“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
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