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The Indonesian archipelago stretches nearly 5,000 km from the west to the east and one
estimate suggests there may be as many as 700 languages. The majority of the languages
belong to the Austronesian language family which occupies an area from Madagascar in the
west to Easter Island (Rapa Nui) in the east of the Pacific Ocean. Within the Austronesian
language family, there are branches. The Western-Malayo-Polynesian (WMP) branch is
found in the west of Indonesia and the Philippines. the Central-Malayo-Polynesian (CMP)
branch is found in the southern part of the Moluccas and Nusa Tenggara (Bellwood, 1997,
Cribb, 2000). The South Halmahera West Papua New Guinea (WHWPNG) branch languages
are spoken in the northern part of Maluku. Papuan languages are found in parts of the east
of East Nusa Tenggara and North Maluku.
West Papua alone has a remarkable diversity of languages, with around 250 languages
most of them spoken by only a few thousand or less. The languages can be divided into
four language sub-groups, West Papuan, East Bird’s Head, Geelvink Bay, and Trans-New
Guinea. Several populations speaking Austronesian languages are also found in the Papuan
coastal areas, notably in the northwest (Bellwood, 1997, Cribb, 2000). Language diversity
contributes to variations in cultural characteristics, and may also reflect genomic diversity.
Attention to detail with all aspects of the research methodology started with
consideration of how to ensure a high-quality sample collection that would accurately
represent the dimensions of diversity among the Indonesian population.
Firstly, the possibility of bias because of sample collection from same location was
avoided. Secondly, on all fieldwork visits the expedition team always included researchers
with medical training or local medical officers who spoke the local languages in order to
reduce misunderstandings and to help obtain informed consent. Detailed questionnaires
were also used to identify cases of marriage with different ethnic groups over three
generations, both from maternal and paternal sides. Third, the sampling strategy
also included historical notes about events that would have had the potential to alter
the original population structure such as war or government transmigration programs
(Marzuki et al., 2003).
At the present time, DNA samples have been collected from approximately 6,000
individuals from more than 80 populations across the Indonesian archipelago. Sequences
of mtDNA HVR1 have been obtained from more than 3,500 individuals. In the initial phase
of the study, we found 474 haplotypes from the D-loop area from a total of 780 samples
and they showed a certain level of difference between individuals. This demonstrates
that Indonesia has haplotype diversity since almost half of the populations analyzed

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