Supplementary Table 1. Worldwide populations included in the comparative analyses

Continent/Population / Ancestry / Reference
Africa
South-East Bantu / African / Kulski and Dunn (2005)
!Kung San / African / “
Sekele San / African / “
Asia
North-East Thais / Asian / Kulski and Dunn (2005)
Khalk Mongolian / Asian / “
Han Chinese (Guangdong province) / Asian / Tian et al. (2008)
Han Chinese (Hunan province) / Asian / “
Han Chinese (Inner Mongolia) / Asian / “
Mongols (Inner Mongolia) / Asian / “
Maonan (Guangxi province) / Asian / Yao et al. (2010)
Bulang (Yunnan province) / Asian / “
Dai (Yunnan province) / Asian / “
Han (Yunnan province) / Asian / “
Hani (Yunnan province) / Asian / “
Jinuo (Yunnan province) / Asian / “
Wa (Yunnan province) / Asian / “
Oceania
Australian / European / Kulski and Dunn (2005)
Europe
Navarre / European / García-Obregón et al. (2012)
Guipuzcoa / European / “
Valencia / European / García-Obregón et al. (2011)

References

García-Obregón S, Alfonso-Sánchez MA, Gómez-Pérez L, Pérez-Miranda AM, Arroyo D, de Pancorbo MM, Peña JA. 2011. Microsatellites and Alu elements from the human MHC in Valencia (Spain): analysis of genetic relationships and linkage disequilibrium. Int J Inmunogenet 38: 483-491

García-Obregón S, Alfonso-Sánchez MA, Pérez-Miranda AM, Gómez-Pérez L, de Parcorbo MM, Peña JA. 2012. Ancestry markers from the human chromosome 6: Alu repeats from the MHC in autochthonous Basques. Hum Immunol 73: 720-725

Kulski JK, Dunn DS, Gaudieri S, Shiina T, Inoko H. 2001. Genomic and phylogenetic analysis of the human CD1 and HLA class I multicopy genes. J Mol Evol 53: 642-650

Tian W, Wang F, Cai JH, Li LX. 2008. Polymorphic insertions in 5 Alu loci within the major histocompatibility complex class I region and their linkage disequilibria with HLA alleles in four distinct populations in mainland China. Tissue Antigens 72: 559-567

Yao Y, Shi L, Shi L, Kulski JK, Chen J, Liu S, Yu L, Lin K, Huang X, Tao Y, Tokunaga K., Chu J. 2010. The association and differentiation of MHC class I polymorphic Alu insertions and HLA-B/Cw alleles in seven Chinese populations Tissue Antigens 76: 194-207


Supplementary Table 2. Five-Alu (AluMicB-AluTF-AluHJ-AluHG-AluHF) haplotype frequencies in Native American samples from Jujuy province (Argentina) and Waorani (Ecuadorian Amazon)

Haplotype a / Frequencies (± SE)
Jujuy / Waorani
1-1-1-1-1 / 0.128 / ± 0.023 / 28 / 0.147 / ± 0.047 / 9
2-1-1-1-1 / 0.210 / ± 0.028 / 45 / 0.023 / ± 0.020 / 1
1-2-1-1-1 / 0.092 / ± 0.020 / 20 / 0.455 / ± 0.066 / 27
1-1-2-1-1 / 0.029 / ± 0.011 / 6 / 0.040 / ± 0.026 / 2
1-1-1-2-1 / 0.090 / ± 0.020 / 20 / 0.057 / ± 0.031 / 3
2-2-1-1-1 / 0.056 / ± 0.016 / 12 / 0.099 / ± 0.040 / 6
2-1-2-1-1 / 0.104 / ± 0.021 / 22 / - / - / -
2-1-1-2-1 / 0.121 / ± 0.022 / 26 / 0.094 / ± 0.039 / 6
1-2-2-1-1 / 0.008 / ± 0.006 / 2 / 0.021 / ± 0.019 / 1
1-2-1-2-1 / 0.076 / ± 0.018 / 16 / 0.038 / ± 0.025 / 2
1-2-1-1-2 / 0.008 / ± 0.006 / 2 / - / - / -
1-1-2-2-1 / 0.007 / ± 0.006 / 2 / - / - / -
1-1-1-2-2 / 0.006 / ± 0.005 / 1 / - / - / -
2-2-2-1-1 / 0.022 / ± 0.010 / 5 / 0.025 / ± 0.021 / 1
2-2-1-2-1 / 0.038 / ± 0.013 / 8 / - / - / -
2-1-2-1-2 / 0.005 / ± 0.005 / 1 / - / - / -

a 1 = absence of the Alu element, 2 = insertion of the Alu element

SE, standard error