Genetics of the Peloponnesean populations and the theory of the extinction of the Medieval Peloponnesean Greeks
SUPPLEMENTARY INFORMATION
Supplementary Figures:
Supplementary Figure 1. Locations of the Populations listed in Supplementary Table 2.
Supplementary Figure 2. Comparisons of Peloponneseans with non –European populations.
Supplementary Figure 3. Testing the hypothesis of Armenian ancestry of Peloponneseans.
Supplementary Figure 4. Unique genetic structure of the populations of Mani.
Supplementary Figure 5. Testing the hypothesis of Mardaitic origin of Maniots.
Supplementary Figure 6. Unique genetic structure of the population of Tsakonia.
Supplementary Tables:
Supplementary Table 1. Districts of origin of the subjects
Supplementary Table 2. Populations used in this study
Supplementary Table 3. IBD Shared between Peloponnesean populations
Supplementary Table 1. Districts of origin of the subjects
Achaea / 25 / 25
Αrgolis / 16 / 16
Αrcadia / 15 / 13
Elis / 24 / 24
Corinthia / 16 / 16
Laconia / 26 / 25
Messenia / 26 / 26
East Tayetos / 23 / 23
West Tayetos / 24 / 24
Deep Mani / 22 / 22
Τsakonia / 24 / 24
TOTAL 241 238
Supplementary Table 2. Populations used in this study1,#.
Population / Region / Samples / ReferenceBelarusian / East Europe / 8 / 1
Belorusians / East Europe / 9 / 2
Russia_A / East Europe / 21 / 3
Russian / East Europe / 25 / 6
Russians / East Europe / 1 / 4
Ukranians / East Europe / 20 / 5
Estonians / North Europe / 15 / 4
Finns / North Europe / 25 / 3
Lithuanians / North Europe / 10 / 2
Swedish / North Europe / 18 / 7
German / Central Europe / 13 / 8
Hungarians / Central Europe / 41 / 3
Polish / Central Europe / 17 / 7
Danes / West Europe / 43 / 3
French / West Europe / 29 / 6
Irish / West Europe / 19 / 3
Orcadian / West Europe / 16 / 6
Basque / SW Europe / 24 / 6
IBS (Iberians)2 / SW Europe / 107 / 9
Spaniards / SW Europe / 12 / 2
Andalusia2 / SW Europe / 9 / 10
Italian / South Europe / 13 / 6
Sardinian / South Europe / 28 / 6
Tuscan / South Europe / 8 / 6
Sicily2 / South Europe / 20 / 12
TSI (Italians) / South Europe / 107 / 9
Veneto2 / South Europe / 10 / 11
Crete2 / SE Europe / 129 / 11,12
Dodecanese2 / SE Europe / 20 (10) / 11,12
Peloponnese2,* / SE Europe / 238 (229) / 13
East Rumelia2,3 / SE Europe / 12 / 12
Macedonia2,3 / SE Europe / 22 / 12
Puglia2,3 / SE Europe / 14 / 13
Serbia2 / SE Europe / 20 / 12
Ashkenazi / Europe / 23 / 3
CEU / Europe / 99 / 9
Pontos2 / Asia Minor / 49 / 13
Cappadocia2 / Asia Minor / 10 / 12
Asia Minor2 / Asia Minor / 49 (31) / 13
Abhkasians / Caucasus / 20 / 5
Adygei / Caucasus / 20 / 3
Adygei / Caucasus / 16 / 6
Armenians / Caucasus / 16 / 5
Chechens / Caucasus / 20 / 5
Georgian / Caucasus / 10 / 7
Georgians / Caucasus / 20 / 2
Kumyks / Caucasus / 14 / 5
Altaians / Siberia / 3 / 4
Dolgans / Siberia / 1 / 4
Evens / Siberia / 2 / 4
Selkups / Siberia / 7 / 4
Yakut / Siberia / 21 / 3
Iranians / Middle East / 20 / 2
Turkmens / Middle East / 15 / 5
Uzbeks / Middle East / 4 / 4
Druze / Near East / 47 / 6
Jordanians / Near East / 19 / 2
Maronites / Near East / 10 / 13
Lebanese / Near East / 7 / 2
Palestinian / Near East / 51 / 6
Syrians / Near East / 16 / 2
Kurds / Near East / 6 / 5
Bedouin / Arabia / 48 / 6
Saudis / Arabia / 20 / 2
Yemenese / Arabia / 10 / 2
Yemenites / Arabia / 37 / 3
Ethiopians / East Africa / 31 / 3
Mozabite / East Africa / 30 / 6
Algeria / North Africa / 19 / 10
Egypt / North Africa / 19 / 10
Libya / North Africa / 17 / 10
Morocco_N / North Africa / 18 / 10
Morocco_S / North Africa / 16 / 10
Sahara_Occ / North Africa / 18 / 10
Tunisia / North Africa / 18 / 10
1 Sample sizes are after QC. For our PCA analyses, the following populations were combined: Russian [6] and Russians [4] into Russia; Adygei [3] and Adygei [6] into Adygei; Belarusian [1] and Belorusians [2] into Belarusian; Georgian [7] and Georgians [2] into Georgian.
2 Population was included in IBD analysis. Population sizes in parentheses are the number of samples included in the IBD analysis.
3 Population was included in IBD analysis but not in PCA analysis.
#In the comparisons of the Peloponneseans with non-Greek populations, the number of commons SNPs in our analyses ranged between 76,000 and 277,000, depending on the particular datasets that were merged and the genotyping platform of each dataset. When the Peloponneseans were compared with other Greek populations that we had genotyped in the past, the number of common SNPs in our analyses was over 1,000,000.
*Of the 241 Peloponneseans 238 were used for PCA analysis and 229 for IBD analysis. Data from 3 individuals were excluded from both the PCA and IBD analyses because they were outliers. Data from 9 individuals were not included in the IBD analysis because they entered the study after the IBD analysis had been completed.
References:
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[13] Present study.
Supplementary Table 3. IBD Shared between Peloponnesean populations
IBD Shared With Deep Mani (n=22)1
Achaea / 21 / 44.2% / 3.0 (1.1) / 1.8
Arcadia / 13 / 57.3% / 3.0 (1.1) / 2.6
Argolis / 16 / 38.4% / 3.1 (1.2) / 1.8
Corinthia / 16 / 43.2% / 3.0 (1.3) / 1.8
East Tayetos / 23 / 94.3% / 3.7 (1.9) / 35.2
Elis / 23 / 53.0% / 3.2 (1.3) / 2.7
Laconia / 26 / 73.8% / 3.4 (1.5) / 11.3
Messenia / 21 / 54.1% / 3.2 (1.2) / 2.8
Northern Tsakonia / 9 / 65.2% / 3.2 (1.3) / 3.9
Southern Tsakonia / 15 / 69.1% / 3.2 (1.4) / 4.2
West Tayetos / 24 / 96.2% / 3.6 (1.8) / 36.9
IBD Shared With Southern Tsakonia (n=15)1
Achaea / 21 / 60.0% / 3.2 (1.3) / 3.3
Arcadia / 13 / 78.5% / 3.4 (1.5) / 5.1
Argolis / 16 / 65.8% / 3.4 (1.6) / 4.2
Corinthia / 16 / 70.4% / 3.1 (1.2) / 3.5
Deep Mani / 22 / 69.1% / 3.2 (1.4) / 4.2
East Tayetos / 23 / 89.0% / 3.2 (1.4) / 7.0
Elis / 23 / 64.1% / 3.2 (1.2) / 3.2
Laconia / 26 / 88.0% / 3.5 (2.0) / 9.7
Messenia / 21 / 64.4% / 3.2 (1.3) / 3.5
Northern Tsakonia / 9 / 100.0% / 4.4 (2.7) / 94.1
West Tayetos / 24 / 82.8% / 3.2 (1.4) / 5.3
1 All values are based on identity by descent (IBD) segments in cross-population pairs, where a cross-population pair is a pair of individuals such that one individual is from Deep Mani or Southern Tsakonia and the other is from the listed population.
2 “Proportion of Pairs with IBD” is the proportion of possible cross-population pairs that share at least one 2 cM IBD segment. A higher proportion indicates that more individuals in the two populations share some IBD with each other.
3 “Mean (SD) Length” is the average and standard deviation of the segment lengths. Longer segments tend to have been inherited from more recent common ancestors.
4 “Mean Pairwise IBD (cM)” is the average amount of IBD shared between an individual in Deep Mani or Southern Tsakonia and an individual in the specified partner population. This is calculated as the sum of the lengths of IBD segments shared between a pair of individuals in the two populations, then divided by the number of unique pairs of individuals in the two populations and by four times the genome length (for the four ways to pair chromosomes between two people). We excluded pairs of individuals who shared more than 40% IBD, i.e., half siblings, full siblings and avuncular pairs.