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

“Taiwan, Southeast Asia and the Pacific, a genetic perspective.” Stephen Oppenheimer Institute of Cognitive and Evolutionary Anthropology, School of Anthropology, Oxford University. ‘Out of Taiwan’ vs. SEA/Pacific ‘Slow boat’. ‘Bellwood/Diamond Express Train rice farmers replacement model’.

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

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  1. “Taiwan, Southeast Asia and the Pacific, a genetic perspective.” Stephen Oppenheimer Institute of Cognitive and Evolutionary Anthropology, School of Anthropology, Oxford University

  2. ‘Out of Taiwan’ vs. SEA/Pacific ‘Slow boat’ ‘Bellwood/Diamond Express Train rice farmers replacement model’ ‘Solheim/Meacham/ Oppenheimer Slow boat Model’ ~4.5 kya ‘Bellwood model’ ~7-14 kya ~3.5 kya ~6 kya ~3 kya 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

  3. Express trains versus slow boat Austro-Asiatic languages Papuan languages Oppenheimer 1998, 2003; Richards, Oppenheimer & Sykes 1998; Capelli et al. 2001; Oppenheimer & Richards 2001a, b)

  4. 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)

  5. Anderson’s 2-phase Neolithic in SE Asia and Oceania

  6. 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

  7. Pacific Clade of domestic pigs (D6) identical to wild boar in Vietnam (Lum)

  8. 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)

  9. 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)

  10. Flooding in Southeast Asia

  11. Bird, et al 2007 The third flood over the Sunda continent measured off Singapore

  12. Sea-level rises as a cause of dispersal in SEA Oppenheimer 1998 Soares et al 2008 ~14 kya, ~11 kya, ~7 kya

  13. Questions 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: • The spread of rice farming, or • Sea-level rises at the end of the Ice Age? • & 3) Where did the colonizers originate?

  14. ATA CHINA BUN AMI TAIWAN PAI PHILIPPINES VIETNAM Wallace’s line MALAY PENINSULA KK MED SULAWESI MND PEK WEST PAPUA PAD BORNEO PAL BGK DNA sampling TOR BAN PLB SUMATRA AMBON UJP JAVA ALOR LOMBOK BALI MTR WAI 1075 from ISEA899 from MSEA 233 from Taiwan519 from China SUMBA

  15. 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)

  16. Source region Target region root Inferring migrations from DNA sequences in a network or tree Fig: after Richards & Macaulay 2000

  17. 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

  18. 16182G 16129 16288 16182 16131 16256 16255 16092 E1b 16294 16172 16311 16324 16172 16093 16248 16129 16261 16093 Aboriginal Taiwanese 16295 16117 16180 E1 Philippines 16291 10834 16140 Malay E1a M9 16390 Singapore 16093 16051 16290 Sumatra 16189 16265T Borneo 16288 16126 16086 Java 16311 16270 8730 16185 Bali 16172 16185 16224 16294 16129 16342 16086 16185 Lombok 16184 Sulawesi 16223 Sumba E2a 16292 16148 16215 East Indonesia 16248 16362 Alor 16258C 16309 E2b 16140 Ambon 16149 16399 Papua New Guinea Vanuatu Haplogroup E Austronesian specific haplogroup 15% of lineages in ISEA and Taiwan

  19. Haplogroup E tree 6.5-9 kya Taiwan + ISEA Taiwan + ISEA ISEA ISEA

  20. Haplogroup E and climate change • 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

  21. An Austronesian-specific marker: hg M7c1c Nauru Alor Lombok 16265T East Indonesia 16145 16129 16179 Sumba 16168 16223 Java 16189 16213 16292 Philippines M7c1 16346C 16362 Sulawesi 16192 China 16356 16311 Sumatra 16278 16093 Aboriginal Malay 16254 16185 Borneo 16150 16274 Taiwan 16337 Malay U.S.A. 16291 Bali Ambon Thailand • ~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

  22. Archaeological counterpart to Early-Holocene genetic expansions: 5 kya Flake–blade industry appearing 5000-6000 years related with ISEA industry 8-6.5 kya

  23. Borneo Ambon Sulawesi China Japan Taiwan Pakistan Singapore Thailand Korea Bali East Indonesia Lombok 16293c 16355 16184 16356 16185 16256 16311 16129 D5d1 16068 16362 16092 16210 16316 16309 • 3% in ISEA • Age of D5d1 = 4000 years • Recent dispersal from China to Sulawesi and East Indonesia: ?via Taiwan or via MSEA 16184 16201A 16171 16223 16245 16093 16148 16126 16369del 16150 16292g 16300 16311 16189 16223 16362 16319 D 16069 16360 Malay Hg D5: MidHolocene dispersal of D5d1 from China 16274 16187 16092 16164 16186 16265C 16273 16172 16357 16355A 16166 16325 16355 16111 16167 16294 16259 16193A 16270? 16311 16187 16256 16228

  24. Mid-Holocene dispersal in western ISEA: hg Y2 16264 16362 16126 16126 16231 16311 N9 213 +A Sulawesi 16093 16284 Borneo 16192 Bali China Taiwan Sumatra Philippines Malay Java • 3% in ISEA • Age of Y2 = 3500 years • ?Recent dispersal through Taiwan, Philippines and western Indonesia -or vice versa

  25. ‘Out of Taiwan’ vs. post-glacial sea-level rises ~4.5 kya ‘Bellwood model’ ~7-14 kya ~3.5 kya ~6 kya ~3 kya

  26. 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

  27. “Out of Taiwan” Bellwood et al.... Lapita technocomplex Neolithic “package”: Rice Red-slipped pottery Pigs, dogs,chickens Polished stone adzes Shell fish-hooks

  28. History of haplogroup B4a1a

  29. That Polynesian motif! Or should it be the ‘Oceanic motif’?

  30. Japan, Korea, China not Taiwan Japan not Taiwan ISEA & Taiwan not China ISEA, (+Pacific & Melanesia) not Taiwan B4a1a1a Taiwan Taiwan +ISEA Taiwan ISEA, Polynesia, Micronesia & Melanesia, not Taiwan B4a1a1a (P. Motif) 9,100 yr (SE 2700) 13,170 yr (SE3840) B4a1a B4a1a1: 9,300 yr (SE 2500)

  31. 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

  32. Conclusions – the mtDNA perspective • 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

  33. 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 Hamburg • Dougie Clarke, Will Meehan, James Blackburn • Dept of Chemical & Biological Sciences, University of Huddersfield • Peter Forster, Petya Blumbach, Matthieu Vizuete-Forster • McDonald Institute for Archaeological Research, University of Cambridge • Jean 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

  34. The 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

  35. The 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

  36. The new mtDNA chronology First colonization of the American continent (~14-21 kya) African L3 (~73 kya) Out of Africa (~70-60 kya) U6b Colonization of Canary Islands – 2450 years Colonization of Polynesia (founder age) – 3450 years Soares, 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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