Genomic Ancestry of North Africans Supports Back-to-Africa Migrations
Identifieur interne : 000198 ( Pmc/Curation ); précédent : 000197; suivant : 000199Genomic 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.
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
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<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>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS Genet</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS Genet</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosgen</journal-id>
<journal-title-group><journal-title>PLoS Genetics</journal-title>
</journal-title-group>
<issn pub-type="ppub">1553-7390</issn>
<issn pub-type="epub">1553-7404</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22253600</article-id>
<article-id pub-id-type="pmc">3257290</article-id>
<article-id pub-id-type="publisher-id">PGENETICS-D-11-00674</article-id>
<article-id pub-id-type="doi">10.1371/journal.pgen.1002397</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Biology</subject>
<subj-group><subject>Evolutionary Biology</subject>
<subj-group><subject>Population Genetics</subject>
<subj-group><subject>Effective Population Size</subject>
<subject>Gene Flow</subject>
<subject>Gene Pool</subject>
<subject>Genetic Drift</subject>
<subject>Genetic Polymorphism</subject>
<subject>Haplotypes</subject>
</subj-group>
</subj-group>
<subj-group><subject>Evolutionary Genetics</subject>
<subject>Evolutionary Processes</subject>
</subj-group>
</subj-group>
<subj-group><subject>Genetics</subject>
<subj-group><subject>Population Genetics</subject>
<subj-group><subject>Effective Population Size</subject>
<subject>Gene Flow</subject>
<subject>Gene Pool</subject>
<subject>Genetic Drift</subject>
<subject>Genetic Polymorphism</subject>
<subject>Haplotypes</subject>
</subj-group>
</subj-group>
<subj-group><subject>Human Genetics</subject>
</subj-group>
</subj-group>
<subj-group><subject>Genomics</subject>
<subj-group><subject>Genome Analysis Tools</subject>
<subj-group><subject>Genome Scans</subject>
</subj-group>
</subj-group>
<subj-group><subject>Genome Evolution</subject>
</subj-group>
</subj-group>
<subj-group><subject>Population Biology</subject>
<subj-group><subject>Population Genetics</subject>
<subj-group><subject>Effective Population Size</subject>
<subject>Gene Flow</subject>
<subject>Gene Pool</subject>
<subject>Genetic Drift</subject>
<subject>Genetic Polymorphism</subject>
<subject>Haplotypes</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Genomic Ancestry of North Africans Supports Back-to-Africa Migrations</article-title>
<alt-title alt-title-type="running-head">Genomic Patterns in North Africa</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Henn</surname>
<given-names>Brenna M.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author" equal-contrib="yes"><name><surname>Botigué</surname>
<given-names>Laura R.</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gravel</surname>
<given-names>Simon</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wang</surname>
<given-names>Wei</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Brisbin</surname>
<given-names>Abra</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Byrnes</surname>
<given-names>Jake K.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Fadhlaoui-Zid</surname>
<given-names>Karima</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zalloua</surname>
<given-names>Pierre A.</given-names>
</name>
<xref ref-type="aff" rid="aff5"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Moreno-Estrada</surname>
<given-names>Andres</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bertranpetit</surname>
<given-names>Jaume</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bustamante</surname>
<given-names>Carlos D.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn1"><sup>¶</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Comas</surname>
<given-names>David</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn1"><sup>¶</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label>
<addr-line>Department of Genetics, Stanford University, Stanford, California, United States of America</addr-line>
</aff>
<aff id="aff2"><label>2</label>
<addr-line>Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain</addr-line>
</aff>
<aff id="aff3"><label>3</label>
<addr-line>Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America</addr-line>
</aff>
<aff id="aff4"><label>4</label>
<addr-line>Laboratory of Genetics, Immunology, and Human Pathology, University Tunis El Manar, Tunis, Tunisia</addr-line>
</aff>
<aff id="aff5"><label>5</label>
<addr-line>The Lebanese American University, Chouran, Beirut, Lebanon</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Schierup</surname>
<given-names>Mikkel H.</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">University of Aarhus, Denmark</aff>
<author-notes><corresp id="cor1">* E-mail: <email>david.comas@upf.edu</email>
(DC); <email>cdbustam@stanford.edu</email>
(CDB)</corresp>
<fn fn-type="con"><p>Conceived and designed the experiments: BMH SG JB CDB DC. Performed the experiments: BMH LRB. Analyzed the data: BMH LRB SG WW AM-E. Contributed reagents/materials/analysis tools: AB JKB KF-Z PAZ JB DC. Wrote the paper: BMH LRB SG CDB DC.</p>
</fn>
<fn id="fn1" fn-type="other"><p>¶ These authors were joint senior authors on this work.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><month>1</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>12</day>
<month>1</month>
<year>2012</year>
</pub-date>
<volume>8</volume>
<issue>1</issue>
<elocation-id>e1002397</elocation-id>
<history><date date-type="received"><day>7</day>
<month>4</month>
<year>2011</year>
</date>
<date date-type="accepted"><day>11</day>
<month>10</month>
<year>2011</year>
</date>
</history>
<permissions><copyright-statement>Henn et al.</copyright-statement>
<copyright-year>2012</copyright-year>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p>
</license>
</permissions>
<abstract><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>
</abstract>
<abstract abstract-type="summary"><title>Author Summary</title>
<p>Proposed migrations between North Africa and neighboring regions have included Paleolithic gene flow from the Near East, an Arabic migration across the whole of North Africa 1,400 years ago (ya), and trans-Saharan transport of slaves from sub-Saharan Africa. Historical records, archaeology, and mitochondrial and Y-chromosome DNA have been marshaled in support of one theory or another, but there is little consensus regarding the overall genetic background of North African populations or their origin and expansion. We characterize the patterns of genetic variation in North Africa using ∼730,000 single nucleotide polymorphisms from across the genome for seven populations. We observe two distinct, opposite gradients of ancestry: an east-to-west increase in likely autochthonous North African ancestry and an east-to-west decrease in likely Near Eastern Arabic ancestry. The indigenous North African ancestry may have been more common in Berber populations and appears most closely related to populations outside of Africa, but divergence between Maghrebi peoples and Near Eastern/Europeans likely precedes the Holocene (>12,000 ya). We also find significant signatures of sub-Saharan African ancestry that vary substantially among populations. These sub-Saharan ancestries appear to be a recent introduction into North African populations, dating to about 1,200 years ago in southern Morocco and about 750 years ago into Egypt, possibly reflecting the patterns of the trans-Saharan slave trade that occurred during this period.</p>
</abstract>
<counts><page-count count="11"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
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