Inference of biogeographical ancestry across central regions of Eurasia.
Identifieur interne : 000291 ( Main/Exploration ); précédent : 000290; suivant : 000292Inference of biogeographical ancestry across central regions of Eurasia.
Auteurs : O. Bulbul [Turquie, Allemagne] ; G. Filoglu [Turquie] ; T. Zorlu [Turquie] ; H. Altuncul [Turquie] ; A. Freire-Aradas [Espagne] ; J. Söchtig [Espagne, Allemagne] ; Y. Ruiz [Espagne] ; M. Klintschar [Allemagne] ; S. Triki-Fendri [Tunisie] ; A. Rebai [Tunisie] ; C. Phillips [Espagne] ; M V Lareu [Espagne] ; Á Carracedo [Espagne, Arabie saoudite] ; P M Schneider [Allemagne]Source :
- International journal of legal medicine [ 1437-1596 ] ; 2016.
Descripteurs français
- KwdFr :
- Analyse discriminante (MeSH), Analyse en composantes principales (MeSH), Asie (MeSH), Europe (MeSH), Fonctions de vraisemblance (MeSH), Fréquence d'allèle (MeSH), Génétique des populations (MeSH), Humains (MeSH), Polymorphisme de nucléotide simple (MeSH), Populations d'origine continentale (génétique), Profilage d'ADN (MeSH), Réaction de polymérisation en chaine multiplex (MeSH).
- MESH :
- génétique : Populations d'origine continentale.
- Analyse discriminante, Analyse en composantes principales, Asie, Europe, Fonctions de vraisemblance, Fréquence d'allèle, Génétique des populations, Humains, Polymorphisme de nucléotide simple, Profilage d'ADN, Réaction de polymérisation en chaine multiplex.
English descriptors
- KwdEn :
- Asia (MeSH), Continental Population Groups (genetics), DNA Fingerprinting (MeSH), Discriminant Analysis (MeSH), Europe (MeSH), Gene Frequency (MeSH), Genetics, Population (MeSH), Humans (MeSH), Likelihood Functions (MeSH), Multiplex Polymerase Chain Reaction (MeSH), Polymorphism, Single Nucleotide (MeSH), Principal Component Analysis (MeSH).
- MESH :
Abstract
The inference of biogeographical ancestry (BGA) can provide useful information for forensic investigators when there are no suspects to be compared with DNA collected at the crime scene or when no DNA database matches exist. Although public databases are increasing in size and population scope, there is a lack of information regarding genetic variation in Eurasian populations, especially in central regions such as the Middle East. Inhabitants of these regions show a high degree of genetic admixture, characterized by an allele frequency cline running from NW Europe to East Asia. Although a proper differentiation has been established between the cline extremes of western Europe and South Asia, populations geographically located in between, i.e, Middle East and Mediterranean populations, require more detailed study in order to characterize their genetic background as well as to further understand their demographic histories. To initiate these studies, three ancestry informative SNP (AI-SNP) multiplex panels: the SNPforID 34-plex, Eurasiaplex and a novel 33-plex assay were used to describe the ancestry patterns of a total of 24 populations ranging across the longitudinal axis from NW Europe to East Asia. Different ancestry inference approaches, including STRUCTURE, PCA, DAPC and Snipper Bayes analysis, were applied to determine relationships among populations. The structure results show differentiation between continental groups and a NW to SE allele frequency cline running across Eurasian populations. This study adds useful population data that could be used as reference genotypes for future ancestry investigations in forensic cases. The 33-plex assay also includes pigmentation predictive SNPs, but this study primarily focused on Eurasian population differentiation using 33-plex and its combination with the other two AI-SNP sets.
DOI: 10.1007/s00414-015-1246-7
PubMed: 26289413
Affiliations:
- Allemagne, Arabie saoudite, Espagne, Tunisie, Turquie
- Basse-Saxe, Galice
- Hanovre, Santiago de Compostela
- Université de Saint-Jacques-de-Compostelle
Links toward previous steps (curation, corpus...)
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Le document en format XML
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Bulbul</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Forensic Sciences, Istanbul University, Istanbul, Turkey. ozlembulbul00@gmail.com.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Institute of Forensic Sciences, Istanbul University, Istanbul</wicri:regionArea><wicri:noRegion>Istanbul</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany. ozlembulbul00@gmail.com.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne</wicri:regionArea><wicri:noRegion>Cologne</wicri:noRegion><wicri:noRegion>Cologne</wicri:noRegion><wicri:noRegion>Cologne</wicri:noRegion></affiliation></author><author><name sortKey="Filoglu, G" sort="Filoglu, G" uniqKey="Filoglu G" first="G" last="Filoglu">G. 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Ruiz</name><affiliation wicri:level="4"><nlm:affiliation>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela</wicri:regionArea><orgName type="university">Université de Saint-Jacques-de-Compostelle</orgName><placeName><settlement type="city">Santiago de Compostela</settlement><region nuts="2" type="region">Galice</region></placeName></affiliation></author><author><name sortKey="Klintschar, M" sort="Klintschar, M" uniqKey="Klintschar M" first="M" last="Klintschar">M. 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Triki-Fendri</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Research Group, Centre of Biotechnology of Sfax, Sfax, Tunisia.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Bioinformatics Research Group, Centre of Biotechnology of Sfax, Sfax</wicri:regionArea><wicri:noRegion>Sfax</wicri:noRegion></affiliation></author><author><name sortKey="Rebai, A" sort="Rebai, A" uniqKey="Rebai A" first="A" last="Rebai">A. Rebai</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Research Group, Centre of Biotechnology of Sfax, Sfax, Tunisia.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Bioinformatics Research Group, Centre of Biotechnology of Sfax, Sfax</wicri:regionArea><wicri:noRegion>Sfax</wicri:noRegion></affiliation></author><author><name sortKey="Phillips, C" sort="Phillips, C" uniqKey="Phillips C" first="C" last="Phillips">C. 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Bulbul</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Forensic Sciences, Istanbul University, Istanbul, Turkey. ozlembulbul00@gmail.com.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Institute of Forensic Sciences, Istanbul University, Istanbul</wicri:regionArea><wicri:noRegion>Istanbul</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany. ozlembulbul00@gmail.com.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne</wicri:regionArea><wicri:noRegion>Cologne</wicri:noRegion><wicri:noRegion>Cologne</wicri:noRegion><wicri:noRegion>Cologne</wicri:noRegion></affiliation></author><author><name sortKey="Filoglu, G" sort="Filoglu, G" uniqKey="Filoglu G" first="G" last="Filoglu">G. Filoglu</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Forensic Sciences, Istanbul University, Istanbul, Turkey.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Institute of Forensic Sciences, Istanbul University, Istanbul</wicri:regionArea><wicri:noRegion>Istanbul</wicri:noRegion></affiliation></author><author><name sortKey="Zorlu, T" sort="Zorlu, T" uniqKey="Zorlu T" first="T" last="Zorlu">T. Zorlu</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Forensic Sciences, Istanbul University, Istanbul, Turkey.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Institute of Forensic Sciences, Istanbul University, Istanbul</wicri:regionArea><wicri:noRegion>Istanbul</wicri:noRegion></affiliation></author><author><name sortKey="Altuncul, H" sort="Altuncul, H" uniqKey="Altuncul H" first="H" last="Altuncul">H. Altuncul</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Forensic Sciences, Istanbul University, Istanbul, Turkey.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Institute of Forensic Sciences, Istanbul University, Istanbul</wicri:regionArea><wicri:noRegion>Istanbul</wicri:noRegion></affiliation></author><author><name sortKey="Freire Aradas, A" sort="Freire Aradas, A" uniqKey="Freire Aradas A" first="A" last="Freire-Aradas">A. Freire-Aradas</name><affiliation wicri:level="4"><nlm:affiliation>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela</wicri:regionArea><orgName type="university">Université de Saint-Jacques-de-Compostelle</orgName><placeName><settlement type="city">Santiago de Compostela</settlement><region nuts="2" type="region">Galice</region></placeName></affiliation></author><author><name sortKey="Sochtig, J" sort="Sochtig, J" uniqKey="Sochtig J" first="J" last="Söchtig">J. Söchtig</name><affiliation wicri:level="4"><nlm:affiliation>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela</wicri:regionArea><orgName type="university">Université de Saint-Jacques-de-Compostelle</orgName><placeName><settlement type="city">Santiago de Compostela</settlement><region nuts="2" type="region">Galice</region></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>Department of Forensic Medicine, Hannover Medical School, Hannover, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Forensic Medicine, Hannover Medical School, Hannover</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Hanovre</settlement></placeName></affiliation></author><author><name sortKey="Ruiz, Y" sort="Ruiz, Y" uniqKey="Ruiz Y" first="Y" last="Ruiz">Y. Ruiz</name><affiliation wicri:level="4"><nlm:affiliation>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela</wicri:regionArea><orgName type="university">Université de Saint-Jacques-de-Compostelle</orgName><placeName><settlement type="city">Santiago de Compostela</settlement><region nuts="2" type="region">Galice</region></placeName></affiliation></author><author><name sortKey="Klintschar, M" sort="Klintschar, M" uniqKey="Klintschar M" first="M" last="Klintschar">M. Klintschar</name><affiliation wicri:level="3"><nlm:affiliation>Department of Forensic Medicine, Hannover Medical School, Hannover, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Forensic Medicine, Hannover Medical School, Hannover</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Hanovre</settlement></placeName></affiliation></author><author><name sortKey="Triki Fendri, S" sort="Triki Fendri, S" uniqKey="Triki Fendri S" first="S" last="Triki-Fendri">S. Triki-Fendri</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Research Group, Centre of Biotechnology of Sfax, Sfax, Tunisia.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Bioinformatics Research Group, Centre of Biotechnology of Sfax, Sfax</wicri:regionArea><wicri:noRegion>Sfax</wicri:noRegion></affiliation></author><author><name sortKey="Rebai, A" sort="Rebai, A" uniqKey="Rebai A" first="A" last="Rebai">A. Rebai</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Research Group, Centre of Biotechnology of Sfax, Sfax, Tunisia.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Bioinformatics Research Group, Centre of Biotechnology of Sfax, Sfax</wicri:regionArea><wicri:noRegion>Sfax</wicri:noRegion></affiliation></author><author><name sortKey="Phillips, C" sort="Phillips, C" uniqKey="Phillips C" first="C" last="Phillips">C. Phillips</name><affiliation wicri:level="4"><nlm:affiliation>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela</wicri:regionArea><orgName type="university">Université de Saint-Jacques-de-Compostelle</orgName><placeName><settlement type="city">Santiago de Compostela</settlement><region nuts="2" type="region">Galice</region></placeName></affiliation></author><author><name sortKey="Lareu, M V" sort="Lareu, M V" uniqKey="Lareu M" first="M V" last="Lareu">M V Lareu</name><affiliation wicri:level="4"><nlm:affiliation>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela</wicri:regionArea><orgName type="university">Université de Saint-Jacques-de-Compostelle</orgName><placeName><settlement type="city">Santiago de Compostela</settlement><region nuts="2" type="region">Galice</region></placeName></affiliation></author><author><name sortKey="Carracedo, A" sort="Carracedo, A" uniqKey="Carracedo A" first="Á" last="Carracedo">Á Carracedo</name><affiliation wicri:level="4"><nlm:affiliation>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Forensic Genetics Unit, Institute of Forensic Science "Luís Concheiro", University of Santiago de Compostela, Santiago de Compostela</wicri:regionArea><orgName type="university">Université de Saint-Jacques-de-Compostelle</orgName><placeName><settlement type="city">Santiago de Compostela</settlement><region nuts="2" type="region">Galice</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.</nlm:affiliation><country xml:lang="fr">Arabie saoudite</country><wicri:regionArea>Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah</wicri:regionArea><wicri:noRegion>Jeddah</wicri:noRegion></affiliation></author><author><name sortKey="Schneider, P M" sort="Schneider, P M" uniqKey="Schneider P" first="P M" last="Schneider">P M Schneider</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne</wicri:regionArea><wicri:noRegion>Cologne</wicri:noRegion><wicri:noRegion>Cologne</wicri:noRegion><wicri:noRegion>Cologne</wicri:noRegion></affiliation></author></analytic><series><title level="j">International journal of legal medicine</title><idno type="eISSN">1437-1596</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Asia (MeSH)</term><term>Continental Population Groups (genetics)</term><term>DNA Fingerprinting (MeSH)</term><term>Discriminant Analysis (MeSH)</term><term>Europe (MeSH)</term><term>Gene Frequency (MeSH)</term><term>Genetics, Population (MeSH)</term><term>Humans (MeSH)</term><term>Likelihood Functions (MeSH)</term><term>Multiplex Polymerase Chain Reaction (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Principal Component Analysis (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse discriminante (MeSH)</term><term>Analyse en composantes principales (MeSH)</term><term>Asie (MeSH)</term><term>Europe (MeSH)</term><term>Fonctions de vraisemblance (MeSH)</term><term>Fréquence d'allèle (MeSH)</term><term>Génétique des populations (MeSH)</term><term>Humains (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populations d'origine continentale (génétique)</term><term>Profilage d'ADN (MeSH)</term><term>Réaction de polymérisation en chaine multiplex (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Continental Population Groups</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populations d'origine continentale</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Asia</term><term>DNA Fingerprinting</term><term>Discriminant Analysis</term><term>Europe</term><term>Gene Frequency</term><term>Genetics, Population</term><term>Humans</term><term>Likelihood Functions</term><term>Multiplex Polymerase Chain Reaction</term><term>Polymorphism, Single Nucleotide</term><term>Principal Component Analysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse discriminante</term><term>Analyse en composantes principales</term><term>Asie</term><term>Europe</term><term>Fonctions de vraisemblance</term><term>Fréquence d'allèle</term><term>Génétique des populations</term><term>Humains</term><term>Polymorphisme de nucléotide simple</term><term>Profilage d'ADN</term><term>Réaction de polymérisation en chaine multiplex</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The inference of biogeographical ancestry (BGA) can provide useful information for forensic investigators when there are no suspects to be compared with DNA collected at the crime scene or when no DNA database matches exist. Although public databases are increasing in size and population scope, there is a lack of information regarding genetic variation in Eurasian populations, especially in central regions such as the Middle East. Inhabitants of these regions show a high degree of genetic admixture, characterized by an allele frequency cline running from NW Europe to East Asia. Although a proper differentiation has been established between the cline extremes of western Europe and South Asia, populations geographically located in between, i.e, Middle East and Mediterranean populations, require more detailed study in order to characterize their genetic background as well as to further understand their demographic histories. To initiate these studies, three ancestry informative SNP (AI-SNP) multiplex panels: the SNPforID 34-plex, Eurasiaplex and a novel 33-plex assay were used to describe the ancestry patterns of a total of 24 populations ranging across the longitudinal axis from NW Europe to East Asia. Different ancestry inference approaches, including STRUCTURE, PCA, DAPC and Snipper Bayes analysis, were applied to determine relationships among populations. The structure results show differentiation between continental groups and a NW to SE allele frequency cline running across Eurasian populations. This study adds useful population data that could be used as reference genotypes for future ancestry investigations in forensic cases. The 33-plex assay also includes pigmentation predictive SNPs, but this study primarily focused on Eurasian population differentiation using 33-plex and its combination with the other two AI-SNP sets. </div></front></TEI><affiliations><list><country><li>Allemagne</li><li>Arabie saoudite</li><li>Espagne</li><li>Tunisie</li><li>Turquie</li></country><region><li>Basse-Saxe</li><li>Galice</li></region><settlement><li>Hanovre</li><li>Santiago de Compostela</li></settlement><orgName><li>Université de Saint-Jacques-de-Compostelle</li></orgName></list><tree><country name="Turquie"><noRegion><name sortKey="Bulbul, O" sort="Bulbul, O" uniqKey="Bulbul O" first="O" last="Bulbul">O. Bulbul</name></noRegion><name sortKey="Altuncul, H" sort="Altuncul, H" uniqKey="Altuncul H" first="H" last="Altuncul">H. Altuncul</name><name sortKey="Filoglu, G" sort="Filoglu, G" uniqKey="Filoglu G" first="G" last="Filoglu">G. Filoglu</name><name sortKey="Zorlu, T" sort="Zorlu, T" uniqKey="Zorlu T" first="T" last="Zorlu">T. Zorlu</name></country><country name="Allemagne"><noRegion><name sortKey="Bulbul, O" sort="Bulbul, O" uniqKey="Bulbul O" first="O" last="Bulbul">O. Bulbul</name></noRegion><name sortKey="Klintschar, M" sort="Klintschar, M" uniqKey="Klintschar M" first="M" last="Klintschar">M. Klintschar</name><name sortKey="Schneider, P M" sort="Schneider, P M" uniqKey="Schneider P" first="P M" last="Schneider">P M Schneider</name><name sortKey="Sochtig, J" sort="Sochtig, J" uniqKey="Sochtig J" first="J" last="Söchtig">J. Söchtig</name></country><country name="Espagne"><region name="Galice"><name sortKey="Freire Aradas, A" sort="Freire Aradas, A" uniqKey="Freire Aradas A" first="A" last="Freire-Aradas">A. Freire-Aradas</name></region><name sortKey="Carracedo, A" sort="Carracedo, A" uniqKey="Carracedo A" first="Á" last="Carracedo">Á Carracedo</name><name sortKey="Lareu, M V" sort="Lareu, M V" uniqKey="Lareu M" first="M V" last="Lareu">M V Lareu</name><name sortKey="Phillips, C" sort="Phillips, C" uniqKey="Phillips C" first="C" last="Phillips">C. Phillips</name><name sortKey="Ruiz, Y" sort="Ruiz, Y" uniqKey="Ruiz Y" first="Y" last="Ruiz">Y. Ruiz</name><name sortKey="Sochtig, J" sort="Sochtig, J" uniqKey="Sochtig J" first="J" last="Söchtig">J. Söchtig</name></country><country name="Tunisie"><noRegion><name sortKey="Triki Fendri, S" sort="Triki Fendri, S" uniqKey="Triki Fendri S" first="S" last="Triki-Fendri">S. Triki-Fendri</name></noRegion><name sortKey="Rebai, A" sort="Rebai, A" uniqKey="Rebai A" first="A" last="Rebai">A. Rebai</name></country><country name="Arabie saoudite"><noRegion><name sortKey="Carracedo, A" sort="Carracedo, A" uniqKey="Carracedo A" first="Á" last="Carracedo">Á Carracedo</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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