“Taiwan, Southeast Asia and the Pacific, a genetic perspective.”

Stephen OppenheimerInstitute of Cognitive and Evolutionary

Anthropology,

School of Anthropology, Oxford University

‘Bellwood model’

‘Out of Taiwan’ vs. SEA/Pacific ‘Slow boat’

~4.5 kya

~3.5 kya

~3 kya ~6 kya

~7-14 kya

‘Bellwood/Diamond Express Train rice farmers replacement model’

Agricultural dispersal of proto-Austronesians from South China/Taiwan from ~5,500 BC Neolithic “package”: Rice,Red-slipped pottery, Pigs, dogs & chickens,Polished stone adzes & Shell fish-hooks

‘Solheim/Meacham/ Oppenheimer

Slow boat Model’

Papuan languages

Austro-Asiatic

languages

Oppenheimer 1998, 2003; Richards, Oppenheimer & Sykes 1998; Capelli et al. 2001; Oppenheimer & Richards 2001a, b)

Express trains versus

slow boat

Archaeological critiques/problems with single late ISEA Neolithic from Taiwan

• Archaeological evidence sparse, but does not indicate a uniform Neolithic ‘package’ (Anderson/Spriggs):

• Complex SE Asian Neolithic elements from Early Holocene i.e. pre-ceramic (O’Connor/Szabo/Terrell)

• Rice Neolithic in ISEA extends only as far as Taiwan and Philippines - and earlier in W. Borneo (rev. Paz) . Red-slipped pottery linked to root crops not rice (Paz)

• Why particularly Taiwan and not S. China or E. Indo-China? (Tsang, Meacham).

• Pre-ceramic arboriculture and horticulture in Sahul including N. Coast NG (Latinis, Denham, Swadling)

Anderson’s 2-phase

Neolithic in SE Asia and

Oceania

Other Problems with two-layer model

• Human genetic evidence that main dispersals may be earlier in Holocene or late Pleistocene (Hill, Richards, Oppenheimer)

• Most plant domestications indigenous to SE Asia and Near Oceania, not Taiwan.

• Genetic evidence linking a) ‘Pacific pig clade’ to Vietnam and b) ISEA pigs to local domestication-not Taiwan (Larson/Lum). c) Chickens (Niu 2002) and dogs (Savolainen 2004) to ISEA

Pacific Clade of domestic pigs (D6)

identical to wild boar in

Vietnam (Lum)

Alternative Demic settlement models

• Sailing and trade in Eastern Sunda (Nusantao) stimulated by rising sea separating ISEA & MSEA (Solheim 1996,2006; Oppenheimer 1998, Soares et al 2008).

• Vietnam as a cultural source for ISEA & Oceania on basis of a Sa Huynh-Kalanay Pottery Complex connection with Lapita (Solheim 2006)

• 2-wave Neolithic model (Anderson 2006) • Main demic dispersals may be earlier in Holocene or

Late Pleistocene (Solheim, Meacham, Oppenheimer)

Three broad phases of settlement of ISEA

& Near Oceania

• First Pleistocene settlement by AMH >40 KYA

• Late- and post-glacial dispersals 5-25 KYA

• Neolithic intrusion (and/or endogenous)

Flooding in Southeast AsiaFlooding in Southeast Asia

Bird, et al 2007

The third flood over the Sunda

continent measured off

Singapore

VIETNAM

CHINATAIWAN

PHILIPPINES

MALAYPENINSULA

SUMATRA

JAVA

BORNEOSULAWESI

WALLACEA

NEW GUINEA

ISLAND SOUTHEAST

ASIA

AUSTRALIA

MAINLAND SOUTHEAST

ASIA

ANCIENT SUNDALAND

WALLACE’S LINE

IRIAN JAYA

PAPUA NEW GUINEA

~14 kya, ~11 kya, ~7 kya

Oppenheimer 1998

Soares et al 2008

Sea-level rises as a cause of dispersal in SEA

Questions to addressQuestions to address

• What were the most important processes in the settlement of Southeast Asia and the SW Pacific

subsequent to the initial colonization over 40,000 years ago:

(1) The spread of rice farming, or

(2) Sea-level rises at the end of the Ice Age?

& 3) Where did the colonizers originate?

CHINA

TAIWAN

ATA

PAI

AMIBUN

PHILIPPINES

Wallace’s line MALAY

PENINSULA

SUMATRA

PAD

MED

PEK

PLB

BGK

JAVA

BORNEO

KK

BAN

SUMBA

BALI

LOMBOK

MTR WAI

SULAWESI MND

UJP

PAL

TOR

WEST PAPUA

AMBON

ALOR

VIETNAM

DNA

sampling 1075 from ISEA899 from MSEA 233 from Taiwan519 from China

Genetic Phylogeography

The study of the geographic spread of genetic lineages

Three components:

1. Detailed gene tree or network (e.g mtDNA/Y chromosome)

2. Geographic distribution of lineages

3. Diversity of clusters of lineages used to estimate time depth.

4. Founder analysis (uses 1-3): identification and dating of specific founder lineages moving from a source to a target region. (Proportional contribution to the modern gene pool of the target region = net gene flow)

Inferring migrations from DNA sequences in a network or tree

root

Source region

Target region

Fig: after Richards & Macaulay 2000

•Schematic global mtDNA tree/network• Root in Africa• Only one major founder type ‘L3’ leaves Africa • This splits into M, N & RThese three founders spread rapidly and diversify in Eurasia

• Regionally specific mtDNA haplogroups evolve

• Coalescence time ~ 200,000 years

Time of founder event ~ 70,000 - 90,000 years

Haplogroup E

Austronesian specific

haplogroup

15% of lineages in ISEA and Taiwan

16324

16256

16093

16248

16390M9

16291

16261

16311

16131

16288

16172

16294

16093

16092

16182

16182G16129

16051

16185

16223

16292

16258C

16309

16184

16215

16399

16140

16189 16290

16126

16093

16117

16129

16148

16140

16180

16288

16311

163421622416294

16172

1624816362

16185

16265T

16270

16295

16086

E1

E2b

E1a

E1b

16129

16172

16255

16149

16086

16185

E2a

10834

8730

Sulawesi

Aboriginal Taiwanese

Sumatra

Sumba

Ambon

Malay

Borneo

Bali

Philippines

Alor

Java

East Indonesia

Lombok

Singapore

Papua New Guinea

Vanuatu

1 2 3 4 5 6 9 107 11 128 14 1513 21 22 23 24 26 2725 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 5351 52 5554 56 57 58 59 60 61 62 63 64 65 66 67 68

94

173

204

482

709

1393

3540

4655

6752

9477

9938

10358

11314

16136

16217

16319

16381

709

5964

6842

7609

7789

12864

16051

16209

16519

6815

7286

15109

1120

1021A

4260

7673

16291

4592

6284

8152

16271

6366

135

13246

16093

16176

150

152

12362

15671

16158

629315607

16319195

7853

9081

16525

7319

11893

15784

16526

8618

153

11963

163907774

16051

3918

5786

7258

9833

7142

7861

14417

16291

30815151

16173

5951

9115

13434

16300

9242

16316

1041

16 17 18 2019

14308

16234

316

3310

7798A

16172

6340

8155

207

9288

14767

5134G

12282

16323

198

961

1821

7364

1452

16223

16324

16256

5662

8551

13933

3866

15235

16174

16519

16189

16255

16291

16311

373

1647416185

9699

16265T

7148

5471

8149

12723

16311

16189

152

3736

11075

16519

8843

131

8577

5277

8953

9020

3345

4120A

9983

709

5417

9129

12358

12522

15596

16270

146

161409983

16172

16248

16362

16291

14766

151

13494

742

8191

12599

374A

7747

13269

16288

13722

207

215

16176

16261

4586

185

527

9018

1047

16261

6620

152

869

9192

69 70 71 72 73 74 75

152879254

16519

5558

92937340

7022

16215

198

5460

6734

9966

12723

16258

16309

16185

9947

63

5460

10909

16189

9063

485

15777

10685

16129

13942 16037

246

10631

12280

16086

161858730

4248

10834

13254

14577

16519195

8440

9080

15178

16051

3027

3705

7598

13626

16390

153

3394

16362

M9

M9a’b

M9a

E

E1

E2

E1b

E1a

E1a2 E1a1E1a1 E2a E2b

10ky

20ky

30ky

40ky

50ky

Ho

loce

ne

Ple

isto

cen

e

0

0

0

0

0

0

0

0

0

0

0

0

0

0

Japan

East Asia

Mainland Southeast Asia

Taiwan

Indonesia/East Malaysia

Philippines

New Guinea

Taiwan + ISEA

ISEA Taiwan + ISEA

ISEA

6.5-9 kya

Haplogroup E tree

• Haplogroup E evolved on Sundaland from haplogroup M9 ~30 kya

• Period of drift >12 kya as area of land halved by rising sea levels

• Major expansions after ~12 kya – perhaps of maritime-adapted populations as the coastline doubled

• Dispersals north to Taiwan, west to Malaysia and east to New Guinea by ~6000 years ago

Haplogroup E and climate changeHaplogroup E and climate change

M7c1 16362 16346C

16292

16192

16311

16189

16213

16168

16265T

16093

16337

16291

1612916145

16179

1618516254

16278

16356

16223

16150

16274

Philippines

SulawesiChinaSumatraAboriginal MalayBorneoTaiwanMalay

U.S.A.

JavaSumba

Alor

AmbonBali

Lombok

Nauru

Thailand

East Indonesia

An Austronesian-specific marker: hg M7c1c

• ~8% of Indonesians - not found in Pacific

• Age = 8,100 years; SE 2200

• Ultimate origin in China

• Dispersal through MSEA to ISEA & to Taiwan; -- too early for migration from Taiwan to ISEA

or from

VIETNAM

CHINATAIWAN

PHILIPPINES

MALAYPENINSULA

SUMATRA

JAVA

BORNEOSULAWESI

WALLACEA

NEW GUINEA

ISLAND SOUTHEAST

ASIA

AUSTRALIA

MAINLAND SOUTHEAST

ASIA

ANCIENT SUNDALAND

WALLACE’S LINE

IRIAN JAYA

PAPUA NEW GUINEA

8-6.5 kya

5 kyaFlake–blade industry appearing 5000-6000

years related with ISEA industry

Archaeological counterpart to Early-Holocene genetic expansions:

16189

16223

16362

1614816093

16309

16092

16311

16256

1618516184

16356

16129

16293c

16355

16311

16319

16201A

16210

16316

16184

16360

D

16369del

16223

16245

16292g

16300

16069

1627416187

16150

16273

16357

16193A16167

16294

16355A

16270?

16172

16259

16187

16256

16171

16068

16362

16265C

16325

1635516111

16311

16228

16126

16166

16092

16164

16186

ChinaJapanTaiwanPakistanSingaporeThailand

SulawesiAmbonBorneo

LombokEast IndonesiaBaliKorea

Hg D5: MidHolocene dispersal of D5d1 from

China

• 3% in ISEA• Age of D5d1 = 4000 years• Recent dispersal from China to

Sulawesi and East Indonesia: ?via Taiwan or via MSEA

D5d1

Malay

Sumatra

Philippines

Taiwan

China

Bali

Borneo

Sulawesi

Malay

Java

Mid-Holocene dispersal in western ISEA: hg Y2

N9161261623116311

16264

16192

213 +A

16362

16284 16093

16126

• 3% in ISEA• Age of Y2 = 3500

years• ?Recent dispersal

through Taiwan, Philippines and western Indonesia -or vice versa

‘Bellwood model’

‘Out of Taiwan’ vs. post-glacial sea-level rises

~4.5 kya

~3.5 kya

~3 kya

~6 kya

~7-14 kya

The “Out of Taiwan” model and the “Polynesian motif”

• The “Out of Taiwan” model suggests that Southeast Asia and the Pacific were re-populated from China/Taiwan in

the Neolithic, 4000-3000 ya

• Alternative models (e.g. Oppenheimer 1998) suggest earlier origins during the sea-level rises in Southeast Asia

or the New Guinea area

• Most Remote Pacific islanders carry a single mtDNA lineage - the “Polynesian motif”

• Therefore the age and distribution of this lineage can test these models

7 - 5.5 kya

4.5 - 4 kya

3.5 kya

>3 kya

Lapita technocomplex

Neolithic “package”:RiceRed-slipped potteryPigs, dogs,chickensPolished stone adzesShell fish-hooks

“Out of Taiwan”

Bellwood et al....

11-9 ky

9-6.5 ky

6-3 ky

3 ky

History of haplogroup B4a1a

That Polynesian motif!

Or should it be the ‘Oceanic motif’?

B4a1a1a (P. Motif)

9,100 yr (SE 2700) B4a1a1: 9,300 yr

(SE 2500)

13,170 yr (SE3840) B4a1a

Japan, Korea, China

not TaiwanJapan not Taiwan

ISEA & Taiwan not China

ISEA, (+Pacific & Melanesia) not Taiwan

TaiwanB4a1a1a

ISEA, Polynesia, Micronesia & Melanesia, not Taiwan

Taiwan Taiwan +ISEA

Summary• There is a signal of early settlement in both the Malay

Peninsula and ISEA

• There are major signals of late-glacial and post-glacial dispersals in ISEA – some involving indigenous lineages, some possibly as a result of movements from the mainland – most likely dispersals in response to climate change and sea-level rise

• There are small signals of mid-Holocene dispersals from China, Indo-China and Near Oceania – possibly associated with farmer-dispersals

• More work needed using complete mtDNA genomes to improve resolution and dating

• Austronesian languages may have been dispersed by small groups of pioneers from Taiwan, but if so the languages were adopted by the mass of the indigenous population of ISEA into which the newcomers were assimilated

• Extant human mtDNA patterns in ISEA and Taiwan seem to have been primarily formed by climate change – in particular the increase in coastline resulting from sea-level rises - rather than by later technological innovation from an external source

Conclusions – the mtDNA perspective

Team & Acknowledgements• Martin Richards, Catherine Hill, Pedro Soares, Maru Mormina

• Dept of Chemical & Biological Sciences, University of Huddersfield• Vincent Macaulay

• Dept of Statistics, University of Glasgow• David Bulbeck

• School of Archaeology & Anthropology, ANU• Patimah Ismael, Joseph Maripa Raja, Norazila Kassim Shaari

• Department of Biomedical Science, Universiti Putra Malaysia• Antonio Torroni, Alessandro Achilli, Chiara Rengo

• Dipartimento di Genetica e Microbiologia, Università di Pavia• Hans–Jürgen Bandelt

• Fachbereich Mathematik, Universität HamburgDougie Clarke, Will Meehan, James Blackburn

Dept of Chemical & Biological Sciences, University of HuddersfieldPeter Forster, Petya Blumbach, Matthieu Vizuete-Forster

McDonald Institute for Archaeological Research, University of CambridgeJean Trejaut, Marie Lin, Jun-Hun Loo

Transfusion Medicine and Anthropology Laboratory, Mackay Memorial Hospital, Tamsui, Taiwan Georgi Hudjashov

The Estonian Biocentre, Tartu, Estonia The British Academy, The Bradshaw Foundation, EU Marie Curie program, The Royal Society, United Productions, Universities of Huddersfield & Leeds

The mtDNA clockThe mtDNA clock

• The most widely used mtDNA rates have been the control-region rate of Forster et al. (1996) and the

coding-region of Mishmar et al. (2003)

1. We need a whole-genome rate (control region as well as coding region) for maximum precision – Mishmar

rate ignores about a third of the variation

2. Some people suggested we also needed to account for purifying selection, which might skew the calibration

• There has been a lot of debate about the rate, with some people suggesting that it is far too slow

The new improved mtDNA clockThe new improved mtDNA clock

We have re-calibrated the mtDNA clock using 2300 complete mtDNA genomes

• We have used new fossil data for the calibration point (human-chimp split now 7 My)

• We have obtained the first rate for the whole mtDNA genome (not just the coding region or control region) –

more precise

• We have corrected for natural selection for the first time – more accurate

50

0

61.9

71.2

58.2

31.8X

9.5X1

20.9 X2

X2a

12.8 14.6

X2b

7.2

X2c

23.9

WW1

17.6

W2

N1

18.9

I26.3

54.2

N1b

21.1

29.2

A25.3

A2

14.6

pA2

A5

20.3

A5c

A5b

13.9 A5a

7.6

N949.1

Y

22.3

Y113.2

Y2

5.0

N9a3

8.9

N9a2

10.1 N9a1

4.7

19.7

N9a5

7.4 N9a4

N9b1

16.8

N9b2

18.4

N9b

29.1

N9b3

8.8

59.1

66.6

54.3

R0 38.8

R0a

13.3

HV27.1

HV1

17.0HV0b

16.6 V13.6

H18.6

H112.2

H211.7

H511.5

H615.3

H14

14.5H412.5

H311.8

H15

14.0

H13

17.5H810.6

H715.5

54.0U

36.9

U1

22.2

U1a

36.0U5

26.9U5a

27.4U5b

18.2

U5a1

20.0

U5a2 24.0

U5b1

22.4

U5b2

U5b3

35.9U6

11.0

U6c

27.7

U6a

13.1

U6b14.9

U6d

53.5

U2

27.5

U2a

34.3

U2b

34.8

U2c

16.7

U2e

40.7

U3

22.9

U3a 27.0

U3b

20.9U4

25.5

U9

21.8

U7

50.2U8

24.9

U8a

34.9

U8b 31.4K26.7

K1

20.5

K1a 25.0

K1b

19.5

K1c

14.1

K2a

25.7K2

50.3JT

13.5

R1

32.6J

24.1J1

11.8

J1a

11.3

J1b

J1b1

23.5

J2

37.5

R5

19.1R5a

51.1

R6

35.6R7

42.1

R8

20.2

R8a

R31a

64.0

R30

B 50.7

B444.2

B4a

25.8

B4a2

18.3

B4a1

24.2

B4a1a

10.4

B4a1b

B4a1c

20.0

B4b

39.0

B4b1

27.5

B214.6

B4b1a

24.3

B4b1b

B4d

28.7

B4c

31.6

B4f

16.2

B542.2

B5a

26.6

B5a2

14.5

B5b

25.9

B5b1

22.5 B5b2

17.4

R11

21.0

R947.2

R9b

21.2

F43.4

10.5

J2b

26.8T

14.7

T1

7.8

T1a

T218.1

8.4

T2b

F1

F1a

22.2 F1b

15.9

F1c

17.3

F1d

F2

17.7

F435.8

48.4

6.2

16.7 16.7

6.0

20.5

19.3 15.6

54.7

21.8

15.5

7.2

4.3

33.5

24.4

53.9

46.042.5

21.1

38.8

6.2

3.9

28.2

6.8

N9a

27.733.5

MitochondrialMitochondrialEveEve Sub-Saharan Africa

North Africa

Near East/Europe

South Asia

East Asia

Americas

L0149.7

L1

L1b

9.7

L1c

85.4

192.4

140.6

L5120.2

89.3L2

48.3

L2a

L2a1

21.5

25.2

L2c

71.6L3

L3b

16.4

L3d

31.0

39.0

L3e

66.7

L3h

34.8

L3i36.1

L3x

53.1 L3f

L0k

11.2

L0a1

26.8

L0a2

25.4

L0a

44.850

100

150

200

100

150

200

0

60.6

M

M125.4

M1a

21.0M1b

20.9

37.6

M2

20.3M2a

12.8

M2b

35.3 M3

M5

21.6

M5a

21.3

M629.8

M3436.5M4

22.2

M18

16.8

M38

34.7

M37

M35

22.3M30

6.4

M41

44.9

M33 32.3

M39

36.5

M36

33.5

M40

D48.3

D6

29.3

D5

38.3

D5c

5.1

D5a

23.8

D5a1

7.6

D5a2

11.5

D5b

21.7

D5b1

16.0

D4

D113.5

D4a15.5

D4a1

6.3

D4a2

10.5

D4a3

13.0

D4a4

12.3

D4b

25.8

D4b1

20.1 D4b2

18.6

D4c22.5

D4c2

2.3

D4c1

19.6

D4e

22.9

D4e1

19.3

D4e2

4.9

D4g

27.0

D4g1

3.7

D4g2

21.1

D4f

2.3

18.1

D4h

17.0

D4i

14.2

D4j

6.3

D4k8.7D4l

3.9

D4m 7.4

D4n

17.2

D4o

M754.8

M7a

27.5

M7a1

18.9 M7a2

21.2 M7a1a

11.8

M7b

28.7

M7b2

6.4

M7c

24.0

M7c1

20.6 M7c3

16.8

M842.7

M8a

25.9

M8a1

2.9

M8a2

18.3

C

28.3

C117.1

C1a

13.9

C1b

14.5C1c

9.0

C4

17.7

Z

24.3

Z1

17.8

Z23.7

Z4

14.8

M953.4

27.4

M9a

15.4

M9a1

4.6M9a2

4.1

M9a3

6.1

M10

27.2

M11

22.7

G

35.7

G1

22.5

G1a

19.0

G2

30.4

G2a

17.7

G3

29.2

G3a

20.9 G3b

14.4 M13

12.4

138.1

108.0

166.8

149.3

114.7

61.8

105.3

86.1

64.1

64.1

53.4

71.5

40.5

34.9

M7b3

13.4

19.9

50.2

HoloceneHolocene

Upper Upper PleistocenePleistocene

Middle Middle PleistocenePleistocene

26.1

46.9

33.4

56.7

E

E1aE1a1a E1b

E114.0

10.0

7.2 6.3

9.9

E2a

6.9

E2

6.6

E2b

14.3L2b

25.3

N49.4

M 39.6

39.6

R

NN

NNNN 64.5

R31

RRRR

African L3 (~73 kya)First colonization of the American continent (~14-21 kya)

Out of Africa (~70-60 kya)

U6b

Colonization of Canary Islands – 2450 years

Colonization of Polynesia (founder age) – 3450 years

The new mtDNA chronologyThe new mtDNA chronologySoares, P., Ermini, L., Mormina, M., Röhl, A., Salas, A., Oppenheimer, S., Macaulay, V., and Richards M.B. Correcting for purifying selection: An improved human mitochondrial molecular clock. AJHG. 84:740-759