supplemental data ancient voyaging and polynesian origins · supplemental data ancient voyaging and...

1

The American Journal of Human Genetics, Volume 88

Supplemental Data

Ancient Voyaging and Polynesian Origins

Pedro Soares, Teresa Rito, Jean Trejaut, Maru Mormina, Catherine Hill,

Emma Tinkler-Hundal, Michelle Braid, Douglas J. Clarke, Jun-Hun Loo,

Noel Thomson, Tim Denham, Mark Donohue, Vincent Macaulay, Marie Lin,

Stephen Oppenheimer, and Martin B. Richards

2

193

709

5201

13281

14751

16299

34

3744

12033

15355

15632A

15940

15941

15983

16092

16399

35

9069

10876

13413

16093

16360

36 37 38 39 40

6620

9812

4823

16324

5824

6131

15777

16129

146

545

11992

12366

16272

3693

5773

16154

10238

5465

9123

31 32 333 4

16261

B4a

B4a2

B4a2a

16129

152

195

4093

5656

6302

6497

6791

9329

14581

16287

5093

13269

4703

6485

11254

13368

16217

150

5237

8248

14968

16261

16363

5108

7789

9968

14905

16292

16261

3666

9177

11914

16213

1

153

513

5824

6969

8158

9856

13581

13720

257

4155

5747

8291

10403

11151

16523

200

1442

4612

5127

6332

7389

11969

13105

16168

16172

16249

16325

16390

2

146

185

189

195

196

348G

513

1719

4048

4926

5460

6026

6614

9288

9921

10759

12358

14133

16291

5

6040

6836

8074

9212

11314

14053

14687

15470

16155

16269

16278

6

146

10757

11428

12732

15083

16240

6722

8379

8855

9701

15512

316

4092

15038

16527

15930

11914

13942

7 8 9 15

146

207

15007

16086

2056

4639

5460

6560

7245

7533

8557

12121

15313

16214

16

498

1719

2220

7993

9128

15301

16309

16354

17

6216

146

4248

199

202

2831

4117

8208

15236

16284

18 19 2012 13 14

14587

16218

207

6023

6413

16136

30

211

3221

4742

5826

7909

13879

14162

16111

16154

16452

16497

4625

4704C

7091

12653

13437

14692

16243

16362

210

2380

5246A

14180

14502

16310

16335

292827

146

3571

4232

8772

9621

12882

16311

150

16140

16274

10310

14133

16311

5379

6416

11770

14001

16287

25

6164

16086

26

709

1007 16265

23 24

3497

150

195

214

5441

10398

13629

15941

16311

7521

9101G

11239

11914

13748

185

8343

9065

11053

16240

1119

15346

146

152

1391

3981

5585

13934

14569

16298

16362

499

4820

13590

827

15535

10 11

3547

4977

6473

9950

11177

180

4122

4123

8875

9682

12738

189

5987

11884

13221

16111

16217

16278

16483

0

0

0

0

0

0

Japan

North Asia

South China

Americas

Mainland Southeast Asia

Taiwan

Indonesia/East Malaysia

Philippines

Trobriand Islands

North coast of New Guinea

Micronesia

Bismarck Archipelago

West New Guinea

Polynesia

Vanuatu

South coast of New Guinea

Bougainville

0

5108

14088

14209

16147

16184A

5379

7340

7598

8958

9103

11017

11653

16093

21

B4

B4g

B4f

B4b’d

B4d

B4d1

B4b

B4b1

B4b1a

B4c

B4c1

B4c1c

B4c1b

43,600 [36,650;51,150]

10,000 years

20,000 years

30,000 years

40,000 years

Ple

isto

ce

ne

Ho

loce

ne

B4b1b

B4b1a2

16357

1189

4025

7664

B4b1a1

B2

B4c2

22

B4c1a

B4h

16094

4025

4769

16360A

6878

16129

ML:8450 [6700;10,250]

CS: 9700 [5000;14,500]

SYN: 12750 [1000;24,500]

12738

4733

6366

12519

310

3394

16274

16311

6492

13350

14659

3357

14449

16223

7510

8525

195

14290

14954

16093

8628

11465

3316

10742

13149

16188

16355

8870 8667

4048

324G

13191

11077

12441

13577

15930

234

6237

16092

1629316178

12290

15712

14587

16478

194

15181

7214A

14470

16288

ML: 6800 [4950;8700]

CS: 7900 [3450;12,450]

SYN: 6500 [2000;11,000]

6083

9103195

6216

302C

6480

8380

16084

16222

15924

93

13708 449

6253

5465

8167

16129

14022

B4a1a1

4080

16048

16551A

408A

3438

4164

10810

61 62 63 64 65 66 67 68 69 70 71 72 73 78 7974 75 76 77 80 81 82 83 84

87 88

85

89 90 91 92 93 94 95

41 42

5894

ML:19,950 [15,450;24,550]

CS: 21,000 [3900;39,500]

SYN: 21,150 [4350;39,700]

150

4218

4907

43 44 45 46

709

150

4679

7533

8679

14148

14569

15663

16169

16239

9254

15292

6891

8595

73C

75

89

5252

47 48

146

12904

32031440

858416317T

49 50 51 52 53 54

310

55 56 57 58 59 60

B4a1

B4a1a

185

6891

7299

9880

11914

12396

16150

9956

14783

16093

16188

16214

7052

7271

9822A

15661

16167

16317

146

281

316

11632

12237

15038

3960

4203

5263

7927

15479

16000

16266G

162126278

12210

9932

10915

13143

16288

16311

8251

15936

16519

16268

5004

9977

4695 7083

146

6719

12239

15746

B4a1c

B4a1b

B4a1d

ML:5650 [4150;7150]

CS: 5850 [3850;7800]

SYN: 7150 [1750;12,550]16247

710

13161

13590

6891 207

6563

1636214249

1443412397

15937

16093

1438

5093

7738 6581

8222

7876195 58225086

5483

2755

152

593

16324

186

310

214

16519

10484

13749

16093

16247

1598

6023

16239

16274

152

16129

9756G

11986

14022

16249

16311

8865

13711

8075 16319

16148

16247

16524

4227

64

9139

16292

12627

12958A

16302

153

226

10966

13135

13943

16219T

4093

4688

4700A

5105

12750

16317

204

14302

6579

7058

5147

11176

16233

6887

6905

614

4742

709

70

6623

16352

16399

4742

16311

215

10529

150435563 16360

B4a1a1a

96 97 98 99 100 101 104 105102 106 107103 109 110 111 112 113108 115 116 117 118 119114 121 122120 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 148146 147 150149 151 152 153 154 156 157

16355

5000years

Ho

loce

ne

B4a1a1a1

151

1692

2416

155

B4a1a2

86

11453

0

0

0

0

0

0

0

0

0

0

3

Figure S1. Phylogeny of 157 Complete mtDNA Genomes from Haplogroup B4

Branch lengths were scaled using maximum likelihood and a time-dependent clock (ML

analysis 1). Age estimates in years for complete genomes (CS) and synonymous mutations

(SYN) are indicated for the most relevant nodes in this study. Synonymous mutations are

underlined. Mutations are transitions at the nucleotide position indicated unless otherwise

specified.

4

Table S1. Complete mtDNA Genomes Used in the Analysis

Haplogroup Region Sub-region/group Sequences ML analysis Notes Reference

1 2 3 4

. R11 China Qingdao, Shandong AY255163 x x x x Kong et al. 20031

. R9b1a Malaysia Semelai AY963579 x x x x Macaulay et al. 20052

. F3a China Yili, Xinjiang AY255167 x x x x Kong et al. 20031

. A6 China Wuhan, Hubei AY255166 x x x x Kong et al. 20031

. Y2 China Qijiang, Chongqing DQ272121 x x x x Kong et al. 20063

. B5a1 China Wuhan, Hubei AY255145 x x x x Kong et al. 20031

. B5b2a China Wuhan, Hubei AY255179 x x x x Kong et al. 20031

1 B4f Japan Aichi AP008788 x x x x Tanaka et al. 20044

2 B4f Japan Tokyo AP008262 x x x x Tanaka et al. 20044

3 B4g China Zhanjiang, Guangdong AY255133 x x x x Kong et al. 20031

4 B4g Vietnam Tay-Nung VNM311 x x x x This study

5 B4e Japan Tokyo AP008436 x x x x Tanaka et al. 20044

6 B4d Japan Chiba AP008492 x x x x Tanaka et al. 20044

7 B4d1 Russia Siberia: Buriat AY519484 x x x x Starikovskaya et al. 20055

8 B4d1 China Qingdao, Shandong AY255140 x x x x Kong et al. 20031

9 B4d1 China Fengcheng, Liaoning AY255135 x x x x Kong et al. 20031

10 B2 America Native American AY195749 x x x x Mishmar et al. 20036

11 B2 America Native American (Pinam) AF347001 x x x x Ingman et al. 20007

12 B4b1b Japan Aichi AP008682 x x x x Tanaka et al. 20044

13 B4b1b Vietnam Hanoi VN016 x x x x This study (Trejaut/Taipei lab data)

14 B4b1b Mongolia DQ272119 x x x x Kong et al. 2006 3

15 B4b1a Russia Siberia: Tubular AY519494 x x x x Starikovskaya et al. 2005 5

16 B4b1a2 Japan Tokyo AP008856 x x x x Tanaka et al. 20044

17 B4b1a2 China Zhanjiang, Guangdong AY255170 x x x x Kong et al. 20031


19 B4b1a1 Japan Aichi AP008594 x x x x Tanaka et al. 20044


21 B4c2 Thailand AY289100 x x x x Ingman and Gyllensten 20038

22 B4c2 Thailand AY289101 x x x x Ingman and Gyllensten 20038

23 B4c1c Japan Chiba AP008450 x x x x Tanaka et al. 20044

24 B4c1c Japan Aichi AP008563 x x x x Tanaka et al. 20044

25 B4c1a Japan Tokyo AP008281 x x x x Tanaka et al. 20044

26 B4c1a Japan Chiba AP008470 x x x x Tanaka et al. 20044

27 B4c1b China Fengcheng, Liaoning AY255149 x x x x Kong et al. 20031

28 B4c1b Japan Chiba AP008472 x x x x Tanaka et al. 20044

29 B4c1b Japan Aichi AP008570 x x x x Tanaka et al. 20044

30 B4c1b Japan Tokyo AP008899 x x x x Tanaka et al. 20044

31 B4a* Taiwan Siraya SL309 x x x x This study (Trejaut/Taipei lab data)

32 B4h China Fujian Fuj4752 x x x x This study (Trejaut/Taipei lab data)

33 B4h China Fujian FC076 x x x x This study (Trejaut/Taipei lab data)

34 B4a Japan Tokyo AP008384 x x x x Tanaka et al. 20044

5

35 B4a Japan Aichi AP008567 x x x x Tanaka et al. 20044

36 B4a2 Japan Gifu AP008257 x x x x Tanaka et al. 20044

37 B4a2a Indonesia Banjarmasin (Borneo) BAN3 x x x x This study

38 B4a2a Taiwan Yami AJ842751 x x x x Trejaut et al. 20059

39 B4a2a Taiwan Paiwan AJ842750 x x x x Trejaut et al. 20059

40 B4a2a Taiwan Saisiat SA030 x x x x This study (Trejaut/Taipei lab data)

41 B4a1d Vietnam Kinh V206 x x x x This study

42 B4a1d Vietnam Hanoi VN014 x x x x This study (Trejaut/Taipei lab data)

43 B4a1c Japan Chiba AP008521 x x x x Tanaka et al. 20044

44 B4a1c Japan Aichi AP008650 x x x x Tanaka et al. 20044


46 B4a1c Japan Tokyo AP008912 x x x x Tanaka et al. 20044

47 B4a1c China GuangXi DQ272120 x x x x Kong et al. 20063

48 B4a1c Thailand Taiwan workers Thai107 x x x x This study (Trejaut/Taipei lab data)

49 B4a1c Russia Siberia: Tuvan AY519495 x x x x Starikovskaya et al. 20055

50 B4a1c Russia Siberia: Tofalar AY519492 x x x x Starikovskaya et al. 20055

51 B4a1c AY195770 x x x x Mishmar et al. 20036

52 B4a1c China Fujian Fuj4547 x x x x This study (Trejaut/Taipei lab data)


54 B4a1c Japan Tokyo AP008412 x x x x Tanaka et al. 20044

55 B4a1b Japan Aichi AP008595 x x x x Tanaka et al. 20044

56 B4a1b Japan Tokyo AP008842 x x x x Tanaka et al. 20044

57 B4a1b Korea AF346993 x x x x Ingman et al. 20007



60 B4a1b Japan Tokyo AP008415 x x x x Tanaka et al. 20044

61 B4a1a Taiwan Ami AJ842749 x x Trejaut et al. 20059

62 B4a1a Taiwan Yami AJ842747 x x Trejaut et al. 20059

63 B4a1a Taiwan Atayal AJ842746 x x Trejaut et al. 20059

64 B4a1a Taiwan Tsou TS039 x x This study (Trejaut/Taipei lab data)

65 B4a1a2 Taiwan Ami AJ842745 x x Trejaut et al. 20059


67 B4a1a Taiwan Ami AMI12 x x This study (Trejaut/Taipei lab data)

68 B4a1a Indonesia Manado MND36 x x This study

69 B4a1a3 Taiwan Ami AM025 x x This study (Trejaut/Taipei lab data)

70 B4a1a3 Taiwan Siraya SL049 x x This study (Trejaut/Taipei lab data)


72 B4a1a3 East Malaysia Kota Kinabalu (Borneo) KK144 x x This study

73 B4a1a3 Indonesia Sumba WAI94 x x This study

74 B4a1a Philippines GQ119021 x x Tabbada et al. 201010

75 B4a1a East Malaysia Kota Kinabalu (Borneo) KK141 x x This study

76 B4a1a Philippines FIL18 x x This study

77 B4a1a Philippines FIL59 x x This study

78 B4a1a Indonesia Banjarmasin (Borneo) BAN75 x x This study

79 B4a1a Indonesia Ambon AMB20 x x This study

80 B4a1a Indonesia Banjarmasin (Borneo) BAN39 x x This study

6

81 B4a1a Indonesia Mataran MTR62 x x This study

82 B4a1a Indonesia Toraja TOR31 x x This study

83 B4a1a Indonesia Java IN101 x x This study(Trejaut/Taipei lab data)

84 B4a1a Indonesia Manado MND37 x x This study

85 B4a1a New Guinea Trobriand Islands DQ372871 Pierson et al. 200611

86 Philippines Mindanao GQ119029 Tabbada et al. 201010

87 B4a1a1 Indonesia Ujung Pandang UJP18 x x This study

88 B4a1a1 Papua New Guinea North Coast AY289076 x Ingman and Gyllensten 20038

89 B4a1a1 Micronesia Majuro Atoll DQ372877 x Pierson et al. 200611

90 B4a1a1 Micronesia Kapingamarangi Atoll DQ372874 x Pierson et al. 200611

91 B4a1a1 Micronesia Kapingamarangi Atoll DQ372875 x Pierson et al. 200611

92 B4a1a1 Bismarch Archipelago Lihir Island L627 x x This study



95 B4a1a1 New Guinea Trobriand Islands DQ372873 x Pierson et al. 200611

96 B4a1a1a Indonesia Ambon AMB39 x x This study

97 B4a1a1a Indonesia Mataran MTR12 x x This study

98 B4a1a1a Indonesia Toraja TOR16 x x This study

99 B4a1a1a Indonesia Mataran MTR8 x x This study

100 B4a1a1a Indonesia Ujung Pandang UJP30 x x This study

101 B4a1a1a Indonesia Manado MND21 x x This study


103 B4a1a1a Indonesia Palangkaraya (Borneo) PRY35 x x This study


105 B4a1a1a Bismarch Archipelago Kavieng K65 x This study

106 B4a1a1a Indonesia Banjarmasin (Borneo) BAN41 x x This study

107 B4a1a1a Bismarch Archipelago Kavieng K73 x x This study

108 B4a1a1a West Papua IR77 x dHPLC + CS This study

109 B4a1a1a Papua New Guinea Madang C12991 x dHPLC + CS This study

110 B4a1a1a Papua New Guinea North Coast AY289077 x Ingman and Gyllensten 20038

111 B4a1a1a Papua New Guinea Madang C7191 x Partly dHPLC This study

112 B4a1a1a Papua New Guinea Madang C11191 x Partly dHPLC This study

113 B4a1a1a Papua New Guinea North Coast AY289080 x Ingman and Gyllensten 20038

114 B4a1a1a Papua New Guinea Madang M4890 x dHPLC + CS This study

115 B4a1a1a Samoa AF347007 x Ingman et al. 20007

116 B4a1a1a Vanuatu Banks and Torres BT5 Partly dHPLC This study




120 B4a1a1a Papua New Guinea Madang M0591 x Partly dHPLC This study

121 B4a1a1a Vanuatu Espiritu Santo DQ372878 x Pierson et al. 200611

122 B4a1a1a Vanuatu Port Olry PO49 Partly dHPLC This study

123 B4a1a1a1 Papua New Guinea North Coast AY289083 Ingman and Gyllensten 20038

124 B4a1a1a1 Bismarch Archipelago Lihir Island L712 x This study

125 B4a1a1a1 Papua New Guinea South Highlands KZ522 x This study


7


128 B4a1a1a1 Bismarch Archipelago Kavieng K95 x x This study






134 B4a1a1a1 Bismarch Archipelago Lihir Island L735 x x This study



137 B4a1a1a1 Vanuatu Banks and Torres BT80 dHPLC + CS This study

138 B4a1a1a1 Vanuatu Port Olry PO76 Partly dHPLC This study

139 B4a1a1a1 Vanuatu Banks and Torres BT79 Partly dHPLC This study

140 B4a1a1a1 Samoa AY289093 Ingman and Gyllensten 20038

141 B4a1a1a1 Cook Islands Atiu AY289069 Ingman and Gyllensten 20038









150 B4a1a1a Samoa AY289094 Ingman and Gyllensten 20038

151 B4a1a1a Bougainville AY963574 x Macaulay et al. 20052

152 B4a1a1a Vanuatu Espiritu Santo DQ372881 Pierson et al. 200611


154 B4a1a1a Vanuatu Port Olry PO44 Partly dHPLC This study

155 B4a1a1a Cook Islands Atiu AY289068 Ingman and Gyllensten 20038

156 B4a1a1a Tonga DQ372886 Pierson et al. 2006 11

157 B4a1a1a Tonga AY289102 Ingman and Gyllensten 20038

Haplogroup, region, sub-region or ethnic group are indicated where the information is available. References and accession numbers for published

sequences are indicated. The inclusion of the sequences in each of the four ML analyses is indicated. Partial dHPLC refers to mtDNA genomes

whose variation was partially assessed through dHPLC with only a portion sequenced. dHPLC + CS refers to genomes initially generated in the

same way but then completely sequenced.

8

Table S2. Control-Region Data for B4a and Additional Coding-Region Markers

Typed in the Laboratories in Leeds and Taipei

Samples and HVS-I

variants from CRS

Haplogroup

n

10

238

67

19

12

239

15

746

14

022

Complete

sequences and

notes

Leeds Laboratory

Taiwan – Ami (n=31)

189 217 261 B4a1a 1 ND 1 1 1 0

189 217 261 311 B4a1a 5 ND 1 1 1 0 Seq. 67

Taiwan – Atayal (n=18)

189 217 261 324 B4a2a 2 ND ND ND ND ND

154 189 217 261 324 B4a2a 1 ND ND ND ND ND

Taiwan – Paiwan (n=21)

189 217 261 B4a1a 2 ND 1 1 1 0

189 217 261 272 324 B4a2a 3 ND ND ND ND ND

189 217 261 272 288 324 B4a2a 1 ND ND ND ND ND

Philippines –

Undetermined (n=61)

189 217 261 B4a1a 4 ND 1 1 1 0 Seq. 76

189 217 261 293 B4a1a 2 ND 1 1 1 0

092 189 217 261 293 B4a1a 5 ND 1 1 1 0 Seq. 77

Indonesia – Alor (n=100)

189 217 261 B4a1a 3 ND 1 1 1 0

189 217 247 261 B4a1a1a 2 ND 1 1 1 ND

Indonesia – Ambon (n=44)

189 217 261 B4a* 1 0 ND ND ND ND Seq. 79

189 217 261 B4a1a 2 ND 1 1 1 0

189 217 223 261 B4a1a 1 ND 1 1 1 0

189 217 223 261 325 B4a1a 1 ND 1 1 1 0

189 217 261 278 B4a1a 1 ND 1 1 1 0 Seq. 96, 102

189 217 247 261 B4a1a 5 ND 1 1 1 0

189 217 247 261 362 B4a1a1a 1 ND 1 1 1 ND Seq. 104

Indonesia – Bali (n=69)

108 189 217 261 B4a1a 1 ND 1 1 1 0

Indonesia – Banjarmasin,

Borneo (n=89)

189 217 261 B4a1a 5 ND 1 1 1 0 Seq. 78

178 189 217 261 B4a1a 2 ND 1 1 1 0 Seq. 80

189 217 247 261 B4a1a1a 1 ND 1 1 1 0

093 189 217 247 261 B4a1a1a 1 ND 1 1 1 0 Seq. 106

189 217 261 324 B4a2a 1 ND ND ND ND ND Seq. 37

Brunei (n=30)

189 217 261 B4a1a 2 ND 1 1 1 0

East Malaysia – Kota

Kinabalu, Borneo (n=76)

189 217 261 B4a1a 4 ND 1 1 1 0 Seq. 75

189 217 223 261 B4a1a 3 ND 1 1 1 0 Seq. 72

092 189 223 217 261 B4a1a 1 ND 1 1 1 0

Indonesia – Manado,

Sulawesi (n=89)

189 217 261 B4a1a 1 ND 1 1 1 0 Seq. 84

9

189 217 261 288 B4a1a 1 ND 1 1 1 0

189 217 261 311 B4a1a 1 ND 1 1 1 0 Seq. 68

189 217 247 261 B4a1a1a 1 ND 1 1 1 ND Seq. 101

Indonesia – Mataram,

Lombok (n=74)

189 217 261 B4a1a 2 ND 1 1 1 0 Seq. 81

189 217 261 400 B4a1a 1 ND 1 1 1 0

189 217 247 261 B4a1a1a 3 ND 1 1 1 ND Seq. 97, 99

Indonesia – Palembang,

Sumatra (n=37)

189 261 B4a* 1 0 ND ND ND ND

Indonesia – Padang,

Sumatra (n=25)

189 217 261 B4a1a 2 ND 1 1 1 0

Indonesia – Palang-

karaya, Borneo (n=112)

189 217 261 B4a1a 4 ND 1 1 1 0

093 189 217 261 B4a1a 1 ND 1 1 1 0

189 217 223 261 B4a1a 2 ND 1 1 1 0

189 217 247 261 B4a1a1a 1 ND 1 1 1 ND Seq. 103

189 217 261 324 B4a2a 3 ND ND ND ND ND

Indonesia – Toraja,

Sulawesi (n=64)

189 217 261 B4a1a 3 ND 1 1 1 0 Seq. 82

189 217 261 311 B4a1a 1 ND 1 1 1 0

189 217 247 261 B4a1a1a 5 ND ND ND ND ND Seq. 98

Indonesia – Ujung Padang,

Sulawesi (n=46)

189 217 261 B4a1a 3 ND 1 1 1 0

189 217 223 261 335 B4a1a 1 ND 1 1 1 0

189 217 261 B4a1a1 1 ND 1 1 1 1 Seq. 87

189 217 247 261 B4a1a1a 3 ND ND ND ND ND Seq. 100

Indonesia – Sumba

188 189 217 223 261 355 1 1 1 1 1 1 0 Seq. 73

Indonesia – West Papua

(n=178)

189 217 261 B4a1a1 1 ND 1 1 1 1

189 217 247 261 B4a1a1a 2 ND 1 1 1 ND

189 217 247 255 261 B4a1a1a 1 ND 1 1 1 ND Seq. 108

Papua New Guinea –

Madang (n=163)

189 217 261 B4a1a1 9 ND 1 1 1 1

086 189 217 261 B4a1a1 2 ND 1 1 1 1

189 217 247 261 B4a1a1a 23 ND 1 1 1 ND Seq. 109, 111,

112, 114, 120

189 217 247 260 261 B4a1a1a 1 ND 1 1 1 ND

189 217 247 261 293C B4a1a1a 1 ND 1 1 1 ND

124 189 217 247 261 293C B4a1a1a 2 ND 1 1 1 ND

189 217 247 B4a1a1a 1 ND 1 1 1 ND

189 217 247 260 261 B4a1a1a 1 ND 1 1 1 ND

189 217 261 B4a* 1 0 0 0 0 ND

Papua New Guinea –

Southern Highlands (n=17)

189 217 247 249 261 B4a1a1a 1 ND 1 1 1 ND Seq. 126

10

126 189 217 247 261 B4a1a1a 1 ND 1 1 1 ND Seq. 125

189 217 247 261 311 B4a1a1a 1 ND 1 1 1 ND Seq. 127

Papua New Guinea – Port

Moresby (n= 114)

189 217 261 B4a1a1 1 ND 1 1 1 1

189 217 260 261 B4a1a1 1 ND 1 1 1 1

189 217 261 274 B4a1a1 2 ND 1 1 1 1

189 217 247 261 B4a1a1 11 ND 1 1 1 1

166C 189 247 261 B4a1a1a 1 ND ND ND ND ND

189 217 247 261 289 B4a1a1a 1 ND ND ND ND ND

Bismarck Archipelago –

Kavieng (n=83)

189 217 261 311 B4a1a1 1 ND 1 1 1 1

051 189 214 217 261 B4a1a1 1 ND 1 1 1 1

189 217 247 261 B4a1a1a 21 ND 1 1 1 ND Seq. 133, 142,

143, 144, 145,

146, 147, 149

148 189 217 261 B4a1a1a 1 ND 1 1 1 ND Seq. 132

189 217 247 261 311 B4a1a1a 10 ND 1 1 1 ND Seq. 128, 130,

131

066 189 247 261 311 B4a1a1a 1 ND 1 1 1 ND

093 189 217 247 261 311 B4a1a1a 3 ND 1 1 1 ND

189 217 247 311 B4a1a1a 1 ND 1 1 1 ND

189 217 247 261 311 319 B4a1a1a 1 ND 1 1 1 ND Seq. 129

093 189 217 247 261 B4a1a1a 2 ND 1 1 1 ND Seq. 107

157 189 217 247 261 B4a1a1a 1 ND 1 1 1 ND

188 189 217 247 261 B4a1a1a 2 ND 1 1 1 ND

189 217 223 247 261 B4a1a1a 2 ND 1 1 1 ND

189 217 233 247 261 B4a1a1a 2 ND 1 1 1 ND Seq. 148

189 217 247 261 292 B4a1a1a 1 ND 1 1 1 ND

189 217 247 261 302 B4a1a1a 1 ND 1 1 1 ND

189 217 247 261 362 B4a1a1a 2 ND 1 1 1 ND Seq. 105

189 217 247 362 B4a1a1a 1 ND 1 1 1 ND

189 217 247 390 B4a1a1a 1 ND 1 1 1 ND

Bismarck Archipelago –

Lihir Island (n=94)

189 217 261 B4a1a1 10 ND 1 1 1 1 Seq. 93

084 189 217 261 B4a1a1 1 ND 1 1 1 1

189 217 222 261 B4a1a1 24 ND 1 1 1 1

084 189 217 222 261 B4a1a1 5 ND 1 1 1 1 Seq. 92

189 217 222 261 302 B4a1a1 2 ND 1 1 1 1

129 189 217 261 B4a1a1 1 ND 1 1 1 1 Seq. 94

189 217 247 261 292 B4a1a1a 3 ND 1 1 1 ND Seq. 134, 135

189 217 247 261 302 B4a1a1a 1 ND 1 1 1 ND Seq. 136

189 217 239 247 261 274 B4a1a1a 3 ND 1 1 1 ND Seq. 124

Solomon Islands (n=21)

189 217 247 261 B4a1a1a 4 ND 1 1 1 ND

189 217 247 261 311 B4a1a1a 3 ND 1 1 1 ND

Vanuatu – Banks and

Torres (n=76)

189 217 247 261 B4a1a1a 7 ND 1 1 1 ND Seq. 116, 117,

118, 119, 137,

153

189 217 219T 247 261 B4a1a1a 2 ND 1 1 1 ND Seq. 139

11

189 194C 217 219T 247 261 B4a1a1a 1 ND 1 1 1 ND

189 217 219T 247 261 345 B4a1a1a 1 ND 1 1 1 ND

Vanuatu – Port Olry

(n=43)

189 217 247 261 B4a1a1a 18 ND ND ND ND ND Seq.122, 138,

154

189 194C 217 247 261 B4a1a1a 2 ND ND ND ND ND

189 217 242 247 294 B4a1a1a 1 ND ND ND ND ND

189 217 247 261 362 B4a1a1a 1 ND ND ND ND ND

189 217 247 294 B4a1a1a 1 ND ND ND ND ND

Cook Islands (n=19)

189 217 247 261 B4a1a1a 15 ND ND ND ND ND

189 217 247 261 294 B4a1a1a 1 ND ND ND ND ND

126 189 217 247 261 B4a1a1a 1 ND ND ND ND ND

126 189 217 261 B4a1a1a 2 ND ND ND ND ND Reversion

16247?

Vietnam (n=397)

189 217 261 B4a1* 2 1 0 0 0 ND

140 189 217 261 B4a1* 1 1 0 0 0 ND

189 217 219 261 286 355 B4a* 1 0 0 0 0 ND

189 217 219 261 286 B4a* 1 0 0 0 0 ND

129 189 217 261 311 B4a* 2 0 0 0 0 ND

189 217 261 294 B4a* 1 0 0 0 0 ND

Thailand (n=132)

093 188 189 214 217 261 B4a* 1 0 0 0 0 ND

Taipei Laboratory

China – Fujian (n=149)

189 217 261 B4a* 1 0 0 ND ND ND

129 189 261 B4h 1 0 0 0 0 0 Seq. 32

189 217 261 299 B4a* 1 0 0 ND ND ND

93 189 217 261 B4a* 1 0 0 ND ND ND

189 217 261 B4a1* 1 1 0 0 0 0 Seq. 52

154 189 217 240 261 B4a1* 1 1 ND ND ND 0

93 189 217 261 311 B4a1* 1 1 0 ND ND ND

Taiwan – Ami (n=98)

189 217 261 B4a1a 18 1 1 ND ND 0 Seq. 65, 69

189 217 261 274 B4a1a 6 1 1 ND ND 0 Seq. 66

189 217 261 311 B4a1a 8 1 1 ND ND 0

93 189 217 223 261 B4a1a 1 1 1 1 1 0 Seq. 71

94 189 217 261 B4a1a 10 1 1 1 1 0 Seq. 61

94 189 217 261 326C B4a1a 1 1 1 ND ND 0

Taiwan – Atayal (n=108)

77 189 217 261 B4a1a 3 1 1 ND ND 0

129 189 217 261 B4a1a 1 1 1 1 1 0 Seq. 63

154 189 217 261 324 B4a2a 1 0 ND ND ND 0

Taiwan – Hakka (n=74)

189 217 240 261 B4a* 1 0 0 ND ND ND

189 217 261 299 B4a* 1 0 0 ND ND ND

189 213 217 261 295 299 B4a* 1 0 0 ND ND ND

189 217 261 304 B4a* 1 0 0 ND ND ND

217 261 299 B4a* 1 0 0 ND ND ND

93 189 217 261 B4a* 2 0 0 ND ND ND

189 217 261 324 B4a2a 1 0 0 ND ND ND

12

Taiwan – Minnan (n=173)

189 217 261 324 B4a2a 1 0 0 ND ND ND

189 217 234 261 B4a* 2 0 0 ND ND ND

129 189 217 261 B4a* 1 0 0 ND ND ND

129 189 217 261 356 B4a* 1 0 0 ND ND ND

189 213 217 235 242 261

292 301

B4a* 1 0 0 ND ND ND

189 217 261 B4a* 2 0 0 ND ND ND

51 129 189 217 261 354 B4a* 1 0 0 ND ND ND

Taiwan – Paiwan (n=55)

189 217 261 272 324 B4a2a 9 0 0 0 0 0 Seq. 39

Taiwan – Pazeh (n=65)

189 217 221 240 261 B4a1* 2 1 0 ND ND 0

154 189 217 261 324 B4a2a 1 0 0 ND ND ND

129 189 217 261 309 B4a* 1 0 0 ND ND ND

136 182 183 189 217 B4a* 1 0 0 ND ND ND

Taiwan – Puyuma (n=52)

189 217 261 272 324 B4a2a 2 ND 0 ND ND ND

Taiwan - Rukai (n=51)

189 217 261 B4a1a 1 1 1 ND ND 0

189 217 261 274 B4a1a 2 1 1 ND ND 0

189 217 261 272 324 B4a2a 5 ND 0 ND ND ND

Taiwan – Saisiat (n=64)

154 189 217 261 B4a2a 1 0 0 ND ND ND

154 189 217 261 324 B4a2a 1 0 0 ND ND 0 Seq. 40

Taiwan – Siraya (n=364)

129 189 217 261 B4a* 3 0 ND ND ND ND

129 189 217 261 287 B4a* 1 0 ND ND ND ND Seq. 31

129 189 217 261 356 B4a* 1 0 ND ND ND ND

189 217 261 B4a1a 1 1 1 ND ND 0

189 217 261 311 B4a1a 1 1 1 ND ND 0

129 189 217 261 B4a1a 1 1 1 ND ND 0

129 189 217 261 311 325 B4a1a 1 1 ND ND ND 0

168 189 217 261 311 B4a1a 1 1 1 ND ND 0

189 217 223 261 B4a1a 3 1 1 ND ND 0 Seq. 70

189 217 261 274 B4a1a 2 1 1 ND ND 0

93 189 217 261 362 B4a1a 1 1 ND ND ND 0

189 217 261 324 B4a2a 12 0 ND ND ND ND

129 189 217 261 324 B4a2a 6 0 ND ND ND ND

189 217 261 272 324 B4a2a 1 0 ND ND ND ND

Taiwan – Toroko (n=53)

154 189 217 261 324 B4a2a 5 0 ND ND ND ND

Taiwan – Tsou (n=60)

189 217 261 B4a1a 6 1 1 ND ND 0 Seq. 64

Taiwan – XinMen (n=38)

189 217 261 B4a1* 6 0 0 ND ND ND

Taiwan – Yami (n=79)

189 217 261 360A B4a1a 9 1 1 1 1 0 Seq. 62

189 217 261 324 B4a2a 1 0 0 ND ND ND

129 189 217 261 324 B4a2a 12 0 0 ND ND 0 Seq. 38

Indonesia – Java (n=228)

189 217 261 B4a1* 1 1 0 ND ND ND Seq. 83

93 189 217 261 B4a1* 3 1 0 ND ND 0

189 217 261 B4a1a 3 1 1 ND ND 0

13

129 189 217 261 B4a1a 1 1 1 ND ND 0

189 217 223 261 B4a1a 1 1 1 ND ND 0

Indonesia (unspecified)

(n=32)

189 217 261 B4a1a 1 1 1 ND ND 0

189 217 261 362 B4a1a 1 1 1 ND ND 0

Indonesia – Kalimantan

(n=42)

189 217 261 B4a1a 2 1 1 ND ND 0

Indonesia – Sumatra (n=29

189 217 261 B4a1a 2 1 1 ND ND 0

Indonesia – Sulawesi

(n=31)

168 189 217 261 311 B4a1* 1 1 0 ND ND 0

189 217 261 B4a1a 1 1 1 ND ND 0

Indonesia – Nusa

Tenggara (n=2)

93 217 261 B4a1a 1 1 1 ND ND 0

Indonesia – Timor (n=33)

189 217 261 B4a1a 1 1 1 ND ND 0

Thailand (n=78)

189 213 217 261 292 B4a* 1 0 0 0 0 0

93 188 189 214 217 261 B4a1* 1 1 0 0 0 0 Seq. 48

Vietnam – Hanoi (n=58)

189 217 219 261 286 B4a* 1 0 0 ND ND 0

189 217 261 274 348 B4a1* 1 1 0 ND ND 0

048 189 217 261 B4a1* 1 1 0 0 0 0 Seq. 41

189 217 261 B4a1* 1 1 0 0 0 0 Seq. 42

Typing is scored as “0” meaning that the position carries the same nucleotide as the

reference sequence, “1” meaning that the nucleotide at that position differs from the

reference sequence and “ND” meaning the sample was not tested at that position. HVS-I

sequence types are indicated as variant positions from the reference sequence, less 16,000,

with transversions indicated by a suffix. Numbers of complete sequences in the last column

refer to the numbering in Table S1 and Figure S1.

14

Table S3. Age Estimates with Associated 95% Confidence Limits of B4a1a in ISEA and

Taiwan, using ML (Maximum Likelihood) with the Complete Genome Clock, and ρ

with Three Different Molecular Clocks, Two of Them with Independent Sources of

Variation (Control-Region and Synonymous Clocks)

Overall (ML11) Taiwan (ML2

1) ISEA (ML3

1)

Maximum likelihood 8450 (6700; 10,250) 8250 (5100;11,450) 8250 (6000; 10,550)

Complete genome

clock, ρ

9700 (5000;14,500) 7900 (5500;10,350) 8000 (5600;10,400)

Control region, ρ 10,700 (4850; 16,550) 9750 (1150; 18,350) 10,850 (4000 ; 17,700)

Synonymous, ρ 12,750 (1000; 24,500) 10,400 (6800;13,950) 10,750 (7300;14,200)

1ML1, ML2 and ML3 refer to the independent ML (maximum likelihood) analyses described

above. Analyses exclude the Pacific data, since the high frequency of B4a1a1a (due to

founder effects) would bias the results.

Table S4. HVS-I Variation of B4a1a in Taiwan and ISEA using ρ, Haplotype Diversity

and π

Region n Age estimate (years)

and 95% CI1

Haplotype diversity π

Taiwan2 82 9750 (1150; 18,350) 0.732 1.055

Philippines 73 9150 (2250; 16,100) 0.606 1.007

Indonesia/East Malaysia 110 11,800 (2800; 20,850) 0.745 1.270

ISEA3 183 10,850 (4000; 17,700) 0.709 1.213

Overall 275 10,700 (4850; 16,550)

1Confidence intervals

2Excluding the Yami, due to their probable recent ancestry in the Philippines

3ISEA (Island Southeast Asia) includes Indonesia/East Malaysia and the Philippines.

Table S5. Pooled Founder Ages, with Associated 95% Confidence Intervals, using the

f1 Criterion, from Taiwan into ISEA and Vice Versa, using ρ and a Control-Region

Clock (HVS-I), a Synonymous Mutation Clock (SYN) and a Time-Dependent Complete

Genome Clock (CS)

Taiwan to ISEA ISEA to Taiwan

HVS-I 8170 (2750; 13,600) 5700 (0; 11,600)

SYN 9750 (2450; 17,100) 8650 (2700; 14,650)

CS 7150 (3700; 10,650) 6300 (3450; 9150)

15

Table S6. Age Estimates and Diversity Measures of Paragroup B4a1a1* (i.e., the Clade

B4a1a1 but Excluding the Polynesian Motif-Derived Subclade, B4a1a1a) in the Pacific,

using the Control-Region Variation between Positions 16051 and 16400

Region n Age estimate

(years) 95% CI

1 (years)

Haplotype

diversity π

North coast of New

Guinea2

24 2800 (0; 6600) 0.292 0.331

Bismarck Archipelago 79 12,250 (0; 25,650) 0.732 1.104

Bougainville 15 6650 (500, 12,800) 0.604 0.781

Solomon Islands 33 9600 (0; 20,200) 0.714 0.981

Polynesia 15 4400 (0; 11,350) 0.420 0.200

Overall 166 8800 (1900; 15,700)

1Confidence interval

2Pooled data from Madang, Sepik Province and Karkar Island

Table S7. Age Estimates (using ρ and the HVS-I Molecular Clock) and Diversity

Measures of B4a1a1a in Indonesia and the Pacific, using the Control-Region Variation

between Positions 16051 and 16400

Region n Age estimate using ρ

(years) and 95% CI1

Haplotype

diversity π

Indonesia 34 3450 (250; 6600) 0.360 0.405

North coast of New Guinea2 62 5400 (1600; 9200) 0.393 0.624

Bismarck Archipelago 290 12,000 (5350; 18,650) 0.781 1.349

Bougainville 89 9500 (2550; 16,400) 0.700 1.082

Solomon Islands 130 5150 (0; 10,500) 0.494 0.566

South coast of New Guinea 16 6650 (500; 12,800) 0.578 0.781

Vanuatu 37 4950 (350; 9550) 0.260 0.571

Polynesia 114 4350 (2050; 6650) 0.411 0.516

Madagascar 35 1900 (0; 4200) 0.160 0.225

Overall Near Oceania3 587 9150 (4750; 13,550)

Overall 807 7700 (4300; 11,100)


2Pooled data from Madang, Sepik Province and Karkar Island

3Pooled data of North Coast of New Guinea, Bismarck Archipelago, Bougainville, Solomon

Islands and South Coast of New Guinea

16

Table S8. Pooled Founder Age of B4a1a1a (the Polynesian Motif-Derived Clade)

Founders into Remote Oceania, Calculated Separately for Vanuatu, Western Polynesia

(Tonga and Samoa), Eastern Polynesia (the Cook Islands and French Polynesia), and

the Overall Dataset, using Three Molecular Clocks and ρ as the Estimator

Molecular Clock Region n Point estimate (years) and 95% CI

1 Control region Vanuatu 35 3600 (0; 7750)

Western Polynesia 73 2950 (1000; 4900)

Eastern Polynesia 41 2450 (200; 4700)

Pooled data 149 3350 (1650; 5050)

Complete sequences Vanuatu 12 3450 (1150; 5800)

Synonymous Vanuatu 12 3250 (0; 6700)


Table S9. mtDNA Lineages Found in Three or More Regions of the Voyaging Corridor

Frequency of mtDNA motif (%)

Hap

logro

up

HV

S-I v

aria

nts (less

16,0

00)

Taiw

an

(n=

977)

Ph

ilipp

ines (n

=556)

Walla

cea (n

=925)

North

coast o

f New

Gu

inea

(n=

403)

Bism

arck

Sea

(n=

1260)

Sou

th co

ast o

f New

Gu

inea

(n=

177)

Solo

mon

s (n=

259)

Rem

ote O

cean

ia (n

=278)

B5b 111 140 189 234 243 399 0.00 1.44 0.00 0.25 0.00 0.56 0.00 0.72

E1b 223 261 362 390 0.00 1.26 3.13 0.50 5.56 2.82 0.00 0.36

M7b1 126 129 192 223 297 0.61 0.90 0.22 0.99 0.08 0.00 0.00 0.00

M28 86 129 148 223 362 (468) 0.00 0.00 0.00 0.50 17.86 0.00 1.16 3.96

P1 176 266 357 0.00 0.00 0.43 1.99 3.02 5.08 0.00 1.80

P1 176 266 270 357 0.00 0.00 0.43 0.99 0.87 4.52 0.00 3.96

P1 176 357 0.00 0.00 0.65 0.50 0.08 6.78 0.00 3.60

P1 176 209 266 357 0.00 0.00 0.00 0.25 1.03 0.00 0.00 0.36

Q1 129 144 148 223 241 265C

311 343

0.00 0.00 1.41 17.12 0.87 12.99 0.77 0.00

Q1 129 144 148 222 241 265C

311 343

0.00 0.00 0.76 7.20 0.24 3.39 0.00 9.35

Q1 129 144 148 241 265C 311

343

0.00 0.00 1.84 6.45 6.03 5.08 4.63 5.76

Q1 129 144 148 172 223 241

265C 311 343

0.00 0.00 1.95 0.25 0.40 2.26 0.00 0.00

Q1 129 144 148 223 241 261

265C 311 343

0.00 0.00 0.00 2.98 0.24 2.82 0.00 0.00

Q1 129 144 148 223 241 264

265C 311 343

0.00 0.00 0.00 0.50 4.30 0.00 3.09 0.00

Q2 66 129 223 241 0.00 0.00 0.76 0.50 7.70 0.00 2.70 0.36

17

Supplemental References

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Phylogeny of East Asian mitochondrial DNA linerages inferred from complete

sequences. Am. J. Hum. Genet. 73:671-676 (erratum 675:157)

2. Macaulay, V., Hill, C., Achilli, A., Rengo, C., Clarke, D., Meehan, W., Blackburn, J.,

Semino, O., Scozzari, R., Cruciani, F. et al. (2005) Single, rapid coastal settlement

of Asia revealed by analysis of complete mitochondrial genomes. Science

308:1034-1036

3. Kong, Q.-P., Bandelt, H.-J., Sun, C., Yao, Y.-G., Salas, A., Achilli, A., Wang, C.-Y.,

Zhong, L., Zhu, C.-L., Wu, S.-F. et al. (2006) Updating the East Asian mtDNA

phylogeny: a prerequisite for the identification of pathogenic mutations. Human

Mol. Genet. 15:2076-2086

4. Tanaka, M., Cabrera, V.M., González, A.M., Larruga, J.M., Takeyasu, T., Fuku, N.,

Guo, L.-J., Hirose, R., Fujita, Y., Kurata, M. et al. (2004) Mitochondrial genome

variation in Eastern Asia and the peopling of Japan. Genome Res. 14:1832-1850

5. Starikovskaya, Y.B., Sukernik, R.I., Derbeneva, O.A., Volodko, N.V., Torroni, A., Ruiz-

Pesini, E., Brown, M.D., Lott, M.T., Hosseini, S.H., Huoponen, K. et al. (2005)

Mitochondrial DNA diversity in indigenous populations of the southern extent of

Siberia, and the origins of Native American haplogroups. Am. J. Hum. Genet.

69:67-89

6. Mishmar, D., Ruiz-Pesini, E., Golik, P., Macaulay, V., Clark, A.G., Hosseini, S.,

Brandon, M., Easley, K., Chen, E., Brown, M.D. et al. (2003) Natural selection

shaped regional mtDNA variation in humans. Proc. Natl Acad. Sci. USA 100:171-

176

7. Ingman, M., Kaessmann, H., Pääbo, S., Gyllensten, U. (2000) Mitochondrial genome

variation and the origin of modern humans. Nature 408:708-713

8. Ingman, M., Gyllensten, U. (2003) Mitochondrial genome variation and evolutionary

history of Australian and New Guinean aborigines. Genome Res. 13:1600-1606

9. Trejaut, J.A., Kivisild, T., Loo, J.H., Lee, C.L., He, C.L., Xi, J.R., Li, Z.Y., Lin, M.

(2005) Traces of archaic mitochondrial lineages persist in Austronesian speaking

Formosan populations. Unambiguous linkage between Aboriginal Taiwanese and

Polynesians to the exclusion of Mainland Asians. PLoS Biol. 3:e247

10. Tabbada, K.A., Trejaut, J., Loo, J.H., Chen, Y.M., Lin, M., Mirazón-Lahr, M., Kivisild,

T., De Ungria, M.C. (2010) Philippine mitochondrial DNA diversity: a populated

viaduct between Taiwan and Indonesia? Mol. Biol. Evol. 27:21-31

11. Pierson, M.J., Martinez-Arias, R., Holland, B.R., Gemmell, N.J., Hurles, M.E., Penny,

D. (2006) Deciphering past human population movements in Oceania: provably

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