prof. mark stonekingthegenetic history of australia, oceania, and southeast asia prof. mark...

The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking

1The screen versions of these slides have full details of copyright and acknowledgements

1

The Genetic History of Australia, Oceania, and Southeast Asia

Prof. Mark Stoneking

Max Planck Institute for Evolutionary Anthropology

Leipzig, Germany

(Part 2 of 2)

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Genetics and the Austronesian expansion

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Austronesian expansion is an expansion of languages

Austronesian archeology, fossils, genes – are all inferences



4Gray et al.

2009

Spread of Austronesian languages from Taiwan is strongly supported by phylogenetic analyses

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Correlations in the archaeological record: movement of people, or movement of ideas?

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1) Role of Taiwan

2) Impact on SE Asia

3) Impact on Oceania



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• 12 groups, 550 individuals

• 8 Highland/Aboriginal groups

• 4 Lowland/Han groups

• Complete mtDNA

genome sequences

• Average coverage ~500X

The role of Taiwan

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New discovery on Liang Island

Matsu Archipelago

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• ~70% complete

• Male, about 30 years old

• Limb bones are robust with prominent muscle attachment

sites, implying he was strong and active

• Radiocarbon dating of a rib bone gave calibrated age

of 8060-8320 BP

• Radiocarbon dating of shells and charcoal from above

the skeletal remains gave calibrated ages of 7400-7900 BP

Liangdao man



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• Extracted DNA from a foot phalanx

and used new single-strand library preparation method

• Obtained ~245X coverage

• Level of contamination T changes

at ends, characteristic

of ancient DNA

Liangdao man

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Liangdao Man• Liangdao Man is from the right place

and the right time to be potentially informative

about origins of Aboriginal Taiwanese...

... and also has the right mtDNA sequence!

• Lingdao Man’s mtDNA sequence is ancestral

to haplogroup E1, sharing two of four

diagnostic positions

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• Liangdao Man’s mtDNA sequence is most closely related

to two E1a sequences from Taiwan

• The closest extant relative of haplogroup E is M9a,

found mostly on the southern coast of China

Has 2 of 4 diagnostic mutations for haplogroup E1

Liangdao Man



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Genetic study of Taiwan

Genetic data strongly suggest

a north to south movement

of people through Taiwan

at

ya

u

n

ma

ka

n

Ami

o

ao

kka

n

0 20 40 60 80 100

Sequence sharingSaisiatAtayal

TsouBunun

PuyumaRukai

PaiwanAmi

MakataoTao

HakkaMinnan

0% 20% 40% 60% 80% 100%

Back to contemporary samples...

Genetic diversity

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Model-based approach to inferring the demographic history of Taiwan

• Either assume

a history, or determine

the best-fitting history

• Carry out simulations

to infer demographic

parameters of interest

Stoneking and Krause 2011

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1) Divergence time between Han and Formosan ancestors

2) Order and timing of population divergences

among Taiwanese groups

3) Migration out of Taiwan




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Results of the simulations

Han Chinese Saisiat Atayal Tsou Bunun Ami Rukai Puyuma Paiwan Malayo-Polynesian

0 1 2 3 4 5 6 7 9 10 8

Divergence me (ka)

South

Central

North


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9.5-11.5 ky

~8 ky

~6 ky

~4-4.5 ky

Putting together archaeology, linguistics, and genetics

Foxtail millet domestication

Rice domestication

Fuzhou

Liangdao Man

8.2-13.5 ky

Rice and Foxtail millet cultivation

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Impact on SE Asia



19 Karafet et al. 2010

Y chromosome analyses suggest four expansion periods in Indonesian history

Initial Pre-Austronesian

Austronesian Late



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Genome-wide data suggest four main ancestries in SE Asia, with a significant Taiwan component

AmiAtayal

Lipson et al. 2014

NegritoMelanesianSE AsiaTaiwanOther Asian

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Analyses of Helicobacter pylori also indicate a Taiwanese origin for the Austronesian expansion

Moodley et al. 2009

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Impact on Oceania



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“Fast train”

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“Entangled bank”

27 Kayser et al. 2006

Asian mtDNA haplogroups

Polynesian mtDNA types are mostly of Asian origin, supporting the "Fast Train" model

Melanesian mtDNA haplogroups



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Asian Y-haplogroups

Polynesian Y-chromosome haplogroupsare mostly of Melanesian origin!

Kayser et al. 2006

Melanesian Y-haplogroups

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• An Asian origin for 94% of Polynesian mtDNAs,

supporting the fast train model

• A Melanesian origin for 66% of Polynesian Y chromosomes,

supporting the entangled bank model

How can we reconcile these results??

Summary

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“Slow-boat” model of Polynesian origins



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Slow boat model

• Migration of Polynesian ancestors from east Asia (Taiwan)

to New Guinea

• Substantial mixing between Polynesian ancestors

and New Guineans

• Mixing was sex-biased, involving primarily women

from the incoming Austronesians and New Guinea men

(influence of matrilocality?)

• In Papuan-speaking coastal New Guinea groups,

more Asian mtDNA than Asian Y-chromosomes

(influence of patrilocality?)

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What about the autosomal gene pool of Polynesians?

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Demographic inference – SNP data

Wollstein et al. 2010

AF EU CH BO PO FI NG

80% 20% ~3000 ya

~500 ya



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• 34 populations

• Grouped by geography/culture

into 6 groups

Near Oceania

Remote Oceania

• 1,331 complete mtDNA

genome sequences

• Average coverage ~450X

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Impact on Oceania: maternal structure

Haplogroup affiliations

• Austronesian: B4a and sublineages

• Melanesian: Q, P, M27, M28, M29

• Other: E, M7c3c

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Rem

ote

Oceania

Near

Oceania



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Widespread sharing of haplogroup B4a lineages

Haplotype sharing

Haplogroup B4a* All other haplogroups

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• Huge impact of haplogroup B4a lineages (~75% of mtDNAs),

associated with the Austronesian expansion

• Most of the remaining mtDNA lineages are autochthonous

Near Oceanian lineages

• Other potential migrations account for ~2% of the mtDNA

lineages and are restricted to specific populations


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Genetic History of Australia, Oceania, and Southeast Asia

• Multiple waves of migration: early southern route to Australia

and Near Oceania followed by subsequent dispersals

• Support for this scenario from both modern and ancient DNA

• Genetic contact from India to Australia ~4,200 years ago



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• Genetic trail into, across, and out of Taiwan

• Spread across island SE Asia

• Huge impact on maternal lineages of Oceania

• Still some puzzles to resolve

‒ How to explain outliers such as Santa Cruz

• Simple models do not account for all of the complexities

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