Prof. Mark StonekingTheGenetic History of Australia, Oceania, and Southeast Asia Prof. Mark...
Transcript of 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)
2
Genetics and the Austronesian expansion
3
Austronesian expansion is an expansion of languages
Austronesian archeology, fossils, genes – are all inferences
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
2The screen versions of these slides have full details of copyright and acknowledgements
4Gray et al.
2009
Spread of Austronesian languages from Taiwan is strongly supported by phylogenetic analyses
5
Correlations in the archaeological record: movement of people, or movement of ideas?
6
Genetics and the Austronesian expansion
1) Role of Taiwan
2) Impact on SE Asia
3) Impact on Oceania
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
3The screen versions of these slides have full details of copyright and acknowledgements
7
• 12 groups, 550 individuals
• 8 Highland/Aboriginal groups
• 4 Lowland/Han groups
• Complete mtDNA
genome sequences
• Average coverage ~500X
The role of Taiwan
8
New discovery on Liang Island
Matsu Archipelago
9
• ~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
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
4The screen versions of these slides have full details of copyright and acknowledgements
10
• 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
11
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
12
• 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
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
5The screen versions of these slides have full details of copyright and acknowledgements
13
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
14
Genetic study of Taiwan
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
15
1) Divergence time between Han and Formosan ancestors
2) Order and timing of population divergences
among Taiwanese groups
3) Migration out of Taiwan
Genetic study of Taiwan
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
6The screen versions of these slides have full details of copyright and acknowledgements
16
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
Genetic study of Taiwan
17
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
18
Genetics and the Austronesian expansion
Impact on SE Asia
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
7The screen versions of these slides have full details of copyright and acknowledgements
19 Karafet et al. 2010
Y chromosome analyses suggest four expansion periods in Indonesian history
Initial Pre-Austronesian
Austronesian Late
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
8The screen versions of these slides have full details of copyright and acknowledgements
22
Genome-wide data suggest four main ancestries in SE Asia, with a significant Taiwan component
AmiAtayal
Lipson et al. 2014
NegritoMelanesianSE AsiaTaiwanOther Asian
23
Analyses of Helicobacter pylori also indicate a Taiwanese origin for the Austronesian expansion
Moodley et al. 2009
24
Genetics and the Austronesian expansion
Impact on Oceania
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
9The screen versions of these slides have full details of copyright and acknowledgements
25
“Fast train”
26
“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
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
10The screen versions of these slides have full details of copyright and acknowledgements
28
Asian Y-haplogroups
Polynesian Y-chromosome haplogroupsare mostly of Melanesian origin!
Kayser et al. 2006
Melanesian Y-haplogroups
29
• 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
30
“Slow-boat” model of Polynesian origins
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
11The screen versions of these slides have full details of copyright and acknowledgements
31
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?)
32
What about the autosomal gene pool of Polynesians?
33
Demographic inference – SNP data
Wollstein et al. 2010
AF EU CH BO PO FI NG
80% 20% ~3000 ya
~500 ya
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
12The screen versions of these slides have full details of copyright and acknowledgements
34
• 34 populations
• Grouped by geography/culture
into 6 groups
Near Oceania
Remote Oceania
• 1,331 complete mtDNA
genome sequences
• Average coverage ~450X
35
Impact on Oceania: maternal structure
Haplogroup affiliations
• Austronesian: B4a and sublineages
• Melanesian: Q, P, M27, M28, M29
• Other: E, M7c3c
36
Impact on Oceania: maternal structure
Rem
ote
Oceania
Near
Oceania
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
13The screen versions of these slides have full details of copyright and acknowledgements
37
Widespread sharing of haplogroup B4a lineages
Haplotype sharing
Haplogroup B4a* All other haplogroups
38
• 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
Impact on Oceania: maternal structure
39
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
-
The Genetic History of Australia, Oceania, and Southeast AsiaProf. Mark Stoneking
14The screen versions of these slides have full details of copyright and acknowledgements
40
Genetics and the Austronesian expansion
• 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
41