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Utility of Genomic Technologies in Anthropology
Wibhu Kutanan
Khon Kaen University, Thailand
A B D E C H G J I L T O N Q R
African Non-African
Molecular Anthropology
Anthropology
Molecular Anthropology
The use of molecular genetic methods to address the question and issues of anthropological interest.
Molecular Genetics Genetics
DNA from modern v.s. ancient human
Source: Wang and Li (2013); https://en.wikipedia.org/wiki/Neanderthal
90.4
4.1 3.20.3 2
16
27
19
36
0
10
20
30
40
50
60
70
80
90
100
Tai-Kadai Austroasiatic Sino-Tibetan Hmong-Mien Austronesian
Percent from 67.9 million No.of languages from 72
Linguistic distribution in Thailand
Source: https://en.wikipedia.orgSource: Lewis et al (2016)
Complex human occupation history in MSEA
Present-day Southeast Asian groups
(Thais)
Hoabinhian hunter-gatherer tradition ~ 44 kya
(Higham, 2014; Ji et al., 2016)
Anatomically Modern Human ~ 50-65 kya
(Higham, 2013; Demeter et al., 2017)
Agricultural/Neolithic expansion from China (Yangtze and Yellow River) ~ 4.0-4.5 kya (Belwood, 2005)
Related to Austroasiatic speaking group (van Driem, 2017)
Iron/Bronze age migration ~ 2.0 kya
(Belwood, 2005)
Related to Tai-Kadai groups
Historical migrations ~600-100
ya from Myanmar, e.g. Mon, Shan, Hilltribes (Karen,
Hmong)
Historical migrations ~250 ya
from Vietnam and Laos, e.g. Phutai, Soa, Nyaw, Lao Isan
Lipson, et al. (2018) McColl, et al. (2018)
Hypotheses of Thai’s origin
1. Altai homeland (Khun Vichit-Matra, 1928)
2. Nan Chao homeland (De Lacouperies, 1885)
3. Southern China homeland (Damrong Rajanubhab, 1949; Benedict, 1975)
4. Indonesian homeland (Phansomboon, 1957)
5. Indigenous theory (Sangvichien, 1966)
Hypotheses of genetic ancestry of Thai/Lao TK people
Demic diffusion
(Immigrant hypothesis)
• a demic expansion of people from southern China that brought their genes, culture, and language to Thailand/Laos
Cultural diffusion
(Endogenous hypothesis)
• a cultural diffusion from southern China that resulted in native AA peoples adopting the TK language and culture
Language and Archaeological evidence Physical anthropological evidence
(O’Connor, 1995; Pittayaporn, 2014) (Sangvichien, 1966; Nakbunlung, 1994)
Admixture?
Hypotheses of genetic ancestry of Thai/Lao TK people
Demic Diffusion
(Immigrant hypothesis)
Cultural Diffusion
(Endogenous hypothesis)
Continuous Migration ?
Source: Premsrirat, S (2002)
18.8% Northern Thais/Khon Mueang
32.14% Northeastern Thais/Lao Isan
43.28 % Central Thais
12.81% Southern Thais
Tai-Kadai (31)
59 populations
Khon Mueang (4)Lao Isan (4)Phuan (2)Black Tai (2)Nyaw (1)Kalueng (1)Phutai (1)Shan (1)Yuan (2)Seak (1)Laotian (2)Lue (2)Khuen (1)Central Thai (7)
Austroasiatic (24)
H’tin (Mal) (1)H’tin (Pray) (2)Lawa (3)Mon (7)Nyahkur (1)So (1)Bru (1)Paluang (1)Blang (1)Khmer (2)Suay/Kui (1)Khamu (1)Mlabri (1)Mani (1)
Skaw Karen (2)Pwo Karen (1)Paduang Karen (1 )
Sino-Tibetan (4)
ผศ.ดร.จตพุล ค ำปวนสำย ผศ.ดร.เมธำวี ศรีค ำมลู
Sequencing
• Preparing genomic libraries for each sample using a double index scheme
(Meyer et al., 2012).
• Enrichment the libraries for ~2.34 mB of the MSY via in-solution hybridization-
capture (Prüfer et al., 2014) using a previously-designed probe set (Kutanan et
al., 2018b) and the Agilent Sure Select system (Agilent, CA, USA) and also
enrichment for mtDNA using design probe (Maricic et al. 2010).
• The libraries were sequenced on the Illumina Hiseq 2500.
Approximate Bayesian Computation (ABC)
Demic Diffusion
(Immigrant hypothesis)
Cultural Diffusion
(Endogenous hypothesis)
Continuous Migration/
Admixture
Major Thai groups mtDNA Y chromosome
Northern Thai Demic diffusion Demic diffusion
Northeastern Thai + Laotian Demic diffusion Admixture
Central Thai Admixture Cultural diffusion
Model based on linguistic and macro-geographic data
Sagart (2004, 2005) Starosta (2005) Peiros (1998)
MSEAISEA
Genetic variation and cultural practice
• Patrilocal groups (i.e., the wife moves into her husband's house) greater genetic divergence among male lineages
• Matrilocal groups (i.e., the husband moves into his wife’s house) greater genetic divergence among female lineage
Nat Genet 2001, 29(1): 20-21
Demographic change
• Female effective population size was greater than male.
• Male and female The early Mesolithic (~10 kya)
• Male specific The Neolithic period (~4-5 kya) (relate to AA and TK)
The Bronze/Iron Age (~2.0-2.5 kya) (related to TK)
0
5000
10000
15000
20000
25000
30000
35000
40000
45000
50000
55000
60000
C-2
6
C1
-7
C2
-19
C2
e-1
7
C2
e1-7
C2
e2-1
0
D-1
9
D1
*-8
D1
a1a-
11
G1
b-7
H-1
3
H1
-11
J-1
5
J2a1
-11
J2b
2-4
N1
c2b
2-2
6
O1
a-4
2
O1
a2-7
O1
a1a-
34
O1
a1a1
-20
O1
a1a2
a-1
4
O1
a1a1
a-1
0
O1
a1a1
b-1
0
O1
b1
a1a1
a-1
48
O1
b1
a1a1
a1a-
10
4
O1
b1
a1a1
a1b
-17
O1
b1
a1a1
a1a1
b-2
3
O1
b1
a1a1
a2a-
27
O1
b1
a1a1
a2a1
a-1
5
O1
b1
a1a1
a2a2
-12
O1
b1
a1a1
b-3
01
O1
b1
a1a1
b*-
18
7
O1
b1
a1a1
b1
a-1
13
O2
a1c-
20
O2
a1c1
a-1
4
O2
a2a-
61
O2
a2a1
a-5
7
O2
a2a1
a2 -
54
O2
a2a1
a2a
-53
O2
a2b
-15
9
O2
a2b
1a-
14
8
O2
a2b
2a-
8
O2
a2b
1a1
a-1
37
O2
a2b
1a1
a*-1
28
O2
a2b
1a2
a1-1
1
R-4
1
R1
-30
R1
a1a1
b-2
8
R2
-11
Coalescent age estimation based on MSY
Human occupation prehistory in Southeast Asia
Present-day Southeast Asian groups
(Thais)
Hoabinhian hunter-gatherer tradition ~ 45 kya
(Higham, 2014; Ji et al., 2016)
Anatomically Modern Human ~ 50-65 kya
(Higham, 2013; Demeter et al., 2017)
Agricultural/Neolithic expansion from China (Yangtze and Yellow River) ~ 4.0-4.5 kya (Belwood, 2005)
Related to Austroasiatic speaking group (van Driem, 2017)
Iron age migration ~ 2.0 kya(Belwood, 2005)
Related to Tai-Kadai (MSEA) and Austronesian groups (ISEA)
Historical migrations ~600-100
ya from Myanmar, e.g. Mon, Shan, Hilltribes (Karen,
Hmong)
Historical migrations ~250 ya
from Vietnam and Laos, e.g. Phutai, Soa, Nyaw, Lao Isan
Lipson, et al. (2018) McColl, et al. (2018)
https://en.wikipedia.org; http://originalpeople.org
The hunter-gatherer groupsMSY NJ tree
mtDNA NJ tree
Data of Thai populations
-MSY sequences = 1,198 sequences (76 populations)
-mtDNA sequences = 2,322 sequences (92 populations)
-GWAS (Affymetrix Axiome GWAS Human Origin 1 array) = 470 individuals (44 populations)
-Genomic sequence of 2000 ya and 13,000 ya samples from Mae Hong Son
Archaeogenetics
รศ.ดร.รศัมี ชทูรงเดช
Woman from Tham Lod Rockshelter (13,000 ya) Long Long Rak Cave (~2,000 ya)
Thai รศ.ดร.รศัมี ชทูรงเดช
ผศ.ดร.จตพุล ค ำปวนสำยรศ.ดร.ดำวรุ่ง กงัวำนพงศ์ผศ.ดร.เมธำวี ศรีค ำมูล
รศ.ดร.พิทยำวฒัน์ พิทยำภรณ์Non-Thai
Prof.Dr. Mark Stoneking, MPI-EVA, GermanyProf.Dr. Svante Pääbo, MPI-EVA, Germany
Prof.Dr. Johanase Krause, MPI- SHH, GermanyAssoc.Prof.Dr. Silvia Ghirotto, U. of Ferrara, Italy
The Max Planck SocietyThe Thailand Research FundKhon Kaen University
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