average +2SD −2SD sdThres nCap Y chromosome no rmalized c overage in the region 28457493 − 28806243 b p, sdThres= 0.4 nCap= 25 1 0 −1 −2

log10 C overage −3

Y chromosome no rmalized c overage in the region 28457493 − 28806243 b p, sdThres= 0.8 nCap= 80 1 0 −1 −2

log10 C overage −3 28.46 28.54 28.62 28.7 28.78 Y chromosome position (Millions of base pairs)

Figure S1. An example of a Y chromosome region filtering by local unique sequence cov- erage (UC). Combinations of filtering parameters (sdThres/nCap) applied to the same chrY region – upper panel 0.4/25; lower panel 0.8/80. In a sample of 307 Y chromosomes we nor- malized each individual’s average UC in 1000 base pair (bp) windows (sliding by 50 bps) to that of the individual’s average UC on chrX, then calculated the log10 average and standard deviation (SD) across all individuals. We then established two parameters for excluding sequence stretches of poor unique coverage: 1) sdThres – wide SD margins (exceeding a set value) indicate that coverage varies between individuals in the region; 2) nCap – very low or very high coverage (+2 SD < 0 or -2 SD > 0) in a set number of consecutive windows suggests a deletion/duplication in the region. Figure S2. The effect of different combinations of nCap/sdThres on the average number of sites retained. The effect of different combinations of nCap/sdThres (filter b) on the sequence length (average number of sites) retained. Within 10.79 MB of chrY regions we applied a re-mapping filter, removed individual bases with less than 5x unique coverage and then tested the effect of nCap/sdThres combina- tions on the average number of nucleotides in the sample of 307 Ychromosomes for which coverage data was available. The combination of these two parameters reaches a plateau approximately at nCap=75/sdThres=0.75 where the gains in retain- ing the sequence length from further relaxing the parameters is negligible – the difference between nCap100/sdThres1.0 and nCap300/sdThres 3.0 is only 0.01%. To retain at least 80% of the original data we picked a point between nCap75/sdThres0.75 and nCap100/sdThres1.0 – and made final analyses with the parameters nCap80/sdThres0.8. Dashed line marks the 10.79MB, orange line marks the point at which 80% of the original sequence length was retained. 25 Kyrgyz_Tdj; KyrgzTJ2 24 Kyrgyz_Tdj; KyrgzTJ3 23 Kyrgyz_Tdj; KyrgzTJ1 26 Altaians; Altai4 22 Altaians; Altai3 21 Ishkasim, Tajiks; Ishk2 27 Assyrians; Assyr1 20 Rushan-Vanch, Tajiks; RVnch2 30 Kyrgyz; Kyrgz3 29 Kyrgyz; Kyrgz4 28 Kyrgyz; Kyrgz2 Altaians; Altai5 36 Kazakhs; Kaz1 19 35 West-Bengal; Beng2 34 Gujaratis; GIH_2 37 Gupta, Uttar-Pradesh; Gupta1 18 33 Gujaratis; GIH_4 38 Middle-caste, Orissa; OrMc1 32 Kurmi, Uttar-Pradesh; Kurmi1 31 Ishkasim, Tajiks; Ishk1 Cossacks; Cosk2 17 Iranians; Iran3 42 Circassians; Cirkas3 41 Shugnan, Tajiks; Shugn1 40 Bashkirs; Bashk4 43 Azerbaijanis; Azerb24 39 Rushan-Vanch, Tajiks; RVnch1 Balkars; Balkar2 52 Russians-North; RusPi2 51 Komis; Komi2 50 Russians-West; RusPs2 53 Karelians; Karel2 49 Karelians; Karel1 R1a1’3 48 Ukrainians_west; UkrnW2 16 47 Ukrainians; Ukr7 54 Ukrainians_east; UkrnE1 Russians-Central; RusRz1 46 60 Cossacks_Kuban; CoskK2 59 Hungarians; Hun_3 56 Ukrainians_north; UkrN1 55 58 Ukrainians_east; UkrnE2 57 Mordvins; Mord2 45 Ukrainians_east; UkrnE3 Ukrainians_west; UkrnW3 62 Circassians; Cirkas2 44 Cossacks; Cosk1 61 Tatars; Tatar3 64 Swedes; Swe2 63 Swedes; Swe1 Saami; Saami6 R1 15 75 Colla, Andean-HA; AndT13 74 Colla, Andean-HA; AndT7 73 Germans; Ger3 72 Portugese; Port1 76 Mordvins; Mord1 71 French; Fra1 78 NW-Europeans; CEU_3 70 77 Christian-Arabs-Israel; CArab2 69 Italians; TSI_2 79 NW-Europeans; CEU_4 United-Kingdom, Britans; UK1 R 14 68 NW-Europeans; CEPH_13 67 Ukrainians_west; UkrnW1 82 Armenians; Armen1 81 Assyrians; Assyr3 66 Tabasarans; Tabas17 80 Avars; Avar9 65 83 Mongolians; Mong4 Bashkirs; Bashk3 Tajiks; Tajik1 R1b 87 Brahmin, Uttar-Pradesh; Brahm2 85 Thakur, Uttar-Pradesh; Thak1 R2 86 Gujaratis; GIH_1 84 Santhal, Jharkhand; Santh1 Brahmin, Uttar-Pradesh; Brahm1 98 Colla, Andean-HA; AndS47 96 Colla, Andean-HA; AndS23 P1 97 Colla, Andean-HA; Colla4 13 95 Andean-Cachi; Cachi5 94 Colla, Andean-HA; AndT12 93 Andean-Cachi; Cachi4 100 Wichi, Andean-LA; Wichi3 99 Wichi, Andean-LA; Wichi4 92 Colla, Andean-HA; AndS41 Q1a 91 101 Andean-Cachi; Cachi3 Colla, Andean-HA; AndS11 90 Eskimo; Esk2 104 Kets; Ket1 103 Selkups; Selkp3 12 Q1 89 Q1c 102 Kets; Ket2 P# Uzbek; Uzbk3 105 Croats; croat11 Brahmin, Nepalese; NepBr1 Q 88 110 Koryaks; KrkG55 109 Koryaks; KrkG11 108 Koryaks; KrkG13 107 Koryaks; KrkG14 11 106 Murut; Murut19 112 Turkmens; TrkUzb2 MR 111 Turkmens; TrkUzb1 Q2 Turkmens; TrkUzb3 Agta; Agta1 116 Bajo; Bajo17 114 Lebbo; Lebb2 115 Aeta; Aeta2 113 Aeta; Aeta1 118 Kosipe; Kosip1 117 Kosipe; Kosip3 Kosipe; Kosip2 137 Buryats; Bur336 MS 136 Buryats; Bur406 135 Kazakhs; Kaz3 134 Mongolians; Mong6 133 Mongolians; Mong1 Mongolians; Mong2 131 127 Koryaks; KrkG233 130 Chukchis; Chuk5 129 Eskimo; Esk3 128 Koryaks; KrkG152 126 132 Chukchis; Chuk9 Koryaks; KrkG294 140 Karelians; Karel3 139 Estonians; Est17 138 Vepsas; Veps2 Cossacks_Kuban; CoskK1 125 146 Latvians; Lat2 145 Estonians; Est2 144 Russians-West; RusPs1 143 Latvians; Lat3 142 Evens_Magadan; Evn31 10 149 Estonians; Est6 147 Estonians; Est21 NR 124 141 148 Saami; Saami5 Saami; Saami4 Russians-North; RusPi1 153 Yakuts; YakM1 152 Yakuts_Sakha; YakS8 N3a 123 151 Yakuts_Kr; YakK3 150 Evens_Sakha; EvenS2 Lebanese; Lebn1 N3# 122 156 Maris; Mari1 155 Udmurds; Udmrd4 154 Udmurds; Udmrd2 Maris; Mari2 Shor; Shor1 Africa 162 Evenks; Evk55 161 Yakuts_Kr; YakK4 121 160 Mongolians; Mong5 163 Tuvinians; Tuva2 159 Tuvinians; Tuva1 165 Forest-Nenets; NenetF3 N# 164 Tundra-Nenets; NentT2 Near–East 158 Tundra-Nenets; NentT1 120 N2a1 157 Evens_Sakha; EvenS3 167 Maris; Mari3 166 Vepsas; Veps4 K# Udmurds; Udmrd3 9 N4 Han; CHB_4 Europe 174 Dusun; Dusun12 172 Dusun; Dusun7 173 Lebbo; Lebb1 171 Gond, Madhya-Pradesh; Gond1 NO 119 176 Vietnamese_south; VietS2 O2a1’2 170 175 Vietnamese_south; VietS1 South–Asia Ho, Jharkhand; Ho1 177 Vietnamese_north; VietN4 Vietnamese_south; VietS3 169 181 Batak; Batak1 180 Murut; Murut13 179 Murut; Murut6 O1 178 Batak; Batak2 Central–Asia Agta; Agta2 182 Agta; Agta3 O 168 189 Burmese; Burm4 188 Burmese; Burm3 187 Burmese; Burm20 O3a1 186 Burmese; Burm8 East & Southeast–Asia 185 Burmese; Burm12 184 Burmese; Burm15 190 Bajo; Bajo21 O3 183 Batak; Batak3 Igorot; Igrt1 192 Tatars; Tatar2 Siberia LT 191 Druze; ISR34 IT 8 Muslim-Arabs-Israel; MArab1 203 Armenians; Armen3 201 Muslim-Arabs-Israel; MArab2 202 Saudi-Arabians; Saudi1 200 Saudi-Arabians; Saudi2 199 Druze; ISR35 Oceania 205 Albanians; Alban3 204 Armenians; Armen2 J1b 198 Jordanians; Jord2 197 Armenians; Armen5 Armenians; Armen4 196 208 Avars; Avar1 Andes J1 J1a 207 Kumyks; Kumk2 195 206 Tabasarans; Tabas4 Lezgins; Lezg2 Azerbaijanis; Azerb13 214 Kyrgyz; Kyrgz1 213 Iranians; Iran1 J 194 212 Kabardins; Kabard3 211 Kapu, Andhra-Pradesh; Kapu1 216 Georgians; Georg2 J2a 210 215 Babtized-Tatars; Kryash4 Assyrians; Assyr4 J2 209 Abkhazians; Abkhaz6 218 Jordanians; Jord1 7 J2b 217 Armenians; Armen7 HT Albanians; Alban2 IJ 193 225 Belarusians; BelaR1 224 Belarusians; BelaR3 223 Chuvashes; Chuv1 222 Lithuanians; Lit2 221 Vepsas; Veps3 227 Croats; croat12 I2’3 220 226 Croats; croat13 Ukrainians; Ukr9 Georgians; Georg1 I 219 231 Mordvins; Mord3 230 Komis; Komi1 229 NW-Europeans; CEPH_15 I1 228 Belarusians; BelaR2 233 Italians; TSI_4 GT 232 Hungarians; Hun2 6 NW-Europeans; CEU_2 240 Dhaka-mixed-popul; Bangl1 238 Kol, Uttar-Pradesh; Kol1 239 Asur, Jharkhand; Asur1 H1a 237 Kshatriya, Uttar-Pradesh; Khsat1 236 Burmese; Burm14 242 Middle-caste, Punjab; PuMc1 235 241 Dhaka-mixed-popul; Bangl2 Balija-Middle-caste, Andhra-Pradesh; Balija1 H 234 Burmese; Burm10 Malayan, Kerala; Mal1 247 North-Ossetians; NOsset2 246 North-Ossetians; NOsset6 245 Abkhazians; Abkhaz5 244 Moldavians; Mold3 G2a 243 Lezgins; Lezg3 249 Kabardins; Kabard4 248 Poles; Pole5 Iranians; Iran2 259 Evens_Magadan; EvenM1 258 Evens_Magadan; EvenM3 CT 257 Evens_Sakha; EvenS1 5 260 Evens_Magadan; EvenM2 256 Evens_Magadan; Evn21 262 Buryats; Bur530 Evenks; Evk14 C3c 255 261 Mongolians; Mong3 265 Koryaks; koryak42 254 264 Koryaks; koryak33 263 Koryaks; Krk119 253 Evenks; Evnk2 Koryaks; Krk116 C3c’h 252 Kazakhs; Kaz2 266 Altaians; Altai6 Koryaks; KrkG3 272 Buryats; Bur383 271 Buryats; Bur578 C3 251 270 Buryats; Bur11 273 Buryats; Bur361 269 Buryats; Bur350 274 Buryats; Bur318 268 Buryats; Bur398 C3f1 267 275 Buryats; Bur2 Buryats; Bur355 C Chinese_PGP, Chinease; Chn1 250 281 Aeta; Aeta3 280 Murut; Murut5 279 Murut; Murut3 282 Lebbo; Lebb3 DT 278 Lebbo; Lebb4 4 277 Low-caste, Madhya-Pradesh; MPlc1 Dusun; Dusun8 276 286 Koinanbe; Koinb3 285 Koinanbe; Koinb1 284 Koinanbe; Koinb2 C2 283 Bajo; Bajo2 C1’7 Bajo; Bajo19 296 Italians; TSI_3 294 United-Kingdom, Britans; UK2 295 Albanians; Alban1 293 Estonians; Est4 292 Mishar-Tatars; TatarM1 E2a 297 Maasai; MKK_1 291 Maasai; MKK_3 290 Iranians; Iran4 299 Christian-Arabs-Israel; CArab3 E2b 298 Christian-Arabs-Israel; CArab1 Sandawe; Sandw2 BT E1’2 300 Sandawe; Sandw3 289 305 Bakola-Pygmies; BakoPy1 3 304 Hadza; Hadza1 303 Baka-Pygmies; BakaPy2 302 Luhya; LWK_4 E# 306 Congo-pygmies; CongPy1 288 Yoruba; YRI_3 E1a 301 310 Sandawe; Sandw1 309 Luhya; LWK_2 308 Luhya; LWK_3 287 307 Bedzan-Pygmies; BedzPy1 Yoruba; YRI_1 AT# Yoruba; YRI_12 312 Chinese_PGP, Chinease; Chn2 2 DE D 311 Tamang, low-caste; NplTA1 Japanese; JPT_1 318 Hadza; Hadza5 316 Hadza; Hadza2 317 Hadza; Hadza3 315 Sandawe; Sandw5 Baka-Pygmies; BakaPy3 1 B4’5 314 319 Baka-Pygmies; BakaPy1 B2’5 313 320 Sandawe; Sandw4 Hadza; Hadza4 Congo-pygmies; CongPy3 A2 321 Congo-pygmies; CongPy6 A00 Ethiopian-Jews; ISR07 Mbos; GRC13292545 322 Mbos; GRC13292546 250000 225000 200000 175000 150000 125000 100000 75000 50000 25000 0

Figure S3. Y chromosome phylogeny based on BEAST analyses. Sample names corre- spond to those reported in Table S6. Age and posterior support estimates for each num- bered clade are reported in Table S7. Six clades that showed significant (p_Delta1 <0.05) phylogenetic asymmetry in SymmeTree analyses are highlighted by # after the haplogroup label. Africa Near East 108 108

105 105 e e N N

107 107

106 106 150 100 50 0 60 40 20 0 Thousands of Years ago Thousands of Years ago Europe Central Asia 108 108

105 105 e e N N

107 107

106 106 60 40 20 0 60 40 20 0 Thousands of Years ago Thousands of Years ago South Asia Southeast & East Asia 108 108

105 105 e e N N

107 107

106 106 60 40 20 0 60 40 20 0 Thousands of Years ago Thousands of Years ago Siberia Andes 108 108

105 105 e e N N

107 107

106 106 60 40 20 0 60 40 20 0 Thousands of Years ago Thousands of Years ago

Figure S4A. NRY and mtDNA Bayesian Skyline Plots for each geographical region. The 95% CI for mtDNA BSPs are represented in red and for NRY in yellow. The BSPs were created using a piecewise-linear coalescence model. 2.0 Africa Andes 1.8 Central Asia Europe 1.6 Near East S-E&E Asia 1.4 Siberia South Asia 1.2 Ne

1.0

0.8 Relative

0.6

0.4

0.2

0.0 012345678910111213 Thousands of Years Ago

Figure S4B. Variation of Y chromosome effective population size over the past 13 kya. The regional NRY BSPs presented in Figure S4A are shown relative to their values at 12 kya. 16 Nf/Nm

12

8

4

0102030405060708090100110120130140150 Thousands of Years Ago

Figure S5 – The temporal dynamics of the ratio of female (Nf) and male (Nm) effective population size in the last 140KY. The ratios of the global accumulative Ne estimates of mtDNA (Nf) and Y chromosome (Nm), as presented in Figure 2, are plotted against the time (in thousands of years) back from the present (0). The BSPs estimates of Ne were obtained in BEAST using a piecewise-linear coalescence model. ) 5 6 Autosomal (predicted) mtDNA 5 NRY

4

3

Effective Population Size (x 10 Size Population Effective 2

1

0 140 120 100 80 60 40 20 0 Thousands of Years Ago

Figure S6 – The temporal dynamics of the autosomal effective population size in the last 140KY as predicted from female (Nf) and male (Nm) effective population sizes. The autosomal estimates were derived applying the 4NfNm/(Nf+Nm) formula on the mtDNA and Y chromosome based estimates. 1 deme, constant, Nm/Nf=1 1 deme, constant, Nm/Nf=0.5 1 deme, constant, Nm/Nf=0.1 Frequency Frequency Frequency 0 100000 250000 0e+00 2e+05 0e+00 2e+05 4e+05 0 200 400 600 800 1000 0 200 400 600 800 1000 0 200 400 600 800 1000

Node age Node age Node age

100 demes, constant, Nm/Nf=1 100 demes, constant, Nm/Nf=0.5 100 demes, constant, Nm/Nf=0.1 Frequency Frequency Frequency 0 100000 250000 0 100000 250000 0e+00 2e+05 0 200 400 600 800 1000 0 200 400 600 800 1000 0 200 400 600 800 1000

Node age Node age Node age

100 demes, exp after, Nm/Nf=1 100 demes, exp after, Nm/Nf=0.5 100 demes, exp after, Nm/Nf=0.1 Frequency Frequency Frequency 0 40000 100000 0 50000 150000 0e+00 4e+04 8e+04 0 200 400 600 800 1000 0 200 400 600 800 1000 0 200 400 600 800 1000

Node age Node age Node age

100 demes, exp, Nm/Nf=1 100 demes, exp, Nm/Nf=0.5 100 demes, exp, Nm/Nf=0.1 Frequency Frequency Frequency 0 20000 60000 0 20000 60000 0 20000 60000

0 200 400 600 800 1000 0 200 400 600 800 1000 0 200 400 600 800 1000

Node age Node age Node age Figure S7 - Distribution of node ages for 1000 coalescent simulation replicates of Y chromosome (red) and mtDNA (blue) lineages under varying scenarios of population growth, deme formation, and effective number of males (Nm) and females (Nf). Plots show histograms of node ages, measured in generations, from fastsimcoal2 coalescent simulations run for four scenarios: Row 1 - one deme with a constant population size; Row 2 - 1 deme divided into 100 equally-sized demes formed 400 generations ago with a constant population size; Row 3 - formation of 100 demes 400 generations ago, with exponential growth starting 200 generations ago; Row 4 - formation of 100 demes 400 generations ago, with exponential growth starting 400 generations ago. The first column shows simulations run, assuming the effective number of males relative to the effective number of females (Nm/Nf) is equal. The second column shows simulations where Nm/Nf = 0.5, and the third column shows simulations with an extreme Nm/Nf=0.1. Nm and Nf are computed assuming a constant autosomal effective size of 10,000. All simulations sample 500 individuals, distributed evenly between demes. 60000 0.00350

H1 H 0.00300 50000

K P 0.00250 E2 IJ mate (years) 40000 O G2a NO G2a1 R I 0.00200 on rate me es me R1 30000 J R2 C J2a J2 R1b Q1 Q 0.00150 N O3 C3

O2a J1 STR muta 20000 R1a2 R1a1 R1a Q1a J1b O3a'b 0.00100 R1a2d O3a1 N3 N2a R1b11 Q2b'c 10000 I2a-L621

STR-based coalescent 0.00050 I1 C3f1 M407 0 0.00000 0 5000 10000 15000 20000 25000 30000 35000 40000 45000 50000 Resequencing-based (BEAST) coalescent me esmate (years)

Figure S8. Comparison of STR and sequence data based coalescent time estimates. STR-based estimates: 21 STR markers, “evolutionary” mutation rate 6.9x10-4 per 25 years (Zhivotovsky et al. 2004). Sequence based estimates: BEAST v.1.8.0, GTR substitution model, lognormal relaxed clock, mutation rate 7.4x10-10 mut/bp/year (SI3). The majority of the STR-based age estimates of “young” haplogroups deviate from the expected linear relationship (black line) with age estimates derived from sequence data. Adjusted STR mutation rates (green line, and the right y-axis) were calculated by 5000 year bins of haplogroup ages assuming linear relationship with sequence data based haplogroup age estimates. The “evolutionary” STR mutation rate that was used to calculate the raw STR- based age estimates is shown as a red line. 8 African Number of coalescent events in clades Time (KYA) African root Non-African involving African and non-African samples 6 70 4

2 60 E

Number of coalescent events Number of coalescent 0 30 35 40 45 50 55 60 65 70 75 52 DC F Time, thousands of years . 50 . K . 47

40

30 D1 D2 D3 D4 D* C3fC3c'h C2 C5 C7a C7b C9 C1 F2 GH1a H1b H1c H2 H4 H3 I J1 J2a J2b L1 L2 TNO1 O2 O3 NO2 K2c K2d S1 S2 S3 M P2 QR

Europe West Asia Caucasus South Asia Northeast Asia SE Asia Oceania Americas

Figure S9. Coalescent times of the oldest Y chromosome haplogroups outside Africa. The tree was generated and coalescent times (presented in thousands of years, KY) calculated in BEAST. Shown are only those 32 branches that had coalescent date older than 30 KY. These branches are shown in solid lines. The plausible branching structure of 11 additional branches that have been reported in the literature is shown in dotted lines. The distribution of relevant clades by geographic regions is presented on the basis of our data and inferences made from literature ignoring cases of the presence of the haplogroup in a region that can be explained by historic gene flow. The distribution of coalescent events in time for African and non-African populations was obtained using a sliding window of 2000 and step size 1000 years. The red and blue line connecting D and E reflects the proposed model of an early back to Africa event involving putative DE* lineages (Hammer et al. 1998). 100 Worldwide Africa NearEast Europe SouthAsia SE&EAsia PNG CentralAsia Siberia Andes

75

50

25

0 mtDNA NRY mtDNANRY mtDNA*NRY mtDNA* NRY mtDNA NRY mtDNA NRY mtDNA*NRYmtDNA* NRY mtDNA NRY mtDNANRY

AmongGroups

Figure S10. Distribution Y chromosome and mitochondrial diversity within and among populations.

5000

mtDNAmtDNA NRYNRY

4000

3000 Co un ts

2000

1000

0 0 20 40 60 80 100 120 140 160 180 200 Pairwise divergence times (π / 2 / µ), KYA

Figure S11. Distribution Y chromosome and mitochondrial DNA pairwise divergence times. The plot is based on the analysis of 320 mtDNA and Y chromosome sequences including African and non-African populations. The two highest peaks in the Y chromosome plot correspond to the two clusters of coalescent nodes in FigureS9, one at 43-48KYA involving non-African coalescent events within haplogroups C, D, and F, and the 62-64KYA cluster to the coalescent events among the non-African founders and between African E lineages and non-Africans. Africa

60 50

4040 30

Co un ts 20 20 Coun ts 10 0 0 0 20 40 60 80 100 120 140 160 180 200 0 20 40Pairwise 60 divergence divergence 80 times 100times (π /(π 2 / 120µ),2 / KYAµ), KYA 140 160 180 200 Near East Europe 150 500

100 400 300

Co un ts 50 Co un ts 200 100 0 0 0 20 40 60 80 100 0 20 40 60 80 100 Pairwise divergence times (π / 2 / µ), KYA Pairwise divergence times (π / 2 / µ), KYA Central Asia South Asia 40 60 50 30 40 20 30 Counts Counts 20 10 10 0 0 0 20 40 60 80 100 0 20 40 60 80 100 Pairwise divergence times (π / 2 / µ), KYA Pairwise divergence times (π / 2 / µ), KYA

Southeast & East Asia Papua New Guinea 150 10

7.5 100 5 ou nt s ou nt s C C 50 2.5

0 0 0 20 40 60 80 100 0 20 40 60 80 100 Pairwise divergence times (π / 2 / µ), KYA Pairwise divergence times (π / 2 / µ), KYA

Siberia Andes 250 30 200 20 150 100 Counts Co un ts 10 50 0 0 0 20 40 60 80 100 0 20 40 60 80 100 Pairwise divergence times (π / 2 / µ), KYA Pairwise divergence times (π / 2 / µ), KYA

Figure S12. Regional plots of Y chromosome and mitochondrial DNA pairwise divergence times. The plot is based on the regional analysis of the 320 mtDNA and Y chromosome sequences as shown combined in Figure S11.

L419 M42 56 596 BT A2'5 M181 M168 282 236 DT B2'5 M145 P143 30 4 CT DE M89 179 156 F C F1329 1 GT F2 M201 M578 SSM 72 198 1 HT G M3035 M523 22 7 IT H M429 M9 45 15 K IJ P326 (M526) 25 0 NR LT F549 P331 5 2 NO MR M214 PR2099 P295 45 6 2 P NO1 NO2 MS B252 M45 M231 M175 46 104 178 61 P1 P2 M242 M207 N O 20 46 R Q M124 M173 168 41 R1 R2 152 17 R1a R1b

Figure S13. Refined topology of the basic branches of the Y-chromosome tree with an emphasis on the short branch lengths defining haplogroup F sub-clades. Mutation counts and branch defining markers (included in counts) are shown on the branches. If no previously named mutation existed on a given branch, a name from the B-series was given to one of the mutations discovered, and the rest were denoted with _eq in the annotations table. Branch lengths include recurrent mutations if such are present in no more than two (exceptionally three) locations in the Y-chromosome phylogeny. Given comparative data from Malaysian high coverage sequences (Wong et al. 2013), we map the position of the F2 clade represented by Malay sample SSM072 and redefine haplogroup NO by F549 and 4 equivalent mutations. NO splits further into NO1-M214 and the novel NO2-F2755, as defined by the SSM016 sequence.

L1086 L1085 V148 V168 M31 V221 A2'T L419 M42 56 596 A2'5 M14 M32 762 1 A3'5 M28 M144 416 A3'4 M51 M13 276 A00 A1A0 A2 A5 A4 A3 BT M10424 M6 CTS3482 PF1 166 32

V70 P28 P262 V243 PF3

517 115 949 7 San San San MKK Baka ISR07 Congo Pygmy 2 Mbos Ethiopian Jew Sardinians 919 identifier 16204 35247 NA21313 HGDP01029 HGDP00987 HGDP01036 GRC13292545 GRC13292546 Sample BT A2c A1a A3a A2* A2b A1b A3b1 A3b2 Karafet 2008 P28 M28 M13 M51 P262 BT A2 A0 A1 A00 A2 A3 A3 Van Oven 2013 BT A0 A1a A00 A1b1a1 A1b1b1 A1b1b2a A3 A1b1b2b A1b1a1a1 A1b1a1a2b A2 ISOGG

FigureS14.RefinedtopologyoftheYchromosomehaplogroupA.Greydashedlines denotebranchesdefinedbypublishedsequencesgeneratedwithIlluminatechnology. M181 2 B L1388 P85 5 B1'5 M236 M182 275 B2'5 M150 M192 155 B4'5 M8495 M7104 18 34 B3 B1 B2 B4 B5 M7583 M8351 M7115 M65 87 124 2 341

B22 M7590 M8035 M30 P6 M6845 264 35 23 329

B23 B24 M7592 L276 M7915 M211 18 96

B27 M7916 92

B25 B26 P70 M2803 517 19 12 209 228 615 y Hadza2 Hadza5 Hadza3 Hadza4 Sandawe5 Sandawe4 CongoPygm PygmyBaka PygmyBaka 9 identifier 91 909 937 319 319 319 319 3124 1807 1577 918, 3125 35246 1100 37 1100 37 1100 37 1100 37 920, Baka927 DNA_C01 DNA_A01 HGDP009 HGDP009 HGDP010 Baka908, DNA_G02 DNA_G01 Baka Sample B1 B2a B2b B2b B2b B2b1 B2b4a B2b4b Karafet 2008 P6 B3 B1 B2a B M7583 M8035 M8351 B2b3 M7104 B B B B Van Oven 2013 B1 B2a B2b1 B2b1 B2b1 B2b1b B2b1a2 B2b1a1c B2b1a1b ISOGG

Figure S15. Refined topology of the Y-chromosome haplogroup B. Grey dashed lines denote branches defined by published sequences generated with Illumina technology.

M145 30 DE M174 M96 146 1 DE N1 M179 P99 L1366 M75 P147 241 124 D1 D2 D3 D4 E1'4 F900 F729 E5 M33 P177 1 E4 E1'3 P75 P2 E3 76 E1'2 V38 M215 11 E1 E2

151 172 400 419 Yoruba Chinese Tamang Japanese Nepalese 37 37 037 424 200 200 Sample identifier NA19239 L2 NA18940 GS000035 GS000010 E2 D2 D3 D* E1a E1b2 2008 D1a* Karafet N1 Oven E2 D2 D3 D* M33* P177* D 2013 E Van E2 D2 D3 D4 E1a D1a E1b2 E ISOGG

Figure S16. Refined topology of the Y-chromosome haplogroup DE. Grey dashed lines denote branches deriving from the respective nodes in previous phylogenetic reports but not found in our sample (Karafet et al 2008; van Oven et al 2013). Branches E1, E2, E1'3 are shown with length 1 because only one of the sub-branches was present in our sample and the rest of the identified mutations were counted to be equal with the sub-branch definition although some of them are actually defining the parent-clade.

V38 1 E1 M329 M2 E1c 211 E1a'b Z5994 M180 61 E1b E1a U174 Page27 M66 P268 U209 45 30 E1a1 E1a3 E1a4 E1a5 E1a2 CTS782 Z1704 CTS3985 CTS11 13 10

CTS9964CTS1313Z873 CTS67 M4465 M4451 U290 M3907 13 2 6

M4438 B399 CTS412 CTS1179B400 M3869 9

B401 CTS283 10

B402 CTS306

128 24 44 44 44 34 37 15 49 36 39 37 28 14 34 NA Luhya Baka Luhya Luhya Hadza Yoruba Yoruba Congo Bakola African African African Bedzan Pygmies pygmies Pygmies Pygmies Sandawe Americans Americans Americans identifier 37 37 37 37 37 37 37 37 245 200 200 200 200 200 200 200 200 200 37 1100 37 1100 37 1100 37 1100 37 1100 37 Sample GS00253 GS00319 GS00319 GS00319 GS00319 GS00319 NA19026 NA19834 NA18504 NA19703 NA19700 NA18501 NA19025 NA19020 DNA_F01_ DNA_E01_ DNA_B02_ GS000035 DNA_B01_ DNA_C02_ DNA_D01_ 2008 E1b1c E1b1a* E1b1a1 E1b1a6 E1b1a9 Karafet E1b1a7a* E1b1a7a3 E1b1a8a* E1b1a8a1* E1b1a8a1a V38* U181 U174 Z5994 Van U290* U209* U209* E1b1a8a* 2013 M180* Oven E E E E E E E E E1b1a2 ISOGG E1b1a1a2 E1b1a1a1e E1b1a1a1h E1b1a1a1a E1b1a1a1g1* E1b1a1a1g1* E1b1a1a1g1a* E1b1a1a1f1a1* E1b1a1a1f1a1d E1b1a1a1f1a1c E1b1a1a1g1a1

Figure S17. Refined topology of the Y-chromosome haplogroup E1. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing.

M215 1 E2

M281 M35 E2e 162 E2a'd Z827 V6 M78 1 113 E2b'c E2a M310 CTS8288 E2d 41 E2c E2b M293 M123 421 81 E2b3 E2b1'2 5414M404B304B 43M 34 E2b2 E2b1 Z841 PF6746 32 76

M6060 Z838 B406 CTS1096 99 01

B405 CTS1885 PF6751 B407 2

M10794 PR1497

41 36 138 107 11 19 88 62 58 st NA Arab- Arab- Mixed Mixed Mixed er fi an-Jews Uzbe ki Sanda we Sanda we 7 7 37 37 iden elpmaS 003 19- 003 19- 002 53- 002 53- GS GS GS GS 0000162 17 0000162 06 0000162 14 0000145 61 0000152 30 GS GS GS GS GS DNA_F01_200_3 _E 02_1100_ DNA _D 02_1100_ DNA _H 01_200_3 DNA 2008 Karafet E1b1b1e E1b1b1d E1b1b1b E1b1b1c* E1b1b1c1a E1b1b1c1* 12 3* E-V6 Van 2013 Oven E-M84 E-M281 E-M310 E-M293 E1b1b1f E-M34* E-M * GGOSI E1b1b2 E1b1b1c E1b1b1b1 E1b1b1b2a* E1b1b1b2b* E1b1b1b2a1a E1b1b1b2a1* E1b1b1b2a1* E1b1b1b2a1d

Figure S18. Refined topology of the Y-chromosome haplogroup E2. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing. (V68) M78 113 E2a M521 Z1902 Z1919 2 5 E2a4 E2a3 E2a1'2 V65 V32 V22 V13 37 73 E2a2 E2a1 L1250 B408 B409 PR4600 B413 CTS141 B476 B415 B416 51

B410 B411 M7149 B414 2

M8166 B412

113 115 84 63 21 27 24 34 31 30 33 30 45 43 US US US Tatars Mixed Mixed Mixed British Maasai Italians Mishar Iranians family(2) Estonians Albanians Australian identifier 37 37 200 200 200 NA21737 Sample 37; GS000015153 GS000035227 GS000013763 GS000015172 GS000017206 GS000015892 GS000035021 GS000016441 GS000011811 GS000016179 GS000015708 GS000014562 NA20510 NA21732 2008 Karafet E1b1b1a* E1b1b1a4 E1b1b1a3* E1b1b1a1b V65 V32 V22 V13 E1b1b1a2* M521 Van E E E E 2013 Oven E ISOGG E1b1b1a1c E1b1b1a1a2 E1b1b1a1a1b E1b1b1a1b1a* E1b1b1a1b2*

FigureS19.RefinedtopologyoftheYchromosomehaplogroupE2a. Greydashedlines denoteknownbrancheswithnosequencedataandbranchesbasedonlowcoverage sequencing. M130 179 C M217 K29 134 2 C3 C1'7 F2645 L1373 7 139 C3c'h L58 Z1338 F914 B473 B79 M48 159 8 28 C3f C3h C3g C3i C3c Page12 B77 B78 M77 B90 75 84 56 C3f1 C3c1a C3c2 B73 M407 B469 B80 B91 B93 83 1 7 12

B100 B99 B97 B470 B87 B471 B81 B94 B92 283 7 28

B101 B102 B103 B104 B105 B98 B89 B88 B472 B86 B83 B82 B96 B95 22

B106 B107 B84 B85 78 8 5 2 3 4 596 5119117 114 129 20 15 15 256 7536 5231 CHS Even Even Even Even Even Kizhi Evenk Evenki Buryat Buryat Buryat Buryat Buryat Buryat Buryat Buryat Buryat Buryat Koryak Koryak Koryak Koryak Koryak Kazakh Chinese Mongol CHB/JPT Zakhchin identifier 15179 22091 14418 22094 22090 13761 20113 22092 22093 22066 13752 22071 22440 19992 35117 20004 20126 34297 22293 16165 22292 16129 19993 16168 16169 14335 HG00628 NA18749 NA19079 NA18612 NA18620 Sample C* C3* C3c Karafet 2008 M48 Z1338 M217* L1373* C C C C Van Oven 2013 C3* C3* C3e C3b2 C3e1a C3b2a ISOGG

Figure S20. Refined topology of the Y-chromosome haplogroup C3. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing.

K29 2 C1'7 K30 CTS824 11 C2'7 C1'8 B477 K281 CTS11043 27 1 CTS5573 C2'4 C5'9 C1'6 M347 M38 B66 B68 V20 M8 180 2 C4 C2 C5'7 C6 C1 C8 B76 M208 M356 B65 P121 CTS786 92 1 1 C5 C7 C9 C1a Z5899 P92 B67 F725 399 387 C2a C5b C5a C7a C7b1 B459 B460 B72 B465 1

B466 B467 92 91 9 6 C2a1a C2a2a B75 B462 B461 B71 B468 3 28

B463 B464 B69 B70 B74 198 19 5 3 7 434 6 10 44 0 1 32 423 JPT JPT JPT Bajo Bajo Aeta Lebbo Lebbo Malay Malay Malay Indian Dusun Murut Murut Murut Koinambe Koinambe Koinambe Australian identifier 8 7 7 ML99 ML84 ML18 17005 17004 35255 35258 35686 17146 16936 16937 19981 22099 20272 35257 20271 NA189 NA189 NA189 Sample WON,M C4 C* C* C2a C5a C1a C2* C5* C1* Karafet 2008 C4 C5 C6 C1 K29* K29* M38* C2a C5b C C C Van Oven 2013 C* C* C4 C2a C5a C1a C2* C5* C1* ISOGG

FigureS21.RefinedtopologyoftheYchromosomehaplogroupC1'7.Greydashedlinesdenoteknownbrancheswithnosequencedataand branchesbasedonlowcoveragesequencing. M201 198 G

M285 P287 47 G1 G2

P15 M377 28 G2a G2b B295 M3294 113 3 G2a1 G2a2`4 Z6178 L30 30 28 G2a4 G2a2`3 P303 PF3359 28 G2a3 G2a2 B296 B297 M6936 L497 U1 12 L91 B376 61 3 L1266 U13 CTS8481 B298 B377 B378 15

L267 B299 27

B300 B375 56 33 29 7 6 114 113 106 34 35 94 90 145 US Jew Jew Pole North North Dutch Lezgin Iranian Mexican Ossetian Ossetian Kabardin Iraqi Abkhazian Moldavian Uzbekistan 0 20 F18 ID 13739 14414 14475 16215 16209 11806 14413 16372 14366 16899 14409 NA19670 unsampled unsampled unsampled unsampled Sample G1* G2* G2c G2a1 G2a* Karafet 2008

*

7

9 L91 U1* 4 U13 P15* P16? P15* M377 M285 M377 L P287* P303* P303* PF3359 Oven G G PF3146* G G G G G G G G G G G G G Van 2013

a

1

a

2

2

a

b

2 G2 G1* G1* G2b G2a 2

G

a

2 G2a2a1b G2a2b2b G2a2b2a G2a2a1b G2a2b2a1b G2a2b2a1b G G2a2b2a1a1 ISOGG

Figure S22. Refined topology of the Y-chromosome haplogroup G. Grey dashed lines denote known branches with no sequence data in our dataset. In the case of haplogroup G all samples generated for this project belonged to clade G2a. Within this clade we distinguish four sub-clades, including G2a1-B295, which was earlier defined by a recurrent marker P16.

M3035 22 H Z5857 M3004 1 H1'4 M282 L902 34 H1'2 B108 M69 26 H3H4 H2 H1 Z5867 M52 P254 74 195 H1b H1a H1c B367 B368 Apt Z4452 M2940 15 84

M2853 Z4507 6 14

B370 B369 M2728 B109 M2702 B372 B371 372 364 274 254 243 147 47 61 47 47 Kol Asur Balija Dhaka Dhaka Punjabi French Malayan Burmese Burmese Kshatriya Cambodian identifier 0528 HGDP 16821 19903 16806 35123 16965 20270 35034 00720 35039 16805 35035 HGDP0 Sample F* H* H* H2 H1a H1* Karafet 2008 Apt Oven H3 H2 M69* Z4507 Z5867 Z4452 M2853 H M3035* H H H H H H 2013 Van H3 H* H2 H1c H1a H1* H1b H1b1 ISOGG

FigureS23.RefinedtopologyoftheYchromosomehaplogroupH.Greydashedlines denoteknownbrancheswithnosequencedataandbranchesbasedonlowcoverage sequencing. M170 144 I M253 M438 213 40 I1 I2`3 B260 Z2891 29 2 I1a`f Z58 B264 Z3319 B51 Z63 CTS6364 1 72 I1g I1a I1f I1e I1b I1c I1d B261 B262 Z138 Z59 PR683 B267 M227 L22 B55 5 10

DF78 Z140 PF7391 Z2539 B53 B52 L300 Z74 22 Z73 B265 B263 CTS4963 M507 L813 L287 6

F2642 B54 20 19 44 40 28 29 31 32 28 52 35 44 48 40 28 21 42 38 US US NW Komi Dutch Dutch mixed mixed mixed mixed mixed mixed Toscan Finnish Finnish Belarus Mordvin Hungarian Utah,CEU European identifier Australian

1

7

3 37 37 37

0

3

5 F19 F11

E

_

2

0

0 15176 16442 11808 10320 35226 15272 10435 15888 16104 13698 14328 16901

A_

0 200 200 200

0

2 N

S

_ HG00189 HG00325 HG00372 HG00186

D

G Sample NA06994 NA12891 NA20511 I1* I1* I1* I1d I1b Karafet 2008 6 L22 Z63 Z59 L813 Z74* Z138 Z140 M227 Z2539 CTS63 I I I M253* M253* I I I I I I I I I Van Oven 2013 I1 I1 I1a3 I1a2a I1a1* I1a2b I1a2a I1a1a I1a1b4 I1a2a1a I1a2a1b I1a1b3a I1a1b3b I1a2a1a2 ISOGG

FigureS24.RefinedtopologyoftheYchromosomehaplogroupI1.Greydashedlinesdenoteknownbranches withnosequencedataandbranchesbasedonlowcoveragesequencing. 40 I2`3 PF3835 L596 4 I2 I3 P37 M436 22 45 I2a'c I2d`e M423 M26 CTS595 M223 L38 63 60 127 I2a I2b I2c I2d I2e L621 L161 Z161 CTS2146 PF4408 F1696 88 61 52 L1400 B258 B62 B61 B57 B266 B259 CTS6433 CTS1977 32 1 B63 B474 B60 CTS5779 B59 Z78 L484 9 10 11 B257 Z190 2 B268 B64 B58 CTS7435 Z79 Z169 6422 19 18 8 12 15 56 35 185 164 25 26 34 42 32 90 109 107 22 48 200 US US US US NA Croat Croat Dutch Dutch Dutch Dutch Vepsa mixed mixed mixed mixed mixed Chuvash Georgian Lithuania Ukrainian identifier Belarusian Belarusian F6 F7 F15 F14 13754 15873 15225 13764 16904 14324 14351 17632 14570 14560 10438 13164 16337 16446 15709 16450 11817 14557 35150 Sample I* I* I2a* I2b* I2a2* Karafet 2008 L38 Z78 M26 L161 I L596 L621 I Z161 I I I I I M223* an I CTS595* CTS1977 I I V 2013 Oven I2c I2a1 I2a2a I2a1a I2a2b I2a1b3 I2a1b2 I2a2a1c2 I2a2a1c2a1 I2a2a1c2a2a I2a2a1c2a2a1a I2a2a1c2a2a1a1 ISOGG

FigureS25.RefinedtopologyoftheYchromosomehaplogroupI2'3. M304 134 J M267 M172 149 24 J1 J2 PF7256 Z2217 2 J1c J1a'b Z1828 P58 119 72 J1a J1b B232 B234 L817 Z1853 2 13 29 J1a1 J1a2 J1b1'6 B233 CTS1460 Z2383 CTS11839 PR6622 L862 2 15 J1b1'5 F1369 F858 CTS11284 PF4881 J1b7 2 J1b1'4 J1b6 B235 Z2329 B246 45 J1b5 J1b1'2 J1b3 L829 B236 B382 B383 J1b4 3 J1b2 J1b1 B237 B239 48 4

B238 PR142 B381 B242 4 12

B240 B241 B243 B244 1

B245 149 44 49 60 39 60 102 75 60 40 44 2 6 28 26 35 43 29 33 Jew USA Avar Azeri saran Druze Malay Lezgin Kumyk Yemen Arabian Arabian Albanian Jordanian Armenian Armenian Armenian Armenian identifier Belarussian Yemeni Tabas Arab Muslim 9929 ML21 13741 14421 14368 14405 13724 11735 35126 35125 14474 16136 16887 16973 13745 16213 16180 16277 35124 35434 Sample J1* J1e 2008 Karafet Oven P58* L858* J1* Z1828 Z1865* Z1865* 2013 J1 J1 J1 van J1 J1 J1a* J1a3a ISOGG J1a2b* J1a2b2*

FigureS26.RefinedtopologyoftheYchromosomehaplogroupJ1. M172 24 J2 M410 M12 82 115 J2a J2b Page55 Z6046 L581 M205 Z1827 22 15 99 4 J2a1'10 J2a11'12 J2b1 J2b2'4 Z2227 Z2220 B438 CTS3233 CTS12568 B247 Z2454 M241 18 3 4 28 J2a1'6 J2a7'10 J2a11 J2b2'3 Z6065 M67 Z2397 L24 Z3406 B248 L1460 L283 14 71 73 J2a12 16 53 J2a6 J2a1'5 J2a7 J2a8'10 J2b2 M166 CTS7523 PF5194 Z1911 F3133 Z387 L243 J2a13 B439 M3670 CTS6272 Z1297 17 J2b3 2 J2a1'4 J2a8 J2b4 Z2242 CTS12244 Z5877 B437 B440 Z631 J2a5 3 11 J2a1'3 J2a9 J2a4 L1483 Z514 J2a10 Z1043 B249 3 J2a1'2 J2a3 Z500 M92 J2a2 J2a1 125 91 113 110 66 43 64 79 81 71 127 39 43 27 29 140 48 46 30 26 Jew Jew USA USA Tatar Dutch Israeli Malay Malay Italian Iranian Andhra Russian Pradesh German Assyrian Kirgizian Albanian unknown Imeretins Jordanian Armenian Georgian Sardinians Sardinians Sardinians Abkhazian Cochin identifier Bene Kabardinian Kapu, S16 867 847 840 ML79 ML82 Sample 15875 16181 16882 13746 35147 16138 15174 13751 35685 10431 16802 16445 13747 16177 35115 15895 14410 10434 16373 F16 860 841 831 J2a* J2b1 J2b* J2a* 2008 J2a2a J2a2* J2a2b J2b2* Karafet M12 M92 L283 L25* L581 Oven M205 M67* M67* F3133 Z6065 J2a J2a J2a J2b 2013 M410* M241* PF7394 PF5172 J2a J2a J2a J2b van J2a J2a J2b J2b* J2a J2a J2a* J2a2 J2b1 J2b* J2a1* J2b2* J2a1* ISOGG J2a1b* J2a1b2 J2a1b1 J2a1h2* J2b2a1* J2b2a1a* J2b2a1a1

FigureS27.RefinedtopologyoftheYchromosomehaplogroupJ2. Greydashedlinesdenoteknownbrancheswithnosequencedataand branchesbasedonlowcoveragesequencing. M9 15 K P326 M526 25 0 LT NR M20 M70 F549 M1221(=P331) 8 5 1 L NO MP L595 M22 M214 PR2099 P295,F115 151 8 45 6 2 L2 L1 T P M357 M349 M27 L1255 L131 L162 NO1 MS B252 M45 B254 M106 46 2 284 P2 S M1 B253 B273 B255 B256 409 1 54 S1'2 M1d M1c P202 B275 B272 B269 147 342 34 107 L1c L1b L1a T1a1 S3a1 S2 S1 P1 B374 B373 B250 B251 B276 B274 B271 B270 M242 M207 64 64 37 32 9311 69410 45 17 16 360 Jew Bajo Arab Aeta Agta Aeta Tatar Druze Lebbo Malay Malay Kosipe Kosipe Kosipe Pathan Papuan Muslim Georgian 8 2 identifier 3592 35256 13705 16135 35250 16935 16941 35260 35365 16210 16212 35249 ML050 ML097 ML016 Sample HGDP0025 HGDP0054 R S Q L* T* P* L1 L3 K* NO M1 L2a Karafet 2008 S R Q 595 NO M27 L131 L162 M1 M357 M317 L1255 M526* M526* K* M526* L L T T L L T K K K Van Oven R S Q K* L2 K* K* NO L1c M1 L1a L1b1 T1a3 T1a2 T1a1

ISOGG

Figure S28. Refined topology of the Y-chromosome haplogroups L, T, S and M. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing.

M231 180 N F2930 L729 17 13 N4 N1'2'3 CTS39 M1786 L666 M46 1 46 N1'2 M128 P43 N3 99 N1 N2a1 L1419 B167 14 1

L1418 B225 B226 B478 11

B168 B169 1 N2a1a B170 B175 15 5

B171 B172 B227 PF3415 269 B173 B174 B228 B176 B178 B179 10

B177 M270 136 126 23 30 37 29 7 19 14 13 9 10 10 10 an ed CHB Mari Even Yakut Vepsa Evenki Forest Tundra Tundra Nenets Nenets Nenets Mongol Udmurd Tuvinian Tuvinian Cambodi Unsampl Identifier 2013 20037 Poznik 35244 14332 35432 16167 16163 16162 15879 35235 20108 22441 17247 16968 Sample N* N1b N1a 2008 N1b1 Karafet N4 Van P63 N3b N3b P43* N3b Oven 2013 M128 N2 ISOGG N1c2a N1c2b N1c2b1

Figure S29. Refined topology of the Y-chromosome haplogroup N. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing. Haplogroup N 1’3 is further split into N 1’2-L166 (former N3b, PhyloTree) and N3-M46 (former N3a, PhyloTree).

M46 46 N3 B187 L708 28 N3b N3a B211 P298 31 10 N3a2'5 M2118 L392 20 19 N3a3'5 CTS10760 Z1936 B197 152 N3a1 N3a2 N3a3 N3a4 N3a5 B180 B181 B182 M1982 F4134 VL29 19 23 5 CTS4556B229 M1932 M1979 L550 VL39 577 15 N3a3a N3a3b B230 B231 B183 M1984 Z4915 B186 B215 B216 B214 11 52 B184 B185 Z4912 M2784 B218 B217 B190 F467 122 B188 L591 B212 B191 B192 B193 3 B213 B189 15

CTS12849 94 39 17 15 15 37 12 10 7 7 44 30 17 25 20 25 17 0113102321 2 Shor Even Mari Mari Even Yakut Yakut Yakut Saami saami Latvian Latvian Udmurt Udmurt Russian Russian Estonian Estonian Estonian Estonian Estonian Estonian Estonian Estonian Lebanese Identifier 13694 35017 14331 17169 22438 15715 16166 20490 14333 22076 14416 15180 20110 15180 16819 35148 35027 17210 16907 35024 35025 17208 17203 17214 17219 Sample et 2008 N1c* N1c1 Karaf N Van N3a N3a N3a N3a 708* Oven 2013 M46* L392* L550* VL29* 1 1a* 1a1 1a1a ISOGG N1c1* N1c1a N1c1a N1c1a N1c1a

Figure S30. Refined topology of the Y-chromosome haplogroup N. We re-define the internal structure of haplogroup N3a-L708 and report several novel subclades. Haplogroup N3a2’5 now has a novel geographically restricted sister clade N3a1, defined by the marker B211, and is further split into previously unreported subclade N3a2-M2118 and subclade N3a3’5 (former N3a-L392).

L392 19 N3a3'5 Z1936 B197 52 N3a4 N3a5 B194 CTS2733 F4205 B202 3 18 17

B195 VL62 B198 B219 B203 B204 10 3 21 15

B220 F2288 B221 B223 B224 B205 B206 3 1 F1356 Z1941 8 B222 B199 B207 B208 10 1 B196 B166 B200 B201 B209 B210 40 23 12 1 020212116 15 6 9 6 7 11 846 Vepsa Buryat Buryat Koryak Koryak Koryak Cossac Kazakh Eskimo Mongol Mongol Mongol Chukchi Chukchi Karelian Estonian Estonian Estonian Estonian Identifier 17380 17213 35116 35236 16190 35127 20491 22077 20002 33948 22068 19998 16186 16971 35149 18757 17207 22069 20001 Sample 2008 Karafet L392* Van N3a N3a 2013 Oven Z1941 Z1936* 2 2a1 ISOGG N1c1a1a N1c1a1a N1c1a1a N Figure S31. Refined topology of the Y-chromosome haplogroups N3a4 and N3a5.

M175 61 O F190 6 O1'2 M119 25 14 137 O3'7 O2'5 O1 B384 M110 287 O1a'b F31(M307) F819 42 63 O1a O1b O1c B385 CTS37 M101 B390 14 41

F343 CTS5709 3

F510 CTS409 9

B386 B398 29 3

B387 B391 B394 B392 2 8

B388 B395 B393 3 2

B389 B396 B397 36 42 50 36 45 41 CHS CHB CHB Agta Agta Batak Batak Malay Malay Malay Malay Malay Murut Malay Malay Malay Malay Malay Murut identifier 35435 35252 19983 19985 35251 35248 ML074 ML100 ML081 ML092 ML091 ML031 ML083 ML055 ML090 ML017 NA18536 NA18606 NA18632 NA18740 HG00577 HG00595 Sample 2008 O1a1 O1a1 O1a2 O1a1a Karafe t P203 M110 O O Van Oven 2013 O1a1 O1a1 O1a2 O1a1a ISOGG

Figure S32. Refined topology of the Y-chromosome haplogroup O1. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing.

M268 14 O2'5 CTS279 M176 52 O2'4 PK4 F883 75 O2 O4 O5 M95 F838 F1669 F2775 CTS298 CTS65 CTS42 41 O2a F1803 CTS350 F857 CTS925 6 O2a1'2 CTS6592 M1284 K4 CTS713 18 37 O2a1 O2a2 O2a3 M88 B418 B426 B417 B420 M1277 L682 F940 CTS9179 31 2 4 F923 F2890 B419 B424 B427 6 1 36 B421 B423 B425 B429 B428 2 B422 53 52 56 52 55 19 12 58 60 S T JP JPT JPT JPT JPT JPT CHS CHS CHS CHS CHB Bihar Gond Malay Malay Malay Malay Lebbo Malay Malay Malay Malay Malay Malay Malay Malay Malay Malay Malay Malay Dusun Dusun 2CH CHB, CHB, CHB, CHS, Ho, JPT Cambodian Vietnamese Vietnamese Vietnamese Vietnamese CHS, 11 identifier ML34 ML89 ML77 ML24 ML80 ML85 ML96 ML94 ML88 ML08 ML62 ML27 ML95 ML37 ML58 ML42 17007 19946 19949 19953 19979 16804 16803 19950 19972 NA18561 NA19007 NA19075 NA19070 NA18638 NA18637 NA18603 NA18534 NA19055 NA18953 NA18962 NA18943 NA18965 NA18563 NA18636 NA19009 HG00701 HG00457 HG00634 HG00442 HG00418 HG00406 HG00530 HG00533 HGDP00711 Sample O2* O2b O2b O2b O2b O2b O2a* O2a1 Karafet 2008 8 * M8 O PK4 O O2b O2b O2b O2b O2b O2b O2b M95 O M268 O Van Oven 2013 PK4 O2* O2b O2b O2b O2b O2b O2b O O2a1* O2a1a ISOGG

Figure S33. Refined topology of the Y-chromosome haplogroup O2. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing.

M122 27 O3'7 CTS152 M324 41 O3'6 KL1 F525 7 O7 O6 O3 JST002611 F964 M188 P164 35 35 O3a'j CTS800 CTS3155 N6 L619 5 27 O3a'b CTS2148 F2055 Page125 Page23 31 34 18 34 O3i'j O3a M209 M159 B451 N7 CTS374 CTS492 9 72 67

B433 F4064 CTS556 F5 1 O6a O3c O3e O3h O3i O3j O3b F11 F238 O6b O3d M7 CTS123 F46 B434 O3f 50 1 O3g O3a1 CTS1346 F275 CTS601 CTS1642 7 39 18

B450 B452 B432 CTS558 B453 B454 B455 B456 CTS1981 5 15 7

B435 B436 B457 B458 121 36 30 73 2153 46 37 46 B S S B B CH JPT JPT CH JPT JPT CHS CHS CHS CHS CHB CHS CHS CHB CHB CHB 3JPT Bajo 4CHB 4CHB 8 Batak Igorot Malay Malay Malay 3CH CH 2CH CHS CHB 4Malays Burmese Burmese Burmese Burmese Burmese Burmese 3CHS JPT JPT CHS 5CHS 3CHB 2CHS 10CHS identifier ML30 ML98 ML75 ML76 ML03 ML46 ML78 17006 35253 22100 19904 19966 19902 19906 19901 19905 NA18959 NA18546 NA18635 NA18609 NA18643 NA19083 NA18622 NA18623 NA18548 NA18624 NA18757 NA18530 NA19076 NA18562 NA18621 NA18544 NA18984 HG00556 HG00589 HG00583 HG00512 HG00524 HG00683 HG00565 HG00592 HG00619 HG00500 HG00448 HG00625 HG00653 HG00559 HG00607 HG00403 HG00472 HG00610 HG00689 HG00656 Sample * 1 O3* 2008 O3a* O3a* O3a3c O3a3c O3a3b O3a3a Karafe t N6 F964 F11 O O O F449 O3 O3 O3 M117 O O3 P201* M134* M188* M122* O O JST0026 Van Oven 2013 O3* O3a1* O3a2* O3a2a O3a1c* O3a2b1 O3a2c2 O3a1c1 O3a1c2 O3a2c1* O3a2c1a ISOGG

Figure S34. Refined topology of the Y-chromosome haplogroup O3. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing.

M242 20 Q M378 L472 33 Q1'2 F1096 M346 22 48 Q3 Q2 Q1 F1202 M25 M323 B28 L53 87 213 40 Q2b'c Q1a'c M120 B143 L330 M1049 M3 37 11 66 215 Q2c Q2b Q2a Q1e Q1d Q1c Q1b Q1a B285 L527 B287 L332 M944 B34 M848 B31 106 71 31 11 2 109 B286 B29 L529 B30 B31 Z784 M943 M825 CTS11699 CTS2731 B35 B42 B47 B48 Y805 23 385 118

B284 B280 B32 B33 M859 CTS5 B36 B37 B43 B46 B49 B50

3 Anzick 3103 Saqqaq B283 B281 M818 CTS398 B39 B38 B44 B45 6 12

B282 B277 B278 B279 B40 B41 277 140 0 51 4 0 754 90 76 101 21 19 41 64 125 109 11 13 6 3124 158 119 113 79 124 n e n i i i r Ket Ket unk CLM MXL MXL MXL MXL MXL Croat Maya Maya Dutch Uzbek AndLA AndLA Selkup AndHA AndHA AndHA AndHA AndHA AndHA Koryak Koryak Koryak Koryak Eskimo Nepales Sardinia PGP AndCach AndCach AndCach Murut19 Turkmen Turkmen Turkmen identifie 8 8 F12 15887 19986 34970 34185 22072 22067 35120 35118 35119 35030 16946 19960 19961 35038 15872 13716 13717 15393 19997 17077 16940 16951 16942 20274 20273 16945 19989 HGDP00 HGDP00 NA19682 NA19795 NA19771 NA19735 NA19729 NA19774 NA19732 NA19786 NA19783 NA19664 HG01124 Sample Q1b Q1a1 Q1a* Q1a2 Q1a6 Q1a3* Q1a3a 2008 Karafet M3 M25 L527 L529 Z780 L330 M120 Q1b Q1a2 Q Q1a1 Q Q Q Q Q Q Van Oven 2013 Q1a* Q1b1 Q1a2* Q1a2* Q1a1a Q1a2c Q1a1b Q1a2b1 Q1a1a1 Q1a2a1a1 Q1a2a1c Q1a2a1b ISOGG

Figure S35. Refined topology of the Y-chromosome haplogroup Q. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing.

M420 143 R1a SRY10831.2 R1a6 R1a1'5 M198 R1a5 R1a1'4 M417 R1a4 R1a1'3 CTS4385 Z645 7 8 R1a3 R1a1'2 B444 B445 Z93 Z283 2 3 R1a2 R1a1 B142 Z94 B110 1 5 R1a2b'd R1a2a Z665 M780 B115 B116 0 3 22 23 R1a2c'd R1a2b R1a2a2 R1a2a1 Z2125 Z2122 B163 M634 B129 B128 B127 B117 1 1 1 1

B446 Z2123 B111 Y50 M582 F1417 L657 B126 B125 7 1 29 18 6 2 R1a2d R1a2c B141 B449 Y874 Y47 B140 B139 B113 B112 B134 B430 B431 F1345 M699 Y9 1 32 1 4 15 3 2

L37 B443 B442 B441 Y910 B138 B137 B136 B135 B447 B165 B133 Y928 Y945 Y944 2 2 3

B164 B448 Y878 Y31 CTS548 B114 1

B132 B131 B130 36 31 51 33 28 33 36 31 6 3 168 31 35 43 6 4 5 9 29 24 9 14 22 44 37 24 21 31 29 36 24 24 27 4 4 3 2 6 i US Jew N/A Tajik Tajik Tajik Tajik Tajik Altay Altay Altay Kurmi Levite mixed mixed family family Gupta Orissa Balkar Kyrgyz Kyrgyz Kyrgyz Kyrgyz Kyrgyz Kyrgyz Iranian Iberian Kazakh Bengali Bashkir Cossack Israelite Assyrian Circassian Azerbaijan unsampled unsampled unsampled 16207 16974 16191 16197 13757 35239 14566 15183 16875 16196 14417 16188 35237 35114 13758 16171 16198 16276 22439 13749 15893 16189 16808 16966 16799 20850 20846 14415 16801 16972 16195 16193 16967 16174 16187 DNA_D01 2008 R1a* R1a1 Karaf R1a 2013 * * 1 R1a* R1a1* ISOGG R1a1a* R1a1a1* R1a1a1b2* R1a1a1b2* R1a1a1b2a* R1a1a1b2a* R1a1a1b2a* R1a1a1b2a1* R1a1a1b2a1a R1a1a1b2a2a R1a1a1b2a2b R1a1a1b2a2b R1a1a1b2a2b

Figure S36. Refined topology of the Y-chromosome haplogroup R1a2 and R1a3. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing. The topology of hg R1a has been covered extensively with our set of 70 samples (excluding 2 duplicates), three of which belong to an Estonian family and two each to two Dutch father-son pairs. In the absence of basal branches in our dataset, the 143 mutations at the root of hg R1a cannot be specifically distributed between the branches R1a1'6. Apart from M420, SRY10831.2, M198 and M417, known to define the branches R1a1'6 as they are drawn, the rest of the mutations (139) are marked in the annotations table as M420_eq, although they may or may not be equivalent to M420.

Z283 3 R1a1 Z284 Z2911 Z91 68 1 R1a1e R1a1d R1a1a'c CTS1123 Z287 L260 CTS11962 M558 Z92 6193 7 R1a1c R1a1a'b CTS2379Z88 B158 L1029 CTS10301 CTS3402 Z685 B145 (M458) 46 11 R1a1b R1a1a B159 B160 B161 B162 B150 B124 Y33 B148 Z1907 CTS8092B146 B56 215 212 13

M3904B157 B156 B155 B154 CTS8816 B123 B149 B118 B119 111

B153 CTS1070 B144 CTS6988B122 B120 16 1

B152 B151 B121 PR4446 28 29 34 26 27 22 26 24 26 43 30 23 9 14 30 35 24 18 21 24 29 32 31 22 13 14 714 ) (2 (2 US US US an i n Tatar i mixed family Saami mixed Swede Swede ra Komi licates ID Russian Russian Russian Cossack Cossack Mordvin Karelian Karelian Estonian p Ukrainian Ukrainian Ukrainian Ukrainian Ukrainian Uk Ukrainian Hungarian Circassian du duplicates) 3 Sample sons: 10327 15891 14329 35018 13704 35113 10494 35238 35041 35179 20417 13755 16338 35176 35174 14330 16797 35121 35177 16970 13765 16796 13756 35026 35240 35178 35109 11805 father: GS0025 DNA B0 2008 R1a1 Karafet Van R1a Oven 2013 b1a3 b1a1 ISOGG b1a3b b1a1a b1a2a b1a2b* R1a1a1 R1a1a1 R1a1a1 R1a1a1 R1a1a1 b1a1b1 R1a1a1 R1a1a1 b1a2b3 R1a1a1

Figure S37. Refined topology of the Y-chromosome haplogroup (hg) R1a1. In one case, the relationship of the branches does not follow previous work: in the Y-chromosome minimal reference phylogeny (van Oven et al. 2013), R-L260 is nested within R-M458, whereas in our dataset, the branch defined by L260 constitutes an outgroup for the group containing the branch carrying M458.

M343 17 R1b M335 B1 L754 13 R1b1'14 V88 P297 M18 25 R1b1'13 M478(M73) M269 106 73 R1b1'12 L23 1 R1b1'11 Z2105 M412 8 1 R1b16 R1b14 R1b12 R1b1'17 R1b15 R1b13 R1b11 B309 CTS7650 B301 B302 B2 B303 B5 B8 2 11 3 1 R1b1'10 R1b17 Z2115 L11 B3 B4 B306 PF7580 B6 B308 7 43 R1b1'19

B304 B7 B9 13R1b10 B305 L945 B307 B10 166 18 20 42 29 30 30 50 39 58 40 42 57 49 2 n US Avar unkn unkn Tadjik Dutch Khalkh PGP Bashkir Mongol TurkJew Assyrian KurdiJew MoroJew PGP PGP Armenian Sardinians Tabassara Sardinians Sardinians Sardinians Sardinians identifier 4 6 3 29 F2 16886 35173 14559 13750 14406 16881 16032 16192 16134 35234 16133 12713 Sample R1b1c R1b1* R1b1b2 14364 R1b1b1 Karafet 2008 R1b* R1b2 R1b1a Van Oven 2013 * R1b1* R1b1c R1b1b R1b1a1 R1b1a2a2 R1b1a2a1 ISOGG

Figure S38. Refined topology of the Y-chromosome haplogroup R1b10-17. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing.

L11 7 R1b1'19 U106 Z1904 1 1 R1b6'9 R1b1'18 L217 Z18 B322 Z381 47 1 R1b9 R1b8 R1b7 R1b6 B313 B314 B332 B333 Z156 Z301 2 1

Z304 B319 B12 L47 Z348 U198 6 18

DF98 DF96 Z9 Z152 DF94 DF89 23 222

B320 B321 B11 L1 Z21 Z327 B328 B323 B324 B334 B335 19 17 13

B318 B315 S512 Z11 B331 B329 11 7 42

B317 B316 B325 B15 B13 B327 B330 B16 1

B326 B14 43 34 32 34 50 47 30 21 21 21 30 48 36 40 17 16 16 16 38 23 35 39 33 32 28 43 US US US US US unkn unkn unkn unkn unkn unkn unkn unkn unkn unkn unkn unkn Dutch Dutch Dutch Dutch Dutch Dutch Dutch Dutch PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP Ukrainian identifier F1 F8 F4 F9 53 F21 F10 F24 F22 9926 9932 9920 9931 6909 Sample 15227 35175 16334 15885 16014 16027 15155 15175 11740 20414 12712 16029 GS002 1 R1b1b2g R1b1b2g R1b1b2g Karafet 2008 Van Oven 2013 a1 a1* a1a a1b a1c1 a1c1 a1b2 a1c2a a1c2* a1c2b1 a1c2b2 a1c2b2a1 a1c2b2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 ISOGG

Figure S39. Refined topology of the Y-chromosome haplogroup R1b6-9. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing.

Z1904 1 R1b1'18 B310 P312 3 1 R1b18 R1b1'5 B311 B312 DF19 L238 DF27 L21 U152 2 1 3 1 R1b5 R1b3 R1b2 R1b1 DF88 S233 R1b4 S227 B20 B344 S359 B21 B336 B341 B345 B351 13 5 1 2 33

B375 B352 B355 CTS956 M153 DF17 B18 Z198 B342 B343 B337 B338 13492

B353 B354 CTS6356 B355 B339 B340 M167 B19 14

Z206 B17

46 42 34 25 26 38 12 137 31 39 29 36 42 32 51 31 34 2 432334036 e US US US US US US US NW unkn unkn unkn unkn Unkn CEPH Rican Rican Dutch Dutch French PGP PGP PGP PGP PGP PGP PGP Puerto Puerto Mordvin pedigree PGP PGP PGP PGP German6 European PGP Portugues AndeanHA AndeanHA identifier 89 82 31 F17 F20 11807 15189 11737 15186 15223 11814 15229 10426 16015 10437 15711 19959 15874 16891 19988 15710 16375 15884 15233 NA128 NA128 HG007 Sample R1b1b2 R1b1b2 R1b1b2 R1b1b2c R1b1b2d Karafet 2008 Van Oven 2013 a2d a2a* a2e1 a2e2 a2a1c a2a1* a2a1* a2a1b1a R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 a2a1a1a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 ISOGG

Figure S40. Refined topology of the Y-chromosome haplogroup R1b3-5. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing.

P312 1

DF19 L238 DF27 L21 U152 2 1 3 1 R1b5 R1b4 R1b3 R1b2 R1b1 DF13 DF63 Z36 (L2) Z192 B348 DF90 Z56 1 11

DF1 Z2542 L20 L408 CTS3080 Z57 PF6656 L654 S47 ` Z43 1 49 1

S530 B365 DF21 B364 DF49 B363 B362 Z253 B357 Z3025 B356 DF41 PR4567 B349 Z68 B350 Z144 B347 Z46 23 1 1 1 8

B366 Z3000 Z246 DF23 Z2534 B359 B358 CTS2376 B346 1129

M222 DF73 Z2184 B361 B360 16 21 37 36 40 36 43 35 35 37 44 18 12 47 38 32 60 57 38 188 21 45 43 28 33 38 34 42 44 31 47 42 34 US US US US US US US US US US US TSI ew CEU CEU PGP MXL Arab unkn unkn unkn unkn unkn unkn unkn unkn unkn unkn unkn Dutch Dutch Dutch British PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP Hispanic Christian PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP PGP reference AshkenaziJ PGP identifier F1 F5 F13 9930 9928 14569 16139 11809 16885 15152 15178 16028 11761 16371 16031 15221 11739 15191 10425 20420 11810 14565 10323 14563 11738 16333 10436 14568 16030 NA07357 NA10851 NA19649 NA20509 Sample R1b1b2 R1b1b2 R1b1b2 R1b1b2f R1b1b2e Karafet 2008 Van Oven 2013 a2c2 a2b* a2b2 a2c1i a2c1* a2c1a a2c1* a2c1* a2b1* a2b3c a2c1k a2c1* a2c1g a2c1f* a2b3b a2c1a1 a2c1b2 a2c1f2* a2b1a1 a2c1f2d a2c1a1a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 R1b1a2a1 ISOGG

Figure S41. Refined topology of the Y-chromosome haplogroup R1b1-2. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing.

M479 1 R2 M124 167 R2a P267 B288 16

B292 B290 1 38

Y1332 Y1376 32

B294 B293 B291 B289 55 45 80 21 23 90 Thakur Santhal Gujara Iran Iran Jew er UP Brahmin UP Brahmin UP 16800 16809 16807 16798 16216 NA20845 Sample iden Sample R* R2 Karafet Karafet 2008 R2 Van Oven 2013

R2a R2* R2a1 ISOGG Figure S42. Refined topology of the Y-chromosome haplogroup R2. Grey dashed lines denote known branches with no sequence data.