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Brief communication Mitochondrial DNA variation suggests extensive gene flow from Polynesian ancestors to indigenous Melanesians in the northwestern Bismarck Archipelago.

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Brief Communication: Mitochondrial DNA Variation
Suggests Extensive Gene Flow from Polynesian
Ancestors to Indigenous Melanesians in the
Northwestern Bismarck Archipelago
Jun Ohashi,1* Izumi Naka,1 Katsushi Tokunaga,1 Tsukasa Inaoka,2
Yuji Ataka,3 Minato Nakazawa,4 Yasuhiro Matsumura,5 and Ryutaro Ohtsuka6
Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, 113-0033 Japan
Department of Environmental Sociology, Faculty of Agriculture, Saga University, Saga, 840-8502 Japan
Research Center for Tropical Infectious Diseases, Institute of Tropical Medicine,
Nagasaki University, Nagasaki, 852-8523 Japan
Socio-Environmental Health Sciences, Graduate School of Medicine, Gunma University, Gunma, 371-8511 Japan
Division of Health Informatics and Education, National Institute of Health and Nutrition, Tokyo, 162-8636 Japan
Department of Human Ecology, Graduate School of Medicine, University of Tokyo, Tokyo, 113-0033 Japan
Austronesian; D-loop; Melanesian; mtDNA; 9-bp deletion; Polynesian
Archaeological, linguistic, and genetic studies show that Austronesian (AN)-speaking Polynesian
ancestors came from Asia/Taiwan to the Bismarck Archipelago in Near Oceania more than 3,600 years ago, and
then expanded into Remote Oceania. However, it remains unclear whether they extensively mixed with indigenous Melanesians who had populated the Bismarck
Archipelago before their arrival. To examine the extent
of admixture between Polynesian ancestors and indigenous Melanesians, mitochondrial DNA (mtDNA) variations in the D-loop region and the cytochrome oxidase
and lysine transfer RNA (COII/tRNALys) intergenic 9-bp
deletion were analyzed in the following three Oceanian
populations: 1) Balopa Islanders as AN-speaking Melanesians living in the northwestern end of the Bismarck
Archipelago, 2) Tongans as AN-speaking Polynesians,
and 3) Gidra as non-Austronesian-speaking Melanesians
in the southwestern lowlands of Papua New Guinea.
Phylogenetic analysis of mtDNA sequences revealed that
more than 60% of mtDNA sequences in the Balopa
Islanders were very similar to those in Tongans, suggesting an extensive gene flow from Polynesian ancestors to
indigenous Melanesians. Furthermore, analysis of pairwise difference distributions for the D-loop sequences
with the 9-bp deletion and the Polynesian motif (i.e.,
T16217C, A16247G, and C16261T) suggested that the
expansion of Polynesian ancestors possessing these variations occurred approximately 7,000 years ago. Am J
Phys Anthropol 130:551–556, 2006. V 2006 Wiley-Liss, Inc.
Recent genetic studies showed that Austronesian
(AN)-speaking Polynesian ancestors came from Asia/Taiwan to the Bismarck Archipelago in Near Oceania, and
then expanded into Remote Oceania. The Bismarck Archipelago had been colonized by Melanesians before the
arrival of the Polynesians ancestors. However, there are
two contradictory models in terms of admixture between
these groups: ‘‘express train’’ (Diamond, 1988; Bellwood,
1989) and ‘‘slow boat’’ (Kayser et al., 2000). The former
model supposes a rapid expansion of Polynesian ancestors along the coast of New Guinea to Polynesia, with
negligible admixture with indigenous Melanesians. The
latter model proposes slow movement of the Polynesian
ancestors, with extensive admixture. Although both geneticists and archaeologists now generally accept some degree of admixture between the Polynesian newcomers
and indigenous Melanesians, the extent of admixture and
direction of gene flow remain under debate.
Early studies of maternally inherited mitochondrial
DNA (mtDNA) supported the express-train model, because a 9-base pair (bp) deletion between the genes for
cytochrome oxidase (COII) and lysine transfer RNA
(tRNALys), here termed the 9-bp deletion, was found in
Southeast Asians and Polynesians, but rarely in Melanesians, and especially not in Papua New Guinea highlanders (Hertzberg et al., 1989; Stoneking et al., 1990).
Recent studies, however, revealed that the 9-bp deletion
occurs frequently in AN-speaking Melanesians in Island
Melanesia, suggesting admixture between Polynesian
ancestors and indigenous Melanesians (Merriwether
et al., 1999).
C 2006
Grant sponsor: Ministry of Education, Culture, Sports, Science,
and Technology of Japan, Grant-in-Aid for Scientific Research.
*Correspondence to: Jun Ohashi, Ph.D., Department of Human
Genetics, Graduate School of Medicine, University of Tokyo, 7-3-1
Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Received 25 March 2005; accepted 11 August 2005.
DOI 10.1002/ajpa.20383
Published online 19 January 2006 in Wiley InterScience
Fig. 1. Map of locations of
populations studied.
The slow-boat model was based on analyses of Y-chromosome polymorphisms (Kayser et al., 2000). Unlike
mtDNA, major Y-haplotypes of Polynesians were also
found in Melanesians but not in Asians, suggesting that
Polynesian ancestors extensively mixed with indigenous
Melanesians, and that many Melanesian genes were
incorporated into Polynesians.
More recently, we reported that the ABO*A102 allele
of the ABO blood-group gene could serve as a genetic
marker reflecting gene flow from Polynesian ancestors to
Melanesians (Ohashi et al., 2004). We compared ABO allele frequencies among three groups: 1) AN-speaking
Melanesians in the Balopa Islands of the Bismarck Archipelago, 2) AN-speaking Polynesians in Tonga, and 3)
the Gidra, a non-Austronesian (NAN)-speaking Melanesian people of the southwestern lowlands of Papua New
Guinea (PNG) (Ohashi et al., 2004). The Balopa Islands
of the Manus province of PNG are located at the northwestern end of the Bismarck Archipelago (i.e., the northwestern end of Near Oceania). Because a Pleistocene
site, the Pamwak rock shelter, was found in Manus
(Fredericksen et al., 1993), and the oldest Lapita potteries, dating to 3,600 years ago, were discovered in
Mussau Island located close to Balopa Island, the Balopa
Islanders are considered to be descendants of the indigenous Melanesians who were initially contacted by the
Polynesian ancestors in Near Oceania. Thus, the genetic
trail of Polynesian newcomers to Near Oceania, if it still
remains, should be detectable in Balopa Islanders. From
the ABO allele-frequency data, we concluded that Balopa
Islanders were genetically more similar to the Polynesian Tongans than to the Melanesian Gidra (Ohashi
et al., 2004).
Because mtDNA and Y-chromosome studies show that
the extent of admixture and direction of gene flow might differ among genetic markers, our perspective, based on the
ABO allele frequency, that Polynesian ancestors mixed with
the ancestors of Balopa Islanders should be reevaluated
with other genetic markers. Thus, in this study, to obtain
more conclusive evidence on the genetic proximity of Balopa
Islanders to Polynesians, mtDNA polymorphisms in the Dloop region and the intergenic COII/tRNALys 9-bp deletion
were analyzed in the same Oceanian populations that we
previously studied: Balopa Islanders, Tongans, and the
Gidra. In addition, pairwise difference distributions for the
D-loop sequences with the 9-bp deletion and the so-called
‘‘Polynesian motif’’ have implications for the evolutionary
history of Polynesian ancestors.
Study populations
Balopa. The Balopa Islands, which consist of three
inhabited islands (Lou, Pam, and Baluan) in the Manus
province of PNG, are located at 1478150 –1478250 East
longitude and 28200 –28350 South latitude. In total, 59
Balopa Islanders were analyzed in this study, and each
individual was not consanguineously related to others
until three generations back, based on villagers’ genealogical records as reconstructed by the authors (Ataka,
1997; Ataka and Ohtsuka, 2000).
Tonga. Twenty Tongans living in Ha’ano and Fakakakai
villages of Ha’apai Island and 23 Tongans in Nukualofa,
the capital city of the Kingdom of Tonga, were recruited
in this study.
Gidra. The Gidra-speaking population, included in the
NAN-speaking group, is located in the southwestern lowlands of PNG. Their population structure and subsistence were described previously (Ohtsuka et al., 1985;
Ohtsuka, 1986). For the analysis of mtDNA variation, 59
Gidra were selected from 192 unrelated individuals living in 12 villages.
The geographic locations of the populations studied
are shown in Figure 1. This study was approved by the
Ethics Committee of the Graduate School of Medicine,
University of Tokyo. The D-loop sequences from nine
aboriginal Taiwanese groups were drawn from Tajima
et al. (2003).
Molecular typing of mtDNA
Typing of the COII/tRNALys intergenic deletion. The
mtDNA 9-bp deletion in the COII/tRNALys intergenic
region was detected by the polymerase chain reaction
(PCR) method established previously (Horai et al., 1996),
with a slight modification of amplification conditions.
The amplified fragments (100 or 91 bp in length) encompassing the intergenic region were separated by electrophoresis on 10% acrylamide gels, followed by staining
with ethidium bromide.
TABLE 1. Frequencies of 9-bp deletion and Polynesian motifs
(T16217c, A16247G, and C16261T) in Oceanian populations1
frequency (%)
Polynesian motif
frequency (%)
37/59 (62.7)
39/43 (90.7)
0/59 (0.0)
29/59 (49.2)
34/43 (79.1)
0/59 (0.0)
All mtDNA sequences with Polynesian motifs have 9-bp deletion.
Direct sequencing of the D-loop region. A fragment
of the D-loop region of mtDNA was amplified with the
primer pair B (15985-50 -AGCACCCAAAGCTAAGATTC30 -16004) and E (100-50 -CAGCGTCTCGCAATGCTATCGCGTG-30 -76), as described elsewhere (Fucharoen et al.,
2001; Qian et al., 2001). The notation of Anderson et al.
(1981) was used for numbering of bases. Amplification
conditions consisted of an initial denaturation at 968C
for 10 min, followed by 30 cycles of denaturation at 968C
for 15 sec, annealing at 528C for 15 sec, and extension at
728C for 35 sec, using a thermal cycler (GeneAmp PCR
System 9700; Perkin-Elmer Applied Biosystems). Nucleotide sequences of both strands were determined with an
automated sequencer (ABI Prism 3100).
Data analysis
Phylogenetic tree and nucleotide diversity. After
eliminating insertion and deletion polymorphisms from the
D-loop sequences, the number of nucleotide substitutions
per site between individual sequences was estimated, based
on the two-parameter method of Kimura (1980). In total,
563 nucleotide sites (positions 16048–16569 followed by
positions 1–41: position numbers which followed the standard numbering system of Anderson et al., 1981) were compared for phylogenetic analysis among the Balopa Islanders,
Tongans, Gidra, and nine aboriginal Taiwanese populations
previously reported (Tajima et al., 2003). Based on the estimated number of substitutions, a phylogenetic tree was constructed by using the unweighted pair group method with
arithmetic mean (UPGMA) method. In addition, nucleotide
diversity within and between populations (dX and dXY,
respectively), and net nucleotide diversity between populations (dA ¼ dXY (dX þ dY)/2; Nei and Li, 1979), were calculated. These analyses were conducted using MEGA version
2.1 (Kumar et al., 2001).
Pairwise difference distributions of D-loop sequences. After eliminating insertion and deletion polymorphisms, pairwise differences of mtDNA D-loop sequences
were calculated for a total of 623 nucleotide sites (positions
16007–16569, followed by positions 1–60) for the Balopa
Islanders, Tongans, and Gidra. The time of population expansion of Polynesian ancestors was inferred based on the
pairwise difference distributions of 63 D-loop sequences
with the Polynesian motif, assuming the sudden-expansion
model (Rogers and Harpending, 1992; Schneider and Excoffier, 1999). These analyses were conducted using Arlequin
version 2.000 (Schneider et al., 2000).
The frequencies of the 9-bp deletion among Balopa
Islanders, Gidra, and Tongans are presented in Table 1.
The frequency was high among Tongans, as previously
reported (Hertzberg et al., 1989; Sykes et al., 1995),
while no mtDNA with the 9-bp deletion was found
among the Gidra. Because the Gidra are NAN-speaking
Melanesians living in the southwestern lowlands of PNG,
they as well as PNG highlanders (Hertzberg et al., 1989)
are believed to be free from gene flow from AN-speaking
groups such as Polynesian ancestors. Thus, the present
result is consistent with this perspective. Among Polynesians, the 9-bp deletion is associated with the following
three transitions: T16217C, A16247G, and C16261T
(Hagelberg and Clegg, 1993; Lum et al., 1994; Melton et al.,
1995; Redd et al., 1995). This haplotype was called the ‘‘Polynesian motif’’ (Melton et al., 1995; Redd et al., 1995). The
frequencies of the Polynesian motif in the populations studied are shown in Table 1. It should be noted here that all
mtDNA sequences with the Polynesian motif had the 9-bp
Figure 2 shows a phylogenetic tree that combines Dloop polymorphisms and the 9-bp deletion for three Oceanian populations and nine aboriginal Taiwanese groups.
The Balopa Islanders’ sequences fell into four clusters.
Of particular interest, the Tongans and Gidra shared
scarcely any sequence features, while the Balopa Islanders
in cluster I shared similar mtDNA sequences with Tongans, and the Balopa Islanders in clusters II–IV had sequences similar to the Gidra.
Figure 3 shows the distributions of pairwise nucleotide
differences within populations. As expected from the results of phylogenetic analysis, a bimodal distribution was
observed in the Balopa Islanders. The peak at one difference reflects the sequence similarity in cluster I of
Figure 2, and the peak at 14 differences result from the
comparison between sequences in clusters I and IV.
To estimate the time of expansion of Polynesian ancestors with the Polynesian motif, we calculated three demographic parameters that could fit the observed pairwise difference distributions of 63 D-loop sequences with
the Polynesian motif, assuming an instantaneous stepwise demographic expansion model (Rogers and Harpending, 1992; Schneider and Excoffier, 1999). This approach enables us to estimate a demographic parameter s ¼ 2 ut), where u is the total mutation rate per
generation, and t measures time in generations since the
sudden expansion. The estimated s was 1.005, with a
95% confidence interval (CI) of 0.034–1.525 obtained
from the bootstrap method with 10,000 replications. The
substitution rate of the mtDNA control region was estimated to be 1.142 3 107 per site per year, based on the
divergence of mtDNA sequences in PNG groups (Stoneking et al., 1992); 623 sites, excluding insertions and deletions, were examined here. The corresponding expansion
time t is therefore 7,060 (95% CI, 240–10,720) years ago.
The frequency of the 9-bp deletion was found to exceed
60% among the Balopa Islanders. Thus, as expected from
our previous study on the ABO blood-group gene (Ohashi
et al., 2004), Balopa Islanders showed genetic proximity
to Tongans. Although the 9-bp deletion had been regarded as a useful marker for tracing the expansion of
Polynesian ancestors, there is increasing evidence that
the same deletion occurred independently in other populations (Ballinger et al., 1992; Soodyall et al., 1996).
Thus, analysis of only the 9-bp deletion does not provide
conclusive evidence, and so we analyzed mtDNA variations in the D-loop region. A phylogenetic tree for the Dloop region in Figure 2 revealed that Balopa Islanders
shared similar mtDNA sequences with Tongans and also
with the Gidra. Because all mtDNA sequences in cluster I
Fig. 2. UPGMA tree for 341 mtDNA sequences from Balopa Islanders, Tongans, Gidra, and nine aboriginal Taiwanese groups.
The mtDNA sequences from Oceanian populations are distinguished as four clusters: cluster I (Polynesian origin), cluster II (Melanesian origin), cluster III (Melanesian origin), and cluster IV (Melanesian origin). Individual sequences at tips of branches are represented by population names followed by sample ID numbers. M, Balopa Islanders; T, Tongans in Ha’ano and Fakakakai villages
of Ha’apai island; TG, Tongans in Nukualifa; G, Gidra. Aboriginal Taiwanese groups are designated as in Tajima et al. (2003): ATA,
Atayal; SAI, Saisiat; BUN, Bunun; TSO, Tsou; RUK, Rukai; PAI, Paiwan; AMI, Ami; PUY, Puyuma; YAM, Yami (Tajima et al.,
2003). The 9-bp deletion appears to have occurred at position indicated by arrow.
of Figure 2 had the 9-bp deletion and the sequences of
aboriginal Taiwanese diverged prior to those of Balopa
and Tonga, the deletion seems to have arisen only once in
these populations. Thus, the mtDNA sequences of Balopa
in cluster I appear to be derived from Polynesian ancestors who came from Asia/Taiwan. In contrast, the mtDNA
sequences of Balopa in clusters II–IV seem to have derived from NAN-speaking Melanesians or indigenous Melanesians who had populated the Bismarck Archipelago
before Polynesian ancestors arrived. This result strongly
suggests that extensive gene flow from Polynesian ancestors to ancestors of the Balopa Islanders occurred when
Polynesian ancestors arrived at the Bismarck Archipelago.
Thus, our data do not support the ‘‘express-train’’ model
hypothesizing that admixture between Polynesian ances-
tors and indigenous Melanesians is negligible. In the ‘‘slowboat’’ model proposed by Kayser et al. (2000), based on
Y-chromosome polymorphisms, Polynesian ancestors moved
gradually across Melanesia and left behind their genes,
but also incorporated many Melanesian genes. The present
data from mtDNA sequences are not compatible with the
incorporation of many Melanesian genes into Polynesian
ancestors. The main direction of gene flow appears to have
been from Polynesian ancestors to indigenous Melanesians.
Of particular interest, this perspective is supported by
mtDNA following maternal inheritance. Thus, not only
males but also many females may have gotten off the ‘‘slow
Although the phylogenetic tree in Figure 2 does not
allow us to infer from which aboriginal Taiwanese groups
Fig. 3. Distributions of pairwise nucleotide differences of Dloop region in Balopa, Tonga, and Gidra.
the Polynesian ancestors are derived, sequences in the
Ami were found to be most similar to those in Tongans.
Furthermore, the net nucleotide diversity dA between the
Ami and Tongans (0.0039) was smaller than that between
the other aboriginal Taiwanese groups and Tongans (data
not shown). Also, dA between the Ami and Balopa
Islanders (0.0020) was smaller than that between the
other aboriginal Taiwanese groups and Balopa (data not
shown). The Ami inhabit the eastern coast of the main
island of Taiwan, geographically close to Near Oceania.
Taking these results together, we speculate that Polynesian ancestors are partly derived from ancestors of the
Ami. This view should be clarified by future studies.
The distributions of pairwise nucleotide differences
within populations were different among three populations (Fig. 3). A unimodal distribution with a strong peak
at one difference was observed in Tongans, suggesting a
recent population expansion of Polynesians (Rogers and
Harpending 1992). In contrast, the Gidra showed multiple
peaks, resulting from three mtDNA lineages indicated by
clusters II–IV in Figure 2. The multiple peaks imply that
the Gidra did not expand recently, unless they mixed with
other populations. The Gidra are thought to be descendants of early migrants into PNG, and have been well-isolated from other Papuan groups due to the linguistic
boundary. It is therefore surprising that the three allelic
lineages that diverged a long time ago have been maintained in the small population of Gidra (approximately
2,000 in 1989), regardless of random genetic drift. Overall,
our results seem to be consistent with demographic histories of the studied populations.
The Polynesian motif was frequently found in Balopa
Islanders as well as in Tongans (Table 1), suggesting that
the appearance of the Polynesian motif had occurred
before Polynesian ancestors arrived at the Bismarck Archipelago. As shown in Figure 2, a number of sequence
features are shared by Balopa Islanders and Tongans in
cluster I. This observation implies a rapid expansion of
Polynesian ancestors before their significant admixture
with indigenous Melanesians. Our estimated time of the
expansion, 7,060 years ago, is similar to the 5,500 years
ago inferred by Redd et al. (1995), based on mtDNA
sequences from Indonesia, coastal PNG, and Samoa. Haplotypes of the 9-bp deletion with the Polynesian motif
have never been found in aboriginal Taiwanese groups
(Melton et al., 1995, 1998; Sykes et al., 1995; Tajima
et al., 2003). Thus, the Polynesian motif appears to have
arisen in Polynesian ancestors after they left Asia/Taiwan.
Interestingly, the estimated expansion time of 7,000 years
ago is consistent with the estimated date, 6,000–6,500
years ago, of the first split with AN languages into Formosan (one or more primary subgroups in Taiwan) and
Malayo-Polynesian (all AN languages outside Taiwan)
(Blust, 1988; Bellwood, 1991). Thus, the population
expansion of Polynesian ancestors with the Polynesian
motif may have occurred soon after they left Asia/Taiwan.
Haplogroups P and Q, as defined by Forster et al. (2001),
are commonly found in Papua New Guinea. We examined if the present D-loop sequences belong to P or Q by
using the same mtDNA sequences in Figures 2 and 4 of
Friedlaender et al. (2005), although such conventional
haplogroups can be distinguished correctly based on
whole-genome sequencing. We found that approximately
20% and 60% of Gidra mtDNA sequences were similar to
haplogroups P and Q, respectively, and 5% and 27% of
Balopa Islanders were similar to P and Q, respectively.
Interestingly, 20% of Gidra mtDNA sequences seemed to
be placed between haplogroups P and Q (data not
shown). In Australian Aborigines, mtDNA sequences belonging to haplogroup P are found, while those belonging
to haplogroup Q are not (Huoponen et al., 2001; Ingman
and Gyllensten, 2003; Friedlaender et al., 2005). Thus
the Gidra, NAN-speaking Melanesians, are considered to
be genetically close to Australian Aborigines compared
to Balopa Islanders, AN-speaking Melanesians.
The analysis of mtDNA variations revealed that
Balopa Islanders were genetically similar to Tongans
rather than the Gidra. The present results suggest that
extensive gene flow occurred from Polynesian ancestors
to indigenous Melanesians. Based on pairwise difference
distributions of D-loop sequences with the Polynesian
motif (i.e., T16217C, A16247G, and C16261T) in Balopa
Islanders and Tongans, the expansion of Polynesian
ancestors possessing the motif was presumed to have
occurred approximately 7,000 years ago.
The sequences reported here were deposited in DDBJ/
EMBL/GenBank under accession numbers AB119285–
The authors are indebted to the people of Papua New
Guinea and Tonga for their cooperation in providing blood
samples for testing. We also thank Drs. Taniela Palu (Ministry of Health, Kingdom of Tonga), Viliami Tangi (Diabetes Clinic, Kingdom of Tonga), and Kazumichi Katayama
(Primate Research Institute, Kyoto University) for research on the Tongan population. We thank three anonymous reviewers for valuable comments and suggestions
about a previous version of the manuscript.
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flow, extensive, archipelago, variation, dna, brief, communication, melanesia, northwestern, indigenous, ancestors, genes, polynesia, bismarck, mitochondria, suggests
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