The investigation of the origin of Southern Tunisians using HLA genes (original) (raw)

References

  1. 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).
    Article CAS PubMed Google Scholar
  2. 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).
    Article CAS PubMed Google Scholar
  3. 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. B 367, 820–829 (2012).
    Article CAS Google Scholar
  4. Brett, M. & Fentress, E. The Berbers, (Blackwell Publishers, Oxford, UK, 1997).
    Google Scholar
  5. 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).
  6. 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
  7. Lucette, V. & Abraham, L. U. Juifs en terre d’islam: les communautés de Djerba 13 (éd. Archives contemporaines, Paris, 1991).
  8. Ibn Khaldūn, A. in The Muqaddimah: An Introduction to History (Trans. Franz Rosenthal, ed. Dawood, N. J., 1967) (abridged).
  9. 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).
    Article CAS PubMed Google Scholar
  10. 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).
    Article CAS PubMed Google Scholar
  11. 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).
    Article CAS PubMed PubMed Central Google Scholar
  12. 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 Antigens 41, 1–14 (1993).
    Article CAS PubMed Google Scholar
  13. 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 Antigens 75, 291–455 (2010).
    Article CAS PubMed PubMed Central Google Scholar
  14. Excoffier, L. & Slatkin, M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol. 12, 921–927 (1995).
    CAS PubMed Google Scholar
  15. 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
  16. 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).
  17. Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987).
    CAS PubMed Google Scholar
  18. Nei, M. Genetic distances between populations. Am. Nat. 106, 283 (1972).
    Article Google Scholar
  19. 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).
    Article CAS PubMed Google Scholar
  20. 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).
  21. 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).
  22. 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 Antigens 69, 192–197 (2007).
    Article CAS PubMed PubMed Central Google Scholar
  23. Ewens, W. The sampling theory of selectively neutral alleles. Theor. Pop. Biol. 3, 87–112 (1972).
    Article CAS Google Scholar
  24. Watterson, G. The homozygosity test of neutrality. Genetics 88, 405–417 (1978).
    CAS PubMed Central PubMed Google Scholar
  25. Slatkin, M. An exact test for neutrality based on the Ewens sampling distribution. Genet. Res. 64, 71–74 (1994).
    Article CAS PubMed Google Scholar
  26. Slatkin, M. A correction to the exact test based on the Ewens sampling distribution. Genet. Res. 68, 259–260 (1996).
    Article CAS PubMed Google Scholar
  27. Glantz, S. A. Primer of Biostatistics 7th edn (McGraw-Hill, New York, NY, 2012).
    Google Scholar
  28. 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 Antigens 55, 239–249 (2000).
    Article CAS PubMed Google Scholar
  29. 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 Antigens 51, 30–40 (1998).
    Article CAS PubMed Google Scholar
  30. Clayton, J. & Lonjou, C. in Genetic Diversity of HLA. Functional and Medical Implications Vol. 1 (ed. Charron, D.) 665–820 (EDK: Paris, 1997).
  31. 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).
    Article CAS PubMed Google Scholar
  32. 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 Antigens 68, 153–162 (2006).
    Article CAS PubMed Google Scholar
  33. 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).
    Article CAS PubMed Google Scholar
  34. 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 ONE 10, e0136909 (2015).
    Article PubMed PubMed Central Google Scholar
  35. 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).
    Article PubMed Google Scholar
  36. 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).
    Article CAS PubMed Google Scholar
  37. 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).
    Article CAS PubMed Google Scholar
  38. Hmida, S., Gauthier, Dridi, A., Quillivic, F., Genetet, B., Boukef et al. HLA class II gene polymorphism in Tunisians. Tissue Antigens 45, 63–68 (1995).
    Article CAS PubMed Google Scholar
  39. 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 Antigens 51, 106–110 (1998).
    Article CAS PubMed Google Scholar
  40. 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 Antigens 76, 177–193 (2010).
    Article CAS PubMed Google Scholar
  41. 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. Probes 29, 197–207 (2015).
    Article CAS PubMed Google Scholar
  42. 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 Antigens 45, 237–245 (1995).
    Article CAS PubMed Google Scholar
  43. 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 Antigens 46, 104–110 (1995).
    Article CAS PubMed Google Scholar
  44. 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 Antigens 57, 308–317 (2001).
    Article CAS PubMed Google Scholar
  45. 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).
  46. 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 Antigens 61, 384–392 (2003).
    Article CAS PubMed Google Scholar
  47. 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).
  48. 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 Antigens 73, 17–32 (2009).
    Article CAS PubMed Google Scholar
  49. Satta, Y., O’hUigin, C., Takahata, N. & Klein, J. Intensity of natural selection at the major histocompatibility complex loci. Proc. Natl Acad. Sci. USA 91, 7184–7188 (1994).
    Article CAS PubMed PubMed Central Google Scholar
  50. 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).
    Article CAS PubMed Google Scholar
  51. 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 Antigens 76, 416–420 (2010).
    Article CAS PubMed Google Scholar
  52. 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).
    Article PubMed Google Scholar
  53. 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 Antigens 64, 520–532 (2004).
    Article CAS PubMed Google Scholar
  54. 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
  55. 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
  56. 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 Antigens 60, 111–121 (2002).
    Article CAS PubMed Google Scholar
  57. Julien, C. A. Histoire de l’Afrique du Nord (Masson et Cie, Paris, 1953).
  58. Murdok, G. P. Africa, Its Peoples and Their Cultural History (McGrawHill, New York, NY, 1959).
  59. 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 Antigens 53, 213–226 (1999).
    Article CAS PubMed Google Scholar
  60. Fischer, T. in The International Geography (ed. Mill, H. R.) 368–377 (Appleton and Company, New York, NY and London, UK, 1920).
  61. Stallaert, C. Ethnogenesis and Ethnicity in Spain: A Historical–Anthropological Approach to Casticismo (Proyecto A: Barcelona, Spain, 1998).
  62. 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. USA 110, 11791–11796 (2013).
    Article PubMed PubMed Central Google Scholar
  63. Currat, M., Poloni, E. S. & Sanchez-Mazas, A. Human genetic differentiation across the Strait of Gibraltar. Evol. Biol. 10, 237 (2010).
    Google Scholar
  64. Le Bon, G. Arab Civilisation (Libairie Firmin Diderot, France, 1884).
  65. Mark, A. & Tessler, A. History of the Israeli-Palestinian Conflict Vol. 329 (Indiana University Press, Bloomington, IN, 1994).
    Google Scholar
  66. 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 Antigens 57, 118–127 (2001).
    Article CAS PubMed Google Scholar
  67. 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).
    Article CAS PubMed PubMed Central Google Scholar
  68. Herodotus. History (Gredos, Madrid, Spain, 1989).
  69. 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 Antigens 64, 486–491 (2004).
    Article CAS PubMed Google Scholar
  70. 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).
    Article PubMed Google Scholar
  71. 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).
    Article CAS PubMed Google Scholar
  72. 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).
    Article PubMed Google Scholar

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