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Human ancient and extant mtDNA from the Gambier Islands (French polynesia) Evidence for an early Melanesian maternal contribution and new perspectives into the settlement of Easternmost Polynesia.

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AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 144:248–257 (2011)
Human Ancient and Extant mtDNA From the Gambier
Islands (French Polynesia): Evidence for an Early
Melanesian Maternal Contribution and New Perspectives
into the Settlement of Easternmost Polynesia
Marie-France Deguilloux,1* Marie-Hélène Pemonge,1 Vincent Dubut,1 Sandrine Hughes,2
Catherine Hänni,2 Lionel Chollet,3 Eric Conte,4 and Pascal Murail1*
1
Université Bordeaux 1, UMR 5199 PACEA, Laboratoire d’Anthropologie des Populations du Passé,
Avenue des Facultés, 33405 Talence Cedex, France
2
Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA,
Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France
3
Centre Hospitalier Intercommunal de Toulon-La Seyne, Département de Biologie Moléculaire, BP 1412,
83056 Toulon Cedex, France
4
Centre International de Recherche Archéologique sur la Polynésie, Université de la Polynésie Française,
BP 6570-98702, Faa’a, Tahiti, Polynésie Française
KEY WORDS
Eastern Polynesia; mtDNA; ancient DNA; settlement; Melanesia
ABSTRACT
Molecular anthropology has been widely
used to infer the origin and processes of the colonization of
Polynesia. However, there are still a lack of representative
geographical studies of Eastern Polynesia and unchallenged
genetic data about ancient Polynesian people. The absence of
both of these elements prevents an accurate description of
the demographic processes of internal dispersion within the
Polynesian triangle. This study provides a twofold analysis of
ancient and modern mtDNA in the eastern part of French
Polynesia: the Gambier Islands. The paleogenetic analyses
conducted on burials of the Temoe Atoll (14th217th centuries)
represent the first fully authenticated ancient human
sequences from Polynesia. The identification of the ‘‘Mela-
nesian’’ Q1 mtDNA lineage in ancient human remains substantiates the Near Oceanic contribution to the early gene
pool of this region. Modern samples originate from Mangareva Island. Genealogical investigations enable us to reliably
identify the conservation of the Melanesian component in
Easternmost Polynesia, despite recent European colonization. Finally, the identification of rare mutations in sequences
belonging to haplogroup B4a1a1a provides new perspectives
to the debate on the internal peopling of the Polynesian
region. Altogether, the results laid out in our study put the
emphasis on the necessity of controlled sampling when discussing the internal settlement of Polynesia. Am J Phys
Anthropol 144:248–257, 2011. V 2010 Wiley-Liss, Inc.
The colonization of Polynesia occurred relatively late in
prehistory and its chronology and progression are still a
matter of debate. The colonization is considered to result
from the dispersal from Southeast Asia to the Pacific of
speakers of Austronesian languages (Kirch, 2000). This
dispersal is archeologically associated with the emergence
(around 1,400 BC in the Bismarck Archipelago) and with
progressive spread (from 900 BC in Western Polynesia)
of the Lapita Cultural Complex (Kirch, 1997). The Lapita
Cultural Complex stemmed from the encounters of these
Austronesian newcomers with populations already present in Near Oceania for several tens of thousands of years,
notably speakers of non-Austronesian languages (Green,
1991). All Polynesian societies are believed to have originated from those which developed the Lapita Cultural
Complex (Kirch, 1997, 2000). However, there is a gap of
1,000 years between the settlement of those societies in
Western Polynesia (Tonga and Samoa) and the period during which the first archipelagos of Eastern Polynesia (Society Islands, Cook Islands, Marquesas, etc.) were populated. This temporal gap leaves open the possibility of
other scenarios (Conte, 2000; Addison and Matisoo-Smith,
2010). The most recent dates recorded for the colonization
of the easternmost inhabited islands of French Polynesia,
the Gambier Islands, correspond only to the 11th–12th centuries AD (Kirch et al., 2010).
For more than a decade, molecular anthropology has
greatly contributed to debates regarding the peopling of
Polynesia. The first studies conducted on mitochondrial
DNA (mtDNA) variation showed a high genetic homogeneity in Polynesia with a single control region haplotype
C 2010
V
WILEY-LISS, INC.
C
Additional Supporting Information may be found in the online
version of this article.
P.M. and E.C. designed research and directed field work; M.F.D.,
M.H.P. (ancient DNA), V.D., L.C. (modern DNA) and S.H., C.H. (ancient DNA replications) performed analyses; M.F.D. and M.H.P. analyzed data; M.F.D. and P.M. wrote the article.
*Correspondence to: M.-F. Deguilloux or P. Murail, Université
Bordeaux 1, UMR 5199 PACEA, Laboratoire d’Anthropologie des
Populations du Passé, Avenue des Facultés, 33405 Talence Cedex,
France. E-mail:
Received 28 May 2010; accepted 25 July 2010
DOI 10.1002/ajpa.21398
Published online 24 September 2010 in Wiley Online Library
(wileyonlinelibrary.com).
MTDNA
MAKEUP OF A FRENCH POLYNESIAN POPULATION
known as the ‘‘Polynesian Motif ’’ (PM) present at high
frequency (Hagelberg and Clegg, 1993; Melton et al.,
1995; Redd et al., 1995; Sykes et al., 1995). The ancestral haplogroup (Hg) of the PM is Hg B4a1 (Kivisild
et al., 2002), which was proven to be shared between
Taiwanese and Polynesian populations and was considered supporting evidence for Polynesian origins in
Taiwan (Lum et al., 1994; Melton et al., 1995). Moreover,
the small proportion of non-PM lineages found in Polynesia was interpreted as support for an Express-Train
model, which proposed little matrilineal interaction
between settlers and the existing inhabitants of Near
Oceania (Diamond, 1988). Since then, studies have
focused on the PM phylogeny, including sequencing of the
entire mitochondrial genome in southeastern Asia and
Oceania. The PM (characterized by an additional transition at np 16247) was shown to be derived from Hg
B4a1a1 and was thus renamed Hg B4a1a1a (Trejaut
et al., 2005; Pierson et al., 2006; Friedlaender et al., 2007).
The geographic region of origin and the age of the PM
haplotype remain a subject of debate, with some researchers suggesting that the haplotype arose in present day
Indonesia earlier than the accepted time frame for a
model of Austronesian expansion from Taiwan (Richards
et al., 1998; Oppenheimer and Richards, 2001; Hill et al.,
2007). However, other analyses have found the timing and
likely place of origin of ancestral sister clades of the PM
(B4a1a1) to be compatible with the ‘‘Out-of-Taiwan’’ model
(Cox, 2005). The discrepancies among the hypotheses are
surely linked to differences in the statistics used as well
as the data under study. Nevertheless, most studies have
demonstrated a predominantly Asian origin for Polynesian maternal lineages, whereas only a few maternal Polynesian Hgs have a Melanesian origin: Hg P1, Q1, Q2
(Kayser et al., 2006) and M28 (Merriwether et al., 2005).
Kayser et al.’s (2006) survey allowed the classification of
all but one of the Polynesian mtDNAs that were analyzed
as either Asian (93.8%) or Melanesian (6.0%) in origin.
Altogether, mitochondrial data favor a very limited Melanesian genetic contribution to the maternal lineages of
Polynesian people.
In contrast to the mtDNA data, studies of paternally
inherited DNA markers from the nonrecombining region
of the Y chromosome (NRY) have revealed significant
Melanesian origins for Polynesian paternal lineages
(Kayser et al., 2000, 2006; Hurles et al., 2002). These
data support the Slow Boat model (Kayser et al., 2000)
that suggests that the ancestors of Polynesians originated in Eastern Asia but mixed intensively with indigenous Melanesians before colonizing the Pacific. The discrepancy between the amounts of Asian and Melanesian
NRY and mtDNA components in Polynesian populations
is often reported as reflecting a sex-biased admixture
that may have been stimulated by cultural elements
such as matrilocality (Hage and Marck, 2003; Trejaut et
al., 2005). Finally, studies of autosomal DNA markers
suggest different scenarios or different proportion of
Melanesian component depending on the loci used (Hill
PM
NRY
PCR
ULD
HVR
np
bp
Abbreviations
Polynesian Motif
nonrecombining region of the Y chromosome
polymerase chain reaction
unrelated lines of descent
hypervariable regions
nucleotide position
base pairs.
249
et al., 1987; Mack et al., 2000; Su et al., 2000; Kayser
et al., 2008; Friedlaender et al., 2008). Overall, the
genetic data reveal a dual origin of Polynesian people, a
major East Asian genetic component and a much lower
but noticeable Melanesian component, the significance of
which depends on the genetic markers used. As a consequence, the genetic origin of Polynesians still remains
contentious. Concerning maternal lineages which can be
traced to a Melanesian origin, their distribution suggests
that Near Oceanic females became some of the first
Remote Oceanic colonists. However, only ancient DNA
could establish the presence of Near Oceanic maternal
lineages in Polynesia before European contact and subsequent gene flow.
Furthermore, although the origin of Polynesians has
received much attention, the dynamics and mode of
human spread into the Polynesian triangle have been
neglected. Archeological evidence shows a pause of
1,000 years between the settlement of Western (Tonga
and Samoa) and Eastern Polynesia (Spriggs and Anderson, 1993). The central islands of Eastern Polynesia (the
Cook Islands, Society Islands, and Marquesas archipelagos) were then probably the centers of dispersion for the
colonization of more peripheral islands (Hawaii, Easter
Island, and New Zealand; Kirch, 2000; Conte, 2000).
However, a more complex pattern of migrations within
Polynesia is suggested by the analysis of mtDNA lineages of the Pacific rat Rattus exulans that supports postsettlement contact and long-distance exchange in the
Polynesian prehistory (Matisoo-Smith et al., 1998).
These conclusions are also supported by geographically
sourced prehistoric inter-island exchanges of raw materials (Weisler, 1998).
FOCUS OF THE STUDY
Molecular anthropology in the context of the Polynesian islands faces several limiting factors. The multiplicity of islands and archipelagos, together with their
recent history, make the sampling strategies crucial. The
genetic pool of the Polynesian islands and the dynamics
of settlement into Polynesia have most often been
deduced from Western Polynesia (Samoa and Tonga, e.g.,
Melton et al., 1995; Redd et al., 1995; Kayser et al.,
2000; Su et al., 2000; Hurles et al., 2002; Pierson et al.,
2006; Friedlaender et al., 2008; Kayser et al., 2008).
When eastern populations are mentioned, they prove to
be unspecified and potentially nonrepresentative (e.g.
Murray-McIntosh et al., 1998). Understanding the
migrations into this far-reaching region cannot be
resolved by the analysis of nonrepresentative samples.
Notably, reliable data from French Polynesia, which covers a large part of the region, are critically missing.
Moreover, to our knowledge, very few previous Polynesian studies detail their sampling strategy, including volunteers’ kinship or volunteers’ own histories, which are
necessary to discard sequences brought by recent postcontact arrivals. Finally, the general debate on the peopling of Polynesia currently lacks reliable paleogenetic
data, useful for interpreting extant data. Previous
genetic analyses of human skeletal remains recovered
from a wide variety of archeological sites and contexts
throughout Oceania (Hagelberg and Clegg, 1993; Hagelberg, 1997) have showed that the people associated with
the Lapita culture in the central Pacific lacked the PM.
However, the authors themselves expressed reservations
about their results, due to their small sample size and
American Journal of Physical Anthropology
250
M.-F. DEGUILLOUX ET AL.
TABLE 1. List of the analyzed archeological samples from Temoe and their radiocarbon dates
Location of genetic
analysis and number of
clones analyzed
Sample
Bone analyzed
Orutu 9a
Orutu 11a
Tupa 18
Tupa 19
Tupa 37
Tutapu 57
Tutapu 68
Adult first right metacarpal bone
Adult left fifth metacarpal bone
Neonate right femur
Adult left third metacarpal bone
Adult left fifth metatarsal bone
Adult second right metatarsal bone
Adult third right metatarsal
Radiocarbon age
1420–1510
1480–1660
nd
1400–1450
1320–1440
1440–1620
1400–1450
cal AD
cal AD
cal
cal
cal
cal
AD
AD
AD
AD
Reference
Beta-214812
Beta-175806
nd
Beta-186752
Beta-175808
Beta-214810
Beta-214811
Bordeaux
79
44
28
40
40
30
65
clones
clones
clones
clones
clones
clones
clones
Lyon
28 clones
42 clones
cal AD, calibrated Anno Domini; nd, not determined.
the caveat of contamination (Hagelberg and Clegg,
1993). As noted by Hagelberg and Clegg (1993), new archeological sites, well characterized and sampled with
precautions against contamination, hold the greatest
promise.
We performed the first combined analysis of mtDNA
in ancient and modern populations from Easternmost
Polynesia, in an attempt to address the following issues:
i) Is the antiquity of the maternal Melanesian component confirmed through a reliable analysis of ancient
Polynesian samples (with full adherence to ancient DNA
criteria)? ii) Is the conservation of a maternal Melanesian component since initial settlement confirmed in
Easternmost Polynesia when reliable characterization of
a modern gene pool is obtained through a genealogical
approach? iii) Can an improved characterization of the
mitochondrial Polynesian gene pool provide new arguments to the debate on internal settlement? To present
pertinent arguments for such questions, we analyzed ancient and modern human samples originating from the
Gambier Islands, the easternmost inhabited islands of
French Polynesia. This region is reported to have been
colonized only in the 11th–12th centuries AD (Kirch et
al., 2010) and provides crucial information concerning
the internal settlement of Polynesia. Ancient human
Polynesian remains under study come from Temoe Atoll
burials located 50 km away from the Gambier Islands.
The remains are dated to the 14th–17th centuries AD
(Table 1), close to the recent colonization of this easternmost part of Polynesia (Kirch et al., 2010). Sampling and
analyses followed all current recommendations for
authentication of ancient sequences. Extant samples
originate from Mangareva, the main island of Gambier
Archipelago, and sampling strategy included genealogical investigations in order to identify nonrelated individuals and to exclude recent arrivals.
MATERIALS AND METHODS
Archeological samples
The ancient bones under study come from recent excavations directed by EC and PM (Murail and Conte,
2005) in the Temoe Atoll, located 50 km southeast of
the Gambier Islands. This atoll was deserted in 1838
and has remained uninhabited to this day. The atoll is
made up of several motus (closely spaced coral islets separated by narrow channels). Burial groups were excavated on the three motus containing such structures
(Tupa, Tutapu and Orutu). Representative graves of
each of these motus were selected for bone sampling.
The graves were in tumuli built with coral blocks. All
American Journal of Physical Anthropology
but one skeleton have been dated by radiocarbon dating
and the range of dating was from the 14th to the 17th
centuries AD (Table 1). Dating put all samples prior to
the first contact with European people, as the Gambier
Islands were identified and named for the first time by
James Wilson in 1797, but the first European to land in
the archipelago was Frederik Beechey in 1826. As the
Gambier Islands are reported to have been colonized
only by the 11th–12th centuries AD (Kirch et al., 2010),
we assume that the ancient remains under study provide
a reliable focus on lineages established during initial settlement of the region.
For each grave excavated, two bones from the feet or
the hands were collected for DNA analysis (a right femur was collected for one neonate individual). Sampling
was conducted by European researchers with all precautions against contamination (including wearing of mask
and gloves). Samples were directly deposited in hermetic
sterile bags and conserved at 2208C as soon as possible.
Ancient DNA extraction, amplification, and
sequencing
Many studies have demonstrated the risks of contamination with external DNA when dealing with ancient
material, all the more likely with ancient human DNA
(Gilbert et al., 2005; Malmström et al., 2005). All analyses performed in our study followed the basic authenticity criteria proposed by paleogeneticists (Richards et al.,
1995; Gilbert et al., 2005) including i) the use of a dedicated laboratory, ii) ensuring the reproducibility of the
results, and iii) the cloning and sequencing of the amplification products to detect polymerase chain reaction
(PCR) artifacts associated with postmortem template
modification and/or contamination.
All analyses of human remains were performed at the
Laboratoire d’Anthropologie des Populations du Passé
(UMR 5199—PACEA, Université Bordeaux 1, Talence,
France) in a laboratory dedicated to analyses of ancient
DNA. The results obtained from two samples were also
independently reproduced in Lyon (PALGENE, Paleogenetics Platform, UMR 5242 - IGFL, ENS and Université
Lyon 1, Lyon) in a dedicated ancient DNA laboratory
using the strict precautions described in Hughes et al.
(2006) and Orlando et al. (2006). The samples selected
for replication were chosen to represent both the Hg Q1
and B4a1a1a haplotypes detected in our study (samples
Orutu 9a and Tutapu 68).
DNA was isolated from the bones of seven individuals
(Table 1), corresponding to four burial groups (motus).
The bone samples were not treated before DNA isolation
as they were excavated specifically for ancient DNA
MTDNA
MAKEUP OF A FRENCH POLYNESIAN POPULATION
251
research and subsequently handled with care to guard
against contamination. Each bone piece was first
reduced to powder and DNA was extracted using a phenol/chloroform protocol (Hughes et al., 2006). The DNA
was then concentrated in 100 lL of sterile distilled water
with a Centricon-30 column (Amicon1). PCR amplifications were performed on the HVR-I and HVR-II regions
of the mtDNA control region, and the 9-base pair deletion located in COII/tRNALys intergenic region (Cann
and Wilson, 1983). To determine the number of 9 bp repetitions, we amplified an 82 bp fragment including the
mitochondrial COII/tRNALys intergenic region, using primers L8215 and H8297 (Kolman and Tuross 2000). The
HVR-I region of the mtDNA control region (nps 1600916301) was obtained using a set of three overlapping primers pairs: Ms1 and Ms2 proposed by Jehaes et al.
(2001), and primers L16190 (nps 16190-16210) and
H16322 (nps 16302-16322). The partial HVR-II sequence
(nps 35-265) was amplified using the primer pairs
F00015/F00285 proposed by Anslinger et al. (2001). PCR
amplifications were performed in a 25 lL reaction volume containing 6.5 mM MgCl2, 0.4 mM dNTP, 0.66 mg/
mL BSA, 1 lM of each primer, 2.5 lL GeneAmp 10X
PCR Buffer (Perkin-Elmer), 0,25 lL DNA extract, and
1.25U AmpliTaq GoldTM. PCR was run for 55 cycles at
948C for 45 s, 568C for 45 s, and 728C for 45 s. At least
two independent DNA isolations were undertaken from
samples and at least two separate amplifications of each
mitochondrial fragment were performed on each DNA
extract. As the products of ancient DNA amplification
generally contain a large number of artifacts generated
by DNA degradation and Taq polymerase errors (Handt
et al., 1996), the PCR products were systematically
cloned using the Topo TA cloning kit (Invitrogen1).
Sequence ambiguities were resolved by analysis of multiple clones (at least 10 clones per fragment) and the most
probable sequences were always deduced from the consensus among several clones of several amplification
products. To detect possible contamination by external
DNA, extractions and amplification blanks were used as
negative controls. Moreover, all six European people
involved in sampling or genetic analyses of ancient samples were genotyped and their HVR-I/II sequences compared with those obtained from ancient Polynesians.
The analyses of the Orutu 9a and Tutapu 68 samples
were replicated in Lyon. DNA was extracted from 200 to
300 mg of bone powder using a standardized phenol/chloroform protocol (Hughes et al., 2006). The DNA was
finally concentrated on a Centricon-30 column, as previously described. Only the primer pairs L16190 and
H16322 were used. The PCR amplifications were performed in 25 lL (2.5 U AmpliTaq GoldTM 2 mM MgCl2, 1
mg/ml BSA, 250 lM of each dNTP, 0.5 lM of each
primer, 0.25 to 1.5 lL of DNA extract diluted to 1/4).
PCR conditions were 10 min at 948C, 35-40 cycles: 948C
for 30 min, 568C for 30 s, 728C for 45 s, and a final elongation at 728C for 10 min. Many independent positive
amplifications obtained were cloned with TOPO-TA Cloning for Sequencing kit (Invitrogen) leading to four and
six PCR products analyzed for each sample respectively
(at least seven clones per product).
viduals corresponding to recent arrivals, complete genealogical investigations of the Mangareva population (three
or more generations back, according to the available archives) allowed us to identify 17 unrelated lines of descent
(ULD) and to sample one living volunteer per ULD. Our
aim was to identify all the ULDs present in the population
three generations ago and to discard lineages corresponding to recent arrivals. This approach allowed the determination of all mitochondrial lineages characterizing the
Mangareva population, but did not provide lineage frequency estimation in the living population.
The molecular analyses were performed in the Département de Biologie Moléculaire of CHITS (La Seyne-sur-mer,
France). Buccal epithelial cell samples were collected and
DNA was extracted as described elsewhere (Dubut et al.,
2009a). Hypervariable regions I and II (HVR-I and HVR-II)
of the mtDNA control region were simultaneously amplified by PCR using primers L15832 (Dubut et al., 2004) and
HV2AS (Mogentale-Profizi et al., 2001) and using the Taq
PCR Core Kit (QIAGEN). PCR was run for 35 cycles at
958C for 30 s, 578C for 30 s, and 728C for 1 min 30 s. Before
sequencing, the PCR products were purified using the QIAquick PCR purification Kit (QIAGEN). The control region
was sequenced using primers L15832 and HV2AS, and primers L16200 and H16350 (described in Dubut et al.,
2009b). The sequencing reaction was performed using BigDye1 Terminator v1.0 Cycle Sequencing Ready Reaction
Kit (Applied Biosystems). The analyses of the sequencing
products were carried out on an ABI PRISM1 310 Genetic
Analyser (Applied Biosystems). Furthermore, the number
of repetitions of the 9 bp motif located in the COII/tRNALys
intergenic region was investigated. The COII/tRNALys
intergenic region was amplified using primers L8215 (Yao
et al., 2002) and H8297B (nps 8297-8310) following the
standard PCR conditions of the Taq PCR Core Kit
(QIAGEN). The number of repetitions of the 9 bp motif was
determined as described in Yao et al. (2002).
Modern population from Mangareva—DNA
isolation and genotyping
RESULTS
This study was approved by the Comité d’Ethique de la
Polynésie Française. After the exclusion of numerous indi-
Sequence analysis
Mitochondrial sequences obtained from ancient and
modern Polynesian specimens reported in this article
have been deposited in the GenBank database (accession
number FJ155566 to FJ155588). These sequences were
compared with mtDNA sequences from the GenBank
international nucleotide sequence database. All sequences were aligned using the MEGA3.1 program (Kumar
et al., 2004). Median-joining networks connecting the
modern Mangareva sequences, ancient Temoe sequences,
and complete mitochondrial genome previously described
(np 16009-16301 and np 35-221; Ingman et al., 2000;
Ingman and Gyllensten, 2003; Mishmar et al., 2003;
Friedlaender et al., 2005; Macaulay et al., 2005; Trejaut
et al., 2005; Pierson et al., 2006; Friedlaender et al.,
2007; Supporting Information Table S1) were constructed for Hg B4a1a and Q1 by using Network 4.201
(www.fluxus-engineering.com). We targeted these complete sequences to take into account the variability
detected in the HVR-II region (since earlier population
studies dealt only with the HVR-I region).
Throughout the following sections, we will use the
term ‘‘Melanesian’’ lineages to make reference to haplotypes frequently described in Melanesia. This improper
American Journal of Physical Anthropology
252
M.-F. DEGUILLOUX ET AL.
appellation is usually used in the literature and has the
advantage of simplifying the discussion.
The haplotype composition observed in the ancient
Temoe samples and the modern Mangareva individuals
is summarized in Table 2. We attempted to isolate DNA
from seven human remains from the Temoe Archipelago, dating from the 14th to the 17th century (Table 1).
Five separate mtDNA segments permitting the identification of partial HVR-I, HVR-II, and COII/tRNALys
intergenic region sequences were successfully amplified
and sequenced for five of the seven ancient samples
(Table 2). The analysis of ancient sequences separated
the Temoe ancient sample into two major lineages: the
PM and Hg Q1, both previously described in Oceanic
populations. Poorer conservation of the DNA for
remaining samples analyzed did not allow complete
determination of sequences for HVR-I (Tupa 18) or for
HVR-II (Orutu 11a). However, despite the partial
sequences, the observed polymorphisms (16217-1624716261; Table 2) permitted us to classify these samples
into the PM. Concerning extant population from
Mangareva, the genealogical analysis of up to three
generations permitted us to retain only 17 maternally
unrelated individuals (corresponding to the 17 ULD
characterized). As with the ancient samples, individuals
from Mangareva clustered into the two divergent
groups PM and Hg Q1.
Fifteen of the seventeen Mangareva ULDs and six
ancient samples (Table 2) showed the characteristic
transitions of the PM (16,217, 16,247, and 16,261) associated with the 9 bp deletion between the COII/tRNALys
(Table 2). One of Mangareva ULDs (Mangareva 2)
exhibited two additional transitions in the HVR-I
sequence at positions 16,126 and 16,278 defining a new
haplotype. Those polymorphisms have already been
described separately among Hg B4a1a1a individuals
from Tonga Island (Ohashi et al., 2006), but never associated. This result enhances the known diversity of PM
sequences. Mangareva 3 showed one additional mutation at position 16,271, which has been described only
once, in the Maori population (Whyte et al., 2005).
Finally, another polymorphism could also be detected in
the HVR-II region, associated with the PM, as five
Mangareva ULDs (Mangareva 1, 9, 15, 16, and 17) and
one ancient sample (Tupa 37) presented a transition at
position 151. This polymorphism is common on multiple
Hg backgrounds, but to our knowledge, this transition
has previously been characterized only in Polynesian
PM sequences originating from Samoa (Lum et al.,
1994; Redd et al., 1995) and the Cook Islands (Ingman
and Gyllensten, 2003). The remaining two ULDs from
the Mangareva sample (representing 12% of the ULDs)
and the ancient sample Tutapu 68 could be affiliated
with Hg Q1 (defined by a series of polymorphisms
in the control region: 89-92-146-16129-16144-1614816241-16265C-16311-16343; Friedlander et al., 2007).
Compared with Q1 sequences previously described, the
sequences characterized presented one additional mutation at position 16,293. The mutation 16,293 has
already been described in Q1 background (in Papua
New Guinea; Vilar et al., 2008), but the specific
haplotype found in Mangareva and the Temoe Atoll
has been previously encountered in only one Samoa
Islander (1/75 individuals; Lum and Cann, 2000), in
14% of Cook Islanders (11/79 individuals; Sykes et al.,
1995; Lum and Cann, 2000; Pierson et al., 2006), and
in 4% of Maori populations (1/27 individuals; Sykes
American Journal of Physical Anthropology
et al., 1995). This haplotype has also been described in
Tahiti and the Austral Archipelago (Sykes et al., 1995),
but the very limited samples concerned do not enable
us to consider its frequency.
All paleogenetic analyses performed in our study followed basic authenticity criteria for aDNA results
(Poinar, 2003). Several lines of evidence support the authenticity of the ancient sequences obtained in our
study: i) Strict precautions were followed during all processes and proved to be effective as all researchers who
directly participated in this study (from people working
in the field to those working in the laboratory) were of
European origin and their sequences were never
observed during analyses. However, typically European
sequences (but different from researchers’ sequences)
were found in 41% of the clones obtained in Bordeaux
lab. These contaminant sequences are regularly observed
in the lab and are not reproducible for a specific sample
(are consequently easily discarded). We consequently
suspect the contamination of PCR reagents (Leonard et
al., 2007). Their high frequency could be linked to the
high number of PCR cycles run in our analyses. ii) For
each human sample, we conducted two independent
DNA extracts, at least two independent PCR amplifications for each extract and mitochondrial fragment, systematically cloned the PCR products, and obtained the
same sequence (the number of clones analyzed for each
sample is indicated in Table 1); iii) The analyses of two
samples were replicated in two different laboratories; iv)
Genetic analysis of modern samples were conducted in a
completely independent manner (by other researchers
and in a lab localized in La Seyne-sur-Mer); v) The pattern of mutations among clones was found to be consistent with that previously described for ancient DNA
(Hofreiter et al., 2001); vi) Different mtDNA fragments
permitted the identification of the same lineage; and
finally, vii) Close correspondence in results between the
ancient and modern aspects of this article reinforces the
aDNA findings, supporting their reliability.
The overall high rate of amplification success indicates
good preservation of ancient DNA in the samples from
Temoe, which can be considered quite unexpected in
light of the conservation conditions. It appears that the
influence of O2, heat, and maybe spindrift have not completely degraded the DNA in the samples. We wonder if
deposits from coral desegregation found on the remains
may have protected the DNA.
All sequences in this study were compared with relevant sequences of the complete mitochondrial genome
previously published (Supporting Information Table S1).
Median Joining Networks for Hg B4a1a and Q1 are
shown in Figure 1. The majority of Mangareva and
Temoe individuals presented sequences belonging to the
central PM node (Fig. 1B). However, a total of seven
Mangareva sequences, and the ancient human remain
sample Tupa 37, showed additional polymorphisms. The
Median Joining Network of Hg Q1 (Fig. 1A) confirms
that the Mangareva and Temoe sequences derived from
other Q1 sequences previously characterized in Papua
New Guinea, Bougainville, Vanuatu, Samoa, and the
Cook Islands.
DISCUSSION
The genetic analysis of human remains from easternmost Polynesia (14th–17th centuries) enables us to demonstrate the ancient presence of the PM and Melanesian
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Sites are numbered (minus 16000) according to the revised Cambridge Reference sequence (rCRS) of Andrews et al. (1999).
nd, not determined; 9 bp, number of 9 bp repetition in the COII/tRNALys intergenic region; Hg, haplogroup.
Orutu 9a
Orutu 11a
Tupa 18
Tupa 19
Tupa 37
Tutapu 57
Tutapu 68
Mangareva 1
Mangareva 2
Mangareva 3
Mangareva 4
Mangareva 5
Mangareva 6
Mangareva 7
Mangareva 8
Mangareva 9
Mangareva 10
Mangareva 11
Mangareva 12
Mangareva 13
Mangareva 14
Mangareva 15
Mangareva 16
Mangareva 17
researcher 1
researcher 2
researcher 3
researcher 4
researcher 5
researcher 6
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9 bp
C – – – G nd
nd nd nd nd nd 1
C – – – G nd
C – – – G
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C – T – G
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C – – – G nd
C – – – G
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C – T nd nd 1
C – – nd nd 1
C – – nd nd 1
C – – nd nd 1
C – – nd nd 1
C – – nd nd 1
C – – nd nd 2
C – – nd nd 1
C – T nd nd 1
C – – nd nd 1
C – – nd nd 1
C – – nd nd 1
C – – nd nd 2
C – – nd nd 1
C – T nd nd 1
C – T nd nd 1
C – T nd nd 1
– – – – G nd
– – – – G nd
– – – – G nd
– – – G G nd
– – – – G nd
– T – – G nd
T
C T
rCRS
HVR-II
69 93 126 129 144 148 182 183 189 209 217 223 234 241 247 261 265 270 271 278 292 293 294 296 304 311 343 519 526 73 89 92 146 150 151 257 263
Variable site location
Sample
HVR-I
Hg
B4a1a1a
B4a1a1a
B4a1a1a
B4a1a1a
B4a1a1a
B4a1a1a
Q1
B4a1a1a
B4a1a1a
B4a1a1a
B4a1a1a
B4a1a1a
B4a1a1a
Q1
B4a1a1a
B4a1a1a
B4a1a1a
B4a1a1a
B4a1a1a
Q1
B4a1a1a
B4a1a1a
B4a1a1a
B4a1a1a
J
H
H
T2b
H
U5
TABLE 2. MtDNA sequence variation in archeological samples from Temoe, modern Mangareva samples, and potential contaminating persons (researchers)
FJ1555585
FJ1555586
FJ1555587
FJ1555588
FJ1555566
FJ1555567
FJ1555568
FJ1555569
FJ1555570
FJ1555571
FJ1555572
FJ1555573
FJ1555574
FJ1555575
FJ1555576
FJ1555577
FJ1555578
FJ1555579
FJ1555580
FJ1555581
FJ1555582
FJ1555583
FJ1555584
Accession nb
254
M.-F. DEGUILLOUX ET AL.
Fig. 1. Median-Joining networks of mitochondrial sequences belonging to Hg Q1 (A) and B4a1a (B). Data encompass mtDNA
HVR-I and HVR-II segments (np 16009-16301 and np 35-221) obtained in our study and sequences compiled from complete mitochondrial genomes listed in Table S1 (positions in parentheses are out of HVR-I region analyzed). The map (C) has been reproduced
from Kirch, (2000).
Hg Q1 in the Gambier region. The new paleogenetic
data we provide in this study prove that females with
Near Oceanic maternal ancestors became some of the
first Remote Oceanic colonists.
The PM (Hg B4a1a1a) is today very common in Polynesia, Micronesia, and many parts of Near Oceania. Its
frequency across Island Southeast Asia (ISEA) and the
Pacific varies from 2% in ISEA (Hill et al., 2007), 38% in
Near Oceania (Friedlaender et al., 2007) to 70% in
Remote Oceania (Kayser et al., 2006). It almost reaches
fixation in Eastern Polynesia (86% in the Cook Islands;
Kayser et al., 2006). The mitochondrial data we obtained
in the ancient Temoe sample, characterized by a predominance of the PM, is in total accordance with previous
surveys. Hg Q is the most common Near Oceanic subdivision of macro Hg M and belongs to those Oceanic
branches of M that developed around the time of initial
American Journal of Physical Anthropology
settlement of New Guinea, more than 30,000 years ago
(Friedlaender et al., 2005). The Q1 branch is today especially common in west New Guinea and has been found
as far east as the Austral Archipelago and Tahiti (Sykes
et al., 1995). To date, Q1 sequences have been revealed
to be present in Remote Oceania, with frequencies varying between 12% in Fiji (Friedlaender et al., 2007) and
4% in Samoa (Sykes et al., 1995; Lum and Cann, 2000;
Kayser et al., 2006). In the Cook Islands, the frequency
of Hg Q1 varied between studies (15% in Sykes et al.,
1995; 18% in Lum and Cann, 2000 and 4% for Kayser et
al., 2006) surely depending on the sampling concerned.
Although the low number of Polynesian people previously sampled in Tahiti and in the Australs (Sykes et
al., 1995) does not allow the determination of a clear profile of the mtDNA distribution in the region, the data
clearly indicated the presence of the Hg Q1 in these
MTDNA
MAKEUP OF A FRENCH POLYNESIAN POPULATION
islands. Overall, the paleogenetic data we provide for
easternmost Polynesia, combined with studies previously
published, demonstrate that the Melanesian Hg Q1
spread along with the PM motif at a much lower frequency throughout Polynesia and reached the easternmost Gambier region during initial settlement. Our
results allow us to rule out a potentially recent introduction (after the arrival of Europeans) of the Melanesian
mtDNA types into Polynesia and substantiate the Near
Oceanic contribution to the early population of the
region (although it cannot offer any definitive resolution
concerning exactly how large or small this minority percentage contribution may be).
Melanesian components were then represented among
the first populations inhabiting the extreme east of
French Polynesia. Genetic drift among small, founding
populations may have been sufficiently strong that Melanesian Hgs at low frequencies in ancestral populations
would have been lost over time (unless continual subsequent migration replenished those lineages). The modern
data obtained for Mangareva population suggest, alternatively, that low frequency Hgs such as Q1 can persist
if the populations expand rapidly after settlement, which
would have been the case for Polynesian populations (as
detected in star-like networks, Fig. 1; Kayser et al.,
2006). Moreover, it is interesting to note that the apparent genetic continuity characterized for the Gambier
Islands (since initial settlement) would support the hypothesis that more recent European colonization has not
profoundly changed the easternmost Polynesian gene
pool. Unfortunately, the methods used to build our modern dataset and the potential recruitment bias in our ancient dataset prevent the analyses from going further for
the time being, at least from a quantitative point of
view. However, Bayesian simulations could be envisaged
to test the continuity between both ancient and modern
populations if more information about haplotype frequencies or burial practices became available.
The modern data presented in this paper constitute the
first description of the extant mitochondrial gene pool of
the Gambier region (Mangareva), the easternmost part of
French Polynesia. Our genealogical approach allows us to
reliably asses the Melanesian component in Easternmost
Polynesia. To our knowledge, population samplings based
on exhaustive genealogical investigations that include
only maternally unrelated individuals are rare. Using this
approach, we were able to determine the presence of 17
unrelated or independent matrilineages in a group of people on Mangareva going back three generations. We suppose that even fewer lineages could be characterized if
genealogies covering more generations were obtained. It
is worth noting that with only 17 mitochondrial lineages
from the population of Mangareva, a relatively high variability in PM sequences was seen, including the detection
of one new haplotype. As a consequence, it would be interesting to test if the very high PM haplotype homogeneity
detected so far in Polynesia could be linked to an analysis
of related individuals (leading to lineage over-representation). This result would also indicate that previous studies
may have underestimated the contribution of non-PM lineages to the original founding populations of Polynesia.
We believe that our genealogical approach provides a demonstration of the value of collecting in-depth genealogical
information to ensure the reliability of the data when
addressing the issue of indigenous population origins.
The ancient and modern data presented in this article
are fully consistent with the hypothesis of a single major
255
settlement of East Polynesia, bringing dual Asian and
Melanesian genetic heritage. Dates of NRY and mtDNA
Hgs (Kayser et al., 2006) which are broadly consistent
with one other already suggested this single major
migration. Concerning the Melanesian component, the
Vanuatu and Polynesian Q1 sequences seem to have
diverged well before the settlement of Remote Oceania,
as they are not closely related to each other or to the
other Q1 sequences from Papua New Guinea and Bougainville (Fig. 1A; age estimate of the Q1 vertex is
22,862 6 4,464 years; Pierson et al., 2006). These observations are consistent with the hypothesis of a single
major settlement of Remote Oceania, bringing these divergent Q1 sequences.
In this study, genealogically controlled sampling, together with broader mitochondrial genome sequencing
(HVR-I plus HVR-II) and paleogenetic data, also provide
important suggestions about the internal peopling of Polynesia. Within the proposed general pattern of west to
east settlement of Polynesia (Kayser et al., 2006), the
detection of a new PM haplotype in Mangareva suggests
a maturation of Hg PM through the directional settlement of Polynesia. Specific haplotypes (in PM motif and
in Hg Q1) detected in ancient samples from the Temoe
Atoll and extant Mangareva population are shown to be
shared only with Samoa, the Cook Islands, and Eastern
Polynesia. The distribution of the Q1 haplotype observed
(characterized by a transition at np 16293) could specifically reinforce the idea that the central islands of Eastern Polynesia were the origin of the colonization of more
peripheral ones. This haplotype appears to be absent
west of Samoa; it has been identified in only one Samoan
(Lum and Cann, 2000) yet is quite common in the Cook
Islands and in easternmost regions of Polynesia (Sykes
et al., 1995; Lum and Cann, 2000; Pierson et al., 2006).
This peculiar distribution could highlight the Cook
Islands as the origin of eastern diffusion. It is worth noting that such a link between the Cook Islands and Mangareva can also be found in oral tradition describing a
Mangareva chief marrying a woman from Rarotonga
(the most populous island of the Cook Islands), along
with other links later on (Buck, 1938).
Finally, a specific substitution at position 16,271 is
shared between modern Mangareva and Maori populations in New Zealand (Whyte et al., 2005). If the time of
the peopling of New Zealand is relatively clear (less than
1,000 years ago; Kirch, 2000), the exact origin of protoMaori has remained until now unspecified. Whyte et al.
(2005) were unable to assign the immediate origins of
the Maori, because some haplotypes they described (such
as the AW7 haplotype presenting the 16,271 transition)
were not known elsewhere in Polynesia. The detection of
this rare mutation in the Gambier Archipelago can be
interpreted in one of the following two ways: it is either
representative of the lack of mitochondrial data in Polynesia (and may be in fact widely distributed in the
region) or it indicates a potential link between the
Gambier Islands and New Zealand.
CONCLUSION
We present the first fully authenticated ancient DNA
recovered from Polynesian specimens. The genetic analysis of ancient human remains (at least 400 years old)
from the Temoe Atoll (Gambier Islands) confirms a dual
genetic heritage (Taiwan/ISEA and Near Oceania) of Polynesians in this region, because the predominance of the
American Journal of Physical Anthropology
256
M.-F. DEGUILLOUX ET AL.
PM and the presence of Melanesian Hg Q1 could be
determined. The ancient data provide evidence for the
ancient arrival of a maternal Melanesian genetic component (Hg Q1) among Polynesian populations, indicating
that the original settlers of easternmost Polynesia were
already bearers of this Melanesian maternal lineage.
The genetic analysis of the modern population from the
neighboring Mangareva Island permits to point out
genetic continuity since initial settlement in Easternmost Polynesia, despite recent European colonization.
The detection of rare or new polymorphisms in ancient
and modern samples from Gambier Archipelago, both for
the PM and for the Hg Q1, supports a maturation of Hgs
through directional settlement of Polynesia. Our mitochondrial data would be in accordance with the hypothesis that the Cook Islands played a dispersal role in eastern migrations. However, apparent genetic links among
the Gambier Archipelago, the Cook Islands, and New
Zealand may be the result of the lack of genetic data for
the region and have to be considered in the light of more
representative mitochondrial data from Polynesia (and
especially French Polynesia).
Polynesia includes some of the last places on earth to have
been settled by humans. We believe that genealogically controlled sampling, together with sequencing the whole mitochondrial genome in representative archipelagos of Polynesia and the incorporation, when possible, of reliable paleogenetic data, are the key to understanding the precise internal
processes of human dispersion in Polynesia.
ACKNOWLEDGMENTS
We thank M. Labbeyie and E. Guifford for their help
in genealogical investigations; the volunteers from Mangareva for their contribution to the sampling and during
archeological field work; S. Vermillard, S. Menut, and M.
Bessou for technical assistance in genetic analysis of ancient remains. Field work and analyses were supported
by the Ministère de la Culture and the sous-direction de
l’Archéologie (France), the Ministère de la Culture de la
Polynésie Française, the Conseil Régional d’Aquitaine,
the Université Bordeaux 1, the ENS de Lyon, the Université Lyon 1 and the CNRS. We also thank A. Gunson
and R. Leahy for their help in the preparation of the
manuscript and for English editing.
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french, contributions, settlements, maternal, extant, human, melanesia, new, early, ancient, islands, gambier, mtdna, easternmost, evidence, polynesia, perspectives
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