ALBERT

Description: Contemporary Jews comprise an aggregate of ethno-religious communities whose worldwide members identify with each other through various shared religious, historical and cultural traditions. Historical evidence suggests common origins in the Middle East, followed by migrations leading to the establishment of communities of Jews in Europe, Africa and Asia, in what is termed the Jewish Diaspora. This complex demographic history imposes special challenges in attempting to address the genetic structure of the Jewish people. Although many genetic studies have shed light on Jewish origins and on diseases prevalent among Jewish communities, including studies focusing on uniparentally and biparentally inherited markers, genome-wide patterns of variation across the vast geographic span of Jewish Diaspora communities and their respective neighbours have yet to be addressed. Here we use high-density bead arrays to genotype individuals from 14 Jewish Diaspora communities and compare these patterns of genome-wide diversity with those from 69 Old World non-Jewish populations, of which 25 have not previously been reported. These samples were carefully chosen to provide comprehensive comparisons between Jewish and non-Jewish populations in the Diaspora, as well as with non-Jewish populations from the Middle East and north Africa. Principal component and structure-like analyses identify previously unrecognized genetic substructure within the Middle East. Most Jewish samples form a remarkably tight subcluster that overlies Druze and Cypriot samples but not samples from other Levantine populations or paired Diaspora host populations. In contrast, Ethiopian Jews (Beta Israel) and Indian Jews (Bene Israel and Cochini) cluster with neighbouring autochthonous populations in Ethiopia and western India, respectively, despite a clear paternal link between the Bene Israel and the Levant. These results cast light on the variegated genetic architecture of the Middle East, and trace the origins of most Jewish Diaspora communities to the Levant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Behar, Doron M -- Yunusbayev, Bayazit -- Metspalu, Mait -- Metspalu, Ene -- Rosset, Saharon -- Parik, Juri -- Rootsi, Siiri -- Chaubey, Gyaneshwer -- Kutuev, Ildus -- Yudkovsky, Guennady -- Khusnutdinova, Elza K -- Balanovsky, Oleg -- Semino, Ornella -- Pereira, Luisa -- Comas, David -- Gurwitz, David -- Bonne-Tamir, Batsheva -- Parfitt, Tudor -- Hammer, Michael F -- Skorecki, Karl -- Villems, Richard -- England -- Nature. 2010 Jul 8;466(7303):238-42. doi: 10.1038/nature09103. Epub 2010 Jun 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel. behardm@usernet.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20531471" target="_blank"〉PubMed〈/a〉

Description: Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3822165/" 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/PMC3822165/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prado-Martinez, Javier -- Sudmant, Peter H -- Kidd, Jeffrey M -- Li, Heng -- Kelley, Joanna L -- Lorente-Galdos, Belen -- Veeramah, Krishna R -- Woerner, August E -- O'Connor, Timothy D -- Santpere, Gabriel -- Cagan, Alexander -- Theunert, Christoph -- Casals, Ferran -- Laayouni, Hafid -- Munch, Kasper -- Hobolth, Asger -- Halager, Anders E -- Malig, Maika -- Hernandez-Rodriguez, Jessica -- Hernando-Herraez, Irene -- Prufer, Kay -- Pybus, Marc -- Johnstone, Laurel -- Lachmann, Michael -- Alkan, Can -- Twigg, Dorina -- Petit, Natalia -- Baker, Carl -- Hormozdiari, Fereydoun -- Fernandez-Callejo, Marcos -- Dabad, Marc -- Wilson, Michael L -- Stevison, Laurie -- Camprubi, Cristina -- Carvalho, Tiago -- Ruiz-Herrera, Aurora -- Vives, Laura -- Mele, Marta -- Abello, Teresa -- Kondova, Ivanela -- Bontrop, Ronald E -- Pusey, Anne -- Lankester, Felix -- Kiyang, John A -- Bergl, Richard A -- Lonsdorf, Elizabeth -- Myers, Simon -- Ventura, Mario -- Gagneux, Pascal -- Comas, David -- Siegismund, Hans -- Blanc, Julie -- Agueda-Calpena, Lidia -- Gut, Marta -- Fulton, Lucinda -- Tishkoff, Sarah A -- Mullikin, James C -- Wilson, Richard K -- Gut, Ivo G -- Gonder, Mary Katherine -- Ryder, Oliver A -- Hahn, Beatrice H -- Navarro, Arcadi -- Akey, Joshua M -- Bertranpetit, Jaume -- Reich, David -- Mailund, Thomas -- Schierup, Mikkel H -- Hvilsom, Christina -- Andres, Aida M -- Wall, Jeffrey D -- Bustamante, Carlos D -- Hammer, Michael F -- Eichler, Evan E -- Marques-Bonet, Tomas -- 090532/Wellcome Trust/United Kingdom -- 260372/European Research Council/International -- DP1 ES022577/ES/NIEHS NIH HHS/ -- DP1ES022577-04/DP/NCCDPHP CDC HHS/ -- GM100233/GM/NIGMS NIH HHS/ -- HG002385/HG/NHGRI NIH HHS/ -- R01 GM095882/GM/NIGMS NIH HHS/ -- R01 GM100233/GM/NIGMS NIH HHS/ -- R01 HG002385/HG/NHGRI NIH HHS/ -- R01_HG005226/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Jul 25;499(7459):471-5. doi: 10.1038/nature12228. Epub 2013 Jul 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23823723" target="_blank"〉PubMed〈/a〉

Description: 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〉