A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Handle URI:
http://hdl.handle.net/10754/550413
Title:
A recent bottleneck of Y chromosome diversity coincides with a global change in culture
Authors:
Karmin, Monika; Saag, Lauri; Vicente, Mário; Sayres, Melissa A. Wilson; Järve, Mari; Talas, Ulvi Gerst; Rootsi, Siiri; Ilumäe, Anne-Mai; Mägi, Reedik; Mitt, Mario; Pagani, Luca; Puurand, Tarmo; Faltyskova, Zuzana; Clemente, Florian; Cardona, Alexia; Metspalu, Ene; Sahakyan, Hovhannes; Yunusbayev, Bayazit; Hudjashov, Georgi; DeGiorgio, Michael; Loogväli, Eva-Liis; Eichstaedt, Christina; Eelmets, Mikk; Chaubey, Gyaneshwer; Tambets, Kristiina; Litvinov, Sergei; Mormina, Maru; Xue, Yali; Ayub, Qasim; Zoraqi, Grigor; Korneliussen, Thorfinn Sand; Akhatova, Farida; Lachance, Joseph; Tishkoff, Sarah; Momynaliev, Kuvat; Ricaut, François-Xavier; Kusuma, Pradiptajati; Razafindrazaka, Harilanto; Pierron, Denis; Cox, Murray P.; Sultana, Gazi Nurun Nahar; Willerslev, Rane; Muller, Craig; Westaway, Michael; Lambert, David; Skaro, Vedrana; Kovačevic´, Lejla; Turdikulova, Shahlo; Dalimova, Dilbar; Khusainova, Rita; Trofimova, Natalya; Akhmetova, Vita; Khidiyatova, Irina; Lichman, Daria V.; Isakova, Jainagul; Pocheshkhova, Elvira; Sabitov, Zhaxylyk; Barashkov, Nikolay A.; Nymadawa, Pagbajabyn; Mihailov, Evelin; Seng, Joseph Wee Tien; Evseeva, Irina; Migliano, Andrea Bamberg; Abdullah, Syafiq; Andriadze, George; Primorac, Dragan; Atramentova, Lubov; Utevska, Olga; Yepiskoposyan, Levon; Marjanovic´, Damir; Kushniarevich, Alena; Behar, Doron M.; Gilissen, Christian; Vissers, Lisenka; Veltman, Joris A.; Balanovska, Elena; Derenko, Miroslava; Malyarchuk, Boris; Metspalu, Andres; Fedorova, Sardana; Eriksson, Anders ( 0000-0003-3436-3726 ) ; Manica, Andrea; Mendez, Fernando L.; Karafet, Tatiana M.; Veeramah, Krishna R.; Bradman, Neil; Hammer, Michael F.; Osipova, Ludmila P.; Balanovsky, Oleg; Khusnutdinova, Elza K.; Johnsen, Knut; Remm, Maido; Thomas, Mark G.; Tyler-Smith, Chris; Underhill, Peter A.; Willerslev, Eske; Nielsen, Rasmus; Metspalu, Mait; Villems, Richard; Kivisild, Toomas
Abstract:
It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
KAUST Department:
Integrative Systems Biology Lab
Citation:
A recent bottleneck of Y chromosome diversity coincides with a global change in culture 2015, 25 (4):459 Genome Research
Publisher:
Cold Spring Harbor Laboratory Press
Journal:
Genome Research
Issue Date:
30-Apr-2015
DOI:
10.1101/gr.186684.114
PubMed ID:
25770088
PubMed Central ID:
PMC4381518
Type:
Article
ISSN:
1088-9051; 1549-5469
Additional Links:
http://genome.cshlp.org/lookup/doi/10.1101/gr.186684.114
Appears in Collections:
Articles

Full metadata record

DC FieldValue Language
dc.contributor.authorKarmin, Monikaen
dc.contributor.authorSaag, Laurien
dc.contributor.authorVicente, Márioen
dc.contributor.authorSayres, Melissa A. Wilsonen
dc.contributor.authorJärve, Marien
dc.contributor.authorTalas, Ulvi Gersten
dc.contributor.authorRootsi, Siirien
dc.contributor.authorIlumäe, Anne-Maien
dc.contributor.authorMägi, Reediken
dc.contributor.authorMitt, Marioen
dc.contributor.authorPagani, Lucaen
dc.contributor.authorPuurand, Tarmoen
dc.contributor.authorFaltyskova, Zuzanaen
dc.contributor.authorClemente, Florianen
dc.contributor.authorCardona, Alexiaen
dc.contributor.authorMetspalu, Eneen
dc.contributor.authorSahakyan, Hovhannesen
dc.contributor.authorYunusbayev, Bayaziten
dc.contributor.authorHudjashov, Georgien
dc.contributor.authorDeGiorgio, Michaelen
dc.contributor.authorLoogväli, Eva-Liisen
dc.contributor.authorEichstaedt, Christinaen
dc.contributor.authorEelmets, Mikken
dc.contributor.authorChaubey, Gyaneshweren
dc.contributor.authorTambets, Kristiinaen
dc.contributor.authorLitvinov, Sergeien
dc.contributor.authorMormina, Maruen
dc.contributor.authorXue, Yalien
dc.contributor.authorAyub, Qasimen
dc.contributor.authorZoraqi, Grigoren
dc.contributor.authorKorneliussen, Thorfinn Sanden
dc.contributor.authorAkhatova, Faridaen
dc.contributor.authorLachance, Josephen
dc.contributor.authorTishkoff, Sarahen
dc.contributor.authorMomynaliev, Kuvaten
dc.contributor.authorRicaut, François-Xavieren
dc.contributor.authorKusuma, Pradiptajatien
dc.contributor.authorRazafindrazaka, Harilantoen
dc.contributor.authorPierron, Denisen
dc.contributor.authorCox, Murray P.en
dc.contributor.authorSultana, Gazi Nurun Naharen
dc.contributor.authorWillerslev, Raneen
dc.contributor.authorMuller, Craigen
dc.contributor.authorWestaway, Michaelen
dc.contributor.authorLambert, Daviden
dc.contributor.authorSkaro, Vedranaen
dc.contributor.authorKovačevic´, Lejlaen
dc.contributor.authorTurdikulova, Shahloen
dc.contributor.authorDalimova, Dilbaren
dc.contributor.authorKhusainova, Ritaen
dc.contributor.authorTrofimova, Natalyaen
dc.contributor.authorAkhmetova, Vitaen
dc.contributor.authorKhidiyatova, Irinaen
dc.contributor.authorLichman, Daria V.en
dc.contributor.authorIsakova, Jainagulen
dc.contributor.authorPocheshkhova, Elviraen
dc.contributor.authorSabitov, Zhaxylyken
dc.contributor.authorBarashkov, Nikolay A.en
dc.contributor.authorNymadawa, Pagbajabynen
dc.contributor.authorMihailov, Evelinen
dc.contributor.authorSeng, Joseph Wee Tienen
dc.contributor.authorEvseeva, Irinaen
dc.contributor.authorMigliano, Andrea Bambergen
dc.contributor.authorAbdullah, Syafiqen
dc.contributor.authorAndriadze, Georgeen
dc.contributor.authorPrimorac, Draganen
dc.contributor.authorAtramentova, Luboven
dc.contributor.authorUtevska, Olgaen
dc.contributor.authorYepiskoposyan, Levonen
dc.contributor.authorMarjanovic´, Damiren
dc.contributor.authorKushniarevich, Alenaen
dc.contributor.authorBehar, Doron M.en
dc.contributor.authorGilissen, Christianen
dc.contributor.authorVissers, Lisenkaen
dc.contributor.authorVeltman, Joris A.en
dc.contributor.authorBalanovska, Elenaen
dc.contributor.authorDerenko, Miroslavaen
dc.contributor.authorMalyarchuk, Borisen
dc.contributor.authorMetspalu, Andresen
dc.contributor.authorFedorova, Sardanaen
dc.contributor.authorEriksson, Andersen
dc.contributor.authorManica, Andreaen
dc.contributor.authorMendez, Fernando L.en
dc.contributor.authorKarafet, Tatiana M.en
dc.contributor.authorVeeramah, Krishna R.en
dc.contributor.authorBradman, Neilen
dc.contributor.authorHammer, Michael F.en
dc.contributor.authorOsipova, Ludmila P.en
dc.contributor.authorBalanovsky, Olegen
dc.contributor.authorKhusnutdinova, Elza K.en
dc.contributor.authorJohnsen, Knuten
dc.contributor.authorRemm, Maidoen
dc.contributor.authorThomas, Mark G.en
dc.contributor.authorTyler-Smith, Chrisen
dc.contributor.authorUnderhill, Peter A.en
dc.contributor.authorWillerslev, Eskeen
dc.contributor.authorNielsen, Rasmusen
dc.contributor.authorMetspalu, Maiten
dc.contributor.authorVillems, Richarden
dc.contributor.authorKivisild, Toomasen
dc.date.accessioned2015-04-21T14:24:00Zen
dc.date.available2015-04-21T14:24:00Zen
dc.date.issued2015-04-30en
dc.identifier.citationA recent bottleneck of Y chromosome diversity coincides with a global change in culture 2015, 25 (4):459 Genome Researchen
dc.identifier.issn1088-9051en
dc.identifier.issn1549-5469en
dc.identifier.pmid25770088en
dc.identifier.doi10.1101/gr.186684.114en
dc.identifier.urihttp://hdl.handle.net/10754/550413en
dc.description.abstractIt is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.en
dc.publisherCold Spring Harbor Laboratory Pressen
dc.relation.urlhttp://genome.cshlp.org/lookup/doi/10.1101/gr.186684.114en
dc.rightsThis article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.en
dc.titleA recent bottleneck of Y chromosome diversity coincides with a global change in cultureen
dc.typeArticleen
dc.contributor.departmentIntegrative Systems Biology Laben
dc.identifier.journalGenome Researchen
dc.identifier.pmcidPMC4381518en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionEstonian Biocentre, Tartu, 51010, Estoniaen
dc.contributor.institutionDepartment of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estoniaen
dc.contributor.institutionDepartment of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51010, Estoniaen
dc.contributor.institutionDivision of Biological Anthropology, University of Cambridge, Cambridge, United Kingdomen
dc.contributor.institutionDepartment of Integrative Biology, University of California Berkeley, Berkeley, California, USAen
dc.contributor.institutionSchool of Life Sciences and The Biodesign Institute, Tempe, Arizona, USAen
dc.contributor.institutionDepartment of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estoniaen
dc.contributor.institutionEstonian Genome Center, University of Tartu, Tartu, 51010, Estoniaen
dc.contributor.institutionDepartment of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estoniaen
dc.contributor.institutionLaboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armeniaen
dc.contributor.institutionInstitute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, Russiaen
dc.contributor.institutionDepartment of Psychology, University of Auckland, Auckland, 1142, New Zealanden
dc.contributor.institutionDepartment of Biology, Pennsylvania State University, University Park, Pennsylvania, USAen
dc.contributor.institutionDepartment of Applied Social Sciences, University of Winchester, Winchester, United Kingdomen
dc.contributor.institutionThe Wellcome Trust Sanger Institute, Hinxton, United Kingdomen
dc.contributor.institutionCenter of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, Albaniaen
dc.contributor.institutionCenter for GeoGenetics, University of Copenhagen, Copenhagen, Denmarken
dc.contributor.institutionDepartment of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russiaen
dc.contributor.institutionInstitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russiaen
dc.contributor.institutionDepartment of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USAen
dc.contributor.institutionSchool of Biology, Georgia Institute of Technology, Atlanta, Georgia, USAen
dc.contributor.institutionDepartment of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USAen
dc.contributor.institutionDNcode Laboratories, Moscow, Russiaen
dc.contributor.institutionEvolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, Franceen
dc.contributor.institutionEijkman Institute for Molecular Biology, Jakarta, Indonesiaen
dc.contributor.institutionStatistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealanden
dc.contributor.institutionCentre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, Bangladeshen
dc.contributor.institutionArctic Research Centre, Aarhus University, Aarhus, DK-8000, Denmarken
dc.contributor.institutionEnvironmental Futures Research Institute, Griffith University, Nathan, Australiaen
dc.contributor.institutionGenos, DNA Laboratory, Zagreb, Croatiaen
dc.contributor.institutionUniversity of Osijek, Medical School, Osijek, Croatiaen
dc.contributor.institutionCentogene AG, Rostock, Germanyen
dc.contributor.institutionInstitute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistanen
dc.contributor.institutionInstitute of Cytology and Genetics, Novosibirsk, Russiaen
dc.contributor.institutionInstitute of Molecular Biology and Medicine, Bishkek, Kyrgyzstanen
dc.contributor.institutionKuban State Medical University, Krasnodar, Russiaen
dc.contributor.institutionL. N. Gumilyov Eurasian National University, Astana, Kazakhstanen
dc.contributor.institutionCenter for Life Sciences, Nazarbayev University, Astana, Kazakhstanen
dc.contributor.institutionDepartment of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russiaen
dc.contributor.institutionLaboratory of Molecular Biology, Institute of Natural Sciences, M. K. Ammosov North-Eastern Federal University, Yakutsk, Russiaen
dc.contributor.institutionMongolian Academy of Medical Sciences, Ulaanbaatar, Mongoliaen
dc.contributor.institutionNational Cancer Centre Singapore, Singaporeen
dc.contributor.institutionNorthern State Medical University, Arkhangelsk, Russiaen
dc.contributor.institutionAnthony Nolan, London, UKen
dc.contributor.institutionDepartment of Anthropology, University College London, London, United Kingdomen
dc.contributor.institutionRIPAS Hospital, Bandar Seri Begawan, Bruneien
dc.contributor.institutionScientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, Georgiaen
dc.contributor.institutionSt. Catherine Specialty Hospital, Zabok, Croatiaen
dc.contributor.institutionEberly College of Science, Pennsylvania State University, University Park, Pennsylvania, USAen
dc.contributor.institutionUniversity of Split, Medical School, Split, Croatiaen
dc.contributor.institutionV. N. Karazin Kharkiv National University, Kharkiv, Ukraineen
dc.contributor.institutionDepartment of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, Bosnia and Herzegovinaen
dc.contributor.institutionInstitute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarusen
dc.contributor.institutionDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlandsen
dc.contributor.institutionResearch Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russiaen
dc.contributor.institutionGenetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russiaen
dc.contributor.institutionDepartment of Zoology, University of Cambridge, Cambridge, United Kingdomen
dc.contributor.institutionDepartment of Genetics, Stanford University School of Medicine, Stanford, California, USAen
dc.contributor.institutionARL Division of Biotechnology, University of Arizona, Tucson, Arizona, USAen
dc.contributor.institutionDepartment of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USAen
dc.contributor.institutionThe Henry Stewart Group, London, United Kingdomen
dc.contributor.institutionVavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russiaen
dc.contributor.institutionUniversity Hospital of North Norway, Tromsøe, Norwayen
dc.contributor.institutionResearch Department of Genetics, Evolution and Environment, University College London, London, United Kingdomen
dc.contributor.institutionEstonian Academy of Sciences, Tallinn, Estoniaen
kaust.authorEriksson, Andersen

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