Genomic Ancestry of North Africans Supports Back-to-Africa Migrations
Identifieur interne : 000242 ( Main/Exploration ); précédent : 000241; suivant : 000243Genomic Ancestry of North Africans Supports Back-to-Africa Migrations
Auteurs : Brenna M. Henn [États-Unis] ; Laura R. Botigué [Espagne] ; Simon Gravel [États-Unis] ; Wei Wang [États-Unis] ; Abra Brisbin [États-Unis] ; Jake K. Byrnes [États-Unis] ; Karima Fadhlaoui-Zid [Tunisie] ; Pierre A. Zalloua [Liban] ; Andres Moreno-Estrada [États-Unis] ; Jaume Bertranpetit [Espagne] ; Carlos D. Bustamante [États-Unis] ; David Comas [Espagne]Source :
- PLoS Genetics [ 1553-7390 ] ; 2012.
Descripteurs français
- KwdFr :
- ADN mitochondrial (génétique), Afrique du Nord, Afrique subsaharienne (ethnologie), Dynamique des populations, Europe, Flux des gènes (génétique), Génomique, Génotype, Haplotypes, Histoire ancienne, Humains, Maroc, Moyen Orient, Polymorphisme de nucléotide simple, Pool des gènes, Population, Population d'origine africaine (génétique), Population d'origine africaine (histoire), Population d'origine européenne (génétique), Population d'origine européenne (histoire), Variation génétique, Égypte, Émigration et immigration.
- MESH :
- ethnologie : Afrique subsaharienne.
- génétique : ADN mitochondrial, Flux des gènes, Population d'origine africaine, Population d'origine européenne.
- histoire : Population d'origine africaine, Population d'origine européenne.
- Afrique du Nord, Dynamique des populations, Europe, Génomique, Génotype, Haplotypes, Histoire ancienne, Humains, Maroc, Moyen Orient, Polymorphisme de nucléotide simple, Pool des gènes, Population, Variation génétique, Égypte, Émigration et immigration.
English descriptors
- KwdEn :
- Africa South of the Sahara (ethnology), Africa, Northern, African Continental Ancestry Group (genetics), African Continental Ancestry Group (history), DNA, Mitochondrial (genetics), Egypt, Emigration and Immigration, Europe, European Continental Ancestry Group (genetics), European Continental Ancestry Group (history), Gene Flow (genetics), Gene Pool, Genetic Variation, Genomics, Genotype, Haplotypes, History, Ancient, Humans, Middle East, Morocco, Polymorphism, Single Nucleotide, Population, Population Dynamics.
- MESH :
- chemical , genetics : DNA, Mitochondrial.
- geographic , ethnology : Africa South of the Sahara.
- geographic : Africa, Northern, Egypt, Europe, Middle East, Morocco.
- genetics : African Continental Ancestry Group, European Continental Ancestry Group, Gene Flow.
- history : African Continental Ancestry Group, European Continental Ancestry Group.
- Emigration and Immigration, Gene Pool, Genetic Variation, Genomics, Genotype, Haplotypes, History, Ancient, Humans, Polymorphism, Single Nucleotide, Population, Population Dynamics.
Abstract
North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.
Url:
DOI: 10.1371/journal.pgen.1002397
PubMed: 22253600
PubMed Central: 3257290
Affiliations:
- Espagne, Liban, Tunisie, États-Unis
- Californie, Catalogne, Gouvernorat de Tunis, État de New York
- Barcelone, Ithaca (New York), Tunis
- Université Cornell, Université Pompeu Fabra
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Henn</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Genetics, Stanford University, Stanford, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Stanford University, Stanford, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Botigue, Laura R" sort="Botigue, Laura R" uniqKey="Botigue L" first="Laura R." last="Botigué">Laura R. Botigué</name><affiliation wicri:level="4"><nlm:aff id="aff2"><addr-line>Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain</addr-line></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona</wicri:regionArea><placeName><settlement type="city">Barcelone</settlement><region nuts="2" type="region">Catalogne</region></placeName><orgName type="university">Université Pompeu Fabra</orgName></affiliation></author><author><name sortKey="Gravel, Simon" sort="Gravel, Simon" uniqKey="Gravel S" first="Simon" last="Gravel">Simon Gravel</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Genetics, Stanford University, Stanford, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Stanford University, Stanford, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Wang, Wei" sort="Wang, Wei" uniqKey="Wang W" first="Wei" last="Wang">Wei Wang</name><affiliation wicri:level="4"><nlm:aff id="aff3"><addr-line>Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York</wicri:regionArea><placeName><region type="state">État de New York</region><settlement type="city">Ithaca (New York)</settlement></placeName><orgName type="university">Université Cornell</orgName></affiliation></author><author><name sortKey="Brisbin, Abra" sort="Brisbin, Abra" uniqKey="Brisbin A" first="Abra" last="Brisbin">Abra Brisbin</name><affiliation wicri:level="4"><nlm:aff id="aff3"><addr-line>Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York</wicri:regionArea><placeName><region type="state">État de New York</region><settlement type="city">Ithaca (New York)</settlement></placeName><orgName type="university">Université Cornell</orgName></affiliation></author><author><name sortKey="Byrnes, Jake K" sort="Byrnes, Jake K" uniqKey="Byrnes J" first="Jake K." last="Byrnes">Jake K. Byrnes</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Genetics, Stanford University, Stanford, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Stanford University, Stanford, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Fadhlaoui Zid, Karima" sort="Fadhlaoui Zid, Karima" uniqKey="Fadhlaoui Zid K" first="Karima" last="Fadhlaoui-Zid">Karima Fadhlaoui-Zid</name><affiliation wicri:level="3"><nlm:aff id="aff4"><addr-line>Laboratory of Genetics, Immunology, and Human Pathology, University Tunis El Manar, Tunis, Tunisia</addr-line></nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Genetics, Immunology, and Human Pathology, University Tunis El Manar, Tunis</wicri:regionArea><placeName><settlement type="city">Tunis</settlement><region nuts="2">Gouvernorat de Tunis</region></placeName></affiliation></author><author><name sortKey="Zalloua, Pierre A" sort="Zalloua, Pierre A" uniqKey="Zalloua P" first="Pierre A." last="Zalloua">Pierre A. Zalloua</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>The Lebanese American University, Chouran, Beirut, Lebanon</addr-line></nlm:aff><country xml:lang="fr">Liban</country><wicri:regionArea>The Lebanese American University, Chouran, Beirut</wicri:regionArea><wicri:noRegion>Beirut</wicri:noRegion></affiliation></author><author><name sortKey="Moreno Estrada, Andres" sort="Moreno Estrada, Andres" uniqKey="Moreno Estrada A" first="Andres" last="Moreno-Estrada">Andres Moreno-Estrada</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Genetics, Stanford University, Stanford, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Stanford University, Stanford, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Bertranpetit, Jaume" sort="Bertranpetit, Jaume" uniqKey="Bertranpetit J" first="Jaume" last="Bertranpetit">Jaume Bertranpetit</name><affiliation wicri:level="4"><nlm:aff id="aff2"><addr-line>Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain</addr-line></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona</wicri:regionArea><placeName><settlement type="city">Barcelone</settlement><region nuts="2" type="region">Catalogne</region></placeName><orgName type="university">Université Pompeu Fabra</orgName></affiliation></author><author><name sortKey="Bustamante, Carlos D" sort="Bustamante, Carlos D" uniqKey="Bustamante C" first="Carlos D." last="Bustamante">Carlos D. Bustamante</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Genetics, Stanford University, Stanford, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Stanford University, Stanford, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Comas, David" sort="Comas, David" uniqKey="Comas D" first="David" last="Comas">David Comas</name><affiliation wicri:level="4"><nlm:aff id="aff2"><addr-line>Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain</addr-line></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona</wicri:regionArea><placeName><settlement type="city">Barcelone</settlement><region nuts="2" type="region">Catalogne</region></placeName><orgName type="university">Université Pompeu Fabra</orgName></affiliation></author></analytic><series><title level="j">PLoS Genetics</title><idno type="ISSN">1553-7390</idno><idno type="eISSN">1553-7404</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Africa South of the Sahara (ethnology)</term><term>Africa, Northern</term><term>African Continental Ancestry Group (genetics)</term><term>African Continental Ancestry Group (history)</term><term>DNA, Mitochondrial (genetics)</term><term>Egypt</term><term>Emigration and Immigration</term><term>Europe</term><term>European Continental Ancestry Group (genetics)</term><term>European Continental Ancestry Group (history)</term><term>Gene Flow (genetics)</term><term>Gene Pool</term><term>Genetic Variation</term><term>Genomics</term><term>Genotype</term><term>Haplotypes</term><term>History, Ancient</term><term>Humans</term><term>Middle East</term><term>Morocco</term><term>Polymorphism, Single Nucleotide</term><term>Population</term><term>Population Dynamics</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN mitochondrial (génétique)</term><term>Afrique du Nord</term><term>Afrique subsaharienne (ethnologie)</term><term>Dynamique des populations</term><term>Europe</term><term>Flux des gènes (génétique)</term><term>Génomique</term><term>Génotype</term><term>Haplotypes</term><term>Histoire ancienne</term><term>Humains</term><term>Maroc</term><term>Moyen Orient</term><term>Polymorphisme de nucléotide simple</term><term>Pool des gènes</term><term>Population</term><term>Population d'origine africaine (génétique)</term><term>Population d'origine africaine (histoire)</term><term>Population d'origine européenne (génétique)</term><term>Population d'origine européenne (histoire)</term><term>Variation génétique</term><term>Égypte</term><term>Émigration et immigration</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Mitochondrial</term></keywords><keywords scheme="MESH" type="geographic" qualifier="ethnology" xml:lang="en"><term>Africa South of the Sahara</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Africa, Northern</term><term>Egypt</term><term>Europe</term><term>Middle East</term><term>Morocco</term></keywords><keywords scheme="MESH" qualifier="ethnologie" xml:lang="fr"><term>Afrique subsaharienne</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>African Continental Ancestry Group</term><term>European Continental Ancestry Group</term><term>Gene Flow</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN mitochondrial</term><term>Flux des gènes</term><term>Population d'origine africaine</term><term>Population d'origine européenne</term></keywords><keywords scheme="MESH" qualifier="histoire" xml:lang="fr"><term>Population d'origine africaine</term><term>Population d'origine européenne</term></keywords><keywords scheme="MESH" qualifier="history" xml:lang="en"><term>African Continental Ancestry Group</term><term>European Continental Ancestry Group</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Emigration and Immigration</term><term>Gene Pool</term><term>Genetic Variation</term><term>Genomics</term><term>Genotype</term><term>Haplotypes</term><term>History, Ancient</term><term>Humans</term><term>Polymorphism, Single Nucleotide</term><term>Population</term><term>Population Dynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Afrique du Nord</term><term>Dynamique des populations</term><term>Europe</term><term>Génomique</term><term>Génotype</term><term>Haplotypes</term><term>Histoire ancienne</term><term>Humains</term><term>Maroc</term><term>Moyen Orient</term><term>Polymorphisme de nucléotide simple</term><term>Pool des gènes</term><term>Population</term><term>Variation génétique</term><term>Égypte</term><term>Émigration et immigration</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Agency, Ci" uniqKey="Agency C">CI Agency</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jasinska Myga, B" uniqKey="Jasinska Myga B">B Jasinska-Myga</name></author><author><name sortKey="Kachergus, J" uniqKey="Kachergus J">J Kachergus</name></author><author><name sortKey="Vilario Gell, C" uniqKey="Vilario Gell C">C Vilario-Gell</name></author><author><name sortKey="Wider, C" uniqKey="Wider C">C Wider</name></author><author><name sortKey="Soto Ortolaza, A" uniqKey="Soto Ortolaza A">A Soto-Ortolaza</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lesage, S" uniqKey="Lesage S">S Lesage</name></author><author><name sortKey="Condroyer, C" uniqKey="Condroyer C">C 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Dermitzakis</name></author><author><name sortKey="Schaffner, S" uniqKey="Schaffner S">S Schaffner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hunter Zinck, H" uniqKey="Hunter Zinck H">H Hunter-Zinck</name></author><author><name sortKey="Musharoff, S" uniqKey="Musharoff S">S Musharoff</name></author><author><name sortKey="Salit, J" uniqKey="Salit J">J Salit</name></author><author><name sortKey="Al Ali, K" uniqKey="Al Ali K">K Al-Ali</name></author><author><name sortKey="Chouchane, L" uniqKey="Chouchane L">L Chouchane</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Purcell, S" uniqKey="Purcell S">S Purcell</name></author><author><name sortKey="Neale, B" uniqKey="Neale B">B Neale</name></author><author><name sortKey="Todd Brown, K" uniqKey="Todd Brown K">K Todd-Brown</name></author><author><name sortKey="Thomas, L" uniqKey="Thomas L">L Thomas</name></author><author><name sortKey="Ferreira, Mar" uniqKey="Ferreira M">MAR Ferreira</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Holsinger, Ke" uniqKey="Holsinger K">KE Holsinger</name></author><author><name sortKey="Weir, Bs" uniqKey="Weir B">BS Weir</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Browning, Sr" uniqKey="Browning S">SR Browning</name></author><author><name sortKey="Browning, Bl" uniqKey="Browning B">BL Browning</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Espagne</li><li>Liban</li><li>Tunisie</li><li>États-Unis</li></country><region><li>Californie</li><li>Catalogne</li><li>Gouvernorat de Tunis</li><li>État de New York</li></region><settlement><li>Barcelone</li><li>Ithaca (New York)</li><li>Tunis</li></settlement><orgName><li>Université Cornell</li><li>Université Pompeu Fabra</li></orgName></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Henn, Brenna M" sort="Henn, Brenna M" uniqKey="Henn B" first="Brenna M." last="Henn">Brenna M. Henn</name></region><name sortKey="Brisbin, Abra" sort="Brisbin, Abra" uniqKey="Brisbin A" first="Abra" last="Brisbin">Abra Brisbin</name><name sortKey="Bustamante, Carlos D" sort="Bustamante, Carlos D" uniqKey="Bustamante C" first="Carlos D." last="Bustamante">Carlos D. Bustamante</name><name sortKey="Byrnes, Jake K" sort="Byrnes, Jake K" uniqKey="Byrnes J" first="Jake K." last="Byrnes">Jake K. Byrnes</name><name sortKey="Gravel, Simon" sort="Gravel, Simon" uniqKey="Gravel S" first="Simon" last="Gravel">Simon Gravel</name><name sortKey="Moreno Estrada, Andres" sort="Moreno Estrada, Andres" uniqKey="Moreno Estrada A" first="Andres" last="Moreno-Estrada">Andres Moreno-Estrada</name><name sortKey="Wang, Wei" sort="Wang, Wei" uniqKey="Wang W" first="Wei" last="Wang">Wei Wang</name></country><country name="Espagne"><region name="Catalogne"><name sortKey="Botigue, Laura R" sort="Botigue, Laura R" uniqKey="Botigue L" first="Laura R." last="Botigué">Laura R. Botigué</name></region><name sortKey="Bertranpetit, Jaume" sort="Bertranpetit, Jaume" uniqKey="Bertranpetit J" first="Jaume" last="Bertranpetit">Jaume Bertranpetit</name><name sortKey="Comas, David" sort="Comas, David" uniqKey="Comas D" first="David" last="Comas">David Comas</name></country><country name="Tunisie"><region name="Gouvernorat de Tunis"><name sortKey="Fadhlaoui Zid, Karima" sort="Fadhlaoui Zid, Karima" uniqKey="Fadhlaoui Zid K" first="Karima" last="Fadhlaoui-Zid">Karima Fadhlaoui-Zid</name></region></country><country name="Liban"><noRegion><name sortKey="Zalloua, Pierre A" sort="Zalloua, Pierre A" uniqKey="Zalloua P" first="Pierre A." last="Zalloua">Pierre A. Zalloua</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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