Table S1. Population names and geographic origin of Y chromosome samples used in this study. Region/Population N Country Lat Long Source Africa (N=26) Baka-Pygmies 3 Cameroon 2.9 14.3 (Lachance et al. 2012) Bakola-Pygmies 1 Cameroon 2.9 14.3 (Lachance et al. 2012) Bedzan-Pygmies 1 Cameroon 2.9 14.3 (Lachance et al. 2012) Congo-Pygmies 3 Congo 0.9 15.9 This study Hadza 5 Tanzania -3.7 35.1 (Lachance et al. 2012) Luhya 3 Kenya 0.6 34.8 (Drmanac et al. 2010) Maasai 2 Kenya -1.3 35.3 (Drmanac et al. 2010) Sandawe 5 Tanzania -4.9 35.8 (Lachance et al. 2012) Yoruba 3 Nigeria 7.4 3.9 (Drmanac et al. 2010) Near East and the Caucasus (N=45) Abkhazians 2 Georgia 43.1 40.6 This study Arab-Christian 3 Israel 32.9 35.3 This study Arab-Muslim 2 Israel 32.8 35.2 This study Arabs 2 Saudi Arabia 33.8 35.6 This study Armenians 6 Armenia 40.2 44.5 This study Assyrians 3 Armenia 40.1 44 This study Avars 2 Russia 42.2 47 This study Azerbaijanis 2 Azerbaijan 40.1 47.5 This study Balkars 1 Russia 43.7 44.2 This study Circassians 2 Russia 44.7 40 This study Druze 2 Israel 32.8 35.2 This study Georgians 1 Georgia 43 41.4 This study Georgians-Imeretins 1 Georgia 41.8 44.7 This study Iranians 4 Iran 35.1 51.2 This study Jordanians 2 Jordan 31.9 35.9 This study Kabardins 2 Russia 43.5 43.6 This study Kumyks 1 Russia 43 47.5 This study Lebanese 1 Lebanon 33.8 35.6 This study Lezgins 2 Russia 41.6 48.3 This study North-Ossetians 2 Russia 43.2 43.9 This study Tabasarans 2 Russia 42 47.9 This study Europe (N=81) Albanians 3 Albania 41.3 19.8 This study Baptized-Tatars 1 Russia 55.9 51.2 This study Bashkirs 2 Russia 51.9 58.2 This study Belarusians 3 Belarus 52.2 24.4 This study Central-Russians 3 Russia 57.8 28.3 This study Chuvashes 1 Russia 53.7 54.7 This study Zaporizhsky Cossacks 2 Ukraine 47.8 35.2 This study Kuban Cossacks 2 Russia 45 38.7 This study Bosnia- Croats 3 43.3 17.8 This study Herzegovina Estonians 5 Estonia 59 22.8 This study Personal Genome Project French 1 France 48.9 2.4 (PGP) Germans 1 Germany 52.5 10.1 This study Hungarians 2 Ukraine 48 24.3 This study Italians 3 Italy 43.6 11 (Drmanac et al. 2010) Karelians 3 Russia 61.2 32.4 This study Komis 2 Russia 62.6 58 This study Latvians 2 Latvia 56.9 24.5 This study Lithuanians 1 Lithuania 55.3 24 This study Maris 3 Russia 55.4 56 This study Mishar-Tatars 1 Russia 54.8 51.4 This study Moldavians 1 Moldova 47.1 28.7 This study Mordvins 3 Russia 54.1 43.3 This study North-Russians 2 Russia 64.7 43.4 This study NW-Europeans 5 Europe 53.4 6.5 (Drmanac et al. 2010) Poles 1 Poland 52.2 21 PGP Portuguese 1 Portugal 38.7 -9 PGP Saami 3 Norway 69.9 25.2 This study Swedes 2 Sweden 59.4 18 This study Tatars 2 Russia 54.6 53.8 This study Udmurts 3 Russia 57.3 54.1 This study Ukrainians 7 Ukraine 51.5 31.4 This study Ukrainians 2 Ukraine 51.5 31.4 PGP British 2 United Kingdom 51.5 -0.1 PGP Vepsas 3 Russia 61.4 34.8 This study Central Asia (N=20) Ishkasim 2 Tajikistan 37 71.7 This study Rushan-Vanch 2 Tajikistan 38.5 71.7 This study Shugnan 1 Tajikistan 37.5 72.4 This study Tajiks 1 Tajikistan 38.4 68.9 This study Kazakhs 3 Kazakhstan 47.5 61.5 This study Kyrgyz 7 Kyrgyzstan 42.2 77 This study Turkmens 3 Uzbekistan 42.6 58.9 This study Uzbek 1 Uzbekistan 41 70.9 This study South Asia (N=25) Asur 1 India 23.7 85.3 This study Balija 1 India 14.7 77.6 This study Bengali 1 India 22.9 88.3 This study Brahmin 2 India 25.3 83.1 This study Bangladeshi 2 Bangladesh 23.7 90.4 This study Gond 1 India 22.2 79.9 This study Gujaratis 3 India 23.5 72.8 (Drmanac et al. 2010) Gupta 1 India 25.5 82.9 This study Ho 1 India 24.1 84.2 This study Kapu 1 India 17.7 83.2 This study Kol 1 India 24.5 83.2 This study Kshatriya 1 India 25.7 82.7 This study Kurmi 1 India 25.2 83 This study Madhya-Pradesh 1 India 23.3 77.1 This study Malayan 1 India 10.4 76.7 This study Orissa 1 India 20.5 85.9 This study Punjabi 1 India 17 75.9 This study Nepalese 2 Nepal 26.8 87.3 This study Santhal 1 India 22.8 85.7 This study Thakur 1 India 27 77.2 This study East and Southeast Asia (N=42) Aeta 3 Philippines 17.6 121 This study Agta 3 Philippines 17.8 121.2 This study Bajo 4 Indonesia -4 122.6 This study Batak 3 Philippines 10.5 119.5 This study Burmese 8 Myanmar 16.4 95.9 This study Chinese 2 China 32 120.3 PGP Dusun 3 Brunei 4.8 114.6 This study Han 1 China 39.9 116.4 (Drmanac et al. 2010) Igorot 1 Philippines 17.1 121 This study Japanese 1 Japan 35.7 139.7 (Drmanac et al. 2010) Lebbo 4 Indonesia 1.7 117.2 This study Murut 5 Brunei 4.5 114.7 This study Vietnamese 4 Vietnam 21 105.9 This study Oceania (N=6) Koinanbe 3 Papua New Guinea -5.5 144.6 This study Kosipe 3 Papua New Guinea -8.5 147.2 This study Siberian and Mongolia (N=62) Altai-Kizhi 3 Russia 51.3 85.4 This study Altai-Telengit 1 Russia 50.8 88.3 This study Buryats 12 Russia 53.8 102.8 This study Chukchis 2 Russia 64.7 177.5 (Clemente et al. 2014) Eskimo 2 Russia 64.5 -172.9 (Clemente et al. 2014) Evenks 3 Russia 58.9 128.7 This study Evens 8 Russia 65.3 130 This study Kets 2 Russia 62.5 86.3 This study Koryaks 12 Russia 59.1 159.9 (Clemente et al. 2014) Forest-Nenets 1 Russia 64.9 77.8 This study Tundra-Nenets 2 Russia 67 78.2 This study Selkups 1 Russia 65.7 87 This study Shor 1 Russia 52.8 87.9 This study Tuvinians 2 Russia 51.5 92.8 This study Yakuts 4 Russia 62.3 132 This study Mongol-Khalkh 1 Mongolia 45.7 106.3 This study Mongol-Khalkh 4 Mongolia 43.5 104.3 This study Mongol-Zakhchin 1 Mongolia 48 91.6 This study Andes (N=13) Calchaquíes 3 Argentina -25.1 -66.2 This study Colla 8 Argentina -24.2 -66.3 This study Wichí 2 Argentina -23.2 -64.1 This study Total 320 Samples not used in geographically explicit analyses (N=153) Jews (N=18) Ashkenazi-Jews 2 France NA NA This study Cochin-Jews 1 India NA NA This study Ethiopian-Jews 1 Ethiopia NA NA This study Georgian-Jews 1 Georgia NA NA This study Iranian-Jews 1 Iran NA NA This study Iraqi-Jews 3 Iraq NA NA This study Kurdistan-Jews 1 Iraq NA NA This study Moroccan-Jews 1 Morocco NA NA This study Mumbai-Jews 2 India NA NA This study Turkey-Jews 1 Turkey NA NA This study Uzbekistan-Jews 2 Uzbekistan NA NA This study Yemenite-Jews 2 Yemen NA NA This study Others (N=33) African-Americans 3 USA (Drmanac et al. 2010) Australian 2 Australia -17.1 132.5 This study CEPH-pedigree 7 Europe NA NA (Drmanac et al. 2010) Estonian-pedigree (6 excluded) 8 Estonia 59 22.8 This study Estonians 2 Estonia 59 22.8 PGP German duplicate sequence 1 Germany 52.5 10.1 This study Komi duplicate sequence 1 Russia 62.6 58 This study Latino/Hispanic 1 Colombia NA NA PGP Mbo 2 Cameroon 5.7 9.9 This Study Mexicans 2 USA NA NA (Drmanac et al. 2010) Murut duplicate sequence 1 Brunei 4.5 114.7 This study Puerto-Ricans 2 Puerto_Rico NA NA (Drmanac et al. 2010) Ukrainians duplicate sequence 1 Ukraine 51.5 31.4 PGP Geographic ancestry not known N.A. NA NA PGP (N=102) Total 473 (456 without 13 relatives and 4 duplicates) Note: The total number of newly reported sequences, excluding 6 relatives and 3 duplicates, is 299, including 16 released under accession number PRJEB7258 (Clemente et al. 2014). Table S2. The effect of different quality filters on the number of Y chromosome SNPs in 475 male samples. L - total length of chrY considered, including variable and non-variable positions; SNPs - total number of binary SNPs; Recurrent – number of SNPs that occur in at least three unique lineages; FS - average number of father – son differences in 24 Dutch father-son pairs, 6 Estonian father-son pairs and 1 brother-brother pair, including cases where father has an ancestral allele and the son or one of the brothers has a derived allele.