Materials and methods
Chapter 1: Autosomal markers
3. Results and discussion 1. Genetic diversity
3.5. Comparison with other populations
To evaluate the genetic relationship between Jewish populations and previously reported data on other populations (Supplementary Table 11), pairwise FST genetic distances were computed (Supplementary Table 12) and represented in an MDS plot (Figure 1). Since no other populations were studied with the full set of 53 X-chromosome markers, genetic distances were assessed separately for the three types of polymorphisms. Stress values in all MDS analyses showed greater structure than would be obtained from a random dataset (Sturrock and Rocha, 2000).
Clustering of the different populations in Figure 1 reveals the ability of the three sets of X-markers to clearly discriminate between continents, with European, Asian, and African populations distantly positioned. With the available data for these markers, Amerindian populations appeared closer to Asians, and North African groups were placed between sub-Saharan and European populations, as expected due to their origin. Within the European cluster, Mediterranean isolates like Ibiza, Sicily, and Calabrian populations showed the most distant positions, as in other genetic studies (Rodríguez et al., 2009).
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Figure 1. Multidimensional scaling analysis (MDS) based on FST genetic distances calculated for 32 X-chromosome Indels, 8 X-Alus and 12 X-STRs. Jewish populations are labelled with stars.
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Regarding the Jewish populations, they do not form a well-defined cluster in any of the sets of markers in the MDS plots, but they do show up as relatively close to their host population or to other populations in the same geographical region, suggesting admixture with their neighbouring populations. These results mirror those obtained in uniparental markers such as mtDNA, which showed that Jewish pairwise comparisons have noticeably greater FST
values than the Jewish-host comparisons, but not when the Y-chromosome was used (Thomas et al., 2002). Indeed, as two thirds of the X-chromosomes descend from maternal origin, X-chromosome polymorphisms will mostly behave as matrilineal markers, showing similar results to those obtained from mtDNA data. Therefore, the results obtained suggest a larger introgression from females in the respective host non-Jewish populations than from males. Nonetheless, it cannot be ruled out that other events in the complex demographic history of the different Jewish groups could also have contributed to the sex-biased genetic pattern observed.
4. Conclusions
This study provides a useful database of 53 X-chromosome markers for populations with Jewish ancestry, including the Chuetas – a converted Sephardic isolate – and their host population (Majorca).A comparison of differentiation patterns between autosomes and X-chromosome between Jewish groups and with non-Jewish populations suggests a sex-biased admixture process. Genetic flow between Jewish communities would have been mediated primarily by males, with preferential introgression from females in the respective non-Jewish host populations, although other scenarios explaining the genetic portrait of these populations with complex histories cannot be ruled out. The results obtained demonstrate that the use of this set of 53 X-markers is highly efficient for forensic purposes.
Genetic distances show that the Jewish populations studied are a heterogeneous group. As such, specific databases for each Jewish community must be used in the forensic field to correctly weigh the value of the evidence based on these X-chromosome markers.
This study follows the guidelines for publication of population data proposed by the journal (Carracedo et al., 2013).
Acknowledgments
This work was partially supported by grant AAEE24/2014 from the Direcció General de R + D + I (Comunitat Autònoma de les Illes Balears) and European Regional Development Fund (ERDF). RP is a recipient of a grant (SFRH/BPD/81986/2011) awarded by the Portuguese Foundation for Science and Technology (FCT) and co-financed by the European Social Fund (Human Potential Thematic Operational Programme— POPH). We are grateful to Maria Trinidad Garcia (from the Serveis Cientificotècnics of the Universitat de les Illes Balears) for her assistance and help with capillary electrophoresis procedures and Meryl Jones for the English language corrections. We would also like to sincerely thank all the Chueta people who volunteered to participate in this study.
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Supplementary Table 2. Short Allele frequencies of 9 X-Alu markers in 569 chromosomes (Sephardic Jews: 103; North African Jews: 77; Middle Eastern Jews: 75; Ashkenazi Jews: 85;
Chuetas: 140 and Majorcans: 89).
Sephardic
Jews
North African Jews
Middle Eastern Jews
Ashkenazi
Jews Chuetas Majorca Ya5DP62 0.1775 0.2198 0.3067 0.2311 0.2599 0.3313 Yb8DP49 0.2638 0.3501 0.2667 0.2911 0.1707 0.1727 Yd3JX437 0.8566 0.9620 0.9867 0.8822 0.9085 0.9098 Yb8NBC634 0.0230 0.0400 0.0667 0.0378 0.0510 0.0226 Ya5DP77 0.0000 0.0267 0.1600 0.0444 0.1014 0.0226 Ya5_491 0.0427 0.0923 0.0133 0.0000 0.0216 0.0300 Yb8NBC578 0.0652 0.0637 0.0667 0.0000 0.0355 0.0226 Ya5DP4 0.9781 0.9877 1.0000 0.9400 0.9848 0.9774 Ya5DP13 0.1026 0.1037 0.0533 0.0111 0.1725 0.1428
Suplementary Table 3. Allele frequencies of 12 X-STR in 470 chromosomes in the 5 Jewish populations studied (Sephardic Jews: 99; North African Jews: 79; Middle Eastern Jews: 80; Ashkenazi Jews:
84 and Chuetas: 127).
DXS10079 DXS10101 DXS10103 DXS10134 DXS10146 DXS10148
Alelle SEP NAJ MEJ ASH CHU SEP NAJ MEJ ASH CHU SEP NAJ MEJ ASH CHU SEP NAJ MEJ ASH CHU SEP NAJ MEJ ASH CHU SEP NAJ MEJ ASH CHU
37.2 0.0171 0.0000 0.0000 0.0111 0.0000
37.3 0.0000 0.0115 0.0000 0.0000 0.0671
38 0.1062 0.0000 0.0500 0.0667 0.0572
38.2 0.0000 0.0133 0.0000 0.0000 0.0000
38.3 0.0171 0.0000 0.0000 0.0472 0.0243
39 0.0403 0.0000 0.0000 0.0250 0.0243
39.2 0.0422 0.0648 0.0115 0.0623 0.0239
39.3 0.0171 0.0000 0.0000 0.0361 0.0461
40 0.0000 0.0230 0.0115 0.0000 0.0072
40.2 0.0175 0.0115 0.0385 0.0230 0.0072
40.3 0.0256 0.0278 0.0628 0.0250 0.0000
41.2 0.0334 0.0382 0.0000 0.0484 0.0167
41.3 0.0171 0.0508 0.0243 0.0000 0.0256
42.2 0.0263 0.0267 0.0128 0.0345 0.0957
42.3 0.0427 0.0254 0.0000 0.0472 0.0171
43.2 0.0652 0.0230 0.0243 0.0369 0.0083
43.3 0.0085 0.0000 0.0000 0.0000 0.0000
44.2 0.0159 0.0139 0.0000 0.0000 0.0000 0.0510 0.0726 0.0716 0.0254 0.0500
44.3 0.0000 0.0000 0.0243 0.0000 0.0000
45.2 0.0159 0.0000 0.0243 0.0460 0.0000
46.2 0.0000 0.0115 0.0128 0.0254 0.0000
47.2 0.0000 0.0000 0.0000 0.0139 0.0000
18-19 0.0000 0.0115 0.0000 0.0000 0.0071 0.0000 0.0000 0.0115 0.0000 0.0000
20-21 0.0000 0.0115 0.0000 0.0000 0.0000
30-31 0.0000 0.0115 0.0000 0.0000 0.0000
35-36 0.0000 0.0000 0.0000 0.0139 0.0000
SEP: Sephardic Jews; NAJ: North African Jews; MEJ: Middle Eastern Jews; ASH: Ashkenazi Jews and CHU: Chuetas.
Supplementary Table 4. Forensic parameters of 32 X-Indel markers in 595 chromosomes (Sephardic Jews: 144; North African Jews: 81; Middle Eastern Jews: 78; Ashkenazi Jews: 84; Chuetas: 96 and Majorcans: 112).
Loci Population Satistical parameters Power of discrimination Mean paternity exclusion change
HET PE PI PD female PD male MEC Krüger MEC Desmarais MEC Desmarais duo
MID2637
MID3712
MID2612
MID357
Combined PE Combined PD female Combined PD male Combined MEC Desmarais Sephardic Jews 1 in 3.91E+01 1 in 2.44E+10 1 in 3.67E+06 1 in 8.29E+04
HET: heterozigosity; PE: power of exclusion; PI: paternity index; PD female: power of discrimination in females; PD male: power of discrimination in males; MEC Krüger: mean exclusion chance in trios involving mother child and putative father (Krüger et al., 1968. Dtsch Z Gerichtl Med 64:127–146); MEC Desmarais: mean exclusion chance in trios involving daughter; MEC Desmarais duo: mean exclusion chance in father/daughter or mother/son duos (Desmarais et al., 1998. J Forensic Sci 43:1046–1049).
Supplementary Table 5. Forensic parameters of 9 X-Alu markers in 569 chromosomes (Sephardic Jews: 103; North African Jews: 77; Middle Eastern Jews:
75; Ashkenazi Jews: 85; Chuetas: 140 and Majorcans: 89).
Loci Population Statistical parameters Power of discrimination Mean paternity exclusion change
HET PE PI PD female PD male MEC Krüger MEC Desmarais MEC Desmarais duo
Yb8NBC578
Sephardic Jews 0.1219 0.0121 0.5694 0.2215 0.1219 0.0572 0.1145 0.0609
North African Jews 0.1193 0.0116 0.5677 0.2172 0.1193 0.0561 0.1122 0.0596
Middle Eastern Jews 0.1245 0.0125 0.5711 0.2258 0.1245 0.0584 0.1168 0.0623
Ashkenazi Jews 0.0000 0.0000 0.5000 0.0000 0.0000 0.0000 0.0000 0.0000
Chuetas 0.0685 0.0041 0.5368 0.1299 0.0685 0.0331 0.0661 0.0342
Majorca 0.0442 0.0018 0.5231 0.0854 0.0442 0.0216 0.0432 0.0221
Ya5DP4
Sephardic Jews 0.0428 0.0017 0.5224 0.0829 0.0428 0.0210 0.0419 0.0214
North African Jews 0.0243 0.0006 0.5125 0.0477 0.0243 0.0120 0.0240 0.0121
Middle Eastern Jews 0.0000 0.0000 0.5000 0.0000 0.0000 0.0000 0.0000 0.0000
Ashkenazi Jews 0.1128 0.0105 0.5636 0.2065 0.1128 0.0532 0.1064 0.0564
Chuetas 0.0299 0.0008 0.5154 0.0585 0.0299 0.0147 0.0295 0.0150
Majorca 0.0442 0.0018 0.5231 0.0854 0.0442 0.0216 0.0432 0.0221
Ya5DP13
Sephardic Jews 0.1841 0.0256 0.6129 0.3174 0.1841 0.0836 0.1672 0.0921
North African Jews 0.1859 0.0260 0.6142 0.3200 0.1859 0.0843 0.1686 0.0929
Middle Eastern Jews 0.1009 0.0085 0.5561 0.1866 0.1009 0.0479 0.0958 0.0505
Ashkenazi Jews 0.0220 0.0005 0.5112 0.0432 0.0220 0.0109 0.0217 0.0110
Chuetas 0.2855 0.0577 0.6998 0.4487 0.2855 0.1224 0.2447 0.1427
Majorca 0.2448 0.0432 0.6621 0.3997 0.2448 0.1074 0.2148 0.1224
Combined PE Combined PD female Combined PD male Combined MEC Desmarais Sephardic Jews 1 in 1.31E+00 1 in 1.81E+01 1 in 5.09E+00 1 in 3.97E+00 North African Jews 1 in 1.38E+00 1 in 2.14E+01 1 in 5.91E+00 1 in 4.32E+00 Middle Eastern Jews 1 in 1.41E+00 1 in 2.12E+01 1 in 5.98E+00 1 in 4.27E+00 Ashkenazi Jews 1 in 1.32E+00 1 in 1.36E+01 1 in 4.53E+00 1 in 3.46E+00 Chuetas 1 in 1.34E+00 1 in 2.41E+01 1 in 5.95E+00 1 in 4.55E+00 Majorca 1 in 1.33E+00 1 in 1.67E+01 1 in 5.07E+00 1 in 3.83E+00
HET: heterozigosity. In bold significant Hady-Weinberg equilibrium p-values; PE: power of exclusion; PI: paternity index; PD female: power of discrimination in females; PD male: power of discrimination in males;
MEC Krüger: mean exclusion chance in trios involving mother child and putative father (Krüger et al., 1968. Dtsch Z Gerichtl Med 64:127–146); MEC Desmarais: mean exclusion chance in trios involving daughter;
MEC Desmarais duo: mean exclusion chance in father/daughter or mother/son duos (Desmarais et al., 1998. J Forensic Sci 43:1046–1049).
Supplementary Table 6. Forensic parameters of 12 X-STR markers in 469 chromosomes (Sephardic Jews: 99; North African Jews: 79; Middle Eastern Jews: 80; Ashkenazi Jews: 84 and Chuetas: 127).
Loci Population Statistical parameters Power of discrimination Mean paternity exclusion change
HET PE PI PD female PD male MEC Krüger MEC Desmarais MEC Desmarais duo
DXS7423
Combined PE Combined PD female Combined PD male Combined MEC Desmarais Sephardic Jews 1 in 2.83E+05 1 in 2.25E+15 1 in 1.05E+09 1 in 2.61E+08 North African Jews 1 in 3.38E+05 1 in 3.00E+15 1 in 1.27E+09 1 in 3.22E+08 Middle Eastern Jews 1 in 1.25E+05 1 in 4.09E+14 1 in 4.30E+08 1 in 9.87E+07 Ashkenazi Jews 1 in 2.33E+05 1 in 1.80E+15 1 in 8.48E+08 1 in 2.12E+08 Chuetas 1 in 1.28E+05 1 in 4.50E+14 1 in 4.34E+08 1 in 1.04E+08
HET: heterozigosity; PE: power of exclusion; PI: paternity index; PD female: power of discrimination in females; PD male: power of discrimination in males; MEC Krüger: mean exclusion chance in trios involving mother child and putative father (Krüger et al., 1968. Dtsch Z Gerichtl Med 64:127–146); MEC Desmarais: mean exclusion chance in trios involving daughter; MEC Desmarais duo: mean exclusion chance in father/daughter or mother/son duos (Desmarais et al., 1998. J Forensic Sci 43:1046–1049).
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Supplemenary Table 7. X-STR haplotypes in 149 males of the 5 Jewish populations studied (Sephardic Jews: 21; North African Jews: 29; Middle Eastern Jews: 28; Ashkenazi Jews: 24 and Chuetas: 47).
LG1 124 haplotypes
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136
137
138
Supplementary Table 9. Haplotype frequencies for MID357-MID356 and MID3690-MID3719-MID2089 in the populations studied.
SEP NAJ MEJ ASH CHU MAJ
MID357-MID356 (N=55) (N=29) (N=28) (N=23) (N=44) (N=46)
SS 0.4909 0.3448 0.4643 0.3043 0.3182 0.1957
SL 0.0000 0.0345 0.0357 0.0000 0.0000 0.0000
LS 0.1091 0.0690 0.0357 0.0870 0.0682 0.0435
LL 0.4000 0.5517 0.4643 0.6087 0.6136 0.7609
MID3690-MID3719-MID2089 (N=56) (N=29) (N=28) (N=24) (N=48) (N=46)
SSS 0.0000 0.0000 0.0000 0.0000 0.0000 0.0217
SSL 0.0000 0.0345 0.0000 0.0000 0.0000 0.0000
SLS 0.0179 0.1379 0.1071 0.0000 0.1667 0.2174
SLL 0.3393 0.2759 0.1429 0.3333 0.2292 0.0870
LSS 0.2321 0.2069 0.2143 0.0833 0.1458 0.1522
LSL 0.0357 0.0000 0.0357 0.0833 0.0000 0.0000
LLS 0.0357 0.0000 0.0000 0.0000 0.0417 0.0000
LLL 0.3393 0.3448 0.5000 0.5000 0.4167 0.5217
N: number of males; SEP: Sephardic Jews; NAJ: North African Jews; MEJ: Middle Eastern Jews; ASH: Ashkenazi Jews; CHU:
Chuetas and MAJ: Majorca.
Supplementary Table 10. FST genetic distances matrix between the Jewish populations in this study, based on 53 X-markers. P-values below diagonal. Significant values (p>0.05) are shown in bold.
SEP NAJ MEJ ASH CHU
SEP - 0.00267 0.01087 0.00397 0.02265
NAJ 0.10941 - 0.01340 0.01117 0.02256
MEJ 0.00000 0.00000 - 0.01324 0.02108 ASH 0.02822 0.00010 0.00000 - 0.02477 CHU 0.00000 0.00000 0.00000 0.00000 -
SEP: Sephardic Jews; NAJ: North African Jews; MEJ: Middle Eastern Jews; ASH: Ashkenazi Jews and CHU: Chuetas.
Darker colours correspond to greater genetic distances.
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Supplementary Table 11. Samples used in the population comparisons, number of chromosomes (N) studied and respective references
Germany 1037 Edelmann et al. (2012)
Sweden 652 Tillmar et al. (2012)
Greenland 129 Pereira et al. (2015) Native American 83 Ibarra et al. (2014) Bangladesh 56 Pereira et al. (2015)
Macau 75 Pereira et al. (2012a)
Taiwan 20 Pereira et al. (2015)
Angola and Mozambique 116 Pereira et al. (2012a)
Somalia 162 Pereira et al. (2012)
Iraq 136 Pereira et al. (2011)
Spain
Zamora 303 Pinto et al. (2015)
Majorca 112 This study
Portugal 324 Pereira et al. (2012a)
Miranda do Douro 182 Pinto et al. (2015)
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Arabs 72 Bentayebi et al. (2011)
Berbers 67 Bentayebi et al. (2011)
High Atlas 151 Athanasiadis et al. (2007) Siwa Oasis 143 Athanasiadis et al. (2007)
Egypt 33 Callinan et al. (2003)
Tunisia 168 Athanasiadis et al. (2007) Ivory Coast 87 Athanasiadis et al. (2007) African American 27 Callinan et al. (2003)
Europe 32 Callinan et al. (2003)
Italy
Consenza 30 Bentayebi et al. (2011)
Catanzaro 61 Bentayebi et al. (2011)
Calabria 164 Bentayebi et al. (2011)
Sicily 84 Bentayebi et al. (2011)
Crete 121 Athanasiadis et al. (2007)
Spain
Basque Country 138 Athanasiadis et al. (2007)
Valencia 60 Bentayebi et al. (2011)
Majorca 89 This study
Minorca 71 Bentayebi et al. (2011)
Ibiza 70 Bentayebi et al. (2011)
Supplemetary Table 12. FST distances matrices of the populations used in the MDS plots for X-Alu insertions, X-STR, and X-Indels. Darker colours correspond to greater genetic distances.
X-Alu
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
1. Sephardic Jews 0.000 2. North African Jews 0.005 0.000 3. Middle Eastern Jews 0.033 0.016 0.000 4. Ashkenazi Jews 0.006 0.013 0.019 0.000
5. Chuetas 0.016 0.026 0.015 0.027 0.000
6. Majorca 0.018 0.026 0.020 0.023 0.000 0.000 7. Minorca 0.024 0.041 0.019 0.036 0.000 0.000 0.000 8. Ibiza 0.029 0.069 0.070 0.044 0.030 0.037 0.021 0.000 9. Valencia 0.000 0.000 0.032 0.018 0.012 0.013 0.023 0.044 0.000 10. Basques 0.012 0.017 0.021 0.000 0.033 0.019 0.039 0.055 0.021 0.000 11. European 0.013 0.033 0.026 0.000 0.018 0.006 0.015 0.000 0.030 0.001 0.000 12. Calabria 0.058 0.108 0.113 0.063 0.074 0.086 0.068 0.028 0.078 0.078 0.031 0.000 13. Catanzaro 0.062 0.108 0.114 0.062 0.077 0.088 0.074 0.041 0.080 0.076 0.036 0.000 0.000 14. Cosenza 0.051 0.108 0.112 0.068 0.068 0.086 0.057 0.000 0.073 0.088 0.029 0.010 0.027 0.000 15. Sicily 0.033 0.070 0.079 0.042 0.052 0.061 0.048 0.010 0.050 0.050 0.007 0.001 0.002 0.009 0.000 16. Crete 0.016 0.048 0.047 0.008 0.030 0.027 0.028 0.009 0.034 0.016 0.000 0.023 0.027 0.019 0.012 0.000 17. Moroccan Arabs 0.001 0.000 0.014 0.012 0.013 0.007 0.023 0.047 0.000 0.010 0.013 0.091 0.093 0.090 0.054 0.033 0.000 18. Moroccan Berbers 0.011 0.040 0.035 0.022 0.020 0.028 0.017 0.033 0.016 0.025 0.024 0.047 0.052 0.034 0.035 0.016 0.031 0.000 19. Moroccan Sahrawis 0.002 0.030 0.030 0.011 0.019 0.022 0.015 0.019 0.011 0.013 0.006 0.040 0.047 0.022 0.024 0.003 0.020 0.000 0.000 20. Tunisia 0.021 0.012 0.000 0.008 0.021 0.023 0.025 0.051 0.026 0.010 0.009 0.088 0.090 0.085 0.054 0.028 0.009 0.026 0.017 0.000 21. High Atlas 0.013 0.046 0.050 0.017 0.039 0.053 0.040 0.033 0.028 0.032 0.027 0.041 0.047 0.024 0.031 0.014 0.043 0.000 0.000 0.034 0.000 22. Siwa oasis 0.018 0.054 0.051 0.020 0.037 0.046 0.035 0.035 0.032 0.031 0.025 0.047 0.054 0.027 0.040 0.013 0.047 0.000 0.000 0.037 0.000 0.000 23. Egypt 0.035 0.073 0.041 0.028 0.020 0.026 0.007 0.009 0.050 0.032 0.000 0.011 0.014 0.010 0.011 0.000 0.053 0.000 0.000 0.031 0.013 0.005 0.000 24. Ivory Coast 0.273 0.281 0.240 0.275 0.246 0.276 0.245 0.340 0.258 0.285 0.327 0.333 0.327 0.340 0.334 0.302 0.290 0.196 0.231 0.264 0.242 0.230 0.238 0.000 25. African Americans 0.215 0.209 0.192 0.227 0.200 0.225 0.201 0.273 0.192 0.229 0.260 0.258 0.250 0.274 0.252 0.244 0.216 0.155 0.181 0.204 0.202 0.197 0.190 0.073 0.000 26. Aymaras 0.227 0.283 0.251 0.241 0.210 0.250 0.197 0.251 0.230 0.266 0.270 0.216 0.215 0.210 0.245 0.223 0.279 0.129 0.161 0.253 0.159 0.144 0.137 0.155 0.182 0.000 27. Quechuas 0.225 0.278 0.245 0.235 0.207 0.241 0.194 0.254 0.227 0.257 0.266 0.224 0.222 0.219 0.251 0.221 0.274 0.127 0.159 0.249 0.161 0.142 0.136 0.133 0.173 0.000 0.000 28.Asia 0.168 0.224 0.219 0.191 0.181 0.213 0.174 0.207 0.170 0.212 0.226 0.174 0.174 0.162 0.195 0.178 0.224 0.085 0.111 0.212 0.109 0.097 0.119 0.143 0.146 0.005 0.007 0.000
X-STR
