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Characterization of population structure from the mitochondrial DNA vis--vis language and geography in Papua New Guinea.

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AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 142:613–624 (2010)
Characterization of Population Structure from the
Mitochondrial DNA Vis-à-Vis Language and Geography
in Papua New Guinea
Esther J. Lee,1* George Koki,2 and D. Andrew Merriwether1
1
2
Department of Anthropology, Binghamton University, Binghamton, NY 13902-6000
Papua New Guinea Institute of Medical Research, Goroka EHP 441, Papua New Guinea
KEY WORDS
Papua New Guinea; mtDNA; language; geography
ABSTRACT
Situated along a corridor linking the
Asian continent with the outer islands of the Pacific,
Papua New Guinea has long played a key role in understanding the initial peopling of Oceania. The vast diversity in languages and unique geographical environments
in the region have been central to the debates on human
migration and the degree of interaction between the Pleistocene settlers and newer migrants. To better understand
the role of Papua New Guinea in shaping the region’s prehistory, we sequenced the mitochondrial DNA (mtDNA)
control region of three populations, a total of 94 individuals, located in the East Sepik Province of Papua New
Guinea. We analyzed these samples with a large data set
of Oceania populations to examine the role of geography
and language in shaping population structure within New
Papua New Guinea constitutes the eastern half of
island New Guinea and includes 600 surrounding
islands, including the large volcanic islands of the
Bismarck Archipelago and Bougainville. The western
part of the island, Western New Guinea, has been
referred to as Irian Jaya and is currently part of Indonesia. Our use of ‘‘New Guinea’’ is restricted to the eastern
part of the island and excludes the surrounding islands
in this work, whereas we use ‘‘Papua New Guinea’’ when
referring to the politically defined region including the
surrounding areas. We use the term ‘‘Near Oceania’’ to
denote the areas of New Guinea, Bismarck Archipelago
and main islands of the Solomon Islands. Islands to the
south and east of the Solomon Islands constitute Remote
Oceania. Lying in the corridor to Remote Oceania, Papua
New Guinea has been the focus of attention in understanding patterns of migration into the Pacific especially
with regards to its cultural, linguistic, and genetic diversity.
The earliest archaeological evidence of human occupation in New Guinea comes from the Huon Peninsula,
located on the east coast, dated to just under 40,000
years before present (YBP) (Groube et al., 1986;
O’Connell and Allen, 2004). Human occupation in the interior mountainous regions of the island occurred by
30,000 YBP in sites such as Nombe and Kosipe (White et
al., 1970; Gillieson and Mountain, 1983; Mountain, 1991;
Chappell, 2000). Other sites in the Bismarck Archipelago, including New Britain and New Ireland, are dated
as early if not earlier than sites discovered in the mainland [review in Summerhayes (2007)]. Interaction
between mainland New Guinea and its surrounding
C 2010
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WILEY-LISS, INC.
Guinea and between the region and Island Melanesia.
Our results from median-joining networks, star-cluster
age estimates, and population genetic analyses show that
while highland New Guinea populations seem to be the
oldest settlers, there has been significant gene flow within
New Guinea with little influence from geography or language. The highest genetic division is between Papuan
speakers of New Guinea versus East Papuan speakers
located outside of mainland New Guinea. Our study supports the weak language barriers to genetic structuring
among populations in close contact and highlights the
complexity of understanding the genetic histories of
Papua New Guinea in association with language and geography. Am J Phys Anthropol 142:613–624, 2010. V 2010
C
Wiley-Liss, Inc.
islands is documented by the movement of animals and
plants beginning around 20,000 YBP (Summerhayes,
2007). Exchange between highland and coastal areas of
New Guinea included not only cultigens but also shell
and stone (White, 1972). Natural sources of obsidian
only occur in West New Britain (Admiralties and Fergusson Island), but obsidian is found in the eastern highlands dated to 4,500 YBP. This illustrates the evidence
of interaction between New Guinea and its surrounding
islands at different times in history (Summerhayes et
al., 1998). It was not until around 3,300 YBP that populations are suggested to have started migrating into
Remote Oceania. This migration is thought to have
introduced a new culture and interacted with those already settled along their migration route (Green, 1991).
Languages in Oceania are classified into Austronesian
and Papuan (also referred as non-Austronesian) language families. The Austronesian language family contains a large number of languages and is widespread,
Additional Supporting Information may be found in the online
version of this article.
*Correspondence to: Esther J. Lee, Department of Anthropology,
Binghamton University, PO Box 6000, Binghamton, NY 13902-6000.
E-mail: elee11@binghamton.edu
Received 8 June 2009; accepted 11 January 2010
DOI 10.1002/ajpa.21284
Published online 3 May 2010 in Wiley InterScience
(www.interscience.wiley.com).
614
E.J. LEE ET AL.
found as far west as Madagascar in the Indian Ocean to
Easter Island in Remote Oceania to the east (Pawley,
2002). It has been proposed that Austronesian speakers
came from the island of Taiwan and rapidly migrated
into Melanesia and outward toward Micronesia and Polynesia (Blust, 1985; Gray et al., 2009). Although Austronesian languages in Oceania are fairly well understood
concerning their history in correlation with archaeological events, far less is understood about Papuan languages. Their geographical range, linguistic, and cultural diversity point to a longer history in situ than Austronesian languages, but little is known of their origins
and expansions (Ross, 2005). Papuan languages are predominant in mainland New Guinea, with no relatives
outside of the Melanesia-East Indonesia region, and
their 40-odd various language groups are not believed to
have close relationships to each other (Pawley, 2007). It
has been suggested that speakers of both families first
encountered one another in the Timor area as evidenced
by the Austronesian languages of east Nusantara showing signs of their speakers’ bilingualism in Papuan languages (Ross, 2005). Furthermore, evidence of contact
between Austronesian speakers and Papuan speakers of
New Guinea and Island Melanesia (IM) is thought to be
reflected in the Austronesian languages spoken in Near
Oceania as well as in Micronesia and Polynesia (Ross,
2005). Among Papuan speakers in New Guinea, some
suggest that Torricelli speakers, located in the highlands
of northern New Guinea, are likely to have been
solely descended from the initial Pleistocene occupants
in the region, based on the idea that their language
appears to be the oldest in Papua New Guinea (Swadling, 1990).
Genetic studies using mitochondrial DNA (mtDNA),
Y-chromosomal, and autosomal data suggest substantial
interaction between people in New Guinea with
migrants coming from East Asia/Taiwan en route to populate Polynesia. The genetic diversity of populations in
Near Oceania has been documented by many (Stoneking
et al., 1990; Merriwether et al., 2005; Ohashi et al.,
2006; Friedlaender et al., 2007; Friedlaender et al., 2008;
Kayser et al., 2008). In particular, admixture between
Polynesian ancestors and indigenous Melanesians is
thought to have taken place in the coastal/lowland of
New Guinea and in the Bismarck Archipelago (Scheinfeldt et al., 2006; Friedlaender et al., 2007). Scholars
have often correlated patterns of cultural, linguistic, and
biological diversity as explained by two major ‘‘waves,’’
which have been distinct temporal events separated by
thousands of years. Some have characterized these two
waves as representing Austronesian-speakers versus
Papuan-speakers. It has been argued that the people
characterized by a variant of mtDNA haplogroup B, also
known as the ‘‘Polynesian-motif,’’ did not often penetrate
into the interiors and especially not into the highlands of
mainland New Guinea and the nearby larger islands of
New Ireland, New Britain, and Bougainville (Stoneking
et al., 1990; Friedlaender et al., 2005). Previous genetic
studies of populations in Papua New Guinea have shown
great diversity in genetic variation and considerable antiquity evidenced by deep roots in the major mtDNA
haplogroups (Ingman and Gyllensten, 2003; Easteal et
al., 2005; Friedlaender et al., 2005, 2007, 2008; Merriwether et al., 2005). It has been suggested that a small
number of people founded the current populations in
New Guinea consisting the major maternal lineages,
haplogroups P, Q, and M (M27–29) (Easteal et al., 2005;
American Journal of Physical Anthropology
Merriwether et al., 2005). These groups are the most
widespread in New Guinea and suggested to have been
the founding population for Papuan speakers. Star-cluster age estimates of these haplogroups correlate with
the earliest date of first settlement in the region
(Friedlaender et al., 2005). On the other hand, early
studies suggested a significant structuring of mtDNA
variation between highland and coastal PNG populations
(Stoneking et al., 1990). Based on these observations,
it has been suggested that the highland New Guinea
populations are remnants of the original, older population that first settled in the region (Easteal et al.,
2005).
In this study, we examine a number of these assumptions about the relationship between language groups
and geography using newly collected mtDNA sequence
data for 94 individuals from three populations in the
East Sepik Province of Papua New Guinea, Dreikikir,
Jama-Sepik Plains, and Kubalia. The samples are from a
region with great linguistic diversity and while previous
studies have examined populations from the vicinity,
they are unlikely to be representative of the region’s history. We examined the mtDNA, because it has the largest available dataset of populations already sequenced
for comparison and is thought to mutate fast enough for
mutations to correspond to the relatively recent linguistic changes over the last 45,000 years. In addition,
because our samples are from an old archival plasma collection, mtDNA was most likely to be successfully recovered than carrying out Y-chromosome typing or whole
mtDNA genome sequencing. We report the haplogroups
present in the region and estimate the ages in each
region based on the diversity and phylogeny of each haplogroup to determine the likely order of the peopling of
Near Oceania. We tested for genetic structuring based
on linguistic and geographical groupings using F-statistics and AMOVA analyses. Nucleotide diversity, in conjunction with tests of neutrality, for each population was
used to identify the most variable (and oldest) and least
bottlenecked populations in each region.
METHODS
Population samples
Blood samples were collected by one of the authors
(GK) and Kuldeep Bhatia from the Institute of Medical
Research in Goroka, Papua New Guinea, in compliance
with institutional review boards. Genealogy information
was obtained, so that unrelated individuals for two to
three generations were selected to be sampled. Samples
are from the East Sepik Province of Papua New Guinea
and include the following populations: Dreikikir (n 5
28), Jama-Sepik Plains (n 5 30), and Kubalia (n 5 36).
Dreikikir is located in the Torricelli Mountains close to
the north coast. Jama-Sepik Plains is located in the
Sepik valley, and Kubalia is situated in the hinterland,
south of the township of Wewak. The location of these
populations is indicated in Figure 1. All three populations speak Papuan languages. Although the language
spoken in Dreikikir is classified in the Torricelli phylum, people from Jama-Sepik Plains and Kubalia speak
languages of the Sepik–Ramu phylum. We screened all
samples for the entire mtDNA control region as
explained below. Sequences are available in Genbank at
the following accession numbers: GQ202742–GQ202835.
mtDNA GENETIC STRUCTURE OF PAPUA NEW GUINEA
615
Fig. 1. Map of Papua New Guinea and location of the three populations, Dreikikir, Jama-Sepik Plains, and Kubalia, along with
the major township in the region, Wewak. Map is modified from maps.yahoo.com.
Laboratory and statistical analyses
DNA was extracted from plasma using the columnbased Qiagen extraction kit following manufacturer’s
protocol (Qiagen, Valencia, CA). Primers spanning nucleotide positions (np) 15938-00429 were used for PCR
amplification of the entire mtDNA control region following standard protocols. Amplification was verified by
agarose gel electrophoresis, and successful amplicons
were purified and prepared for sequencing using BigDye
Terminator v.3.1 reaction kits (Applied Biosystems, Foster City, CA). Direct sequencing was carried out on an
ABI PRISMTM 377XL DNA Sequencer (Applied Biosystems). Sequence data were aligned with Sequencher:
Forensic Version (GeneCodes). Samples were also
screened for the intergenic COII/tRNALys 9-bp deletion.
Additional sequences from Papua New Guinea and
Oceania were compiled using data from the literature
(Friedlaender et al., 2005; Merriwether et al., 2005; Vilar
et al., 2008). We only used the hypervariable region 1
(HV1) sequences for this broader comparison (np 16,019–
16,351). Sequences were aligned using ClustalX (Jeanmougin et al., 1998) and edited in MacClade 4.03 (Maddison and Maddison, 2000). Median-joining networks
were calculated for haplogroups P and Q in Network
4.502 (www.fluxus-engineering.com; Bandelt et al. 1999).
On the basis of the distribution of samples in haplogroups P and Q median-joining networks, we describe
shared and derived haplotypes based on geography and
language family. We define shared haplotypes as samples
that have the same haplotype while derived haplotypes
are defined as being one mutation away from the node
located closer to the central node. Thus, either derived
haplotypes are derived from the population of the haplotype closer to the central node or both derived and preceding haplotypes have a shared parental population.
This is another way to infer gene flow between populations.
Population statistics were calculated using ARLEQUIN (Schneider et al., 2000), which included analysis
of AMOVA and F-statistic values as well as diversity
indices and neutrality tests. In particular, F-statistic values were generated based on shared haplotype frequencies by permutating individuals for 10,000 simulated
random migrations between populations. Furthermore,
F-statistic estimates were used to generate a two-dimensional scaling to illustrate the inferred distances using
ALSCAL in SPSS (Statistical Package for Social Sciences, Chicago, IL).
RESULTS
Haplogroup characterization
Fifty-nine distinct haplotypes were identified based
on the mtDNA control region. The majority of haplotypes are assigned to haplogroups P and Q (Table 1).
Two individuals from Kubalia are assigned to haplogroup B4a1a1a (Table S4). The two haplotypes
assigned to B4 were confirmed by the 9-bp deletion at
the COII/tRNALys intergenic region. One B4 haplotype
(RW248) shows the same mutations in HV1 that are
also found in the East Sepik of New Guinea (Vilar et
al., 2008). One haplotype from Jama-Sepik and one
from Dreikikir are unassigned. One haplotype shows
mutations at 16,362; 16,519; 73; and 185 (RW160) and
American Journal of Physical Anthropology
616
E.J. LEE ET AL.
the other shows mutations at 16,051; 16,086; 16,129;
16,148; 16,223; 16,362; 16,519; 73; 152; 195; 207; 263;
and 269 (RW36). The latter shares mutations that are
characterized for haplogroup M28 but lacks the mutation at 16,468. Thirty-one individuals are assigned to
haplogroup P (33%), whereas 59 are assigned to haplogroup Q (63%) (Table 1). Among haplotypes assigned
to P, one is identified as P2 with mutations at 16,362;
16,519; 73; 185; and 263. The frequencies of P and Q
are similar to those that have been previously reported
in New Guinea (e.g. Friedlaender et al. 2005). All identified haplotypes and their mutations are shown in Supporting Information Tables S1–S4.
We compared published HV1 sequence data from the
Pacific with our samples for each haplogroup medianjoining network. In addition to the three populations
examined in this study, the remaining populations were
divided into Lowland New Guinea, Highland New
Guinea, and IM, which includes all islands outside of
New Guinea. Figures 2 and 3 show median-joining networks for haplogroups P and Q. The median-joining net-
TABLE 1. Distribution of haplogroups from the three
populations analyzed in this study
Haplogroups
Population
Region
P
Q
P1 P2 Q1 Q3 B M28 Other Total
Dreikikir
Torricelli Mt 12
Jama-Sepik Sepik Plains 9
Kubalia
Sepik Plains 10
Total
31
1
1
12 2
14 6
18 6 2
44 14 2
1
1
1
1
28
30
36
94
work for haplogroup P is not clearly resolved due to a
number of reticulations, which have been reported previously (Friedlaender et al., 2005). Haplogroup Q (see
Fig. 3) shows two distinct clusters, which differentiates
subhaplogroups Q1 and Q3. Within haplogroup P, while
some individuals from Jama-Sepik share one of the central nodes and are separated by just one mutation,
others are branched off at three or four mutations away
from the central node. Individuals from Dreikikir are
not more than two mutations away from the central
node while some individuals from Kubalia are separated
by three mutations from the central node. Haplogroup Q
shows a similar pattern, in which the three populations
are present in the central nodes, both in Q1 and Q3,
while others appear as derived haplotypes in the network.
To further examine shared and derived haplotypes,
Tables 2 and 3 list haplotypes that are shared and
derived between geographical regions for haplogroups P
and Q. Overall, the number of shared haplotypes does
not appear to be significantly different between any
regions, though haplotypes for haplogroup P in Kubalia
are only shared with lowland New Guinea and not with
other regions or populations. The number of shared haplotypes between IM and New Guinea populations ranges
from two to four in both haplogroups. In both haplogroups, there are more derived haplotypes in highland
New Guinea from lowland New Guinea (six) than vice
versa (three and one; Tables 2 and 3). In haplogroup P,
highland New Guinea shows a high number of derived
haplotypes from IM (six) and Dreikikir (five). Lowland
New Guinea also has a high number of derived haplotypes from IM (five) in haplogroup P. The highest number of derived haplotypes in haplogroup Q (nine) is in
Fig. 2. Median-joining network of haplogroup P from the Pacific (only HV1). Nodes are patterned as follows: Dreikikir 5 gray;
Jama-Sepik 5 black; Kubalia 5 white; lowland New Guinea 5 crossed pattern; highland New Guinea 5 vertical stripes; Island
Melanesia 5 horizontal stripes.
American Journal of Physical Anthropology
617
mtDNA GENETIC STRUCTURE OF PAPUA NEW GUINEA
Fig. 3. Median-joining network of haplogroup Q from the Pacific (only HV1). Coding follows Figure 2.
TABLE 2. Shared and derived haplotypes for haplogroup P between the three populations and Lowland New Guinea, Highland
New Guinea, and Island Melanesia (IM)
Shared/derived1
Dreikikir
Jama-Sepik
Kubalia
Lowland NG
Highland NG
IM
Dreikikir
Jama-Sepik
Kubalia
Lowland NG
Highland NG
IM
–
1/1
0/2
3/2
2/5
3/1
1/0
–
0/2
2/0
2/0
2/0
0/0
0/1
–
2/1
0/2
0/3
3/0
2/1
2/2
–
5/6
4/2
2/0
2/0
0/3
5/4
–
2/1
3/0
2/1
0/3
4/5
2/6
–
1
Regions listed on the rows are derived from the regions listed on the columns. For example, the last column for the first row, Dreikikir, 0 is interpreted as number of derived haplotypes from Island Melanesia that are found in Dreikikir.
TABLE 3. Shared and derived haplotypes for haplogroup Q between the three populations and regions in the Pacific
Shared/derived
Dreikikir
Jama-Sepik
Kubalia
Lowland NG
Highland NG
IM
Dreikikir
Jama-Sepik
Kubalia
Lowland NG
Highland NG
IM
–
1/2
3/0
1/5
2/2
2/0
1/0
–
2/0
3/5
1/2
1/1
3/0
2/2
–
2/5
2/3
4/1
1/3
3/2
2/1
–
3/6
4/3
2/0
1/3
2/0
3/1
–
2/0
2/1
1/3
4/1
4/9
2/4
–
lowland New Guinea, which is derived from IM haplotypes (Table 3).
Tables 4 and 5 show shared and derived haplotypes
between populations by language groups. Papuan languages were further categorized into individual phyla,
East Papuan, Trans New Guinea (TNG), Sepik-Ramu,
and Torricelli. The Torricelli phylum is only represented
by Dagua. Haplotypes within haplogroup P in the TNG
phylum show a high number of shared haplotypes with
the Austronesian language family (five) as well as
derived haplotypes nine from the language family. The
number of derived haplotypes from Dreikikir is also high
(nine). In haplogroup Q, on average, more haplotypes
are shared between the Austronesian language family
and other groups, ranging from two to four (Table 5).
There is also a higher number of derived haplotypes
from the Austronesian language family found in Papuan
languages, ranging from five to nine.
Using a mutation rate of 20,180 years for HV1, we
calculated the haplogroup ages for P, Q, Q1, and Q3
(Saillard et al., 2000). Ages were also calculated separately by geographical region and language family: IM
American Journal of Physical Anthropology
618
E.J. LEE ET AL.
TABLE 4. Shared and derived haplotypes for haplogroup P between the three populations and language groups
Shared/derived
Dreikikir
Jama-Sepik
Kubalia
Torricelli
Sepik-Ramu
TNG
East Papuan
Austronesian
–
1/1
0/2
0/1
3/0
2/9
1/2
3/1
1/2
–
1/2
0/0
3/0
2/0
1/2
1/1
0/0
0/1
–
1/0
1/1
0/0
0/0
1/2
0/0
0/0
1/0
–
0/0
0/0
0/0
0/0
3/1
3/0
1/3
0/1
–
2/2
1/2
3/0
2/2
2/0
0/2
0/0
2/1
–
2/3
5/3
1/1
1/0
0/0
0/0
1/0
2/0
–
1/2
3/2
1/2
1/2
0/0
3/0
5/9
1/4
–
Dreikikir
Jama-Sepik
Kubalia
Torricelli
Sepik-Ramu
TNG1
East Papuan
Austronesian
1
TNG, Trans New Guinea phylum.
TABLE 5. Shared and derived haplotypes for haplogroup Q between the three populations and language groups
Shared/derived
Dreikikir
Jama-Sepik
Kubalia
Torricelli
Sepik-Ramu
TNG
East Papuan
Austronesian
–
1/2
3/0
1/1
2/3
1/2
1/0
2/0
1/0
–
2/0
2/1
2/4
2/2
1/0
3/0
3/0
2/1
–
0/1
3/5
1/2
1/1
3/0
1/0
2/0
0/0
–
1/1
3/0
2/0
3/0
2/2
2/1
3/1
1/1
–
3/0
1/0
2/0
1/2
2/0
1/1
3/2
3/1
–
2/0
4/0
1/0
1/0
1/0
2/0
1/2
2/0
–
4/1
2/2
3/1
3/2
3/5
2/9
4/6
4/5
–
Dreikikir
Jama-Sepik
Kubalia
Torricelli
Sepik-Ramu
TNG1
East Papuan
Austronesian
1
TNG, Trans New Guinea phylum.
TABLE 6. Rho estimates1 for haplogroups P and Q (Q1 and Q3)
Haplogroup
q
q (years)
r
r (years)
P
IM-AN
IM-Papuan
PNG highland
PNG lowland Papuan
PNG lowland AN
Q
IM-AN
IM-Papuan
PNG highland
PNG lowland Papuan
PNG lowland AN
Q1
IM-AN
IM-Papuan
PNG highland
PNG lowland Papuan
PNG lowland AN
Q3
IM-AN
IM-Papuan
PNG highland
PNG lowland Papuan
PNG lowland AN
3.0533
2.5313
1.4000
3.4074
3.7647
2.7188
3.6997
2.9750
3.8166
3.1364
3.0783
3.9487
1.6810
1.2031
1.6719
2.2162
1.7500
1.5200
2.3860
1.0455
0.6271
1.6000
1.7222
0.6364
61615
51081
28252
68761
75972
54864
74660
60036
77018
63292
62119
79685
32653
24279
33738
44723
35315
30674
48149
21097
12655
32288
34754
12842
0.80308
0.92333
0.52493
0.914
1.2062
0.84433
1.0546
0.89739
1.2028
0.89014
0.99621
1.2027
0.39662
0.48235
0.67874
0.52407
0.35755
0.5246
0.95618
0.40401
0.37557
0.61644
0.42673
0.35209
16206
18633
10593
18444
24340
17039
21282
18109
24272
17963
20104
24270
8004
9734
13697
10576
7215
10586
19296
8153
7579
12440
8611
7105
1
Estimates are calculated for the entire haplogroup and broken
down by geographical/linguistic region.
Austronesian (IM-AN), IM Papuan, New Guinea Highland (all Papuan), New Guinea Lowland Papuan, and
New Guinea Lowland Austronesian (Table 6). Haplogroup Q is slightly older than P with q values showing
3.6997 for Q while 3.0533 for P. Within haplogroup Q,
Q3 appears to be older at 2.386 compared with 1.681 for
Q1. For haplogroup P, Papuan-speaking populations
from lowland and highland PNG appear to be the oldest.
This is similar to that seen in subhaplogroups Q1 and
Q3. On the other hand, Austronesian-speaking populations from lowland PNG and Island Melanesian PapuanAmerican Journal of Physical Anthropology
speaking populations seem to be as old if not older in
haplogroup Q.
Gene flow inferred from AMOVA, pairwise
comparisons, and two-dimensional analysis
Using F-statistics and AMOVA tests (Excoffier et al.,
1992), gene flow was inferred by grouping populations
by geographical region and by language group (Table 7).
F-statistics were estimated by AMOVA between New
Guinea and the surrounding islands and between highland and lowland New Guinea populations. Furthermore, populations were grouped by Papuan and Austronesian languages, and within Papuan, further divided
into East Papuan languages, which are spoken outside
of New Guinea, and TNG, Sepik-Ramu, and Torricelli
languages, which are spoken within New Guinea. The
highest FST value from AMOVA was between Papuan
speakers in New Guinea versus Papuan speakers outside
of New Guinea, who are classified in the East Papuan
phylum (0.337), indicating relatively high-genetic division. This value is slightly higher than comparing Papuan and Austronesian-speaking populations (0.2894) or
between geographical groupings of New Guinea and
other islands (0.3116). The lowest genetic division comes
from comparisons between populations speaking Papuan
languages of different phyla within New Guinea (FST \
0.09). In addition, FST value between highland and lowland New Guinea is relatively low at 0.1267 also suggesting a low level of population genetic division
between populations from the regions.
Table 8 shows pairwise population comparisons
between the three populations and other populations in
the Pacific, which were carried out by calculating the
F-statistics from shared haplotype frequencies (Slatkin,
1995). F-statistics with P values below 0.05 are in bold.
A complete table with values between each population is
available upon request. The three populations examined
in our study show similar genetic affinities with each
other (0.031–0.052), but other populations appear to
mtDNA GENETIC STRUCTURE OF PAPUA NEW GUINEA
619
TABLE 7. AMOVA-derived F-statistics between populations by geography and language
Grouping
FST
FSC
FCT
NG versus Bismarck and Bougainville
Highland versus Lowland NG
Papuan versus Austronesian languages
NG Papuan versus East Papuan phylum
TNG versus Sepik-Ramu and Torricelli phylum
Sepik-Ramu versus Torricelli phylum
0.3116
0.1267
0.2894
0.3370
0.0873
0.0073
0.2667
0.1257
0.2566
0.2617
0.0789
0.0143
0.0612
0.0012
0.0441
0.1020
0.0091
-0.0071
TABLE 8. F-statistics values estimated between Dreikikir,
Jama-Sepik, Kubalia, and other populations in the Pacific with
significant values (P < 0.05) in bold
Populations
Dreikikir
FST
Jama-Sepik
FST
Kubalia
FST
Dreikikir
Jama-Sepik
Kubalia
Markham
Fringe Highlands
Garaina
Kayagar
Wahgi-Minj
Mandobo
Rigo
Walis
St Martin
Dagua
Boiken
Wingei
Warabung
Witupe
Kiniambu
Aita
Eivo
Nagovisi
Rotokas
Nasioi
Teop
Saposa
Ata
Marabu
Rangulit
Malasait
Sulka
Kol
Tolai
Kuot
Mamusi
Melamela
Mengen
Mussau
Nailik
Nakanai
Notsi
Tigak
Madak
Anem
Kove
Fiji
New Caledonia
Vanuatu
Ontong Java
Santa Cruz
Solomon Islands
–
0.03127
0.0359
0.02933
0.13926
0.10569
0.04245
0.04645
0.08388
0.1148
0.01783
0.05968
0.02493
0.02236
0.00882
0.01289
0.03205
0.01747
0.31962
0.0901
0.19722
0.06877
0.0463
0.06968
0.03038
0.14341
0.16812
0.10712
0.16739
0.06225
0.0864
0.05695
0.16024
0.12778
0.07078
0.05151
0.01803
0.0174
0.15362
0.03957
0.06186
0.04953
0.06778
0.03247
0.03841
0.0306
0.04575
0.14749
0.09874
0.06626
0.03127
–
0.05209
0.04421
0.15173
0.12113
0.05539
0.06277
0.09875
0.12728
0.05059
0.07101
0.02693
0.04472
0.01956
0.03119
0.04224
0.04137
0.3303
0.10269
0.20943
0.08139
0.05859
0.08246
0.04314
0.15512
0.17944
0.11997
0.17903
0.08782
0.09827
0.06983
0.1717
0.14048
0.08409
0.06864
0.03117
0.03
0.16462
0.05277
0.07441
0.06178
0.08063
0.04568
0.05601
0.04096
0.05985
0.15956
0.11043
0.07863
0.0359
0.05209
–
0.04612
0.15137
0.12304
0.07175
0.06411
0.09945
0.12534
0.05311
0.05704
0.03528
0.03697
0.03381
0.02989
0.03983
0.0417
0.31101
0.08992
0.18855
0.07701
0.06078
0.08429
0.04565
0.15441
0.17805
0.12085
0.17718
0.08634
0.09552
0.07151
0.17008
0.14022
0.09298
0.06526
0.03388
0.03263
0.16392
0.05521
0.07523
0.06391
0.08251
0.04823
0.05075
0.04385
0.05657
0.15068
0.10502
0.07407
have closer or similar genetic affinities. For example,
Dreikikir shows the lowest F-statistic value with Nailik,
an Austronesian-speaking population from New Ireland
(0.017), and Kiniambu (0.017) from the Sepik plains.
Dreikikir also shows close genetic affinities with Dagua
(0.024) and Boiken (0.022), both from the north coast of
New Guinea in the same province. Jama-Sepik has the
lowest F-statistic value with Wingei (0.019), and Kubalia
has the lowest value with Warabung (0.029). Both
Wingei and Warabung are from the Prince Alexander
Mountains in the same province.
The two-dimensional scaling of all populations shows
that most are clustered together by geographic proximity
(see Fig. 4). All scaling had a fitness level higher than
0.85. Examining populations in New Guinea, the three
populations from this study are included in the main
central cluster while Rigo, Mandobo, and a population
from the Fringe Highlands (see Fig. 5). Rigo is an Austronesian-speaking coastal population, and Mandobo is a
Papuan-speaking population from the lowland riverine
area. Papuan-speaking populations were analyzed separately in Figure 6, and the three populations from this
study are clustered with the main central cluster. Two
Bougainville populations appear to be outliers (Aita and
Nagovisi) while some populations from New Britain and
New Ireland clustered together apart from the main central cluster. Fringe Highland is clustered more closely to
this smaller cluster of New Britain and New Ireland
populations. Furthermore, populations such as Nasioi
(Bougainville), Kol (New Britain), and Sulka (New Britain) are clustered more closely with New Guinea populations.
Nucleotide diversity and neutrality
We calculated the nucleotide diversity for populations
with a sample size above 10 and carried out Tajima’s D
neutrality tests (Tajima, 1989; Slatkin, 1994). Nucleotide
diversity was slightly higher in populations of New
Guinea compared to populations from New Britain and
other surrounding islands, which is consistent with the
New Guinea populations being older than the island populations (Table 9). All populations except Tigak and New
Caledonia are statistically insignificant for the Tajima’s
D test, thus neutrality is assumed (P \ 0.05).
DISCUSSION
In this study, we examined several questions regarding
the genetic patterns in New Guinea: (1) Are populations
in New Guinea older than the surrounding outer islands?
(2) Can we see significant genetic structuring between
highland and lowland New Guinea populations? (3) Can
we see significant genetic structuring based on language
families (Austronesian and Papuan) in New Guinea? (4)
Can we predict genetic affinity based on geographical
proximity and language affinities in Near Oceania?
Previous studies have suggested that inhabitants of
the highlands in New Guinea are an older population
American Journal of Physical Anthropology
620
E.J. LEE ET AL.
Fig. 4. Two-dimensional analysis of populations from the Pacific based on mtDNA HV1 F-statistic values from shared haplotype
frequencies. Fitness level is 0.864.
Fig. 5. Two-dimensional analysis of populations from New Guinea based on mtDNA HV1 F-statistic values from shared haplotype frequencies. Fitness level is 0.966.
who had limited interaction with those in the lowlands
or outside of the mainland. Our results agree and show
star-cluster age estimates of highland inhabitants of
New Guinea to be very old as old as the haplogroup in
its entirety. In particular, Papuan speakers represented
American Journal of Physical Anthropology
by subhaplogroup Q1 are oldest in the highlands of New
Guinea, and age estimates are younger in the lowlands
and outside of New Guinea. On the other hand, Papuan
speakers outside of New Guinea are younger than Austronesian speakers in the same region for haplogroup P
mtDNA GENETIC STRUCTURE OF PAPUA NEW GUINEA
621
Fig. 6. Two-dimensional analysis of Papuan-speaking populations based on mtDNA HV1 F-statistic values from shared haplotype frequencies. Fitness level is 0.899.
and subhaplogroup Q3. This may suggest that Papuan
speakers represented by haplogroups P and Q3 were settled in New Guinea for at least several thousands of
years before migrating to the outer islands while Q1 can
be an example of the older lineages found in IM seen
from previous studies (e.g. Friedlaender et al., 2005).
Thus, there seems to be diverse genetic patterns of
migration among the founding lineages that arrived in
New Guinea.
Within New Guinea, gene flow estimates show weak
structuring of population between the highlands and
lowlands. Two-dimensional analysis shows that most
New Guinea populations are clustered together and the
few populations that appear to be distant from the main
cluster include both Austronesian and Papuan-speaking
populations (see Fig. 5). This suggests that the genetic
differentiation between highland and lowland New
Guinea does not seem to be as significant as previously
thought, in contrast to previous studies (e.g. Stoneking
et al., 1990). This may reflect more recent population
history and interaction between populations regardless
of geographic proximity as well as languages. On the
other hand, there seems to be greater differentiation
between New Guinea and outer islands, rather than differentiation within New Guinea proper. This differentiation is congruent with languages spoken, as our results
show that the structuring between Papuan speakers in
New Guinea and East Papuan speakers is equivalent to
Papuan versus Austronesian speakers. The separate language histories of Austronesian and Papuan languages
have been described by others (e.g. Blust, 1995; Pawley,
2002), and the East Papuan phylum has been suggested
to include five or possibly six families and several isolates (Ross, 2005). Thus, there seems to be a broad range
of variation within Papuan languages that is reflected in
the genetic patterns.
Genetic affinity is also inferred from shared and
derived haplotypes between different geographical
regions. Our results show that more highland New
Guinea haplotypes are derived from lowland New
Guinea and IM than vice versa (Tables 2 and 3). This
may suggest that either (1) more highland haplotypes
are derived from populations in lowland New Guinea
than vice versa, (2) both share a recent common ancestral population, or (3) there has been extensive interaction between these populations, which may have
obscured any prehistoric interaction or lack thereof.
Although the ancestral population for haplogroups P and
Q can be traced back to around 50,000 years ago (Friedlaender et al., 2005), it seems plausible that the
relationship between these haplotypes may reflect the
interaction in the past few thousands of years. This is
also supported by the AMOVA tests, which show relatively high-genetic affinity between populations within
New Guinea.
Examining the number of shared and derived haplotypes according to language groups, overall the number
of shared haplotypes between Austronesian and other
language groups are equal to or slightly higher than the
number of shared haplotypes between Papuan languages. For example, the number of shared haplotypes
between Austronesian and Papuan speakers in haplogroup Q ranges from two to four with an average of
three haplotypes, while the number of shared haplotypes
between the Sepik-Ramu phylum and other Papuan languages is between one and three (Table 5). This may
simply indicate that the commonly used dichotomy
between Austronesian and Papuan speakers does not
American Journal of Physical Anthropology
622
E.J. LEE ET AL.
TABLE 9. Nucleotide diversity and neutrality tests for populations in New Guinea and the Pacific1
Population
Region
Language
Sample size
Dreikikir*
Dagua
Boiken
Jama-Sepik*
Kubalia*
Witupe
Kiniambu
Wingei
Warabung
Walis
St. Martin
Markham
Rigo
Kayagar
Fringe Highlands
Wahg-Minj
Mandobo
Ata
Marabu
Malasait
Kol
Sulka
Tolai
Mamusi
Melamela
Nakanai
Nailik
Notsi
Kuot
Tigak
Madak
Aita
Rotokas
Nagovisi
Nasioi
Saposa
Teop
Santa Cruz
Solomon Islands
Fiji
New Caledonia
Vanuatu
Ontong Java
Torricelli Mt
North Coastal NG
North Coastal NG
Sepik Plains
Sepik Plains
Sepik Plains
Sepik Plains
Prince Alexander Mt
Prince Alexander Mt
Island NG
Island NG
Coastal NG
Coastal NG
Southwest Riverine NG
Highlands NG
Western highlands NG
Lowland riverine NG
New Britain
New Britain
New Britain
New Britain
New Britain
New Britain
New Britain
New Britain
New Britain
New Ireland
New Ireland
New Ireland
New Ireland
New Ireland
Bougainville
Bougainville
Bougainville
Bougainville
Bougainville
Bougainville
Torricelli**
Torricelli**
Sepik-Ramu**
Sepik-Ramu**
Sepik-Ramu**
Sepik-Ramu**
Sepik-Ramu**
Sepik-Ramu**
Sepik-Ramu**
Sepik-Ramu**
Austronesian
Austronesian
Austronesian
Trans-New Guinea**
Trans-New Guinea**
Trans-New Guinea**
Trans-New Guinea**
East Papuan**
East Papuan**
East Papuan**
East Papuan**
East Papuan**
Austronesian
Austronesian
Austronesian
Austronesian
Austronesian
Austronesian
East Papuan**
Austronesian
Austronesian
East Papuan**
East Papuan**
East Papuan**
East Papuan**
Austronesian
Austronesian
East Papuan**
Austronesian
Austronesian
Austronesian
Austronesian
Austronesian
28
22
22
30
36
29
32
27
26
32
32
91
18
34
16
19
26
43
75
38
52
26
67
61
14
74
22
12
60
21
33
38
19
14
31
18
16
69
26
15
35
22
24
Nucleotide diversity
Tajima’s D
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
0.64244
20.33091
20.46693
0.49036
20.30192
0.32372
0.53893
20.26964
20.51896
0.20899
0.67344
20.59466
0.36325
0.26386
20.20469
20.70137
20.58126
0.05018
0.47456
1.61876
0.23966
20.6116
20.30458
1.89388
20.43928
0.00705
0.84979
0.28172
21.19116
21.48884
20.36874
20.65946
2.74579
0.17874
1.51875
20.57534
20.30872
0.73126
21.15399
20.21909
21.75746
21.03098
1.73489
0.021831
0.028765
0.024372
0.020873
0.021822
0.02202
0.02491
0.021663
0.022073
0.02704
0.028701
0.027869
0.018246
0.025019
0.017338
0.021934
0.016549
0.01128
0.012992
0.00686
0.020513
0.017363
0.025429
0.015762
0.021388
0.016867
0.017004
0.009282
0.006849
0.011571
0.015607
0.013482
0.025068
0.002013
0.025928
0.012699
0.021747
0.026568
0.021346
0.025113
0.020554
0.024565
0.01539
0.011732
0.015295
0.013114
0.011246
0.011596
0.011806
0.013175
0.011666
0.011884
0.014216
0.015027
0.014309
0.010181
0.013203
0.009803
0.012005
0.009160
0.006442
0.007199
0.004276
0.010885
0.009553
0.013196
0.008567
0.011980
0.009065
0.009457
0.005835
0.004220
0.006753
0.008617
0.007537
0.013568
0.001838
0.013688
0.007390
0.012045
0.013740
0.011522
0.013808
0.011014
0.013210
0.008611
1
Papuan languages are indicated by their phylum name.
* Populations from this study.
** Phyla classified in the Papuan language family.
exist and that language has not prevented any interaction between these people. A previous study has argued
based on autosomal data that languages were not a significant barrier to genetic exchange in northern IM
(Hunley et al., 2008). Furthermore, the higher F-statistic
value based on the AMOVA tests (0.337) between Papuan speakers within New Guinea versus Papuan speakers outside the main island compared with Papuan
speakers and Austronesian speakers (0.2894) suggests
that geographical separation may have a stronger influence in the genetic division than language (Table 7). The
high F-statistic value between New Guinea and surrounding islands (0.3116) also corroborates this view.
Interestingly, TNG populations have a high number of
derived haplotypes from the Austronesian language family in both haplogroup P (nine) and haplogroup Q (six) as
well as a relatively high number of shared haplotypes
(five and four) (Table 8 and 9). TNG populations also have
a high number of derived haplotypes from Dreikikir (nine)
in haplogroup P but a low number in haplogroup Q (two).
The TNG hypothesis proposes that TNG speakers
American Journal of Physical Anthropology
expanded from the central highlands of New Guinea at
around 6,000 YBP or as early as 10,000 YBP to the east
and west, most likely correlating with the expansion of
agriculture (Swadling, 1990; Pawley, 1998; Denham et al.,
2003; Pawley, 2005). Among the nine derived haplotypes
from Dreikikir found in TNG speakers, six are haplotypes
from the highlands, which may suggest that TNG speakers possibly descended from an ancestral population to
both TNG and Torricelli speakers who are located in the
highlands and expanded across New Guinea including the
lowlands. Still, interaction between Austronesian speakers and TNG must have also been very extensive based on
the number of shared and derived haplotypes. A previous
study suggested that the TNG expansion played a more
important role in Y-chromosome diversity of New Guinea
(Mona et al., 2007). Further investigation of the mtDNA
from different TNG and Torricelli speakers across New
Guinea may provide further understanding of this proposed expansion.
Our analysis included Sepik-Ramu speakers from six
populations located in the Sepik plains and the moun-
mtDNA GENETIC STRUCTURE OF PAPUA NEW GUINEA
tainous regions (Table 9). The rising sea levels during
the mid-Holocene formed an inland sea in the SepikRamu basin, which reached its full extent at around
6,500–7,500 YBP and then slowly transformed to the
current riverine floodplain by sedimentation (Swadling
et al., 1989; Chappell, 2005). It has been proposed that
the change in landscape shifted the focus of interaction
from between people of the basin and the highlands to
the basin and outer islands (Swadling and Hide, 2005).
This interaction may be reflected in the high number of
derived haplotypes from the Austronesian language family found in haplotypes assigned to the Sepik-Ramu phylum for haplogroup Q (nine). Some previous studies have
suggested limited contact between Austronesian-speaking populations and Papuan-speaking populations (e.g.
Vilar et al., 2008), but our study proposes that interaction between people between different language families
occurred more frequently than previously thought.
SUMMARY AND CONCLUSIONS
Our study corroborates the common view that populations in New Guinea are in general older than those in
the surrounding islands, and Papuan speakers are in general older than Austronesian speakers. Furthermore, we
show the existence of genetic structuring between New
Guinea and its surrounding islands, as evidenced in comparison with the East Papuan phylum as well as other
Papuan languages within New Guinea. Within New
Guinea, our data suggest that highlanders are older
inhabitants of the region but also had stronger interaction
with lowland populations than perhaps previously
thought. Although highland and lowland inhabitants
speak a range of different languages, there does not seem
to be strong genetic structuring between different language groups in New Guinea. In other words, interaction
seems to have occurred with little influence from the languages spoken or the locations of settlement. Although
genetic evidence does show remnants of an ‘‘Austronesian
expansion’’ along the route to Oceania as seen in previous
studies (e.g. Kayser et al., 2008), there does not seem to
have been strong barriers to genetic exchange. Furthermore, our conclusion supports the argument of weak or
absent language barriers to genetic structuring in Near
Oceania, especially when in close contact, which has also
been shown in eastern Indonesia (Hunley et al., 2008;
Friedlaender et al., 2009; Mona et al., 2009). Future studies examining more populations of different Papuan languages and information from other genetic systems such
as the Y-chromosomal and autosomal data in association
with ethnographic data may provide information on other
aspects of the complexities in New Guinea prehistory
since the Holocene. In sum, we believe that the simple dichotomy of the two ‘‘waves’’ oversimplifies the complex
prehistories of New Guinea and its surrounding islands
and our results emphasize its rich linguistic, cultural, geographical, and genetic diversity.
ACKNOWLEDGMENTS
We thank all the donors who provided the samples for
this study. We are grateful to Jonathan Friedlaender for
sample selection from the IMR collection and helpful
suggestions on this paper. All procedures were approved
by the institutional review boards. The authors thank
Miguel Vilar for assisting in the initial analysis. We
acknowledge the two anonymous reviewers for their
helpful comments and advice on this work.
623
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