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

DNA MarkersBi-parentally inherited marker

mtDNAY chromosome

Source: Skaletsky et al. (2003)

Uni-parentally inherited marker

Coalescence theoryMutation

0.0000000167 /base/years (mtDNA)

Source: https://en.wikipedia.org

mtDNA haplogroup distribution

Source: https://en.wikipedia.org

Y haplogroup distribution

Source: Mann et al. (2009)

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

Genetic difference in major Thai groups

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

Mon

Tai-Kadai

Austronesian

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

Genetic variation and cultural practice

Patrilocal

Patrilocal

Matrilocal

Matrilocal

Bayesian Skyline Plot (BSP)

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

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D-1

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48

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20

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R-4

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-30

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a1a1

b-2

8

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-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

McColl et al., Science 361, 88–92 (2018)

Lipson et al., Science 361, 92–95 (2018)

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