MBE Advance Access published July 28, 2012

Evolutionary History of Continental Southeast Asians:“Early Train” Hypothesis Based on Genetic Analysis of
Mitochondrial and Autosomal DNA Data
Timothy A. Jinam,1,2 Lih-Chun Hong,3 Maude E. Phipps,4 Mark Stoneking,5 Mahmood Ameen,3Juli Edo,6 HUGO Pan-Asian SNP Consortium,7 and Naruya Saitou*,1,2
1Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
Division of Population Genetics, National Institute of Genetics, Mishima, Japan3
Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
4
Jeffrey Cheah School of Medicine and Health Sciences, Monash University (Sunway Campus), Selangor, Malaysia
5
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
6
Department of Anthropology, Faculty of Arts and Social Sciences, University of Malaya, Kuala Lumpur, Malaysia
7
Human Genome Organisation, Singapore*Corresponding author: E-mail: saitounr@lab.nig.ac.jp.
Associate editor: Anne Stone
The complete mtDNA sequences for all 86 individuals have been submitted to DDBJ/EMBL/Genbank (accession nos.
AP012346–AP012431).
2

The population history of the indigenous populations in island Southeast Asia is generally accepted to have been shaped by two
major migrations: the ancient “Out of Africa” migration !50,000 years before present (YBP) and the relatively recent “Out of
Taiwan” expansion of Austronesian agriculturalists approximately 5,000 YBP. The Negritos are believed to have originated fromthe ancient migration, whereas the majority of island Southeast Asians are associated with the Austronesian expansion. We
determined 86 mitochondrial DNA (mtDNA) complete genome sequences in four indigenous Malaysian populations, together
with a reanalysis of published autosomal single-nucleotide polymorphism (SNP) data of Southeast Asians to test the plausibility
and impact of those migration models. The three Austronesian groups (Bidayuh, Selatar, and Temuan) showed high frequencies
of mtDNA haplogroups, which originated from the Asian mainland !30,000–10,000 YBP, but low frequencies of “Out of
Taiwan” markers. Principal component analysis and phylogenetic analysis using autosomal SNP data indicate a dichotomy
between continental and island Austronesian groups. We argue that both the mtDNA and autosomal data suggest an“Early Train” migration originating from Indochina or South China around the late-Pleistocene to early-Holocene period,
which predates, but may not necessarily exclude, the Austronesian expansion.
Key words: Austronesian, Negrito, mitochondrial DNA, Southeast Asia, Orang Asli.

Introduction
The Southeast Asian region is home to a rich variety ofhuman populations, each with their own ethnic cultures
and traditions. The history and diversity of the various indigenous groups that still populate the region had been described by using archaeological, linguistic, and mostrecently, genetic data. Archaeological evidence points to thepresence of modern humans in Southeast Asia at least 40,000
years before present (YBP) (Brothwell 1960; Barker et al.
2007). Those early migrants eventually reached the Sahul
landmass, which today is split into Papua New Guinea,
Australia, and Tasmania (Leavesley and Chappell 2004;
O’Connell and Allen 2004). That ancient wave of migration
was believed to have brought the ancestors of several“Australoid” populations found in Southeast Asia andAustralia. These include the Papuans and Australian
Aboriginals, as well as several groups in the Andaman,

Philippines, and West Malaysia, which are collectively
known as Negritos (Cavalli-Sforza et al. 1994). Up until theLast Glacial Maximum approximately 20,000 YBP, the current
islands of Sumatra, Java, and Borneo were joined together tothe Asian mainland, forming a landmass known as Sundaland(Glover and Bellwood 2004), which was separated from the
Sahul landmass by multiple islands collectively referred to as
Wallacea; Wallace’s line separates Wallacea and Sundaland(fig. 1).
Another significant epoch with respect to human migrations in island Southeast Asia occurred much later during themid-Holocene period (5,000–7,000 YBP). With Taiwan as theprobable starting point, this migration wave eventually spreadsouthward throughout island Southeast Asia and into theislands of Oceania, bringing with it agriculture, domesticatedlivestock, and Austronesian languages (Bellwood 2005). This
“Out of Taiwan” migration was largely supported by! The Author 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, pleasee-mail: journals.permissions@oup.com

Mol. Biol. Evol. doi:10.1093/molbev/mss169

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Research
articleAbstractJinam et al. . doi:10.1093/molbev/mss169

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archaeological data (Bellwood 2005, 2007) and the linguistic
phylogeny of Austronesian languages (Diamond 1988; Grayand Jordan 2000). This migration model, termed the “express
train,” assumes a rapid expansion from Taiwan to Polynesia
with little or no admixture between the expanding and extant
populations. This model was later expanded to involve a
series of pulses and pauses but remains fundamentally similar(Gray et al. 2009). On the other side of the discussion is
the possible origin in island Southeast Asia. The “Southeast
Asian” model posits complex interactions between
Melanesians, Southeast Asians, and Polynesians and ultimately an Austronesian origin probably in East Indonesia instead of Taiwan (Terrell 1988; Oppenheimer and Richards
2001).
2

Genetic data have been used to argue for and against those
two models: the Taiwanese or Southeast Asian origin ofAustronesians. The “Southeast Asian origin” model was initially based on the age estimates of mitochondrial DNA(mtDNA) haplogroup B4a1a, which was found at high frequencies in the Polynesians, hence the name Polynesian motif(Oppenheimer and Richards 2001). This was later supplemented by a study based on mtDNA haplogroup E distribution, which proposed a dispersal originating from insularSoutheast Asia driven by climate change (Soares et al.
2008). Genetic evidence for the “express train” model,
which predicts a rapid expansion from Taiwan with little orno admixture with extant populations has been lacking.
Instead, most genetic studies advocate a slower movement,

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FIG. 1. A map of Southeast Asia. Numbers indicate locations of populations listed in supplementary table S1, Supplementary Material online. Areas
shaded light gray indicate the extent of the landmass up to the Last Glacial Maximum.

“Early Train” Hypothesis for Evolution of Southeast Asians . doi:10.1093/molbev/mss169

Materials and Methods
Population Samples
DNA samples from the Jehai, Temuan, and Bidayuh werepreviously collected on several occasions as part of studies
on general health among indigenous communities (Jinam
et al. 2008) and genetic analysis of autosomal markers(HUGO PASNP Consortium 2009; Jinam et al. 2010). We
also included samples collected from a Proto Malay subpopulation called Seletar. Based on their family information obtained during field sampling, only samples from unrelated
individuals were used in genetic analyses. The Jehai,

Temuan, and Seletar represent the Orang Asli groups from
West Malaysia, whereas the Bidayuh is one of the many indigenous groups from East Malaysia on the island of Borneo.
The geographical locations for the Jehai, Temuan, Seletar, andBidayuh are 1–4 as depicted in figure 1. This study was approved by the respective institutional review boards of the
National Institute of Genetics in Japan, University of Malaya in
Malaysia, Max Planck Institute for Evolutionary Anthropology
in Germany, Ministry of Health Malaysia, Monash University
in Malaysia, and the Department of Indigenous Affairs(Jabatan Kemajuan Orang Asli Malaysia, JAKOA). Informed
consent was obtained from all participants.

Complete mtDNA Genome Sequencing
Sequencing of mtDNA complete genomes was performed ina total of 68 samples (8 Temuan, 22 Jehai, 17 Bidayuh, and 21
Seletar) using 11 pairs of polymerase chain reaction (PCR)
primers and 32 sequencing primers from Torroni et al.
(2001). A slight modification to their protocol involved optimizing annealing temperatures for all PCR reactions to
60 " C, instead of 55 " C. PCR products were purified using
ExoSAP-IT reagent before being subjected to sequencing
reactions using the BigDye Terminator kit (Applied
Biosystems). Capillary separation was performed on the
ABI3130xl Genetic Analyzer (Applied Biosystems). For
each sample, the resulting 32 traces were aligned to
the revised Cambridge Reference Sequence (Genbank
ID NC_012920) using CodonCode Aligner software(CodonCode Corporation, Dedham, MA, USA) to obtainthe consensus sequence. In addition, complete mtDNA sequences from 18 samples (10 Temuan, 2 Jehai, and 6
Bidayuh) were generated using a high-throughput sequencing platform as described previously (Gunnarsdottir et al.
2011a), resulting in a total of 86 complete mtDNA
genome sequences from four groups.

Nucleotide Sequence Data Analysis
Nucleotide sequences of all mtDNAs determined in this study
were assigned to mtDNA haplogroups according to nomenclature at http://www.phylotree.org (last accessed April 2011;see van Oven and Kayser 2009). mtDNA haplogroup frequencies from the Kensiu, another Negrito subgroup from West
Malaysia (Hong LC, Fong MY, Phipps ME, unpublished data),
and other Southeast Asian populations listed in supplementary table S1, Supplementary Material online, were used forprincipal component analysis (PCA) using R software package(http://www.R-project.org; last accessed April 2009).
Coding region sequences (nucleotide positions 577–
16,023) were extracted from the newly determined complete
mtDNA sequences and also from available literature (supplementary table S1, Supplementary Material online). A
neighbor-joining tree (Saitou and Nei 1987) was generatedusing MEGA software version 5 (Tamura et al. 2011) with 500
bootstrap replications. Using a subset of sequences that represent the haplogroups found in our samples in addition witha chimpanzee mtDNA sequence (Genbank ID D38113; Horaiet al. 1992) as an outgroup, we estimated the mutation rate
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which allows for sex-biased admixture between migrants ofAsian ancestry (possibly from Taiwan) with existing
Melanesian populations with respect to Polynesian origins(Kayser et al. 2000, 2008; Wollstein et al. 2010; Mirabal et al.
2012). In addition, some studies offered a differing perspective:
possible earlier migration(s) from the Asian mainland during
the late-Pleistocene to early-Holocene period, which predates
the Austronesian expansion, based on mtDNA (Hill et al.
2006, 2007) and Y-chromosomal (Karafet et al. 2010) analyses
of island Southeast Asian populations.
Analysis of autosomal DNA markers in Southeast Asian
populations tended to be scattered and very limited incontrast to analyses using uniparental mtDNA and
Y-chromosomal markers. However, the development ofhigh-throughput single-nucleotide polymorphism (SNP) genotyping platforms allowed for more comprehensive genetic
studies such as that by the Pan-Asian SNP Consortium(PASNP) (HUGO PASNP Consortium 2009). Although thearticle mainly focused on the migration histories of East
Eurasian populations as a whole, the data generated should
allow for a more focused analysis of Southeast Asian
populations.
In addressing questions regarding the origin and genetic
diversity of Austronesians, genetic studies using both uniparental markers and autosomal SNP data mostly focused on
Polynesian populations. A more comprehensive examinationof both mtDNA and autosomal SNP diversity in island
Southeast Asian populations may provide more insight into
the origins and migration patterns of humans in Southeast
Asia. Given this current backdrop, we conducted an in-depth
genetic analysis of Southeast Asian populations using available SNP data from PASNP (HUGO PASNP Consortium 2009)
and HGDP-CEPH panel database (Li et al. 2008), together with
newly generated complete mtDNA sequences in four indigenous Malaysian groups. These include three Austronesiangroups (Temuan, Seletar, and Bidayuh) and a Negrito(Jehai). The Negritos from West Malaysia, who are also referred to as Semang, currently speak Austro-Asiatic languages
and may be the descendants of ancient migrants to theSoutheast Asian region. By exploring the diversity of the maternally inherited mtDNA and genome-wide autosomal SNP
in these four groups and comparing them with other populations within the Southeast Asian region, we attempt to shedlight on some questions regarding their demographic andmigration histories.

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Jinam et al. . doi:10.1093/molbev/mss169

Genome-Wide SNP Data Analysis
Genotype data from the Jehai, Kensiu, Temuan, and Bidayuh
were retrieved from the Pan-Asian SNP database (http://
www4a.biotec.or.th/PASNP, last accessed April 2011). The
geographical locations of the PASNP populations are depicted
in supplementary figure S1, Supplementary Material online. In
addition, other Southeast Asian populations from the PASNP(HUGO PASNP Consortium 2009) and HGDP-CEPH (Li et al.
2008) data sets listed in supplementary table S2,
Supplementary Material online, were also retrieved. There
were 12,150 SNPs that were common to both data sets. To
assess the relatedness between individuals, PCA was conducted using the smartpca program in the EIGENSOFT software package (Patterson et al. 2006) by using the SNP
genotype data.
The populations were further grouped into 17 broader
categories listed in supplementary table S3, Supplementary
Material online, for phylogenetic tree and network analysis.
PHYLIP software (Felsenstein 2005) was used to generate
5,000 bootstrap replicates of SNP allele frequencies, and genetic distance matrices between populations were calculatedusing Nei’s (1972) standard genetic distance. An unrooted

Neighbor-Joining tree and a phylogenetic network based on
the Neighbor-Net method was constructed from the pairwise
genetic distances between populations using the SplitsTree4
software (Huson and Bryant 2006).

Results
mtDNA Analysis
Sequence Diversity and Haplogroup Distribution
Complete mtDNA sequences were newly determined from86 individuals (24 Jehai, 18 Temuan, 21 Seletar, and 23
Bidayuh). The summary statistics for the sequence variation in those groups are listed in table 1. The highest haplotype diversity was observed in the Temuan, whereas thelowest was in the Seletar, in which only five distinct
mtDNA haplotypes were observed. Negative values for
Tajima’s D test were observed in the Bidayuh, Seletar, andTemuan, suggesting a history of population expansion.
However, the P values did not indicate statistically significant
deviation from expectation assuming a constant populationsize.
All individuals were assigned to specific haplogroups belonging to M and N macrohaplogroups by following the nomenclature in www.phylotree.org as much as possible. A totalof 23 haplogroups were observed, and the specific mutations
that define M and N haplogroups are shown in supplementary figures S2 and S3, Supplementary Material online, respectively. In addition to haplogroup-defining mutations,additional mutations that were population specific were observed. For example, additional mutations in haplogroup
N9a6a differ between the Bidayuh, Jehai, and Temuan (supplementary fig. S3, Supplementary Material online). In mostcases, the haplogroups observed have been reported previously, but there are instances where some haplotypes share
only the basal mutations with known haplogroups, and additional mutations did not match any existing ones. Those
haplotypes were therefore assigned to the closest basal
haplogroup, for example, B4a and F1a’c in supplementary
figure S3, Supplementary Material online. The mtDNA haplogroup frequencies of the four populations and the Kensiu(Hong LC, Fong MY, Phipps ME, unpublished data) are presented in table 2. The most frequent haplogroup in the
Bidayuh is N9a6a, whereas in the Temuan, the most frequent
haplogroups are M21a, N22, and N21, which are lineages thatbranch off directly from basal M and N haplogroups(Macaulay et al. 2005). The low nucleotide diversity observedin the Seletar was further demonstrated by the limited

Table 1. Summary statistics for complete mtDNA sequences in four Malaysian groups.
Statistics
No. of sequences
No. of haplotypes
Haplotype diversity ± SD
Mean no. pairwise difference
No. of polymorphic sites
Nucleotide diversity
Tajima’s D (P value)
NOTE.—NS, not significant; SD, standard deviation.

4

Bidayuh23
13
0.88 ± 0.05
30.5
157
0.00184$1.14495 (NS)

Jehai
24
11
0.89 ± 0.04
32.1
87
0.00194
1.4924 (NS)

Seletar21
50.54 ± 0.11
15.9
65
0.00096$0.49193 (NS)Temuan18
140.94 ± 0.05
29.1
135
0.00175$1.09762 (NS)

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and age of haplogroups using a Bayesian Markov chain
Monte Carlo (MCMC) method as implemented in the
BEAST software (Drummond and Rambaut 2007). A divergence time of 6.5 million years between humans and chimpanzee (Goodman et al. 1998; Mishmar et al. 2003) was used
as a calibration point. Using Tamura and Nei (1993) substitution model and assuming a strict molecular clock, the mutation rate was estimated using a normally distributed priorwith a mean of 1.71 # 10$8 for coding-region sequences(Soares et al. 2009). The trees were generated on a run of
40,000,000 steps, sampling every 4,000 steps, and the first
4,000,000 steps were regarded as burn-in. Bayesian skyline
plots (BSP) were generated for the Jehai, Temuan, Seletar,and Bidayuh groups using the above parameters but with acoalescent-based tree prior with a piecewise linear model. A
maximum-likelihood (ML) tree was also constructed using
the same set of coding-region sequences as above to estimate
the time depth of mtDNA haplogroups. Using the MEGA5
software, the Tamura and Nei (1993) substitution model was
implemented, and two mutation rates were used for molecular clock calibration: 1.71 # 10$8 (Soares et al. 2009) and1.36 # 10$8, which was estimated using Bayesian MCMC as
described earlier.

“Early Train” Hypothesis for Evolution of Southeast Asians . doi:10.1093/molbev/mss169

number of observed haplogroups and the very high frequency
of one particular haplogroup, N9a6 at 71%. Haplogroups
M21a and R21 are the most frequent in the Jehai and
Kensiu, respectively, who are both Negrito groups.
Table 2. mtDNA haplogroup frequencies (%) in five indigenous
Malaysian groups.

aBidayuh

Jehai

Seletar
4.8

TemuanKensiua

27.8
5.6
5.6
5.6

43.2

4.3
4.3
37.5

8.7
4.3
4.3
4.3

2.7
19.0

5.6
4.8
2.7
4.3
5.6
30.4
12.5
8.3
25.0

2.7
43.2
22.2
16.7
71.4

34.8
23

16.7
24

21

Hong LC, Fong MY, Phipps ME, unpublished data.

5.6
18

5.4
37

Relationship with Other Populations
To further elucidate the relationship between the indigenous
Malaysian populations and other surrounding populations,
PCA was performed using haplogroup frequencies from thisstudy and from selected populations from the literature (supplementary table S1, Supplementary Material online). The
resulting PCA plot is shown in figure 2. We added population
ID after the name of each population in this paragraph for abetter understanding of population identity. A clear divisionappears along the first principal component (PC) on the X
axis, which places the Negrito populations from West
Malaysia (Jehai_1, Kensiu_5, Batek_6, and Mendriq_7) at
one end and most other Austronesian-speaking populations
from Southeast Asia at the other end. On the second PC on
the Y axis, there appears to be a geographical divide between
the Austronesians groups. Populations in West Malaysia,
Sumatra, and Java (Malay_11, Jakun_10, Java_17, Bali_18,
and Lombok_19) tend to cluster with mainland or continental groups (Thai_30, Vietnamese_31, South Chinese_33, andCham_32). On the other hand, populations from Taiwan,
Philippines, and other Indonesian islands to the east
(Alor_14, Ambon_15, and Sulawesi_22) tend to group together. It seems that PC1 represents a Negrito-Austronesian
divide, whereas PC2 corresponds to a continental-island division of Austronesian groups. However, not all population affinities fall nicely into these two generalized trends.
The Temuan_2 in West Malaysia are Austronesian speakers and are physically distinct from the Malaysian Negritos,
but they clustered with them in the PCA plot of figure 2. Thismay be due to the high frequencies of haplogroup M21a in
both the Temuan and Negritos, suggesting either gene flow
between these populations or parallel increases of this haplogroup frequency. The populations from Borneo (Bidayuh_4,
Iban_12, Banjarmasin_16, and Kota_Kinabalu_13) also displayed somewhat irregular patterns. The Iban_12 and

FIG. 2. PCA plot based on haplogroup frequencies. Numbers in circles are population labels as listed in supplementary table S1, Supplementary Material
online. Red circles are populations from current study and black circles are from literature.

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Haplogroup
G1c
M20
M74b
M21a
M22a
M7b1
M7c2
M7c3c
E1b
B4a
B4a1a1aB4b1a2a
B4c2
B5a
B5b2
B6
F1a’c
F1a1a
F1a1a1
R21
N21
N22
N9a6
N9a6a
Total individuals

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Jinam et al. . doi:10.1093/molbev/mss169

Banjarmasin_16 appeared closer to the continental clusters,
whereas Kota_Kinabalu_13 appear closer to the island cluster.
The Bidayuh_4 clustered with two other Proto-Malay groups(Seletar_3 and Semelai_9) from West Malaysia. The kinshipstructure may also have a significant bearing on mtDNA diversity, as shown by the Besemah_23 and Semende_24 of
Sumatra. The Semende tribe is matrilocal and is closer tothe continental populations, whereas the Besemah tribe ispatrilocal and is closer to island Southeast Asians. This may
suggest that the mtDNA diversity in the Besemah is shapedby female migrations from island Southeast Asia.

The mean value of the mutation rate was used to calibrate
the molecular clock of the ML tree. In addition, we used themutation rate of 1.71 # 10$8 as reported by Soares et al.
(2009). Age estimates using the ML tree and Bayesian
methods were based on the coalescence time of all mtDNA
sequences that belong to the same haplogroup. In general,the higher mutation rate of Soares et al. (2009) resulted inyounger age estimates of haplogroups compared with theages obtained using the mutation rate estimated from ourown data. The haplogroup ages obtained from the Bayesian
MCMC analysis tended to give slightly older time frames
compared with the ML estimates and this may be attributed
to the differences between Bayesian and ML methods. The
resulting ML tree using the mutation rate of 1.36 # 10$8 isshown in figure 3, whereas the other age estimates (ML andBayesian) are listed in table 3.
Diversity of M Haplogroup Lineages
The M haplogroups observed in this study included thosewhich were considered indigenous to the Orang Asli,

FIG. 3. ML tree constructed using mtDNA coding-region sequences. The molecular clock was calibrated with a mutation rate of 1.36 # 10$8 substitutions per site per year. Gray horizontal bar represents time frame of the Austronesian expansion from 7,000 years ago, and haplogroups withcoalescent times within that period are indicated with a green dot. Haplogroups that support the “early train” hypothesis are indicated with red
diamonds and orange boxes. (A) Subtree of haplogroup M lineages. (B) Subtree of hapologroup N lineages.

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Phylogenetic Analysis and Coalescence Time Estimation
The Neighbor-Joining tree for haplogroups M and N are
shown separately in supplementary figure S4A and S4B,
Supplementary Material online, respectively. Estimation of
the mutation rate for the mtDNA coding region using
Bayesian MCMC analysis resulted in a mean value of
1.36 # 10$8, with a 95% highest posterior density range of
1.07 # 10$8–1.65 # 10$8, substitutions per site per year.

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Table 3. Age estimates of selected haplogroups based on mtDNA coding-region sequences using ML and Bayesian MCMC methods.
ML
41,300–51,900
4,400–5,500
22,600–28,400
22,500–28,500
31,300–39,300
20,400–25,600
17,800–22,400
4,900–6,200
12,900–16,300
23,200–29,000
5,100–6,400
10,700–13,500
38,800–48,000
22,900–28,700
11,500–14,400
4,900–6,100
19,300–24,100
30,500–38,200
4,100–5,100
28,600–35,800
8,900–11,100
24,100–30,100
8,100–10,000
21,700–27,200
8,100–10,200
22,900–28,600
8,400–10,500
11,700–14,700
19,100–23,800
13,800–17,300
6,900–8,600

MCMC (95% highest posterior density interval)
79,000 (59,000–98,700)
8,500 (1,600–16,900)
31,100 (16,900–46,600)
34,400 (17,500–51,500)
52,300 (34,100–70,300)
35,400 (20,800–49,600)
27,600 (14,300–41,500)
9,300 (900–19,200)
18,600 (6,800–30,600)
36,300 (20,500–52,100)
8,200 (1,500–15,700)
15,100 (5,400–25,500)
78,500 (58,400–99,200)
35,400 (16,800–55,600)
17,200 (8,500–26,900)
8,200 (2,600–14,900)
27,300 (13,700–42,200)
64,600 (46,100–86,300)
8,600 (1,500–17,100)
54,700 (37,100–73,500)
16,300 (5,800–27,100)
37,100 (23,700–52,500)
12,300 (3,200–22,200)
34,600 (20,600–50,500)
13,200 (4,800–23,000)
36,000 (20,400–53,000)
13,300 (3,400–24,100)
20,900 (9,600–33,500)
29,900 (17,700–42,100)
21,100 (11,100–31,500)
10,300 (3,500–18,200)

The range of dates obtained by ML method was obtained by using the mutation rate reported by Soares et al. (2009) (lower limit) and the rate obtained by Bayesian MCMC
estimation (upper limit).

namely M21a and M22 (Macaulay et al. 2005; Hill et al. 2006).
M21a was most frequent in the Temuan and Jehai, as well asother Negrito subgroups in West Malaysia (Hill et al. 2006).
Outside of West Malaysia, M21a was also present in appreciable frequencies in the Sakai (also a Negrito group) and in
the Chiang Mai population from Thailand (Fucharoen et al.
2001) and very rarely in some Philippine populations(Tabbada et al. 2009; Gunnarsdottir et al. 2011a). The otherM21 subtypes, M21b and M21c, which were reported at low
frequencies in the Orang Asli (Hill et al. 2006) but frequent in
the Moken of Myanmar (Dancause et al. 2009), were notobserved in any of our current samples. M22 was earlier reported in the Proto Malays (Macaulay et al. 2005), and recent
reports showed that it was present in the Vietnamese (Penget al. 2010) and Southern Chinese (Kong et al. 2011) but has
so far not been reported in any island Southeast Asians (Hillet al. 2007).
Haplogroup E, which was proposed to be a marker for
postglacial expansion centering in Island Southeast Asia
(Soares et al. 2008), was found in the form of E1b in the

Seletar and Bidayuh. Haplogroup M7 lineages that are present
in the Malaysian samples included M7c3c in the Bidayuh. This
haplogroup seems to be restricted to Southeast Asia and wassuggested to be a marker for the Austronesian expansion
during mid-Holocene (Hill et al. 2007), consistent with ourage estimates. Other M7 lineages found in the Temuan include M7b1 and M7c2, and they coalesce with lineages fromthe mainland (Kong et al. 2003) (fig. 3). We also observed
several haplogroups that have not been reported in any
Southeast Asian population to date. These included G1c in
the Seletar and M74b and M20 in the Bidayuh. G1c was earlier
reported in Koreans (Derenko et al. 2007) and Han Chinese(Kong et al. 2003). The ancestral M74a haplotype was reported in southern Chinese populations (Kong et al. 2011),
whereas a derived type M74b was found in the Bidayuh in
Borneo and Hani of south China (Kong et al. 2011). The
M74b1 subtype has been found in Surigaonon and
Mamanwa in the Philippines (Gunnarsdottir et al. 2011a; reported as M*) and also in the Besemah in Sumatra(Gunnarsdottir et al. 2011b, reported as M4). Figure 3
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Haplogroup
M
M20
M21a
M22
M74
M74b
M7c2
M7c3c
M7b1
E
E1b
G1c
N
N21
N9a6
N9a6a
N22
R
R21
B5
B5b2
B4a
B4a1a1aB4b
B4b1a2
B4c
B4c2
B6
F1
F1a’c
F1a1a

MBE

Jinam et al. . doi:10.1093/molbev/mss169shows that the deepest branch of M74 is found in a SouthernChinese, whereas the subgroups M74b were found in the
Bidayuh and Besemah, suggesting a dispersal originatingfrom southern China and into island Southeast Asia.
Haplogroup M20 found in one Bidayuh individual coalesces
with the sequence found in a southern Chinese group (Konget al. 2011), and these two M20 lineages clustered with haplogroup M51 found in the Cham of Vietnam (Peng et al.
2010) and the Besemah in Sumatra (Gunnarsdottir et al.
2011b), as shown in supplementary figure S4A,
Supplementary Material online.

8

Changes in Effective Population Size
The BSP, which were generated using coding-region sequences, are shown in supplementary figure S6,
Supplementary Material online. When all 86 sequenceswere analyzed together (supplementary fig. S6A,
Supplementary Material online), the observed pattern isthat of an increase in population size from approximately
60,000 to 40,000 YBP. What appears to be a stable population
size from 30,000 to 10,000 YBP was then followed by a decline
which lasted until several hundred YBP. A similar pattern wasobserved when the Jehai (Negrito) was omitted (supplementary fig. S6B, Supplementary Material online) or when all four
populations were analyzed separately (supplementary fig.
S6C–F, Supplementary Material online). However, in thecase of Temuan (supplementary fig. S6D, Supplementary
Material online) and Seletar (supplementary fig. S6E,
Supplementary Material online), there were no indicationsof population size increase from 40,000 YBP or older.
Although the pattern of population increase from 60,000 to
40,000 YBP may suggest signals of population expansion asdemonstrated in other worldwide populations (Atkinson
et al. 2008; Fagundes et al. 2008), any interpretations should
be taken with caution given the large confidence intervals forthe estimates. A consistent pattern that appeared was that ofa population size decrease from 10,000 YBP, and similar patterns were also observed in some Philippine populations(Gunnarsdottir et al. 2011a). The BSP plots also showed atrend of increasing population size in all four groups!1,000 YBP. The underlying cause for the observed patterns
can only be speculated and as such would warrant further
investigation.

Genome-Wide SNP analysis
The results of PCA analysis using genome-wide autosomal
SNP markers are shown in figure 4. In figure 4A where all
Southeast Asian populations were analyzed, the first PC(PC1) distinguishes between the Melanesians and Southeast
Asians. The Indonesians from the Alor Island and surroundingislands seem to be intermediate between the Melanesians
and other Southeast Asians. The second PC (PC2) separates
the Malaysian Negritos from other populations, whereas thethird PC (PC3) in supplementary figure S7, Supplementary
Material online, showed that PC3 separates the Philippine
Negritos from the other populations. A recurring patternobserved in the Malaysian Negritos, Philippine Negritos, andAlorese is that the individuals are spread apart in a gradient,or comet-like pattern, suggesting recent admixture between
these groups with Thai, Chinese, or other Austronesians whoform a tight cluster in the PCA plot. This comet-like pattern
was also observed in PCA analyses of Patterson et al. (2006),
Bryc et al. (2010), and McEvoy et al. (2010), who all interpreted the comet-like patterns as results of recent
admixtures.

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Diversity of N Haplogroup Lineages
As with haplogroup M, we found rare N lineages, which werepreviously only reported in the Orang Asli, namely N21, N22,
and R21 (Hill et al. 2006, 2007). N21 lineages in the Temuan
appeared to be derived from an ancestral type found in the
Cham of Vietnam (supplementary figure S4, Supplementary
Material online), implying an origin in Indochina during late
Pleistocene based on our age estimates. N22 appears to belimited to the Temuan, as observed in this study and by Hillet al. (2006), although it also appears in very low frequencies
in the Philippines (Tabbada et al. 2009), Sumatra(Gunnarsdottir et al. 2011b), and Sumba islands (Hill et al.
2007). Haplogroup R21 appears to be limited to Negrito populations in West Malaysia, although it was also found at appreciable frequencies in the Senoi (Hill et al. 2006), who arethought to have arrived from Indochina (Glover and
Bellwood 2004). Haplogroup N9a is widespread in East Asia,
but the subclade N9a6 appears to be restricted to island
Southeast Asian populations where it is found at low frequencies in Sumatra and Java, Indonesia, but not in the Philippines
or Taiwan (Hill et al. 2007). However, we found N9a6 and its
daughter clade N9a6a to be quite frequent in the Malaysiangroups, particularly in the Bidayuh and Seletar.
Haplogroup B, which is characterized by a 9-bp deletion at
position 8272, is fairly common in island Southeast Asia andparticularly in Polynesia. The distribution of this haplogroup isvaried among the Malaysian populations, with B4a and B5bfound in the Bidayuh, B4b and B6 in the Temuan, and B4c in
the Seletar. The two B4a lineages in the Bidayuh included
B4a1a1a, also known as the Polynesian motif, and it mightreflect recent gene flow from the Pacific during themid-Holocene period (Soares et al. 2011). The other is an
undefined B4a haplogroup, which shares the same basal mutations as B4a but could not be further designated to any of
its daughter clades. The branching patterns of the NJ tree
(supplementary fig. S4, Supplementary Material online)
show that the ancestral types of haplogroups B4b, B4c, andB5b were found in South Chinese populations, suggesting an
origin in the mainland and dispersal to island Southeast Asia.
Interestingly, the B4c2 haplogroup found in the Seletar was
also extracted from ancient Negrito hair samples (Ricaut et al.
2006), indicating a diffusion from the mainland during the late
Pleistocene. Haplogroup F is another common clade inSoutheast Asia, with F1a1a previously reported to be frequentin the Temiar, a Senoi group (Hill et al. 2006). Haplogroup
F1a’c shares the same basal mutations as F1a except at

nucleotide position 4086 and is present in the Bidayuh, aswell as the Besemah and Semende of Sumatra (Gunnarsdottir
et al. 2011b).

“Early Train” Hypothesis for Evolution of Southeast Asians . doi:10.1093/molbev/mss169

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FIG. 4. Individual-based PCA using SNP genotype data. (A) PCA plot using all individuals listed in supplementary table S2, Supplementary Material
online. (B) PCA plot after excluding Malaysian Negrito, Philippine Negrito, Melanesian, and Alorese individuals.

9

Jinam et al. . doi:10.1093/molbev/mss169

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To explore this tight clustering of groups, PCA was rerun
after omitting Melanesian, Alorese, and Negrito (bothMalaysian and Philippine) individuals, and the resulting
PCA plot is shown in figure 4B. Generally, the SouthernChinese and Thai individuals tend to cluster together,whereas the other Austronesian populations appear to be
spread out roughly according to geographic order, with indigenous Taiwanese, Filipinos, and Sulawesi individuals at one
end and the Temuan, Bidayuh, and Javanese at the other.
Further examination of other PCs (supplementary fig. S8,
Supplementary Material online) show that the Temuan andBidayuh individuals are also spread apart in a comet-like pattern, suggesting that these two groups also experienced
recent admixture with other groups. Estimation of individual
ancestry proportions using frappe software (Tang et al. 2005)10

in supplementary figure S10, Supplementary Material online,
reveals a mosaic of Taiwanese (green), Southeast Asian (blue),and East Asian (orange) ancestry components at k = 3. The
Taiwanese ancestry component decreases gradually according to the geographical order of populations, and the same
pattern was observed for the Southeast Asian component in
the opposite direction. At k = 4 and k = 5, the Temuan andBidayuh appear to be distinguished from other Southeast
Asian populations.
The Neighbor-Joining tree and Neighbor-Net network
based on SNP allele frequencies of Southeast Asian groups(supplementary table S3, Supplementary Material online)
were constructed. The Neighbor-Joining tree (fig. 5A) showsthat populations that are geographically located east of theWallace line (Filipino, Taiwanese, Toraja, Philippine Negrito,

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FIG. 5. (A) Neighbor-Joining tree and (B) Neighbor-Net network constructed from Nei’s standard genetic distance matrix between populations listed insupplementary table S3, Supplementary Material online. SNP allele frequencies were used to generate the distance matrix. Bootstrap values above 90%
are shown on the Neighbor-Joining tree.

“Early Train” Hypothesis for Evolution of Southeast Asians . doi:10.1093/molbev/mss169

Discussion
This study includes the first description of mtDNA diversity infour indigenous Malaysian populations using complete sequence data from all individuals sampled. This is in contrast
to most studies in which complete mtDNA sequencing was
performed only on selected haplotypes based initially on control region diversity. Such biased sampling can lead to exaggerated results in some analyses as demonstrated in
Gunnarsdottir et al. (2011a). A striking feature that we observed from our data was the limited mtDNA diversity in the
Seletar. There were only four distinct haplogroups detected,
reflected in the very low haplotype diversity statistic of 0.54,
although not as extreme as the value of 0.167 observed in the
Moken Sea Gypsies from Myanmar (Dancause et al. 2009).
This limited mtDNA diversity in the Seletar may be the resultof genetic drift, exacerbated by their small population size,
which numbers approximately 800 individuals (Nicholas
2000). This may explain how haplogroup N9a6, which wasreported at low frequencies in island Southeast Asia (Hill et al.
2007), rose to such high frequencies in the Selatar. We also
took advantage of the availability of genome-wide SNP datafrom Southeast Asian populations reported in the PASNP(HUGO PASNP Consortium 2009) and the HGDP-CEPH(Li et al. 2008) studies to supplement the mtDNA data andto provide some insights into the migratory and demographic
histories of Southeast Asian populations.
Regarding the Australoid populations in Southeast Asia,
our mtDNA data do not appear to show any similarities inthe extant mtDNA lineages of the Negrito groups (Andaman,
West Malaysia, and the Philippines), Melanesians, andAustralian Aboriginals. The mtDNA diversity in each ofthese Australoid groups is characterized by distinct markers,
namely M31 and M32 in the Andamanese (Thangaraj et al.
2003, 2005; Barik et al. 2008), N11b in the Mamanwa of thePhilippines (Gunnarsdottir et al. 2011a; this haplotype waslabeled as N* in their article), M21a and R21 in the Jehai
and Kensiu from West Malaysia, and haplogroups P, Q, S,
and O in the Melanesians and Australian Aboriginals. We
found that those mtDNA lineages have a time depth ranging
from 30,000 to 50,000 YBP and is consistent with earlier reports (Ingman et al. 2000; Macaulay et al. 2005; Thangaraj
et al. 2005; Gunnarsdottir et al. 2011a). This suggests theirlong-term presence in the Southeast Asia, probably datingback to the original inhabitants of the region. The diversityof the mtDNA lineages within these Australoid groups andtheir branching pattern on the NJ tree (supplementary fig. S4,
Supplementary Material online) may imply multiple foundereffects followed by long time isolation but whether there wasa single, rapid entry (Macaulay et al. 2005) is still open todebate.
It also appears that these Australoid groups have experienced substantial gene flow with their neighboring populations. For example, haplogroups such as F1a1a and N9a6a in
the Malaysian Negritos or E1a1a1 and B4b1a2 in thePhilippine Negritos (Gunnarsdottir et al. 2011a) may havebeen introduced by admixture with the neighboring
Austronesian populations. The effect of this admixture isalso demonstrated in the comet-like patterns in the PCA
plots using SNP data (fig. 4) and the reticulations in the
Neighbor-Net network (fig. 5). Although the relatedness between these geographically distinct Australoid groups is notapparent based on the mtDNA diversity, SNP PCA plots, andNeighbor-Joining tree, the NeighborNet network (fig. 5B)shows that the Malaysian Negritos may have some commonalities with other Australoid groups (Philippine Negrito andMelanesian). A study of archaic hominin (Denisovan) admixture in Southeast Asia (Reich et al. 2011) showed that theAustraloid populations (Jehai, Mamanwa, Australians, and
New Guineans) share an ancient common ancestry but
have since experienced different admixture episodes with different populations. A more exhaustive survey involving more
Australoid populations with a denser set of autosomal SNP
markers would therefore be desirable to paint a clearer picture regarding their interesting past.
As for the history of Austronesians, our mtDNA data
points to a more substantial influence from the mainland
in shaping the haplotype diversity of the three
Austronesian groups we studied: Temuan, Seletar, andBidayuh. The putative markers for the “Out of Taiwan” expansion, B4a1a and M7c3c account for less than 10% of the
mtDNA lineages in all three Austronesian groups combined.
Furthermore, other markers such as Y2, D5, M7b3, F3b, and11

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Melanesian, and Alorese) form a cluster with 100% bootstrap
probability. We refer to this cluster as “island” cluster.
Populations from the west of the Wallace line (Bidayuh,
Javanese, Malaysian Negrito, and Temuan) form another cluster with populations from mainland Asia (South Chinese,Thai, and Cambodian) and we refer to this cluster as “continental” cluster. There are exceptions to this general clustering,whereby the Sumatrans and Mentawai (west coast of
Sumatra) that are geographically located west of theWallace line but are clustered with the Filipino andTaiwanese on the “island” cluster. The Neighbor-Net network(fig. 5B) generally displays the same clustering pattern with
the Neighbor-Joining tree and also highlights the division between “island” and “continental” clusters. The main difference is that the network shows the Malaysian Negritos as
being closer to other “Australoid” populations (Philippine
Negrito, Melanesian, and Alorese) than to other
Austronesian groups, suggesting they may share some ancientcommonalities.
Although the populations from the Indonesian islands ofAlor and its vicinity speak Austronesian languages, they forma cluster with Melanesians. The reticulation observed between the Alorese and Melanesians on the network andthe very short branch leading to the Alorese on the NJ treesuggests admixture between those two groups, and this was
further confirmed by Xu et al. (2012). The reticulation observed between the Temuan and Malaysian Negrito may also
be indicative of admixture events as suggested by the“comet-like” pattern in SNP-based PCA (fig. 4) and also thesharing of mtDNA haplogroups between the two groups. In
general, the tree and the network appear to show the dichotomy between island and continental Southeast Asians asshown earlier by the mtDNA and SNP-based PCA results.

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F4, which were proposed to have followed the movement outof Taiwan (Hill et al. 2007; Tabbada et al. 2009), were notobserved in any of the Austronesian groups in our study.
An alternative explanation for the lack of “Out of Taiwan”
haplogroups in the Austronesian groups we studied may bethat the Austronesian expansion involved incorporation of
females from existing populations, rather than replacingthem. However, a study by Jordan et al. (2009) suggested
that the ancestral Austronesian populations mostly practiced
matrilocal postmarital residence. This would mean that the
expanding Austronesian populations were more likely toretain their own mtDNA lineages. This casts some doubt
on the incorporation of existing females by the expanding
Austronesians, which would mask the Out of Taiwan signal.
Instead we found a sizeable proportion of haplogroups withlinks to the mainland around the vicinity of Indochina orSouth China with ages predating the Austronesian expansion.
This is characterized by haplogroups M21a, N9a6, N21, N22,
and F1a’c, which account for more than 60% of the mtDNA
lineages in the three Austronesian groups. This is in addition
to haplogroups M74b, M22, G1c, M7b1, B5b2, M7c2, andB4c2, which also have roots in the mainland. These haplogroups are not found or very infrequent in populations
around the vicinity of Taiwan and the ages range from approximately 30,000 to 10,000 YBP (fig. 3), corresponding to
the late-Pleistocene to early-Holocene period.
The PCA plots using mtDNA (fig. 2) and SNP data (fig. 4)
together with the Neighbor-Net network and NeighborJoining tree (fig. 5) appear to indicate a dichotomy inAustronesian populations. Populations from the mainland
Asia (Thai, Southern Chinese, and Cambodian) tend to becloser to populations that were previously part of the
Sundaland landmass (populations from Malaysia and Javaand Borneo islands). This “continental” cluster of populations
12

is separate from the “island” cluster of populations, which
include Taiwanese, Filipino, and Sulawesi. The Malay from
West Malaysia and Dayak from Borneo tend to be in intermediate positions of these two major clusters. This dichotomy is even clearer when Australoid populations wereomitted from the network and tree analysis (supplementary
fig. S9, Supplementary Material online). The high-bootstrap
values lend support to the dichotomy of these two clusters(island and continental). Taken together, there results suggestthat Austronesians might have originated from two or possibly more, separate migration events.
We therefore propose an “early train” hypothesis (fig. 6A)
which differs from the “express train” (fig 6B), for explaining
the observed results from mtDNA and SNP analysis inAustronesian groups. It essentially involved migration(s) originating from Indochina or South China, which spread south
to West Malaysia, Sumatra, Java, and Borneo when they werestill connected as Sundaland during the Last Glacial
Maximum. The origin of this “early train” migration is inferred from the phylogenetic analysis of mtDNA lineages,
which indicate that the ancestral types of lineages found in
the continental cluster (West Malaysia, Borneo, and Java)tend to be found in Indochina or South China. The timingof this migration may have ranged from 30,000 to 10,000 YBP
based on the age estimates of mtDNA haplogroups indicatedin figure 3. Furthermore, the BSP plots in the three
Austronesian groups studied (supplementary fig. S6,
Supplementary Material online) do not indicate any signsof population expansion that might have taken place
5,000–7,000 YBP if they indeed originated from the “express
train” expansion from Taiwan. The dichotomy between
island and continental cluster of Austronesian populations
based on PCA, network, and tree analyses lend further

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FIG. 6. Migration models relating to the origins of Austronesians. (A) “Early train” model originating from Indochina/South China !30,000–10,000
years ago. (B) “Express train” model originating from Taiwan !7,000–5,000 years ago.

“Early Train” Hypothesis for Evolution of Southeast Asians . doi:10.1093/molbev/mss169

Although we do not have direct archaeological evidence tosupport our “early train” dispersal from the mainland, someclues may lie within the existence of the Hoabinhian tradition,
characterized by flaky pebble tools (Glover and Bellwood2004). The Hoabinhian are thought to have emerged from
Indochina during the early-Holocene period (14,000–
10,000 YBP) based on dating of the stone tools and spreadsouthward, as evidenced by the archaeological sites found in
Sumatra and West Malaysia (Cavalli-Sforza et al. 1994; Glover
and Bellwood 2004). We conjecture that the Hoabinhian may
have made it all the way south to Java and Borneo. Linguistics
may also provide some clues regarding human movementfrom continental Southeast Asia. Austro-Asiatic languages
are mostly spoken in Indochina but are also used by the
Senoi and the Negritos in Peninsular Malaysia. The ancestorsof the Senoi are thought to have migrated southward from
Indochina and introduced Austro-Asiatic languages to theextant Negrito populations in the Malay Peninsula(Bellwood 2005). However, the time of 4,000 YBP proposedby Bellwood (2005) for that migration is very recent compared with our “Early Train” model.
Other lines of evidence that corroborate our data include
Y-chromosomal markers, which suggests a Paleolithic(30,000–15,000 YBP) contribution from mainland Asia
(Karafet et al. 2010) and autosomal short tandem repeat
markers which also show a dichotomy between
Austronesians in Java and Samoa (Shepard et al. 2005).
Other supporting data include that from domesticated animals which tend to accompany humans in their migrations.
Genetic analysis of domesticated pig (Larson et al. 2007) anddog (Oskarsson et al. 2012) both propose a migration frommainland Asia by Sundaland and into the Pacific region,
which may have been accompanied by humans.
Taken together, our results suggest an “early train” wave(s)of migration originating from South China or Indochina
during late Pleistocene to early Holocene (30,000–
10,000 YBP), predating the Neolithic expansion from Taiwan(Glover and Bellwood 2004; Bellwood 2005, 2007). We do notpreclude the Out of Taiwan migration, but it appears improbable that it contributed wholly to the genetic diversity in all
Austronesian groups, particularly those west of the Wallace
line. In conclusion, our data suggest a more intricate migration history than the generally accepted, if not oversimplified,
two-wave hypothesis regarding the peopling of island
Southeast Asia.

Supplementary Material
Supplementary figures S1–S10 and tables S1–S3 are available
at Molecular Biology and Evolution online (http://www.mbe.oxfordjournals.org/).

Acknowledgments
The authors thank Anuar Zaini, Khalid Kadir, Badariah
Ahmad, Siti Harnida, Mah Yong Cheng, and other membersof the Cardio-Metabolic RS at the Jeffrey Cheah School of
Medicine and Health Sciences, MUSC; JAKOA officers who
participated in the field study of the Orang Seletar; Roland
13

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support to our idea of a separate, earlier migration from themainland which predates the “express train” from Taiwan.
Our proposed “early train” movement from the mainland
does not preclude the episode of a Neolithic expansion from
Taiwan involving Austronesian agriculturalists (Bellwood2005), depicted in figure 6B. This is because the populations
from Taiwan and its vicinity (the Philippines and Sulawesi)
cluster together with high confidence based on the
Neighbor-Joining tree, whereas the PCA plot in figure 4B
also points to a relationship among the Taiwan, Philippine,
and Sulawesi populations, which extend to the other island
Austronesian groups such as the Mentawai and Sumatrans.
The frappe analysis (supplementary fig. S10, Supplementary
Material online) also shows a signal of Austronesian expansion at k = 3 to k = 5 as indicated by an ancestry component(in green) that is most frequent in Taiwan, which then decreases sequentially in the Philippine, Indonesian, and Malay
groups who are all Austronesian speakers. Furthermore, the
mtDNA lineages found in the Philippines and Taiwan tend tohave time depths of less than 10,000 YBP (supplementary fig.
S5, Supplementary Material online). The presence of haplogroups B4a1a and M7c3c in the Bidayuh from Borneo canbe taken as an indication for the impact of the “Out of
Taiwan” expansion on continental groups. It may be possiblethat Borneo was an intersection between the “early train”
and “express train” movements given its location as the outeredge of the Sundaland landmass (fig. 1). Interestingly, although the Sumatrans and Mentawai are geographically located on the west of the Wallace line, thus on the continentalside, they cluster with other populations on the “island” cluster on the NJ tree and network (fig. 5). These groups could
have been part of the subsequent “express train” migration
instead of the “early train” movement, hence their clusteringwith the “island” cluster of populations. Furthermore, theadmixture between Asian and Melanesian ancestry in eastern
Indonesian populations was dated back to !4,000–5,000 YBP(Xu et al. 2012), which is consistent with the timing for theAustronesian expansion.
It should be noted that some caveats are in order wheninterpreting these results. The age of an mtDNA haplotype
does not necessarily equate to its age in a population. It may
well be possible that an “old” haplotype was introduced into
a population by recent migrations, thus the haplogroup age
estimates of 30,000 YBP may represent the upper limit for the
possible time window of migration. However, even if we takeage estimates of mtDNA lineages as the upper limit for thetime of human migration events, we found that age estimatesof mtDNA haplogroups associated with the Austronesian
expansion (supplementary fig. S5, Supplementary Material
online) are not too far off from the time estimated by archaeological data, which is 5,000 YBP. On the basis of our current
analyses, we could not make any conclusions as towhether our “early train” migration involved a single entry
or multiple waves of migration. It would therefore be desirable
in future studies to vigorously test our “early train” model
against other competing and plausible scenarios using demographic modeling, such as those reported by Batini et al.
(2011).

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Jinam et al. . doi:10.1093/molbev/mss169

Schroeder, Anne Butthof, and Mingkun Li at MPI, Leipzig;
Yoshimi Noaki at NIG, Mishima; and all participants/families
who generously gave us their time. This work was supported
by research grants # FP066-2007C from University of Malaya
and # 5140060 from Monash University (Sunway Campus);
SOKENDAI Strategic Research Project Grant; and The Max
Planck Society.

References14

primates based on DNA evidence complemented by fossil evidence.
Mol Phylogenet Evol. 9:585–598.
Gray RD, Drummond AJ, Greenhill SJ. 2009. Language phylogenies reveal
expansion pulses and pauses in Pacific settlement. Science 323:
479–483.
Gray RD, Jordan FM. 2000. Language trees support the express-train
sequence of Austronesian expansion. Nature 405:1052–1055.
Gunnarsdottir ED, Li M, Bauchet M, Finstermeier K, Stoneking M. 2011a.
High-throughput sequencing of complete human mtDNA genomes
from the Philippines. Genome Res. 21:1–11.
Gunnarsdottir ED, Nandineni MR, Li M, Myles M, Gil D, Pakendorf B,
Stoneking M. 2011b. Larger mitochondrial DNA thanY-chromosome differences between matrilocal and patrilocalgroups from Sumatra. Nat Commun. 2:228.
Hill C, Soares P, Mormina M, et al. (12 co-authors). 2006.
Phylogeography and ethnogenesis of aboriginal Southeast Asians.
Mol Biol Evol. 23:2480–2491.
Hill C, Soares P, Mormina M, et al. (11 co-authors). 2007. A mitochondrial stratigraphy for island southeast Asia. Am J Hum Genet. 80:
29–43.
Horai S, Satta Y, Hayasaka K, Kondo R, Inoue T, Ishida T, Hayashi S,
Takahata N. 1992. Man’s place in Hominoidea revealed by mitochondrial DNA genealogy. J Mol Evol. 35:32–43.
HUGO Pan-Asian SNP Consortium. 2009. Mapping human genetic diversity in Asia. Science 326:1541–1545.
Huson DH, Bryant D. 2006. Application of phylogenetic networks inevolutionary studies. Mol Biol Evol. 23:254–267.
Ingman M, Kaessmann H, Paabo S, Gyllensten U. 2000. Mitochondrial
genome variation and the origin of modern humans. Nature 408:
708–713.
Jin H-J, Tyler-Smith C, Kim W. 2009. The peopling of Korea revealed byanalyses of mitochondrial DNA and Y-chromosomal markers. PLoS
One. 4:e4210.
Jinam T, Phipps M, Indran M, Kuppusamy U, Mahmood AA, Hong LC,
Edo J. 2008. An update of the general health status in the indigenous
populations of Malaysia. Ethn Health. 13:277–287.
Jinam T, Saitou N, Edo J, Mahmood A, Phipps M. 2010. Molecularanalysis of HLA class I and class II genes in four indigenous
Malaysian populations. Tissue Antigens. 75:151–158.
Jordan FM, Gray RD, Greenhill SJ, Mace R. 2009. Matrilocal residence isancestral in Austronesian societies. Proc R Soc B. 276:1957–1964.
Karafet TM, Hallmark B, Cox MP, Sudoyo H, Downey S, Lansing JS,
Hammer MF. 2010. Major east–west division underlies Y chromosome stratification across Indonesia. Mol Biol Evol. 27:1833–1844.
Kayser M, Brauer S, Weiss G, Underhill P, Roewer L, Schiefenhövel W,
Stoneking M. 2000. Melanesian origin of Polynesian Y chromosomes.
Curr Biol. 10:1237–1246.
Kayser M, Choi Y, van Oven M, Mona S, Brauer S, Trent RJ, Suarkia D,
Schiefenhövel W, Stoneking M. 2008. The impact of theAustronesian expansion: evidence from mtDNA and Y chromosome diversity in the Admiralty Islands of Melanesia. Mol Biol
Evol. 25:1362–1374.
Kong QP, Sun C, Wang HW, et al. (16 co-authors). 2011. Large-scale
mtDNA screening reveals a surprising matrilineal complexity in East
Asia and its implications to the peopling of the region. Mol Biol Evol.
28:513–522.
Kong QP, Yao YG, Sun C, Bandelt HJ, Zhu CL, Zhang YP. 2003. Phylogenyof East Asian mitochondrial DNA lineages inferred from completesequences. Am J Hum Genet. 73:671–676.

Downloaded from http://mbe.oxfordjournals.org/ at National Institute of Genetics on August 9, 2012

Atkinson QD, Gray RD, Drummond AJ. 2008. mtDNA variation predicts
population size in humans and reveals a major Southern Asian
chapter in human prehistory. Mol Biol Evol. 25:468.
Barik SS, Sahani R, Prasad BVR, et al. (14 co-authors). 2008. Detailed
mtDNA genotypes permit a reassessment of the settlement andpopulation structure of the Andaman Islands. Am J Phys Anthropol
136:19–27.
Barker G, Barton H, Bird M, et al. (27 co-authors). 2007. The ‘humanrevolution’ in lowland tropical Southeast Asia: the antiquity andbehavior of anatomically modern humans at Niah Cave (Sarawak,
Borneo). J Hum Evol. 52:243–261.
Batini C, Lopes J, Behar DM, Calafell F, Jorde LB, van der Veen L,
Quintana-Murci L, Spedini G, Destro-Bisol G, Comas D. 2011.
Insights into the demographic history of African Pygmies from complete mitochondrial genomes. Mol Biol Evol. 28(2): 1099–1110.
Bellwood P. 2005. The first farmers: the origins of agricultural societies.
Victoria, Australia: Blackwell Publishing.
Bellwood P. 2007. Prehistory of the Indo-Malaysian Archipelago.
Canberra, Australia: ANU E Press.
Brothwell DR. 1960. Upper Pleistocene human skull from Niah caves,
Sarawak. Sarawak Museum J. 9:323–350.
Bryc K, Velez C, Karafet T, Moreno-Estrada A, Reynolds A, Auton A,
Hammer M, Bustamante CD, Ostrer H. 2010. Genome-wide patterns of population structure and admixture among Hispanic/
Latino populations. Proc Natl Acad Sci U S A. 107:8954–8961.
Cavalli-Sforza LL, Menozzi P, Piazza A. 1994. The history and geographyof human genes. Princeton, NJ: Princeton University Press.
Dancause KN, Chan CW, Arunotai NH, Lum JK. 2009. Origins of the
Moken Sea Gypsies inferred from mitochondrial hypervariable
region and whole genome sequences. J Hum Genet. 54:86–93.
Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Dambueva I,
Perkova M, Dorzhu C, Luzina F, Lee H, Vanecek T. 2007.
Phylogeographic analysis of mitochondrial DNA in Northern
Asian populations. Am J Hum Genet. 81:1025–1041.
Diamond JM. 1988. Express train to Polynesia. Nature 336:307–308.
Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis
by sampling trees. BMC Evol Biol. 7:214.
Fagundes NJR, Kanitz R, Eckert R, Valls ACS, Bogo MR, Salzano FM,
Smith DG, Silva WA Jr, Zago MA, Ribeiro-dos-Santos AK. 2008.
Mitochondrial population genomics supports a single pre-clovis
origin with a coastal route for the peopling of the Americas. Am J
Hum Genet. 82:583–592.
Felsenstein J. 2005. PHYL0IP (Phylogeny Inference Package). Seattle:
Department of Genome Sciences, University of Washington.
Fucharoen G, Fucharoen S, Horai S. 2001. Mitochondrial DNA polymorphisms in Thailand. J Hum Genet. 46: 115–125.
Glover I, Bellwood PS. 2004. Southeast Asia: from prehistory to history.
Oxford, UK: Routledge.
Goodman M, Porter CA, Czelusniak J, Page SL, Schneider H, Shoshani J,
Gunnell G, Groves CP. 1998. Toward a phylogenetic classification of

MBE

“Early Train” Hypothesis for Evolution of Southeast Asians . doi:10.1093/molbev/mss169

Saitou N, Nei M. 1987. The neighbor-joining method: a new
method for reconstructing phylogenetic trees. Mol Biol Evol.
4(4):406–425.
Shepard EM, Chow RA, Suafo’a E, Addison D, Pérez-Miranda AM,
Garcia-Bertrand RL, Herrera RJ. 2005. Autosomal STR variation in
five Austronesian populations. Hum Biol. 77:825–851.
Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A,
Oppenheimer S, Macaulay V, Richards MB. 2009. Correcting for
purifying selection: an improved human mitochondrial molecular
clock. Am J Hum Genet. 84:740–759.
Soares P, Rito T, Trejaut J, et al. (16 co-authors). 2011. Ancient voyaging
and polynesian origins. Am J Hum Genet. 88:239–247.
Soares P, Trejaut J, Loo JH, et al. (14 co-authors). 2008. Climate change
and postglacial human dispersals in Southeast Asia. Mol Biol Evol. 25:
1209–1218.
Tabbada KA, Trejaut J, Loo JH, Chen YM, Lin M, Mirazon-Lahr M, Kivisild
T, De Ungria MCA. 2009. Philippine mitochondrial DNA diversity: apopulated viaduct between Taiwan and Indonesia? Mol Biol Evol. 27:
21–31.
Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans
and chimpanzees. Mol Biol Evol. 10:512–526.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011.
MEGA5: molecular evolutionary genetics analysis using maximum
likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731–2739.
Tang H, Peng J, Wang P, Risch NJ. 2005. Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol. 28:
289–301.
Terrell J. 1988. Prehistory in the Pacific Islands. Cambridge, UK:
Cambridge University Press.
Thangaraj K, Chaubey G, Kivisild T, Reddy AG, Singh VK, Rasalkar AA,
Singh L. 2005. Reconstructing the origin of Andaman Islanders.
Science 308:996.
Thangaraj K, Singh L, Reddy AG, Rao VR, Sehgal SC, Underhill PA,
Pierson M, Frame IG, Hagelberg E. 2003. Genetic affinities of theAndaman islanders, a vanishing human population. Curr Biol. 13:
86–93.
Torroni A, Rengo C, Guida V, et al. (12 co-authors). 2001. Do the four
clades of the mtDNA haplogroup L2 evolve at different rates. Am J
Hum Genet. 69:1348–1356.
van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic
tree of global human mitochondrial DNA variation. Hum Mutat.
30:E386–E394.
Wollstein A, Lao O, Becker C, Brauer S, Trent RJ, Nürnberg P, Stoneking
M, Kayser M. 2010. Demographic history of Oceania inferred fromgenome-wide data. Curr Biol. 20:1983–1992.
Xu S, Pugach I, Stoneking M, Kayser M, Jin L. 2012. Genetic dating
indicates that the Asian–Papuan admixture through Eastern
Indonesia corresponds to the Austronesian expansion. PNAS. 109:4574–4579. Available from: http://www.pnas.org/content/early/
2012/03/05/1118892109.

15

Downloaded from http://mbe.oxfordjournals.org/ at National Institute of Genetics on August 9, 2012

Larson G, Cucchi T, Fujita M, et al. (32 co-authors). 2007. Phylogeny andancient DNA of Sus provides insights into neolithic expansion in
Island Southeast Asia and Oceania. Proc Natl Acad Sci U S A. 104:4834–4839.
Leavesley M, Chappell J. 2004. Buang Merabak: additional early radiocarbon evidence of the colonisation of the Bismarck Archipelago,
Papua New Guinea. Antiquity 78(301). Available from: http://
antiquity.ac.uk/projgall/leavesley/index.html.
Li JZ, Absher DM, Tang H, et al. (11 co-authors). 2008. Worldwide
human relationships inferred from genome-wide patterns of variation. Science 319:1100–1104.
Macaulay V, Hill C, Achilli A, et al. (21 co-authors). 2005. Single, rapid
coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308:1034–1036.
McEvoy BP, Lind JM, Wang ET, Moyzis RK, Visscher PM, van Hoslt
Pellekaan SM, Wilton AN. 2010. Whole-genome genetic diversity
in a sample of Australians with deep Aboriginal ancestry. Am J
Hum Genet. 87:297–305.
Mirabal S, Herrera KJ, Gayden T, Regueiro M, Underhill PA, GarciaBertrand RL, Herrera RJ. 2012. Increased Y-chromosome resolutionof haplogroup O suggests genetic ties between the Ami aboriginesof Taiwan and the Polynesian Islands of Samoa and Tonga. Gene 492:
339–348.
Mishmar D, Ruiz-Pesini E, Golik P, et al. (13 co-authors). 2003. Natural
selection shaped regional mtDNA variation in humans. Proc Natl
Acad Sci U S A. 100:171–176.
Nei M. 1972. Genetic distance between populations. Am Nat. 106:283–292.
Nicholas C. 2000. The Orang Asli and the contest for resources.
Indigenous politics, development and identity in peninsular
Malaysia. Denmark: IWGIA & Center for Orang Asli Concerns.
O’Connell JF, Allen J. 2004. Dating the colonization of Sahul (Pleistocene
Australia-New Guinea): a review of recent research. J Archaeol Sci.
31:835–853.
Oppenheimer SJ, Richards M. 2001. Slow boat to Melanesia? Nature 410:
166.
Oskarsson MCR, Klütsch CFC, Boonyaprakob U, Wilton A, Tanabe Y,
Savolainen P. 2012. Mitochondrial DNA data indicate an introduction through Mainland Southeast Asia for Australian dingoes andPolynesian domestic dogs. Proc Biol Sci. 279:967–974.
Patterson N, Price AL, Reich D. 2006. Population structure andEigenanalysis. PLoS Genet. 2:e190.
Peng MS, Quang HH, Dang KP, Trieu AV, Wang HW, Yao YG, Kong QP,
Zhang YP. 2010. Tracing the Austronesian footprint in mainland
Southeast Asia: a perspective from mitochondrial DNA. Mol Biol
Evol. 27:2417–2430.
Reich D, Patterson N, Kircher M, et al. (15 co-authors). 2011. Denisova
admixture and the first modern human dispersals into Southeast
Asia and Oceania. Am J Hum Gen. 89:516–528.
Ricaut FX, Bellatti M, Lahr MM. 2006. Ancient mitochondrial DNA from
Malaysian hair samples: some indications of Southeast Asian population movements. Am J Hum Biol. 18:654–667.

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