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India. [2] Amgen, 33 Kazantzaki Str, Ilioupolis 16342, Athens, Greece (T.L.); Banaras Hindu University, Varanasi 221 005, India (L.S.). ; CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India. ; 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. ; Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain. ; 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA. ; 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. ; 1] Institute for Archaeological Sciences, University of Tubingen, Tubingen 72074, Germany. [2] Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tubingen, 72070 Tubingen, Germany. [3] Max Planck Institut fur Geschichte und Naturwissenschaften, Jena 07745, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25230663" target="_blank"〉PubMed〈/a〉

Description: Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years. We identified events whose dates and participants suggest they describe genetic impacts of the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209567/" 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/PMC4209567/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hellenthal, Garrett -- Busby, George B J -- Band, Gavin -- Wilson, James F -- Capelli, Cristian -- Falush, Daniel -- Myers, Simon -- 090532/Wellcome Trust/United Kingdom -- 098386/Wellcome Trust/United Kingdom -- 098386/Z/12/Z/Wellcome Trust/United Kingdom -- 098387/Wellcome Trust/United Kingdom -- 098387/Z/12/Z/Wellcome Trust/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Feb 14;343(6172):747-51. doi: 10.1126/science.1243518.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24531965" target="_blank"〉PubMed〈/a〉

Description: The expansion of Bantu-speaking agropastoralist populations had a great impact on the genetic, linguistic, and cultural variation of sub-Saharan Africa. It is generally accepted that Bantu languages originated in an area around the present border between Cameroon and Nigeria approximately 5,000 years ago, from where they spread South and East becoming the largest African linguistic branch. The demic consequences of this event are reflected in the relatively high genetic homogeneity observed across most of sub-Saharan Africa populations. In this work, we explored genome-wide single nucleotide polymorphism data from 28 populations to characterize the genetic components present in sub-Saharan African populations. Combining novel data from four Southern African populations with previously published results, we reject the hypothesis that the "non-Bantu" genetic component reported in South-Eastern Africa (Mozambique) reflects extensive gene flow between incoming agriculturalist and resident hunter-gatherer communities. We alternatively suggest that this novel component is the result of demographic dynamics associated with the Bantu dispersal.

Description: A consensus on Bantu-speaking populations being genetically similar has emerged in the last few years, but the demographic scenarios associated with their dispersal are still a matter of debate. The frontier model proposed by archeologists postulates different degrees of interaction among incoming agropastoralist and resident foraging groups in the presence of "static" and "moving" frontiers. By combining mitochondrial DNA and Y chromosome data collected from several southern African populations, we show that Bantu-speaking populations from regions characterized by a moving frontier developing after a long-term static frontier have larger hunter-gatherer contributions than groups from areas where a static frontier was not followed by further spatial expansion. Differences in the female and male components suggest that the process of assimilation of the long-term resident groups into agropastoralist societies was gender biased. Our results show that the diffusion of Bantu languages and culture in Southern Africa was a process more complex than previously described and suggest that the admixture dynamics between farmers and foragers played an important role in shaping the current patterns of genetic diversity.

Description: The malaria parasite Plasmodium falciparum invades human red blood cells by a series of interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy-number variants affecting the host invasion receptor genes GYPA and GYPB . We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently increased in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.