ALBERT

Description: North African Jews constitute the second largest Jewish Diaspora group. However, their relatedness to each other; to European, Middle Eastern, and other Jewish Diaspora groups; and to their former North African non-Jewish neighbors has not been well defined. Here, genome-wide analysis of five North African Jewish groups (Moroccan, Algerian, Tunisian,...

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: Mutations in the human neurotrypsin gene are associated with autosomal recessive mental retardation. To further understand the pathophysiological consequences of the lack of this serine protease, we studied Tequila (Teq), the Drosophila neurotrypsin ortholog, using associative memory as a behavioral readout. We found that teq inactivation resulted in a long-term memory (LTM)-specific defect. After LTM conditioning of wild-type flies, teq expression transiently increased in the mushroom bodies. Moreover, specific inhibition of teq expression in adult mushroom bodies resulted in a reversible LTM defect. Hence, the Teq pathway is essential for information processing in Drosophila.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Didelot, Gerard -- Molinari, Florence -- Tchenio, Paul -- Comas, Daniel -- Milhiet, Elodie -- Munnich, Arnold -- Colleaux, Laurence -- Preat, Thomas -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):851-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genes et Dynamique des Systemes de Memoire, UMR CNRS 7637, Ecole Superieure de Physique et de Chimie Industrielles, 10 Rue Vauquelin 75005 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16902143" 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: 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: 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〉

Description: Tuberculosis (TB) is a global health problem estimated to kill 1.4 million people per year. Recent advances in the genomics of the causative agents of TB, bacteria known as the Mycobacterium tuberculosis complex (MTBC), have allowed a better comprehension of its population structure and provided the foundation for molecular evolution analyses. These studies are crucial for a better understanding of TB, including the variation of vaccine efficacy and disease outcome, together with the emergence of drug resistance. Starting from the analysis of 73 publicly available genomes from all the main MTBC lineages, we have screened for evidences of positive selection, a set of 576 genes previously associated with drug resistance or encoding membrane proteins. As expected, because antibiotics constitute strong selective pressure, some of the codons identified correspond to the position of confirmed drug-resistance-associated substitutions in the genes embB , rpoB, and katG . Furthermore, we identified diversifying selection in specific codons of the genes Rv0176 and Rv1872c coding for MCE1-associated transmembrane protein and a putative l -lactate dehydrogenase, respectively. Amino acid sequence analyses showed that in Rv0176, sites undergoing diversifying selection were in a predicted antigen region that varies between "modern" lineages and "ancient" MTBC/BCG strains. In Rv1872c, some of the sites under selection are predicted to impact protein function and thus might result from metabolic adaptation. These results illustrate that diversifying selection in MTBC is happening as a consequence of both antibiotic treatment and other evolutionary pressures.