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  • 1
    Publication Date: 2014-01-28
    Description: Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Brana-Arintero site in Leon, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Brana individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4269527/" 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/PMC4269527/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Olalde, Inigo -- Allentoft, Morten E -- Sanchez-Quinto, Federico -- Santpere, Gabriel -- Chiang, Charleston W K -- DeGiorgio, Michael -- Prado-Martinez, Javier -- Rodriguez, Juan Antonio -- Rasmussen, Simon -- Quilez, Javier -- Ramirez, Oscar -- Marigorta, Urko M -- Fernandez-Callejo, Marcos -- Prada, Maria Encina -- Encinas, Julio Manuel Vidal -- Nielsen, Rasmus -- Netea, Mihai G -- Novembre, John -- Sturm, Richard A -- Sabeti, Pardis -- Marques-Bonet, Tomas -- Navarro, Arcadi -- Willerslev, Eske -- Lalueza-Fox, Carles -- F32 GM106656/GM/NIGMS NIH HHS/ -- F32GM106656/GM/NIGMS NIH HHS/ -- R01 HG007089/HG/NHGRI NIH HHS/ -- R01-HG007089/HG/NHGRI NIH HHS/ -- England -- Nature. 2014 Mar 13;507(7491):225-8. doi: 10.1038/nature12960. Epub 2014 Jan 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain [2]. ; 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark [2]. ; Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain. ; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, USA. ; 1] Department of Integrative Biology, University of California, Berkeley, California 94720, USA [2] Department of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, Pennsylvania 16802, USA. ; Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark. ; I.E.S.O. 'Los Salados', Junta de Castilla y Leon, E-49600 Benavente, Spain. ; Junta de Castilla y Leon, Servicio de Cultura de Leon, E-24071 Leon, Spain. ; Center for Theoretical Evolutionary Genomics, University of California, Berkeley, California 94720, USA. ; Department of Medicine and Nijmegen Institute for Infection, Inflammation and Immunity, Radboud University Nijmegen Medical Centre, 6500 Nijmegen, The Netherlands. ; Department of Human Genetics, University of Chicago, Illinois 60637, USA. ; Institute for Molecular Bioscience, Melanogenix Group, The University of Queensland, Brisbane, Queensland 4072, Australia. ; 1] Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA. ; 1] Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain [2] Institucio Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Catalonia, Spain. ; 1] Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain [2] Institucio Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Catalonia, Spain [3] Centre de Regulacio Genomica (CRG), Barcelona 08003, Catalonia, Spain [4] National Institute for Bioinformatics (INB), Barcelona 08003, Catalonia, Spain. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24463515" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/history ; *Alleles ; Biological Evolution ; Caves ; European Continental Ancestry Group/*genetics ; Eye Color/genetics ; *Fossils ; Genome, Human/genetics ; Genomics ; History, Ancient ; Humans ; Immunity/*genetics ; Lactose Intolerance/genetics ; Male ; Pigmentation/*genetics ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Skeleton ; Skin Pigmentation/genetics ; Spain/ethnology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2013-07-05
    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〉
    Keywords: Africa ; Animals ; Animals, Wild/genetics ; Animals, Zoo/genetics ; Asia, Southeastern ; Evolution, Molecular ; Gene Flow/genetics ; *Genetic Variation ; Genetics, Population ; Genome/genetics ; Gorilla gorilla/classification/genetics ; Hominidae/classification/*genetics ; Humans ; Inbreeding ; Pan paniscus/classification/genetics ; Pan troglodytes/classification/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Population Density
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2014-09-12
    Description: Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation approximately 5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249732/" 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/PMC4249732/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carbone, Lucia -- Harris, R Alan -- Gnerre, Sante -- Veeramah, Krishna R -- Lorente-Galdos, Belen -- Huddleston, John -- Meyer, Thomas J -- Herrero, Javier -- Roos, Christian -- Aken, Bronwen -- Anaclerio, Fabio -- Archidiacono, Nicoletta -- Baker, Carl -- Barrell, Daniel -- Batzer, Mark A -- Beal, Kathryn -- Blancher, Antoine -- Bohrson, Craig L -- Brameier, Markus -- Campbell, Michael S -- Capozzi, Oronzo -- Casola, Claudio -- Chiatante, Giorgia -- Cree, Andrew -- Damert, Annette -- de Jong, Pieter J -- Dumas, Laura -- Fernandez-Callejo, Marcos -- Flicek, Paul -- Fuchs, Nina V -- Gut, Ivo -- Gut, Marta -- Hahn, Matthew W -- Hernandez-Rodriguez, Jessica -- Hillier, LaDeana W -- Hubley, Robert -- Ianc, Bianca -- Izsvak, Zsuzsanna -- Jablonski, Nina G -- Johnstone, Laurel M -- Karimpour-Fard, Anis -- Konkel, Miriam K -- Kostka, Dennis -- Lazar, Nathan H -- Lee, Sandra L -- Lewis, Lora R -- Liu, Yue -- Locke, Devin P -- Mallick, Swapan -- Mendez, Fernando L -- Muffato, Matthieu -- Nazareth, Lynne V -- Nevonen, Kimberly A -- O'Bleness, Majesta -- Ochis, Cornelia -- Odom, Duncan T -- Pollard, Katherine S -- Quilez, Javier -- Reich, David -- Rocchi, Mariano -- Schumann, Gerald G -- Searle, Stephen -- Sikela, James M -- Skollar, Gabriella -- Smit, Arian -- Sonmez, Kemal -- ten Hallers, Boudewijn -- Terhune, Elizabeth -- Thomas, Gregg W C -- Ullmer, Brygg -- Ventura, Mario -- Walker, Jerilyn A -- Wall, Jeffrey D -- Walter, Lutz -- Ward, Michelle C -- Wheelan, Sarah J -- Whelan, Christopher W -- White, Simon -- Wilhelm, Larry J -- Woerner, August E -- Yandell, Mark -- Zhu, Baoli -- Hammer, Michael F -- Marques-Bonet, Tomas -- Eichler, Evan E -- Fulton, Lucinda -- Fronick, Catrina -- Muzny, Donna M -- Warren, Wesley C -- Worley, Kim C -- Rogers, Jeffrey -- Wilson, Richard K -- Gibbs, Richard A -- 095908/Wellcome Trust/United Kingdom -- 15603/Cancer Research UK/United Kingdom -- 260372/European Research Council/International -- HG002385/HG/NHGRI NIH HHS/ -- P30 AA019355/AA/NIAAA NIH HHS/ -- P30CA006973/CA/NCI NIH HHS/ -- P51 RR000163/RR/NCRR NIH HHS/ -- R01 GM059290/GM/NIGMS NIH HHS/ -- R01 GM59290/GM/NIGMS NIH HHS/ -- R01 HG002385/HG/NHGRI NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- R01 HG005226/HG/NHGRI NIH HHS/ -- R01 MH081203/MH/NIMH NIH HHS/ -- R01_HG005226/HG/NHGRI NIH HHS/ -- T15 LM007088/LM/NLM NIH HHS/ -- U41 HG007497/HG/NHGRI NIH HHS/ -- U41 HG007497-01/HG/NHGRI NIH HHS/ -- U41HG007234/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- U54HG003273/HG/NHGRI NIH HHS/ -- WT095908/Wellcome Trust/United Kingdom -- WT098051/Wellcome Trust/United Kingdom -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Oregon Health &Science University, Department of Behavioral Neuroscience, 3181 SW Sam Jackson Park Road Portland, Oregon 97239, USA. [2] Oregon National Primate Research Center, Division of Neuroscience, 505 NW 185th Avenue, Beaverton, Oregon 97006, USA. [3] Oregon Health &Science University, Department of Molecular &Medical Genetics, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA. [4] Oregon Health &Science University, Bioinformatics and Computational Biology Division, Department of Medical Informatics &Clinical Epidemiology, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA. ; Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, Texas 77030, USA. ; Nabsys, 60 Clifford Street, Providence, Rhode Island 02903, USA. ; 1] University of Arizona, ARL Division of Biotechnology, Tucson, Arizona 85721, USA. [2] Stony Brook University, Department of Ecology and Evolution, Stony Brook, New York 11790, USA. ; IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain. ; 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA. [2] Howard Hughes Medical Institute, 1705 NE Pacific Street, Seattle, Washington 98195, USA. ; Oregon Health &Science University, Department of Behavioral Neuroscience, 3181 SW Sam Jackson Park Road Portland, Oregon 97239, USA. ; 1] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. [2] The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK. [3] Bill Lyons Informatics Center, UCL Cancer Institute, University College London, London WC1E 6DD, UK (J.He); Seven Bridges Genomics, Cambridge, Massachusetts 02138, USA (D.P.L.); Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA (F.L.M.); BioNano Genomics, San Diego, California 92121, USA (B.t.H.); University of Chicago, Department of Human Genetics, Chicago, Illinois 60637, USA (M.C.W.); Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138, USA (C.W.W.); The CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (B.Z.). ; Leibniz Institute for Primate Research, Gene Bank of Primates, German Primate Center, Gottingen 37077, Germany. ; 1] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. [2] European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ; University of Bari, Department of Biology, Via Orabona 4, 70125, Bari, Italy. ; Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA. ; Louisiana State University, Department of Biological Sciences, Baton Rouge, Louisiana 70803, USA. ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ; University of Paul Sabatier, Toulouse 31062, France. ; The Johns Hopkins University School of Medicine, Department of Oncology, Division of Biostatistics and Bioinformatics, Baltimore, Maryland 21205, USA. ; University of Utah, Salt Lake City, Utah 84112, USA. ; Texas A&M University, Department of Ecosystem Science and Management, College Station, Texas 77843, USA. ; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA. ; Babes-Bolyai-University, Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Cluj-Napoca 400084, Romania. ; Children's Hospital Oakland Research Institute, BACPAC Resources, Oakland, California 94609, USA. ; University of Colorado School of Medicine, Department of Biochemistry and Molecular Genetics, Aurora, Colorado 80045, USA. ; Max Delbruck Center for Molecular Medicine, Berlin 13125, Germany. ; Centro Nacional de Analisis Genomico (CNAG), Parc Cientific de Barcelona, Barcelona 08028, Spain. ; Indiana University, School of Informatics and Computing, Bloomington, Indiana 47408, USA. ; The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA. ; Institute for Systems Biology, Seattle, Washington 98109-5234, USA. ; The Pennsylvania State University, Department of Anthropology, University Park, Pennsylvania 16802, USA. ; University of Arizona, ARL Division of Biotechnology, Tucson, Arizona 85721, USA. ; University of Pittsburgh School of Medicine, Department of Developmental Biology, Department of Computational and Systems Biology, Pittsburg, Pennsylvania 15261, USA. ; Oregon Health &Science University, Bioinformatics and Computational Biology Division, Department of Medical Informatics &Clinical Epidemiology, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA. ; 1] The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA. [2] Bill Lyons Informatics Center, UCL Cancer Institute, University College London, London WC1E 6DD, UK (J.He); Seven Bridges Genomics, Cambridge, Massachusetts 02138, USA (D.P.L.); Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA (F.L.M.); BioNano Genomics, San Diego, California 92121, USA (B.t.H.); University of Chicago, Department of Human Genetics, Chicago, Illinois 60637, USA (M.C.W.); Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138, USA (C.W.W.); The CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (B.Z.). ; Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, USA. ; 1] University of Arizona, ARL Division of Biotechnology, Tucson, Arizona 85721, USA. [2] Bill Lyons Informatics Center, UCL Cancer Institute, University College London, London WC1E 6DD, UK (J.He); Seven Bridges Genomics, Cambridge, Massachusetts 02138, USA (D.P.L.); Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA (F.L.M.); BioNano Genomics, San Diego, California 92121, USA (B.t.H.); University of Chicago, Department of Human Genetics, Chicago, Illinois 60637, USA (M.C.W.); Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138, USA (C.W.W.); The CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (B.Z.). ; Oregon National Primate Research Center, Division of Neuroscience, 505 NW 185th Avenue, Beaverton, Oregon 97006, USA. ; 1] European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. [2] University of Cambridge, Cancer Research UK-Cambridge Institute, Cambridge CB2 0RE, UK. ; 1] University of California, Gladstone Institutes, San Francisco, California 94158-226, USA. [2] Institute for Human Genetics, University of California, San Francisco, California 94143-0794, USA. [3] Division of Biostatistics, University of California, San Francisco, California 94143-0794, USA. ; Paul Ehrlich Institute, Division of Medical Biotechnology, 63225 Langen, Germany. ; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ; Gibbon Conservation Center, 19100 Esguerra Rd, Santa Clarita, California 91350, USA. ; 1] Oregon Health &Science University, Bioinformatics and Computational Biology Division, Department of Medical Informatics &Clinical Epidemiology, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA. [2] Oregon Health &Science University, Center for Spoken Language Understanding, Institute on Development and Disability, Portland, Oregon 97239, USA. ; 1] Children's Hospital Oakland Research Institute, BACPAC Resources, Oakland, California 94609, USA. [2] Bill Lyons Informatics Center, UCL Cancer Institute, University College London, London WC1E 6DD, UK (J.He); Seven Bridges Genomics, Cambridge, Massachusetts 02138, USA (D.P.L.); Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA (F.L.M.); BioNano Genomics, San Diego, California 92121, USA (B.t.H.); University of Chicago, Department of Human Genetics, Chicago, Illinois 60637, USA (M.C.W.); Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138, USA (C.W.W.); The CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (B.Z.). ; Louisiana State University, School of Electrical Engineering and Computer Science, Baton Rouge, Louisiana 70803, USA. ; 1] Institute for Human Genetics, University of California, San Francisco, California 94143-0794, USA. [2] Division of Biostatistics, University of California, San Francisco, California 94143-0794, USA. ; 1] University of Cambridge, Cancer Research UK-Cambridge Institute, Cambridge CB2 0RE, UK. [2] Bill Lyons Informatics Center, UCL Cancer Institute, University College London, London WC1E 6DD, UK (J.He); Seven Bridges Genomics, Cambridge, Massachusetts 02138, USA (D.P.L.); Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA (F.L.M.); BioNano Genomics, San Diego, California 92121, USA (B.t.H.); University of Chicago, Department of Human Genetics, Chicago, Illinois 60637, USA (M.C.W.); Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138, USA (C.W.W.); The CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (B.Z.). ; 1] Oregon Health &Science University, Center for Spoken Language Understanding, Institute on Development and Disability, Portland, Oregon 97239, USA. [2] Bill Lyons Informatics Center, UCL Cancer Institute, University College London, London WC1E 6DD, UK (J.He); Seven Bridges Genomics, Cambridge, Massachusetts 02138, USA (D.P.L.); Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA (F.L.M.); BioNano Genomics, San Diego, California 92121, USA (B.t.H.); University of Chicago, Department of Human Genetics, Chicago, Illinois 60637, USA (M.C.W.); Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138, USA (C.W.W.); The CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (B.Z.). ; 1] IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003 Barcelona, Spain. [2] Centro Nacional de Analisis Genomico (CNAG), Parc Cientific de Barcelona, Barcelona 08028, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25209798" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Evolution, Molecular ; Genome/*genetics ; Hominidae/classification/genetics ; Humans ; Hylobates/*classification/*genetics ; *Karyotype ; Molecular Sequence Data ; *Phylogeny ; Retroelements/genetics ; Selection, Genetic ; Transcription Termination, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2015-09-30
    Description: Despite the increasing knowledge about DNA methylation, the understanding of human epigenome evolution is in its infancy. Using whole genome bisulfite sequencing we identified hundreds of differentially methylated regions (DMRs) in humans compared to non-human primates and estimated that ~25% of these regions were detectable throughout several human tissues. Human DMRs were enriched for specific histone modifications and the majority were located distal to transcription start sites, highlighting the importance of regions outside the direct regulatory context. We also found a significant excess of endogenous retrovirus elements in human-specific hypomethylated. We reported for the first time a close interplay between inter-species genetic and epigenetic variation in regions of incomplete lineage sorting, transcription factor binding sites and human differentially hypermethylated regions. Specifically, we observed an excess of human-specific substitutions in transcription factor binding sites located within human DMRs, suggesting that alteration of regulatory motifs underlies some human-specific methylation patterns. We also found that the acquisition of DNA hypermethylation in the human lineage is frequently coupled with a rapid evolution at nucleotide level in the neighborhood of these CpG sites. Taken together, our results reveal new insights into the mechanistic basis of human-specific DNA methylation patterns and the interpretation of inter-species non-coding variation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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