The investigation of the origin of Southern Tunisians using HLA genes (original) (raw)
References
Shiina, T., Hosomichi, K., Inoko, H. & Kulski, J. K. The HLA genomic loci map: expression, interaction, diversity, and disease. J. Hum. Genet.54, 15–39 (2009). ArticleCASPubMed Google Scholar
Robinson, J., Soormally, A. R., Hayhurst, J. D. & Marsh, S. G. The IPD-IMGT/HLA database—new developments in reporting HLA variation. Hum. Immunol.77, 233–237 (2016). ArticleCASPubMed Google Scholar
Vina, M. A., Hollenbach, J. A., Lyke, K. E., Sztein, M. B., Maiers, M., Klitz, W. et al. Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations. Philos. Trans. R. Soc. Lond. Ser. B367, 820–829 (2012). ArticleCAS Google Scholar
Brett, M. & Fentress, E. The Berbers, (Blackwell Publishers, Oxford, UK, 1997). Google Scholar
Stearns, P. N. & Leonard, W. L. in The Encyclopedia of World History: Ancient, Medieval, and Modern, Chronologically Arranged 6th edn, 129–131 (Houghton Mifflin Harcourt, New York, NY, USA, 2001).
Austin, R. A. The Transaharian Slave Trade. Essays in the Economic History of the Atlantic Slave Trade, (New York Academy Press, New York, NY, 1979). Google Scholar
Lucette, V. & Abraham, L. U. Juifs en terre d’islam: les communautés de Djerba 13 (éd. Archives contemporaines, Paris, 1991).
Ibn Khaldūn, A. in The Muqaddimah: An Introduction to History (Trans. Franz Rosenthal, ed. Dawood, N. J., 1967) (abridged).
Hajjej, A., Hajjej, G., Almawi, W. Y., Kaabi, H., El-Gaaied, A. & Hmida, S. HLA class I and class II polymorphism in a population from south-eastern Tunisia (Gabes Area). Int. J. Immunogenet.38, 191–199 (2011). ArticleCASPubMed Google Scholar
Hajjej, A., Hmida, S., Kaabi, H., Dridi, A., Jridi, A., El Gaaled, A. et al. HLA genes in Southern Tunisians (Ghannouch area) and their relationship with other Mediterraneans. Eur. J. Med. Genet.49, 43–56 (2006). ArticleCASPubMed Google Scholar
Miller, S. A., Dykes, D. D. & Polesky, H. F. A sample salting out procedure for extraction DNA from human nucleated cells. Nucleic Acids Res.16, 1215–1218 (1988). ArticleCASPubMedPubMed Central Google Scholar
Buyse, I., Decorte, R., Baens, M., Cuppens, H., Semana, G., Emonds, M. P. et al. Rapid DNA typing of class II HLA antigens using the polymerase chain reaction and reverse dot blot hybridization. Tissue Antigens41, 1–14 (1993). ArticleCASPubMed Google Scholar
Marsh, S. G. E., Albert, E. D., Bodmer, W. F., Bontrop, R. E., Dupont, B., Erlich, H. A et al. Nomenclature for factors of the HLA system, 2010. Tissue Antigens75, 291–455 (2010). ArticleCASPubMedPubMed Central Google Scholar
Excoffier, L. & Slatkin, M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol.12, 921–927 (1995). CASPubMed Google Scholar
Schneider, S., Kueffer, J. M., Roessli, D. & Excoffier, L. Arlequin: A Software Environment for the Analysis of Population Genetics Data, (Genetics and Biometry Lab, Geneva, Switzerland, 1996). Google Scholar
Imanishi, T., Akaza, T., Kimura, A., Tokunaga, K., Gojrobi, T. in HLA 1991 Vol. I (eds Tsuji, K., Aizawa, M. & Sasazuki, T.) 76–79 (Oxford University Press, Oxford, UK, 1992).
Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4, 406–425 (1987). CASPubMed Google Scholar
Nei, M. Genetic distances between populations. Am. Nat.106, 283 (1972). Article Google Scholar
Nei, M., Tajima, Y. & Tateno, Y. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J. Mol. Evol.19, 153–170 (1983). ArticleCASPubMed Google Scholar
Young, F. W. & Bann, C. M. in Statistical Computing Environments for Social Researches (eds Stine, R. A. & Fox, J.) 207–236 (Sage Publications, New York, NY, 1996).
Lancaster, A. K., Nelson, M. P., Single, R. M., Meyer, D. & Thomson, G. in Pacific Symposium on Biocomputing Vol. 8 (eds Altman, R. B., Dunker, K., Hunter, L., Jung, T. & Klein, T.) 514–525 (World Scientific, Singapore, Singapore, 2003).
Lancaster, A. K., Single, R. M., Solberg, O. D., Nelson, M. P. & Thomson, G. PyPop update—a software pipeline for large-scale multilocus population genomics. Tissue Antigens69, 192–197 (2007). ArticleCASPubMedPubMed Central Google Scholar
Ewens, W. The sampling theory of selectively neutral alleles. Theor. Pop. Biol.3, 87–112 (1972). ArticleCAS Google Scholar
Slatkin, M. An exact test for neutrality based on the Ewens sampling distribution. Genet. Res.64, 71–74 (1994). ArticleCASPubMed Google Scholar
Slatkin, M. A correction to the exact test based on the Ewens sampling distribution. Genet. Res.68, 259–260 (1996). ArticleCASPubMed Google Scholar
Glantz, S. A. Primer of Biostatistics 7th edn (McGraw-Hill, New York, NY, 2012). Google Scholar
Gomez-Casado, E., del Moral, P., Martinez-Laso, J., García-Gómez, A., Allende, L., Silvera-Redondo et al. HLA gene in Arabic-Speaking Moroccans: close relatedness to Berbers and Iberians. Tissue Antigens55, 239–249 (2000). ArticleCASPubMed Google Scholar
Comas, D., Mateu, E., Calafell, F., Pérez-Lezaun, A., Bosch, E., Martínez-Arias, R. et al. HLA class I and class II DNA typing and the origin of Basques. Tissue Antigens51, 30–40 (1998). ArticleCASPubMed Google Scholar
Clayton, J. & Lonjou, C. in Genetic Diversity of HLA. Functional and Medical Implications Vol. 1 (ed. Charron, D.) 665–820 (EDK: Paris, 1997).
Arnaiz-Villena, A., Benmamar, D., Alvarez, M., Diaz-Campos, N., Varela, P., Gomez-Casado, E. et al. HLA allele and haplotype frequencies in Algerians. Relatedness to Spaniards and Basques. Hum. Immunol.43, 259–268 (1995). ArticleCASPubMed Google Scholar
Hajjej, A., Kâabi, H., Sellami, M. H., Dridi, A., Jeridi, A., El Borgi, W. et al. The contribution of HLA class I and II alleles and haplotypes to the investigation of the evolutionary history of Tunisians. Tissue Antigens68, 153–162 (2006). ArticleCASPubMed Google Scholar
Hajjej, A., Sellami, M. H., Kaabi, Hajjej, G., El-Gaaied, A., Boukef, K. et al. HLA class I and class II polymorphisms in Tunisian Berbers. Ann. Hum. Biol.38, 156–164 (2011). ArticleCASPubMed Google Scholar
Hajjej, A., Almawi, W. Y., Hattab, L., El-Gaaied, A. & Hmida, S. HLA class I and class II alleles and haplotypes confirm the Berber Origin of the Present Day Tunisian Population. PLoS ONE10, e0136909 (2015). ArticlePubMedPubMed Central Google Scholar
Sánchez-Velasco, P., Karadsheh, N. S., García-Martín, A., Ruíz de Alegría, C. & Leyva-Cobián, F. Molecular analysis of HLA allelic frequencies and haplotypes in Jordanians and comparison with other related populations. Hum. Immunol.62, 901–909 (2001). ArticlePubMed Google Scholar
Galgani, A., Mancino, G., Martínez-Labarga, C., Cicconi, R., Mattei, M., Amicosante, M. et al. HLA-A, -B and -DRB1 allele frequencies in Cyrenaica population (Libya) and genetic relationships with other populations. Hum. Immunol.74, 52–59 (2013). ArticleCASPubMed Google Scholar
Arnaiz-Villena, A., Elaiwa, N., Silvera, C., Rostom, A., Moscoso, J., Gómez-Casado, E. et al The origin of Palestinians and their genetic relatedness with other Mediterranean populations [retraction] Hum. Immunol.62, 889–900 (2001). ArticleCASPubMed Google Scholar
Hmida, S., Gauthier, Dridi, A., Quillivic, F., Genetet, B., Boukef et al. HLA class II gene polymorphism in Tunisians. Tissue Antigens45, 63–68 (1995). ArticleCASPubMed Google Scholar
Izaabel, H., Garchon, H. J., Caillat-Zucman, S., Beaurain, G., Akhayat, O., Bach, J. F. et al. HLA class II DNA polymorphism in a Moroccan population from the Souss, Agadir area. Tissue Antigens51, 106–110 (1998). ArticleCASPubMed Google Scholar
Canossi, A., Piancatelli, D., Aureli, A., Oumhani, K., Ozzella, G., Del Beato, T. et al. Correlation between genetic HLA class I and II polymorphisms and anthropological aspects in the Chaouya population from Morocco (Arabic speaking). Tissue Antigens76, 177–193 (2010). ArticleCASPubMed Google Scholar
Brick, C., Atouf, O., Bouayad, A . & Essakalli, M. Moroccan study of HLA (-A, -B, -C, -DR, -DQ) polymorphism in 647 unrelated controls: Updating data. Mol. Cell. Probes29, 197–207 (2015). ArticleCASPubMed Google Scholar
Martinez-Laso, J., De Juan, Martinez-Quiles, N., Gomez-Casado, E., Cuadrado, E. & Arnaiz-Villena, A. The contribution of the HLA-A, -B, -C and -DR, -DQ DNA typing to the study of the origins of Spaniards and Basques. Tissue Antigens45, 237–245 (1995). ArticleCASPubMed Google Scholar
Roitberg-Tambur, A., Witt, C. S., Friedmann, Safirman, C., Sherman, Battat, S. et al. Comparative analysis of HLA polymorphism at the serologic and molecular level in Moroccan and Ashkenazi Jews. Tissue Antigens46, 104–110 (1995). ArticleCASPubMed Google Scholar
Arnaiz-Villena, A., Karin, M., Bendikuze, N., Gomez-Casado, E., Moscoso, J., Silvera, C. et al. HLA alleles and haplotypes in the Turkish population: relatedness to Kurds, Armenians and other Mediterraneans. Tissue Antigens57, 308–317 (2001). ArticleCASPubMed Google Scholar
Imanishi, T., Akaza, T., Kimura, A., Tokunaga, K. & Gjobori, T. in HLA 1991 Vol. 1 (eds Tsuji, K., Aizawa, M. & Sasazuki, T.) 1065–1220 (Oxford University Press, Oxford, UK, 1992).
Sanchez-Velasco, P., Gomez-Casado, E., Martinez-Laso, J., Moscoso, J., Zamora, J., Lowy, E. et al. HLA alleles in isolated populations from North Spain: origin of the Basques and the ancient Iberians. Tissue Antigens61, 384–392 (2003). ArticleCASPubMed Google Scholar
Single, R., Meyer, D., Mack, S. J., Lancaster, A., Nelson, M. P. & Erlich, H. et al. in Immunobiology of the Human MHC (ed. Jansen, J. A.) 705–746 (International Histocompatibility Working Group Press, Seattle, WA, 2006).
Mack, S. J., Tu, B., Lazaro, A., Yang, R., Lancaster, A. K., Cao, K. et al. HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies distinguish Eastern European Americans from the general European American population. Tissue Antigens73, 17–32 (2009). ArticleCASPubMed Google Scholar
Satta, Y., O’hUigin, C., Takahata, N. & Klein, J. Intensity of natural selection at the major histocompatibility complex loci. Proc. Natl Acad. Sci. USA91, 7184–7188 (1994). ArticleCASPubMedPubMed Central Google Scholar
Abdennaji Guenounou, B., Yacoubi Loueslati, B., Buhler, S., Hmida, S., Ennafaa, H., Khodjet-Elkhil, H. et al. HLA class II genetic diversity in Southern Tunisia and the Mediterranean area. Int. J. Immunogenet.33, 93–103 (2006). ArticleCASPubMed Google Scholar
Fadhlaoui-Zid, K., Buhler, S., Dridi, A., Benammar El Gaaied, A. & Sanchez-Mazas, A. Polymorphism of HLA class II genes in Berbers from Southern Tunisia. Tissue Antigens76, 416–420 (2010). ArticleCASPubMed Google Scholar
Mahfoudh, N., Ayadi, I., Kamoun, A., Ammar, R., Mallek, B. & Maalej, L. et al. Analysis of HLA-A, -B, -C, -DR, -DQ polymorphisms in the South Tunisian population and a comparison with other populations. Ann Hum Biol.40, 41–47 (2013). ArticlePubMed Google Scholar
Ayed, K., Ayed-Jendoubi, S., Sfar, I., Labonne, M. P. & Gebuhrer, L. HLA class-I and HLA class-II phenotypic, gene and haplotypic frequencies in Tunisians by using molecular typing data. Tissue Antigens64, 520–532 (2004). ArticleCASPubMed Google Scholar
Solberg, O. D., Mack, S. J., Lancaster, A. K., Single, R. M., Tsai, Y. & Sanchez-Mazas, A. et al. Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. Hum. Immunol.69, 43–464 (2008). Article Google Scholar
Apanius, V., Penn, O. & Slev, P. R. et al. The nature of selection on the major histocompatibility complex. Crit. Rev. Immunol.15, 179–224 (1997). Article Google Scholar
Arnaiz-Villena, A., Gomez-Casado, E. & Martinez-Laso, J. Population genetic relationships between Mediterranean populations determined by HLA allele distribution and a historic perspective. Tissue Antigens60, 111–121 (2002). ArticleCASPubMed Google Scholar
Julien, C. A. Histoire de l’Afrique du Nord (Masson et Cie, Paris, 1953).
Murdok, G. P. Africa, Its Peoples and Their Cultural History (McGrawHill, New York, NY, 1959).
Arnaiz-Villena, A., Iliakis, P., González-Hevilla, M., Longás, J., Gómez-Casado, E., Sfyridaki, K. et al. The origin of Cretan populations as determined by characterization of HLA alleles. Tissue Antigens53, 213–226 (1999). ArticleCASPubMed Google Scholar
Fischer, T. in The International Geography (ed. Mill, H. R.) 368–377 (Appleton and Company, New York, NY and London, UK, 1920).
Stallaert, C. Ethnogenesis and Ethnicity in Spain: A Historical–Anthropological Approach to Casticismo (Proyecto A: Barcelona, Spain, 1998).
Botigué, L. M., Henn, B. M., Gravel, S., Maples, B. K., Gignoux, C. R. & Corona, E. et al. Gene flow from North Africa contributes to differential human genetic diversity in southern Europe. Proc. Natl Acad. Sci. USA110, 11791–11796 (2013). ArticlePubMedPubMed Central Google Scholar
Currat, M., Poloni, E. S. & Sanchez-Mazas, A. Human genetic differentiation across the Strait of Gibraltar. Evol. Biol.10, 237 (2010). Google Scholar
Le Bon, G. Arab Civilisation (Libairie Firmin Diderot, France, 1884).
Mark, A. & Tessler, A. History of the Israeli-Palestinian Conflict Vol. 329 (Indiana University Press, Bloomington, IN, 1994). Google Scholar
Arnaiz-Villena, A., Dimitroski, K., Pacho, A., Moscoso, J., Gómez-Casado, E. & Silvera-Redondo, C. et al. HLA genes in Macedonians and the Sub-Saharan origin of the Greeks. Tissue Antigens57, 118–127 (2001). ArticleCASPubMed Google Scholar
Dork, T., El-Harith, E. -H. A., Stuhrmann, M., Macek, M. Jr, Egan, M., Cutting, G. R. et al. Evidence for a common ethnic origin of cystic fibrosis mutation 3120+1G-to-A in diverse populations. Am. J. Hum. Genet.63, 656–662 (1998). ArticleCASPubMedPubMed Central Google Scholar
Herodotus. History (Gredos, Madrid, Spain, 1989).
Petlichkovski, A., Efinska-Mladenovska, O., Trajkov, D., Arsov, T., Strezova, A. & Spiroski, M. High-resolution typing of HLA-DRB1 locus in the Macedonian population. Tissue Antigens64, 486–491 (2004). ArticleCASPubMed Google Scholar
Fadhlaoui-Zid, K., Martinez-Cruz, B., Khodjet-el-khil, H., Mendizabal, I., Benammar-Elgaaied, A. & Comas, D. Genetic structure of Tunisian ethnic groups revealed by paternal lineages. Am. J. Phys. Anthropol.146, 271–280 (2011). ArticlePubMed Google Scholar
Fadhlaoui-Zid, K., Plaza, S., Calafell, F., Ben Amor, M., Comas, D. & Bennamar El gaaied, A. Mitochondrial DNA heterogeneity in Tunisian Berbers. Ann. Hum. Genet.68, 222–233 (2004). ArticleCASPubMed Google Scholar
Frigi, S., Cherni, L., Fadhlaoui-Zid, K. & Benammar-Elgaaied, A. Ancient local evolution of African mtDNA haplogroups in Tunisian Berber populations. Hum. Biol.82, 367–384 (2010). ArticlePubMed Google Scholar