c.

a.

O-M175
T_9

S_73**

R_62

Q_32

O_230*

N_27
Haplogroups with N>8

M_52**

L_14

J_48

I_13

S-B254
H_23

G_13

E_47

C3_32

C_97**

b.
Frequency in the whole dataset N=793

M-P256
30

20

10

0
600 620 640 660 680 700 720
Number of mutations from BT

C-M130

BT

2.0E-4
Figure S1 Distribution of the number of mutations from terminal tips to the BT node (gray circle) on the Maximum Likelihood (ML) tree.
a. violin plots for haplgroups (hgs) with N>8, number of samples is next to the hg label, main hgs discussed in the text are marked with **.
b. histogram for the whole dataset of 793 individuals with mean (648) and standard deviation (18).
c. the ML tree as in Figure 1, yellow boxes highlight the main hgs discussed in text.
The two rooting samples from hg A are excluded from calculations.
 CBL002 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* C8-MY1025
BRE05 Flores_Bere (Flores) Wallacea Jacobs et al. 2019* C8-MY1025
n73 BRE06 Flores_Bere (Flores) Wallacea Jacobs et al. 2019* C8-MY1037
n76 CBL33 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* C8-MY1038
n70 RAM067 Flores_Rampasasa (Flores) Wallacea Jacobs et al. 2019* C8-MY1026
CBL019 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* C8-MY1027
CBL018 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* C8-MY1036
n71
CBL34 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* C8-MY1035
n81 RAM005 Flores_Rampasasa (Flores) Wallacea Jacobs et al. 2019* C8-MY1039
n80RAM025 Flores_Rampasasa (Flores) Wallacea Jacobs et al. 2019* C8-MY1040
n68 n78
CBL010 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* C8-MY1041
n79CBL022 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* C8-MY1042
CBL027 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* C8-MY1043
C8-MY1021 n77
RAM022 Flores_Rampasasa (Flores) Wallacea Jacobs et al. 2019* C8-MY1044
n67
RAM105 Flores_Rampasasa (Flores) Wallacea Jacobs et al. 2019* C8-MY1045
RAM024 Flores_Rampasasa (Flores) Wallacea Jacobs et al. 2019* C8-MY1034
n82 RAM038 Flores_Rampasasa (Flores) Wallacea Jacobs et al. 2019* C8-MY1047
n66 TL097 Ma'anyan (Borneo) Sundaland Jacobs et al. 2019* C8-MY1051
n65 TL119 Ma'anyan (Borneo) Sundaland Jacobs et al. 2019* C8-MY1052
n58 n64 TL113 Ma'anyan (Borneo) Sundaland Jacobs et al. 2019* C8-MY1053
n63 SS6002751 Malay Sundaland Wong et al. 2013 C8-MY1054
GS000035257-ASM Aeta (Luzon) PhilTwn Karmin et al. 2015 C8-B468
n61 SS6002817 Malay Sundaland Wong et al. 2013 C8-MY1056
n59
KJG18 Sulawesi_Kajang (Sulawesi) Wallacea Jacobs et al. 2019* C8-MY1057
GS000020272-ASM Murut (Borneo) Sundaland Karmin et al. 2015 C8-B71
n60 GS000022099-ASM Murut (Borneo) Sundaland Karmin et al. 2015 C8-B71
GS000019981-ASM Murut (Borneo) Sundaland Karmin et al. 2015 C8-B72
n56 n88 MTW-MDB-020 Mentawai (Mentawai) Sundaland This study C8-MY1060
n87 MTW-MDB-032 Mentawai (Mentawai) Sundaland This study C8-MY1061
n86 MTW078 Mentawai (Mentawai) Sundaland Jacobs et al. 2019* C8-MY1064
C8-F725 n85 MTW-MDB-025 Mentawai (Mentawai) Sundaland This study C8-MY1062
n84
MTW-MDB-002 Mentawai (Mentawai) Sundaland This study C8-MY1063
n55 MTW-MDB-011 Mentawai (Mentawai) Sundaland This study C8-MY1065
n89
n83 MTW-MDB-024 Mentawai (Mentawai) Sundaland This study C8-MY1066
MTW-TLL-022 Mentawai (Mentawai) Sundaland This study C8-MY1067
HGDP01310 Dai East Asia Bergström et al. 2020 C8-MY1068
n54 NA20889 Gujarati World 1000 Genome Consortium 2015 C5-MY1081
n53 NA21118 Gujarati World 1000 Genome Consortium 2015 C5-Z31734
n52 GS000017146-ASM Low-caste_MP World Karmin et al. 2015 C5-MY1085
n51
C5-M356 SS6002781 Malay Sundaland Wong et al. 2013 C5-MY1087
NA21133 Gujarati World 1000 Genome Consortium 2015 C5-Z39947
n48
HGDP00029 Brahui World Bergström et al. 2020 C5-SK989
n40 n50 HG03593 Bengali World 1000 Genome Consortium 2015 C5-Z31714
n49
HG03228 Punjabi World 1000 Genome Consortium 2015 C5-Z31779
n46 CBL006 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* C7-MY1074
CBL054 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* C7-MY1075
n45 CBL025 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* C7-MY1076
n39 n44
C7-B67 n43 RAM008 Flores_Rampasasa (Flores) Wallacea Jacobs et al. 2019* C7-MY1077
n41 FLT020 Lembata_Timur_Kadakewa (Lembata) Wallacea Jacobs et al. 2019* C7-MY1079
GS000016936-ASM Lebbo (Borneo) Sundaland Karmin et al. 2015 C7-B69
C9-B68 n42 GS000016937-ASM Lebbo (Borneo) Sundaland Karmin et al. 2015 C7-B70
GS000020271-ASM Dusun (Borneo) Sundaland Karmin et al. 2015 C9-B68
n107 GRC15491812 Raiatea (Raiatea) Remote Oceania Hudjashov et al. 2018 C2-MY1583
n106 GRC15491810 Tahaa (Tahaa) Remote Oceania Hudjashov et al. 2018 C2-MY1581
n104 n105
GRC15491811 Raiatea (Raiatea) Remote Oceania Hudjashov et al. 2018 C2-MY1582
GRC15491815 Tahaa (Tahaa) Remote Oceania Hudjashov et al. 2018 C2-FT12774
n101 B00IEVJ Nagum_Boiken (New Guinea) SahulN Brucato 2021* C2-MY1580
n103 GS000035258-ASM Koinanbe (New Guinea) SahulN Karmin et al. 2015 C2-B463
n102
GS000035686-ASM Koinanbe (New Guinea) SahulN Karmin et al. 2015 C2-B464
GS000035255-ASM Koinanbe (New Guinea) SahulN Karmin et al. 2015 C2a2a-B462
n100 LP6005443-DNA_C08 Papuan (New Guinea) SahulN Mallick et al. 2016 C2-MY1104
n109
n111 SS6004472 Papua_Sim (New Guinea) SahulN Mallick et al. 2016 C2-MY1103
GS000017004-ASM Bajo (Sulawesi) Wallacea Karmin et al. 2015 C2-Z32832
n108 n110 SS6002832 Malay Sundaland Wong et al. 2013 C2-MY1105_eq
n99
n112 B00IEVL Nagam-Boikin-Kakra (New Guinea) SahulN Brucato 2021* C2-MY1108
n38 n98 LP6005443-DNA_D07 Papuan (New Guinea) SahulN Mallick et al. 2016 C2-MY1106
MKT-TBR-007 Tanimbar (Tanimbar) Wallacea Jacobs et al. 2019* C2-MY1109
C2-Y25191 MPI-389 Mappi, Korowai (New Guinea) SahulN This study C2-F10054.2
n97 n115 EGAN00001279035 Bundi (New Guinea) SahulN Malaspinas et al. 2016 C2-MY1097
n114 EGAN00001279031 Bundi (New Guinea) SahulN Malaspinas et al. 2016 C2-MY1096
EGAN00001279033 Bundi (New Guinea) SahulN Malaspinas et al. 2016 C2-MY1098
n113
EGAN00001279032 Bundi (New Guinea) SahulN Malaspinas et al. 2016 C2-MY1099
n116 EGAN00001279034 Bundi (New Guinea) SahulN Malaspinas et al. 2016 C2-MY1100
n122 SMB-ANK-026 Anakalang (Sumba) Wallacea This study C2-MY1111
C2-M38 n121 SMB-WNG-021 Wunga (Sumba) Wallacea This study C2-MY1112
n96 n120
FLT018 Lembata_Timur_Kadakewa (Lembata) Wallacea Jacobs et al. 2019* C2-MY1114
SLW51 Sulawesi_Mandar (Sulawesi) Wallacea Jacobs et al. 2019* C2-MY1113
n119
DTT-KEI-031 Kei (Kei) Wallacea Jacobs et al. 2019* C2-MY1115
n118 n123 SMB-ANK-027 Anakalang (Sumba) Wallacea This study C2-MY1116
n35 n125 UV944 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 C2-MY1120
n124 UV925 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 C2-MY1119
SMB-WNG-002 Wunga (Sumba) Wallacea This study C2-MY1121
C2-FT71648 n130 FLT022 Lembata_Timur_Kadakewa (Lembata) Wallacea Jacobs et al. 2019* C2-MY1125
n117 SLW40 Sulawesi_Mandar (Sulawesi) Wallacea Jacobs et al. 2019* C2-MY1126
n129
n90 n128 ALR03 Alor (Alor) Wallacea Jacobs et al. 2019* C2-MY1127
n127 SLD-TBR-001 Tanimbar (Tanimbar) Wallacea Jacobs et al. 2019* C2-MY1128
n126 GS000017005-ASM Bajo (Sulawesi) Wallacea Karmin et al. 2015 C2-B76
ALR11 Alor (Alor) Wallacea Jacobs et al. 2019* C2-MY1129
n94 EGAN00001088616 Karryarra_WA (Australia) SahulS Bergström et al.2016 C4-Z40252
n93 EGAN00001089017 Karryarra_WA (Australia) SahulS Bergström et al.2016 C4-Z40414
C4-M347 EGAN00001192721 Broome_WA (Australia) SahulS Bergström et al.2016 C4-Z40247
n92
C4-MY1088 EGAN00001192719 Queensland_N_Atherston (Australia) SahulS Bergström et al.2016 C4-Z40419
n91 n95 SS6004477 Queensland_Australian (Australia) SahulS Mallick et al. 2016 C4-MY1091
EGAN00001072788 Queensland_Norm (Australia) SahulS Bergström et al.2016 C4-Z40423
HGDP00758 Japanese (Japan) East Asia Bergström et al. 2020 C1-MY1020
C1-M8 n36 n37 NA18971 Japanese (Japan) East Asia 1000 Genome Consortium 2015 C1-Z31839
NA18989 Japanese (Japan) East Asia 1000 Genome Consortium 2015 C1-CTS5225
GS000022293-ASM Even_Magadan World Karmin et al. 2015 C3-B86
n34
n33GS000034297-ASM Even_Magadan World Karmin et al. 2015 C3-B472
C-M130 HGDP01204 Oroqen East Asia Bergström et al. 2020 C3-MY1589
n30
n3 GS000022292-ASM Even_Magadan World Karmin et al. 2015 C3-B84
n32
GS000020129-ASM Even_Magadan World Karmin et al. 2015 C3-B85
n31
n26 GS000016165-ASM Even World Karmin et al. 2015 C3-B83
n29GS000020004-ASM Evenk World Karmin et al. 2015 C3-B89
n28 GS000020126-ASM Buryat World Karmin et al. 2015 C3-B88
n25
n27 LP6005442-DNA_D01 Xibo East Asia Mallick et al. 2016 C3-MY1590
GS000035117-ASM Mongolian World Karmin et al. 2015 C3-B470
n21 HGDP01302 Uygur World Bergström et al. 2020 C3-F8473
GS000016168-ASM Koryak World Karmin et al. 2015 C3-B96
n24
n23 GS000016169-ASM Koryak World Karmin et al. 2015 C3-B95
n22 GS000019993-ASM Koryak World Karmin et al. 2015 C3-B94
n14 GS000014335-ASM Evenk World Karmin et al. 2015 C3-M93
n20 GS000022440-ASM Altaian World Karmin et al. 2015 C3-Z32844
n19 HGDP01244 Xibo East Asia Bergström et al. 2020 C3-F10085
n18 GS000022071-ASM Koryak World Karmin et al. 2015 C3-B77
n1 C3-L1373 n17 LP6005443-DNA_F05 Chipewyan World Mallick et al. 2016 C3-BY728
n13 SS6003406 Malay Sundaland Wong et al. 2013 C3-MY1592
n15
n16 GS000013752-ASM Kazakh World Karmin et al. 2015 C3-F9700
HGDP01205 Oroqen East Asia Bergström et al. 2020 C3-F10283
C3-M217 GS000019992-ASM Koryak World Karmin et al. 2015 C3-B79
n4
n12 GS000014418-ASM Buryat World Karmin et al. 2015 C3-M407
n11 NA18749 Han Chinese East Asia 1000 Genome Consortium 2015 C3-CTS1003
C3f-Page12 GS000015179-ASM Han Chinese East Asia Personal Genomes Project C3-Z31684
n9 HG02141 Kinh MSEA 1000 Genome Consortium 2015 C3-F12752
n10
HG02373 Dai East Asia 1000 Genome Consortium 2015 C3-K536
n5
HG00628 Han Chinese East Asia 1000 Genome Consortium 2015 C3-MY1588
C3-CTS4660 GS000016863-ASM Han Chinese East Asia 1000 Genome Consortium 2015 C3-MY1570
n6 GS000016861-ASM Han Chinese East Asia 1000 Genome Consortium 2015 C3-MY1585
SS6004467 Dai East Asia Mallick et al. 2016 C3-MY1595
J-M304 GS000013747-ASM Iranian World Karmin et al. 2015 J-PF4901
n2 GS000016136-ASM Druze World Karmin et al. 2015 J-P58

70000 60000 50000 40000 30000 20000 10000 0

Years before present
Figure S2. Dated phylogenetic tree of haplogroup (hg) C-M130. Main hg labels shown on branches, tree file and more labels in File S1, node ages
with CI are in Table S3. Samples from hg J-M304 are used as outgroup and calibration point is hg C-M130 (Table S2). Labels colorcoded as on Figure 1.
 B00IWTR Kamea (New Guinea) SahulN Brucato 2021* S9j1-MY160
n137
n136 EGAN00001279051 Marawaka (New Guinea) SahulN Malaspinas et al. 2016 S9j1-MY162
S9j-MY153 EGAN00001279053 Marawaka (New Guinea) SahulN Malaspinas et al. 2016 S9j1-MY161
n133 EGAN00001279052 Marawaka (New Guinea) SahulN Malaspinas et al. 2016 S9j2-MY158
n135
S9i'j-MY151 n131 n134 EGAN00001279055 Marawaka (New Guinea) SahulN Malaspinas et al. 2016 S9j2-MY157
EGAN00001279054 Marawaka (New Guinea) SahulN Malaspinas et al. 2016 S9j2-MY155
SLW54 Sulawesi_Mandar (Sulawesi) Wallacea Jacobs et al. 2019* S9i-MY152
n132
SS6002786 Malay Sundaland Wong et al. 2013 S9i-MY152
S9i'k-F16114 n123
n129 EGAN00001279046 Tari (New Guinea) SahulN Malaspinas et al. 2016 S9k1-MY171
n127 EGAN00001279050 Tari (New Guinea) SahulN Malaspinas et al. 2016 S9k1-FT61388
n128 EGAN00001279047 Tari (New Guinea) SahulN Malaspinas et al. 2016 S9k1-MY170
n126 EGAN00001279049 Tari (New Guinea) SahulN Malaspinas et al. 2016 S9k1-MY169
S9k-M828 n130
EGAN00001279045 Mendi (New Guinea) SahulN Malaspinas et al. 2016 S9k1-MY167
n124 EGAN00001279048 Tari (New Guinea) SahulN Malaspinas et al. 2016 S9k1-MY166
S9c'k-Z41356 n115
EGAN00001279041 Mendi (New Guinea) SahulN Malaspinas et al. 2016 S9k-MY165
n125 EGAN00001279043 Mendi (New Guinea) SahulN Malaspinas et al. 2016 S9k2-MY164
GS000016935-ASM Lebbo (Borneo) Sundaland Karmin et al. 2015 S9h1-MY147
n122
n121 SLW36 Sulawesi_Mandar (Sulawesi) Wallacea Jacobs et al. 2019* S9h2-MY146
n119 B00IEW8 Maisin (New Guinea) SahulN Brucato 2021* S9g-MY150
ALR06 Alor (Alor) Wallacea Jacobs et al. 2019* S9f-MY149
n120
S9c'h- n116 LP6005443-DNA_H07 Papuan (New Guinea) SahulN Mallick et al. 2016 S9e-Z41506
S9-P202 Z41398 n118
LP6005443-DNA_G07 Papuan (New Guinea) SahulN Mallick et al. 2016 S9d-Z41351
n117 NG06 Papuan (New Guinea) SahulN Jacobs et al. 2019* S9d-MY144
n107
LP6005443-DNA_E07 Papuan (New Guinea) SahulN Mallick et al. 2016 S9c-M226.1
n112 EGAN00001279036 Kundiawa (New Guinea) SahulN Malaspinas et al. 2016 S9b1-MY143
EGAN00001279039 Kundiawa (New Guinea) SahulN Malaspinas et al. 2016 S9b1-MY142
n110 n111 EGAN00001279038 Kundiawa (New Guinea) SahulN Malaspinas et al. 2016 S9b1-MY140
S7'9-Z42413 S9b-MY131 B00IWU3 Oksap_Meng (New Guinea) SahulN Brucato 2021* S9b2-MY138
n104 n109 EGAN00001279044 Mendi (New Guinea) SahulN Malaspinas et al. 2016 S9b3-MY136
S9a'b- n114
n113 PNG001 Enga (New Guinea) SahulN This study S9b3-MY135
n108 B00IWTU Kewabi-Poroma (New Guinea) SahulN Brucato 2021* S9b3-MY133
MY129 FLT042 Lembata_Timur_Kadakewa (Lembata) Wallacea Jacobs et al. 2019* S9a-MY130
S7'8-FGC38729 S8-P60 n106
EGAN00001192720 Pilbara_WA (Australia) SahulS Bergström et al.2016 S8-Z41753
n105 EGAN00001196790 Queensland_Mount_Isa (Australia) SahulS Bergström et al.2016 S8-Z41759
S4'9 n102
EGAN00001089016 Queensland_Gunganji (Australia) SahulS Bergström et al.2016 S7-MY128
UV1263 Pasismanua (New Britain) SahulN Vernot et al. 2016 S6d1-MY127
-Z41335 n88
n101 UV1266 Pasismanua (New Britain) SahulN Vernot et al. 2016 S6d1-MY126
S6b'd- n100 UV923 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 S6d2-MY124
UV1003 Nakanai Loso (New Britain) SahulN Vernot et al. 2016 S6d3-MY122
MY115 n98 n103
UV1134 Ata (New Britain) SahulN Vernot et al. 2016 S6d3-MY121
n99 GRC15491807 Raiatea (Raiatea) Remote Oceania Hudjashov et al. 2018 S6c-MY117
n97 UV518 Mussau (Mussau) SahulN Vernot et al. 2016 S6b-MY116
S5'6-FT178878 UV1042 Mamusi (New Britain) SahulN Vernot et al. 2016 S6a-MY114
n93 n96 UV919 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 S5-MY112
S5-MY106 n95 UV986 Nakanai (New Britain) SahulN Vernot et al. 2016 S5-MY111
S4'6-PR495.2 n89
n94 UV1196 Melamala (New Britain) SahulN Vernot et al. 2016 S5-MY109
UV946 Nakanai (New Britain) SahulN Vernot et al. 2016 S5-MY107
S4c-Z41921 EGAN00001072789 Queensland_SE (Australia) SahulS Bergström et al.2016 S4c-Z41924
S4b'c-Z41923 n92
UV940 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 S4c-MY104
S4-P315 n90
n91
UV1260 Mangseng (New Britain) SahulN Vernot et al. 2016 S4b-MY103
EGAN00001196788 Queensand_N_Kuranda (Australia) SahulS Bergström et al.2016 S4a-P401
n87
n148 FAN-KEI-011 Kei (Kei) Wallacea Jacobs et al. 2019* S10c-MY101
FAN-KEI-024 Kei (Kei) Wallacea Jacobs et al. 2019* S10c-MY102
n146
FLT078 Lembata_Waipukang (Lembata) Wallacea Jacobs et al. 2019* S10c-MY98
n147
n143 TL004 Ma'anyan (Borneo) Sundaland Jacobs et al. 2019* S10c-MY97
B00IEVO Enga (New Guinea) SahulN Brucato 2021* S10b-MY94
n145
n144 B00IEWR Maipi (New Guinea) SahulN Brucato 2021* S10b-MY93
PNG076 Enga (New Guinea) SahulN This study S10b-MY99
n142
n153 UV573 Nailik (New Ireland ) SahulN Vernot et al. 2016 S10e1-MY88
n86 n152 UV580 Nailik (New Ireland ) SahulN Vernot et al. 2016 S10e1-MY88
B00IWTX Karkar (New Guinea) SahulN Brucato 2021* S10e2-MY89
S10-SK1807 n149 DTT-KEI-006 Kei (Kei) Wallacea Jacobs et al. 2019* S10f1-MY82
n151
n139 n150 MPI-030 Korowai, Mappi (New Guinea) SahulN Jacobs et al. 2019* S10f2-MY83
KJG25 Sulawesi_Kajang (Sulawesi) Wallacea Jacobs et al. 2019* S10g-MY84
S-B254 n138
n82
n141 EGAN00001279037 Kundiawa (New Guinea) SahulN Malaspinas et al. 2016 S10a-MY75
LP6005443-DNA_F08 Papuan (New Guinea) SahulN Mallick et al. 2016 S10a-MY76
n140 LP6005443-DNA_C07 Papuan (New Guinea) SahulN Mallick et al. 2016 S10a-MY77
S11-B275 GS000016941-ASM Bajo (Sulawesi) Wallacea Karmin et al. 2015 S11-B275
S12-Z41926 EGAN00001072787 Queensland_Gunganji (Australia) SahulS Bergström et al.2016 S12-Z41926
S1-B273 n85
GS000035249-ASM Aeta (Luzon) PhilTwn Karmin et al. 2015 S1-B276
GS000035250-ASM Aeta (Luzon) PhilTwn Karmin et al. 2015 S1-Z33750
n83 S2'3-BY62222 n84
ALR21 Alor (Alor) Wallacea Jacobs et al. 2019* S2-MY68
SLW13 Sulawesi_Mandar (Sulawesi) Wallacea Jacobs et al. 2019* S3-MY69
GS000035256-ASM Kosipe (New Guinea) SahulN Karmin et al. 2015 M1c4-B271
n58
n57 GS000035365-ASM Kosipe (New Guinea) SahulN Karmin et al. 2015 M1c4-B270
GS000035260-ASM Kosipe (New Guinea) SahulN Karmin et al. 2015 M1c5-Z33740
n54 B00IEWJ Melpa (New Guinea) SahulN Brucato 2021* M1c1-MY60
n56
n53 n55 LP6005443-DNA_F07 Papuan (New Guinea) SahulN Mallick et al. 2016 M1a3-MY35
EGAN00001279042 Mendi (New Guinea) SahulN Malaspinas et al. 2016 M1c2-MY57
B00IWTM Sasinalin-Era (New Guinea) SahulN Brucato 2021* M1c3-MY61
n59
LP6005443-DNA_A08 Papuan (New Guinea) SahulN Mallick et al. 2016 M1c3-SK1889
n52
BRE10 Flores_Bere (Flores) Wallacea Jacobs et al. 2019* M1c6-MY53
n63
CBL55 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* M1c6-MY52
M1c-B256 M1c6- n62
RAM087 Flores_Rampasasa (Flores) Wallacea Jacobs et al. 2019* M1c6-MY50
n51 n60
Z42300 n61
EGAN00001089015 Mer (Australia) SahulS Bergström et al.2016 M1c6-Z42323
EGAN00001196789 Mer (Australia) SahulS Bergström et al.2016 M1c6-Z42330
B00IWTT Gapapainwa (New Guinea) SahulN Brucato 2021* M1c7-Z43832
n44 B00IEWG Melpa (New Guinea) SahulN Brucato 2021* M1b1-MY48
n50
n49 B00IWTN Melpa (New Guinea) SahulN Brucato 2021* M1b1-MY47
n48 B00IEVQ Enga (New Guinea) SahulN Brucato 2021* M1b1-MY45
n47 B00IWU1 Enga (New Guinea) SahulN Brucato 2021* M1b1-MY43
MS-PR2099 M1b- LP6005443-DNA_B08 Papuan (New Guinea) SahulN Mallick et al. 2016 M1b2-P51
n45
n30
n43
MY39 n46
B00IEVW Melpa (New Guinea) SahulN Brucato 2021* M1b3-MY41
EGAN00001279040 Kundiawa (New Guinea) SahulN Malaspinas et al. 2016 M13b-MY40
n70 MPI-025 Korowai, Mappi (New Guinea) SahulN Jacobs et al. 2019* M1a1-MY28
M1a'd- n68
MPI-065 Korowai, Mappi (New Guinea) SahulN Jacobs et al. 2019* M1a1-MY28
BNA01 Flores_Bena (Flores) Wallacea Jacobs et al. 2019* M1a2-MY31
Z30917 M1a-
n69
BNA05 Flores_Bena (Flores) Wallacea Jacobs et al. 2019* M1a2-MY30
n42 n64 SLD-TBR-022 Tanimbar (Tanimbar) Wallacea Jacobs et al. 2019* M1a3-MY38
n67
MY26 n66 TMB-TBR-027 Tanimbar (Tanimbar) Wallacea Jacobs et al. 2019* M1a3-MY37
n65 ALK-TBR-025 Tanimbar (Tanimbar) Wallacea Jacobs et al. 2019* M1a3-MY35
WAR-KEI-030 Kei (Kei) Wallacea Jacobs et al. 2019* M1a4-MY34
n41
LP6005441-DNA_A10 Papuan (New Guinea) SahulN Mallick et al. 2016 M1d-FGC24709
n74 ALR04 Alor (Alor) Wallacea Jacobs et al. 2019* M1e2-MY25
M1e- WAR-KEI-005 Kei (Kei) Wallacea Jacobs et al. 2019* M1e3-MY24
n72 n73 MPI-074 Korowai, Mappi (New Guinea) SahulN Jacobs et al. 2019* M1e1-MY22
M1a'g-Page1 MY19
MPI-376 Korowai, Mappi (New Guinea) SahulN Jacobs et al. 2019* M1e1-MY21
M1e'f- n71 NG66 Papuan (New Britain) SahulN Jacobs et al. 2019* M1f-Z43414
n40
Z43413 n79
B00IEVB Bannoni (Bougainville) SahulN Brucato 2021* M1g1-MY18
n78 B00IEWM Telei (New Guinea) SahulN Brucato 2021* M1g1-MY17
UV1230 Ata (New Britain) SahulN Vernot et al. 2016 M1g2-MY15
n21 M1-M106 n36 M1g-P87
n77
n76 UV931 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 M1g3-MY13
n75 UV500 Lavongai North (New Hanover ) SahulN Vernot et al. 2016 M1g4-MY11
UV305 Baining (New Britain) SahulN Vernot et al. 2016 M1g5-MY9
n39 UV979 Nakanai (New Britain) SahulN Vernot et al. 2016 M1h1-MY8
n32
M1h-MY6 n38
UV927 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 M1h1-MY8
n37 UV971 Nakanai (New Britain) SahulN Vernot et al. 2016 M1h1-MY8
B00IWTQ Wiru (New Guinea) SahulN Brucato 2021* M1h2-P94
M3b'c-MY3 UV043 Baining (New Britain) SahulN Vernot et al. 2016 M3b-MY5
M-P256 M3-MY113 n33
n35
UV1224 Mamusi (New Britain) SahulN Vernot et al. 2016 M3c-MY4
n31 n34 UV886 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 M3a-MY2
UV958 Nakanai (New Britain) SahulN Vernot et al. 2016 M3a-MY2
n81 UV910 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 M4-MY8891
M4-MY62 n80 UV952 Nakanai (New Britain) SahulN Vernot et al. 2016 M4-MY64
UV964 Nakanai (New Britain) SahulN Vernot et al. 2016 M4-MY65
K2-M526 R1a-M417 GS000035240-ASM Swede World Karmin et al. 2015 R1a1e-Z287
n10 R-M207 n29
SS6003431 Malay Sundaland Wong et al. 2013 R1a2b-L657
P1-M45
n27 R2a-FGC18147 n28 NA20845-200-37-ASM Gujarati World Drmanac et al. 2010 R2a-B294
n25 SS6002826 Malay Sundaland Wong et al. 2013 R2a-Y1299
Q1'2-L472 LP6007076-DNA_A01 Kashmiri_Pandit World Mallick et al. 2016 Q2a-M25
P-P295 n26
SS6004476 Karitiana World Mallick et al. 2016 Q1a-M848
n22
n24 SS6002783 Malay Sundaland Wong et al. 2013 P2-MY1512
P2-B252 n23 SS6002830 Malay Sundaland Wong et al. 2013 P2-MY1513
GS000035392-ASM Agta (Luzon) PhilTwn Karmin et al. 2015 P2-B253
O1-M119 n16
FLT060 Lembata_Waipukang (Lembata) Wallacea Jacobs et al. 2019* O1a-MY237
GT-F1329 O-M175 n14
FLT077 Lembata_Waipukang (Lembata) Wallacea Jacobs et al. 2019* O1a-MY250
n6 NO1-M214 O3i-B451 n15
KJG04 Sulawesi_Kajang (Sulawesi) Wallacea Jacobs et al. 2019* O3i-MY977
n12 SMT01 Sumatra (Sumatra) Sundaland Jacobs et al. 2019* O3i-MY984
N-M231 n13
GS000022076-ASM Yakut World Karmin et al. 2015 N-L708
NA18558-200-37-ASM ChineseEast Asia Personal Genomes Project N-M231
NO- n11 SLW42 Sulawesi_Mandar (Sulawesi) Wallacea Jacobs et al. 2019* NO2-MY1510
M2308 NO2-MY1507 n20
SMT12 Sumatra (Sumatra) Sundaland Jacobs et al. 2019* NO2-MY1509
NO2-MY1506 n19
F-M819 n17
n18 SMT03 Sumatra (Sumatra) Sundaland Jacobs et al. 2019* NO2-MY1508
SS6002749 Malay Sundaland Wong et al. 2013 NO2-MY1505
n3 NO2- HG03742 Telugu World 1000 Genome Consortium 2015 NO2b-MY1504
GRC15560180 Jewish World Behar et al.2017 G2-Y12978
MY1503 G2-CTS1868 n9
G-M201 n8 GS000010844-ASM Jewish World Carmi et al. 2014 G2-MY1514
GS000013739-ASM North_Ossetian World Karmin et al. 2015 G2-A200
n7
n1 GRC15560107 Jewish World Behar et al.2017 G1-Z26333
SS6002805 Malay Sundaland Wong et al. 2013 F3-MY1502
F- n4 n5 HG02040 KinhMSEA Polaris Diversity F4-Z40734
C-M130 MY1500
LP6005443-DNA_E01 LahuEast Asia Mallick et al. 2016 F-M427
n2 DTT-KEI-031 Kei (Kei) Wallacea Jacobs et al. 2019* C2-MY1115
GS000013752-ASM Kazakh World Karmin et al. 2015 C3-L1373

Years Before Present

70000 60000 50000 40000 30000 20000 10000 0

Figure S3. Dated phylogenetic tree of haplogroup (hg) MS-PR2099. Main hg labels shown on branches, tree-file with more labels in File S2, node ages with CI are in Table S4.
For phylogeneitc structure, similarly for the hg O-M175 tree (Figure S4, File S3), same set of samples from hgs N-M231, NO2-MY1503, P-P259, G-M201, F-MY1500 are
included, samples from hg C-M130 are used as outgroup and calibration point is GT-F1329 (Table S2). Labels colorcoded as on Figure 1.
 n171
NIAS17 Nias_Gomo (Nias) Sundaland Jacobs et al. 2019* O1a-MY207
n169 NIAS38 Nias_Gomo (Nias) Sundaland Jacobs et al. 2019* O1a-MY207
n168 170NIAS15 Nias_Gomo (Nias) Sundaland Jacobs et al. 2019* O1a-MY208
n167 NIAS21 Nias_Gomo (Nias) Sundaland Jacobs et al. 2019* O1a-MY1534
n166 NIAS26 Nias_Gomo (Nias) Sundaland Jacobs et al. 2019* O1a-MY236
n165 NIAS02 Nias_Hilitobara (Nias) Sundaland Jacobs et al. 2019* O1a-MY235
NIAS33 Nias_Gomo (Nias) Sundaland Jacobs et al. 2019* O1a-MY234
SMT39 Sumatra (Sumatra) Sundaland Jacobs et al. 2019* O1a-MY233
O1a-MY200 n163 NIAS04 Nias_Hilitobara (Nias) Sundaland Jacobs et al. 2019* O1a-MY232
n161 n164 NIAS08 Nias_Hilitobara (Nias) Sundaland Jacobs et al. 2019* O1a-MY209
O1a-F78 n162 MTW071 Mentawai (Mentawai) Sundaland Jacobs et al. 2019* O1a-MY231
NIAS16 Nias_Gomo (Nias) Sundaland Jacobs et al. 2019* O1a-MY229
n160 n173 SAMEA104038928 Dai East Asia Polaris Diversity O1a-Z23484
n174 LP6005441-DNA_C05 Han Chinese East Asia Mallick et al. 2016 O1a-F18517
n172 SAMEA104038841 Han Chinese East Asia Polaris Diversity O1a-Z23496
n156
LP6005519-DNA_D06 Igorot (Luzon) PhilTwn Mallick et al. 2016 O1a-MY211
n159 B00IEV8 Motuna (Bougainville) SahulN Brucato 2021* O1a-MY227
n157 B00IWTW Pidgin (New Guinea) SahulN Brucato 2021* O1a-MY226
O1a-F140 DNG06 Java_Dieng (Java) Sundaland Jacobs et al. 2019* O1a-MY213
n158 DNG34 Java_Dieng (Java) Sundaland Jacobs et al. 2019* O1a-MY255
n155 SS6002823 Malay Sundaland Wong et al. 2013 O1a-MY222
n177 SS6002788 Malay Sundaland Wong et al. 2013 O1a-MY219
n181
n178
TL032 Ma'anyan (Borneo) Sundaland Jacobs et al. 2019* O1a-MY220
n180 GS000035248-ASM Agta (Luzon) PhilTwn Karmin et al. 2015 O1a-B389
n152
n175 n179 SS6002816 Malay Sundaland Wong et al. 2013 O1a-MY218
UV1043 Mamusi (New Britain) SahulN Vernot et al. 2016 O1a-MY217
n176 LP6005442-DNA_E07 Atayal (Taiwan) PhilTwn Mallick et al. 2016 O1a-MY223
O1a-F31 SS6002750 Malay Sundaland Wong et al. 2013 O1a-MY224
n154 HG02079 Kinh MSEA 1000 Genome Consortium 2015 O1a-F23485
n148 n153 HG02360 Dai East Asia 1000 Genome Consortium 2015 O1a-F20634
SAMEA104038844 Kinh MSEA Polaris Diversity O1a-MY1554
n151 SAMEA104038917 Dai East Asia Polaris Diversity O1a-Z7773
n150 SAMN00006498 Han Chinese East Asia Polaris Diversity O1a-CTS352
n149
SAMN00000455 Han Chinese East Asia Polaris Diversity O1a-CTS11040
FLT060 Lembata_Waipukang (Lembata) Wallacea Jacobs et al. 2019* O1a-MY237
n146 n147 SS6002814 Malay Sundaland Wong et al. 2013 O1c-MY266
n132 SS6002833 Malay Sundaland Wong et al. 2013 O1c-MY265
SS6002807 Malay Sundaland Wong et al. 2013 O1c-MY264
n145 GS000019985-ASM Murut (Borneo) Sundaland Karmin et al. 2015 O1c-B396
n136 n144 GS000035251-ASM Batak (Palawan) PhilTwn Karmin et al. 2015 O1c-B397
n143 GS000019983-ASM Murut (Borneo) Sundaland Karmin et al. 2015 O1c-B395
LP6005592-DNA_H03 Hawaiian (Hawaii) Remote Oceania Mallick et al. 2016 O1c-MY263
n137 n141 NIAS13 Nias_Hilitobara (Nias) Sundaland Jacobs et al. 2019* O1c-MY258
O1c-M110 O1c-MY253 NIAS01 Nias_Hilitobara (Nias) Sundaland Jacobs et al. 2019* O1c-MY257
n140 n142 NIAS10 Nias_Hilitobara (Nias) Sundaland Jacobs et al. 2019* O1c-MY256
O1-M119 n133 n139 NIAS03 Nias_Hilitobara (Nias) Sundaland Jacobs et al. 2019* O1c-MY259
n138 NIAS12 Nias_Hilitobara (Nias) Sundaland Jacobs et al. 2019* O1c-MY260
n131 SS6002764 Malay Sundaland Wong et al. 2013 O1c-MY261
n135 GS000035252-ASM Batak (Palawan) PhilTwn Karmin et al. 2015 O1c-B394
n134 KJG08 Sulawesi_Kajang (Sulawesi) Wallacea Jacobs et al. 2019* O1c-MY268
B00IEW5 Suau-Wedau (New Guinea) SahulN Brucato 2021* O1c-MY269
n188 GS000035435-ASM Agta (Luzon) PhilTwn Karmin et al. 2015 O1b-B391
n189 SS6002824 Malay Sundaland Wong et al. 2013 O1b-MY239
KJG32 Sulawesi_Kajang (Sulawesi) Wallacea Jacobs et al. 2019* O1b-MY238
n186 n187 MTW007 Mentawai (Mentawai) Sundaland Jacobs et al. 2019* O1b-MY242
n183 MTW024 Mentawai (Mentawai) Sundaland Jacobs et al. 2019* O1b-MY243
O1b-F819 n185 SMT05 Sumatra (Sumatra) Sundaland Jacobs et al. 2019* O1b-MY248
n182 n184 SS6002825 Malay Sundaland Wong et al. 2013 O1b-MY249
FLT077 Lembata_Waipukang (Lembata) Wallacea Jacobs et al. 2019* O1b-MY250
NA18647 Han Chinese East Asia 1000 Genome Consortium 2015 O1b-MY1533
HG01844 Kinh MSEA 1000 Genome Consortium 2015 O2a2-A22938
HG02407 Dai East Asia 1000 Genome Consortium 2015 O2a2-MY1528
n258 HG02389 Dai East Asia 1000 Genome Consortium 2015 O2a2-F18676
n250 n255
LP6005443-DNA_B01 Dai East Asia Mallick et al. 2016 O2a2-MY1530
n257 RAM003 Flores_Rampasasa (Flores) Wallacea Jacobs et al. 2019* O2a2-MY283
n256 GS000019979-ASM Dusun (Borneo) Sundaland Karmin et al. 2015 O2a2-B420
O2a2-F789 n254 LP6005442-DNA_G01 Yi East Asia Mallick et al. 2016 O2a2-MY282
n221 n253 SS6002760 Malay Sundaland Wong et al. 2013 O2a2-MY284
n251 BLI615 Bali_Gadon (Bali) Sundaland Jacobs et al. 2019* O2a2-MY901
n252 GS000019953-ASM Dusun (Borneo) Sundaland Karmin et al. 2015 O2a2-B417
SMT23 Sumatra (Sumatra) Sundaland Jacobs et al. 2019* O2a2-MY900
n249 SS6002829 Malay Sundaland Wong et al. 2013 O2a2-MY297
n247 SS6002821 Malay Sundaland Wong et al. 2013 O2a2-F16164
n248 SS6002827 Malay Sundaland Wong et al. 2013 O2a2-MY296
n222 SS6002784 Malay Sundaland Wong et al. 2013 O2a2-MY295
n238 n246 DNG05 Java_Dieng (Java) Sundaland Jacobs et al. 2019* O2a2-MY290
n241 SS6002791 Malay Sundaland Wong et al. 2013 O2a2-MY292
n245 SS6002787 Malay Sundaland Wong et al. 2013 O2a2-MY289
n242 SS6002770 Malay Sundaland Wong et al. 2013 O2a2-MY288
n244 SS6002828 Malay Sundaland Wong et al. 2013 O2a2-MY287
n243 DNG09 Java_Dieng (Java) Sundaland Jacobs et al. 2019* O2a2-MY286
GS000016803-ASM Gond World Karmin et al. 2015 O2a2-B422
n240 SS6002818 Malay Sundaland Wong et al. 2013 O2a2-MY299
n223 GS000017007-ASM Lebbo (Borneo) Sundaland Karmin et al. 2015 O2a2-MY298
n130 SS6002775 Malay Sundaland Wong et al. 2013 O2a2-MY275
n237
n235 SS6002813 Malay Sundaland Wong et al. 2013 O2a2-MY276
n236 SS6002741 Malay Sundaland Wong et al. 2013 O2a2a-MY280
SS6002767 Malay Sundaland Wong et al. 2013 O2a2-MY273
n206 n234 SS6002810 Malay Sundaland Wong et al. 2013 O2a2-MY274
SS6002822 Malay Sundaland Wong et al. 2013 O2a2-MY277
n224 n233 GS000019972-ASM Vietnamese MSEA Karmin et al. 2015 O2a2-B428
n230 HG02061 Kinh MSEA 1000 Genome Consortium 2015 O2a2-MY1525
n232
n231 GS000019950-ASM Vietnamese MSEA Karmin et al. 2015 O2a2-B429
n225 HG01865 Kinh MSEA 1000 Genome Consortium 2015 O2a2-MY1522
SS6002757 Malay Sundaland Wong et al. 2013 O2a2-MY281
n228 GS000016804-ASM Ho World Karmin et al. 2015 O2a2-MY271
n229
n226 LP6005519-DNA_E05 Khonda_Dora World Mallick et al. 2016 O2a2-MY272
n227 SS6002795 Malay Sundaland Wong et al. 2013 O2a2-MY279
LP6005441-DNA_G03 Cambodian MSEA Mallick et al. 2016 O2a2-MY278
n219 n220 GS000019946-ASM Vietnamese MSEA Karmin et al. 2015 O2a1-FGC79915
O2a-M95 SAMEA104038832 Kinh MSEA Polaris Diversity O2a1-F1399
n217 LP6005442-DNA_C11 Kinh MSEA Mallick et al. 2016 O2a1-MY904
n203 n218 B00IEVR Orokolo (New Guinea) SahulN Brucato 2021* O2a1-MY902
n214 SAMEA104038812 Dai East Asia Polaris Diversity O2a1-MY903
n213 n216 SAMEA104038808 Dai East Asia Polaris Diversity O2a1-Z39410
SAMEA104038815 Kinh MSEA Polaris Diversity O2a1-MY906
O2a1-M88 n215 LP6005443-DNA_A02 Tujia East Asia Mallick et al. 2016 O2a1-MY905
LP6005441-DNA_C08 Miao East Asia Mallick et al. 2016 O2a1-MY907
O2-PK4 n211
n212 GS000019949-ASM Vietnamese MSEA Karmin et al. 2015 O2a1-Z24014
n202 SAMEA104038793 Dai East Asia Polaris Diversity O2a1-F18990
n207
n210 SAMEA104038811 Dai East Asia Polaris Diversity O2a1-MY908
n208 SAMEA104038860 Dai East Asia Polaris Diversity O2a1-MY909
n209 SAMEA104038931 Dai East Asia Polaris Diversity O2a1-MY910
O2'4-CTS279 SAMN00000459 Han Chinese East Asia Polaris Diversity O2a1-CTS9884
n198 n205 GS000016869-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O2a-MY912
SAMN00004683 Han Chinese East Asia Polaris Diversity O2a2-MY270
n204 SAMN00006438 Han Chinese East Asia Polaris Diversity O2a-MY914
SS6004469 Han Chinese East Asia Mallick et al. 2016 O2b-F838
O4-Page59 n201 GS000016662-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O4-MY915
O2'5-M268 n199 SAMEA104038929 Kinh MSEA Polaris Diversity O4-MY916
n190 n200 SAMN00000460 Han Chinese East Asia Polaris Diversity O4-CTS1127
SAMN00001618 Han Chinese East Asia Polaris Diversity O4-MY917
n197 NA19070 Japanese (Japan) East Asia 1000 Genome Consortium 2015 O5-F787
NA19005 Japanese (Japan) East Asia 1000 Genome Consortium 2015 O5-CTS3926
n196 GS000016719-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O5-MY918
n192
O5-P49 n195
SAMN00006474 Han Chinese East Asia Polaris Diversity O5-F940
n193 SAMN00006471 Han Chinese East Asia Polaris Diversity O5-MY919
n191 LP6005441-DNA_G05 Hezhen East Asia Mallick et al. 2016 O5-Z39506
n194
SAMN00001603 Han Chinese East Asia Polaris Diversity O5-PH40
SAMN00001605 Han Chinese East Asia Polaris Diversity O5-CTS562
SAMN00000446 Han Chinese East Asia Polaris Diversity O3a-F1754
n124 n129 GS000016842-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O3a-MY933
SAMN00000447 Han Chinese East Asia Polaris Diversity O3a-CTS5488
n125 n128 GS000019904-ASM Burmese MSEA Karmin et al. 2015 O3a-B453
n127 SAMN00006522 Han Chinese East Asia Polaris Diversity O3a-MY931
n126 SAMEA104038856 Dai East Asia Polaris Diversity O3a-F20963
SAMN00000448 Han Chinese East Asia Polaris Diversity O3a-MY932
n111 LP6005519-DNA_A06 Burmese MSEA Mallick et al. 2016 O3a1-MY926
n123 GS000019902-ASM Burmese MSEA Karmin et al. 2015 O3a1-B454
n115 GS000019906-ASM Burmese MSEA Karmin et al. 2015 O3a1-B455
n121
n122 GS000019901-ASM Burmese MSEA Karmin et al. 2015 O3a1-B457
n116
GS000019905-ASM Burmese MSEA Karmin et al. 2015 O3a1-MY921
n120 LP6005443-DNA_E09 Naxi East Asia Mallick et al. 2016 O3a1-MY922
n112 SAMEA104038939 Dai East Asia Polaris Diversity O3a1-MY923
n117 SAMEA104038889 Dai East Asia Polaris Diversity O3a1-MY924
O3a1-CTS4658 n118
n119
SAMEA104038927 Dai East Asia Polaris Diversity O3a1-MY925
SAMEA104038801 Dai East Asia Polaris Diversity O3a1-Z26012
LP6005592-DNA_E05 Sherpa World Mallick et al. 2016 O3a1-MY1006
O3a'b-F450 n114
SAMEA104038900 Dai East Asia Polaris Diversity O3a1-MY927
O-M175 n96 n113 LP6005441-DNA_C06 Japanese (Japan) East Asia Mallick et al. 2016 O3a1-MY930
n30
n106
GS000016839-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O3b-A9472
GS000022100-ASM Burmese MSEA Karmin et al. 2015 O3b-B432
n107 n110 LP6005443-DNA_A07 Thai MSEA Mallick et al. 2016 O3b-MY934
n105 n109 SAMN00006468 Han Chinese East Asia Polaris Diversity O3b-MY935
n108 LP6005443-DNA_C02 Xibo East Asia Mallick et al. 2016 O3b-MY937
LP6005441-DNA_E08 Mongola World Mallick et al. 2016 O3b-SK1769
n98 SAMEA104038878 Han Chinese East Asia Polaris Diversity O3b-F3607
SAMN00006444 Han Chinese East Asia Polaris Diversity O3b-A9473
n104
O3b-F46 GS000016987-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O3b-MY939
O3b-F114 n100 n103 SAMN00006555 Han Chinese East Asia Polaris Diversity O3b-MY940
LP6005443-DNA_D06 Korean East Asia Mallick et al. 2016 O3b-MY941
n97 n101
n99 n102 SAMN00001604 Han Chinese East Asia Polaris Diversity O3b-MY942
SAMN00001621 Han Chinese East Asia Polaris Diversity O3b-MY943
O3a'j-P164 SAMN00001610 Han Chinese East Asia Polaris Diversity O3b-F14370.2
n74 SAMN00000458 Han Chinese East Asia Polaris Diversity O3b-MY944
SS6002808 Malay Sundaland Wong et al. 2013 O3i-MY986
n94
n95 SMT01 Sumatra (Sumatra) Sundaland Jacobs et al. 2019* O3i-MY984
O3i-B452 n93 SMT22 Sumatra (Sumatra) Sundaland Jacobs et al. 2019* O3i-MY985
n92 SS6002809 Malay Sundaland Wong et al. 2013 O3i-MY987
n89
GS000035253-ASM Batak (Palawan) PhilTwn Karmin et al. 2015 O3i-B436
n91 KJG02 Sulawesi_Kajang (Sulawesi) Wallacea Jacobs et al. 2019* O3i-MY976
n90 SS6002811 Malay Sundaland Wong et al. 2013 O3i-Z44781
O3i-B451 KJG04 Sulawesi_Kajang (Sulawesi) Wallacea Jacobs et al. 2019* O3i-MY977
n76 n88 FDT-TBR-004 Tanimbar (Tanimbar) Wallacea Jacobs et al. 2019* O3i-MY963
n86 SS6002763 Malay Sundaland Wong et al. 2013 O3i-MY964
n87 TL003 Ma'anyan (Borneo) Sundaland Jacobs et al. 2019* O3i-MY965
TL038 Ma'anyan (Borneo) Sundaland Jacobs et al. 2019* O3i-MY966
O3i-B450 n85 CBL49 Flores_Cibol (Flores) Wallacea Jacobs et al. 2019* O3i-MY969
O3i'j-N6 n77 GS000017006-ASM Bajo (Sulawesi) Wallacea Karmin et al. 2015 O3i-MY1013
B00IEVE Magu (New Guinea) SahulN Brucato 2021* O3i-MY954
n75 n78 n80 GRC15491808 Raiatea (Raiatea) Remote Oceania Hudjashov et al. 2018 O3i-MY957
n84
B00IEVG Motu (New Guinea) SahulN Brucato 2021* O3i-MY955
n81 n83 UV929 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 O3i-MY951
O3-F525 n79 n82 UV956 Nakanai (New Britain) SahulN Vernot et al. 2016 O3i-MY952
n53 UV897 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 O3i-MY953
SS6002831 Malay Sundaland Wong et al. 2013 O3i-MY958
SAMN00006486 Han Chinese East Asia Polaris Diversity O3j-F4068
n73 SS6002779 Malay Sundaland Wong et al. 2013 O3f-MY989
n72 SS6002736 Malay Sundaland Wong et al. 2013 O3f-MY988
NO1-M214 n71 SS6002800 Malay Sundaland Wong et al. 2013 O3f-MY990
n28 n68 SS6002765 Malay Sundaland Wong et al. 2013 O3f-MY1012
n67 n70 HG02035 Kinh MSEA 1000 Genome Consortium 2015 O3f-MY1524
n69 SAMEA104038840 Kinh MSEA Polaris Diversity O3f-MY1552
LP6005443-DNA_F01 She East Asia Mallick et al. 2016 O3f-N5
O3f-F1276 GS000016867-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O3f-CTS123
n62 n66 SAMEA104038792 Kinh MSEA Polaris Diversity O3f-MY1551
n64 HG01861 Kinh MSEA 1000 Genome Consortium 2015 O3f-MY1521
O3f-M7 n63 n65 HG02137 Kinh MSEA 1000 Genome Consortium 2015 O3f-MY1527
n59 HG02023 Kinh MSEA 1000 Genome Consortium 2015 O3f-MY1523
HG01816 Dai East Asia 1000 Genome Consortium 2015 O3f-MY1520
O3-F2055 O3f-Y26403 n60 n61 LP6005442-DNA_C07 Ami (Taiwan) PhilTwn Mallick et al. 2016 O3f-MY993
n56 LP6005443-DNA_G05 Ami (Taiwan) PhilTwn Mallick et al. 2016 O3f-MY994
O3'6-M324 O3-M188 GS000019966-ASM Igorot (Luzon) PhilTwn Karmin et al. 2015 O3f-B433
n32 n58 SAMN00006546 Han Chinese East Asia Polaris Diversity O3h-M159
n54 GS000016977-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O3h-MY996
n57 SAMEA104038915 Han Chinese East Asia Polaris Diversity O3h-MY1000
n55 GS000016860-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O3-CTS8490
SAMN00000445 Han Chinese East Asia Polaris Diversity O3-F1226
n51 LP6005441-DNA_C03 Brahui World Mallick et al. 2016 O6a-F15966
n52 SAMEA104038807 Kinh MSEA Polaris Diversity O6a-CTS5409
GS000016660-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O6a-CTS4241
NO/K2a-M2308 n23 n45 O6a-F17 n48
GRC15491809 Raiatea (Raiatea) Remote Oceania Hudjashov et al. 2018 O6a-MF31684
SAMN00006441 Han Chinese East Asia Polaris Diversity O6a-F18858
n49 GS000016683-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O6a-MF21617
n44 n47 n50
SAMEA104038932 Han Chinese East Asia Polaris Diversity O6a-F1418
O3'7-M122 O6a-F11
n46 SAMN00000436 Han Chinese East Asia Polaris Diversity O6a-CTS7271
n31 SAMN00000456 Han Chinese East Asia Polaris Diversity O6a-PH83
O6a-IMS-JST002611 n43 LP6005441-DNA_F05 Hazara World Mallick et al. 2016 O6a-SK1692
n40 GS000016843-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O6a-CTS2107
O6a-F283 n41 n42 LP6005519-DNA_B06 Burmese MSEA Mallick et al. 2016 O6a-F18913
SAMN00006453 Han Chinese East Asia Polaris Diversity O6a-F20523
O6-L127.1 SAMEA104038836 Han Chinese East Asia Polaris Diversity O6a-CTS679
n33 n37 GS000016681-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O6b-MY1005
SAMN00006456 Han Chinese East Asia Polaris Diversity O6b-MY1004
n35
n38 GS000017031-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O6b-MY1002
n39 SAMN00006462 Han Chinese East Asia Polaris Diversity O6b-MY1003
n34 n36 GS000016714-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O6b-CTS1933
K2-M526 O6b-F2159 SAMN00004689 Han Chinese East Asia Polaris Diversity O6b-Z24958
SAMN00001619 Han Chinese East Asia Polaris Diversity O6b-PH954
n10
N-M231 GS000016835-ASM Han Chinese East Asia 1000 Genome Consortium 2015 O7-F1025
n29 GS000022076-ASM Yakut World Karmin et al. 2015 N-L708
NO2-MY1503 NA18558-200-37-ASM Chinese East Asia Personal Genomes Project N-M231
HG03742 Telugu World 1000 Genome Consortium 2015 NO2b-MY1504
n24 SS6002749 Malay Sundaland Wong et al. 2013 NO2-MY1505
n25
NO2-MY1507 n26 n27 SMT12 Sumatra (Sumatra) Sundaland Jacobs et al. 2019* NO2-MY1509
SLW42 Sulawesi_Mandar (Sulawesi) Wallacea Jacobs et al. 2019* NO2-MY1510
SMT03 Sumatra (Sumatra) Sundaland Jacobs et al. 2019* NO2-MY1508
R-M207 n22 GS000035240-ASM Swede World Karmin et al. 2015 R1a1e-Z287
n20 SS6003431 Malay Sundaland Wong et al. 2013 R1a2b-L657
GT-F1329 P1-M45 n21 NA20845-200-37-ASM Gujarati World Drmanac et al. 2010 R2a-B294
n6 n18
Q1'2-L472 SS6002826 Malay Sundaland Wong et al. 2013 R2a-Y1299
LP6007076-DNA_A01 Kashmiri_Pandit World Mallick et al. 2016 Q2a-M25
P-P295 n19
SS6004476 Karitiana World Mallick et al. 2016 Q1a-M848
n15
P2-B252 P2-MY1511 n17 SS6002783 Malay Sundaland Wong et al. 2013 P2-MY1512
MP-M1221 n16 SS6002830 Malay Sundaland Wong et al. 2013 P2-MY1513
n11 GS000035392-ASM Agta (Luzon) PhilTwn Karmin et al. 2015 P2-B253
M-P256
F-M89 n12
n14 ALK-TBR-025 Tanimbar (Tanimbar) Wallacea Jacobs et al. 2019* M1a3-MY35
UV043 Baining (New Britain) SahulN Vernot et al. 2016 M3b-MY5
n3 MS-PR2099 n13 B00IEWR Maipi (New Guinea) SahulN This study S10b-MY93
S-B254 UV919 Nakanai Bileki (New Britain) SahulN Vernot et al. 2016 S5-MY112
G-M201 n9 GRC15560180 Jewish World Behar et al.2017 G2-Y12978
n8 GS000010844-ASM Jewish World Carmi et al. 2014 G2-MY1514
n1 n7 GS000013739-ASM North_Ossetian World Karmin et al. 2015 G2-A200
GRC15560107 Jewish World Behar et al.2017 G1-Z26333
F-MY1500 n4 LP6005443-DNA_E01 Lahu East Asia Mallick et al. 2016 F-M427
n5 SS6002805 Malay Sundaland Wong et al. 2013 F3-MY1502
C-M130 HG02040 Kinh MSEA Polaris Diversity F4-Z40734
n2_ GS000013752-ASM Kazakh World Karmin et al. 2015 C3-L1373
DTT-KEI-031 Kei (Kei) Wallacea Jacobs et al. 2019* C2-MY1115

70000 60000 50000 40000 30000 20000 10000 0

Years before present

Figure S4. Dated phylogenetic tree of haplogroup (hg) O-M175. Main hg labels shown on branches, tree file and more labels in File S3, node ages with CI are in Table S5.
For phylogeneitc structure, similarly for the hg MS-PR2099 tree (Figure S3, File S2), same set of samples from hgs N-M231, NO2-MY1503, P-P259, G-M201, F-MY1500 are included, samples from
hg C-M130 are used as outgroup and calibration point is GT-F1329 (Table S2). Labels colorcoded as on Figure 1.