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mitochondrial DNA sequences from all subjects showed very high diversity and pointed
to the presence of intensive admixture between Austronesian-speaking and Papuan-
speaking populations. The conclusions were reached by looking at the total number
of polymorphic sites where site refers to bases position on DNA which has different
nucleotides and occurs in several locations. In addition, this diversity was also illustrated by
the number of haplotypes. A haplotype is analogous to a certain motif which is a collection
of several unique bases obtained from the DNA sequencing. Haplotype determination
is not conducted randomly but follows a well- established consensus in naming. The
communities with highest variations were found in the eastern part of Indonesia (Sumba,
Flores, Pantar, and Alor) where both Asian and Papuan genetic derivatives were observed.
To be able to reconstruct Indonesian human migration pattern, the huge environmental
and geological changes’ impact on the archipelago’s inhabitants cannot be ignored. The
archipelago’s geographical identity as a cross roads for human migration is an important
part of why Indonesia became a settlement location with highly diverse ethnicities,
languages, and genetics. The history of Melanesia cannot be separate from Indonesia as
its people’s genetic makeup shows the same ancestral traces. Melanesia, as elsewhere in
Indonesia, is inhabited by Austronesian-speaking and non-Austronesian-speaking people
and this is reflected in the genetic background of its populations. Explaining this is a
multi-disciplinary task. Anthropologists support numerous new algorithms in population
genetics that illustrate unimpeded human society. Modern science has rejected studies
based on the concept of ‘race’. It looks at processes such as cultural change over time and
emphasizes interregional contacts and interactions. By using population genetics, the
natural borders in the Indo Pacific area, the Wallace bio-geographical line, and the line
separating Near and Remote Oceania can finally be illuminated reliably.
Analysis using mtDNA and Y-chromosome genetic markers exhibits that genetic
variation in Indonesia was shaped primarily by two migration processes, the movements
of early humans due to the sea level change and the migration of populations with
agricultural technology from mainland Asia to the Southeast Asian archipelago. The
initial settlers of Indo Pacific were known to possess a particular mitochondrial genetic
background (P and Q) which is owned to some extent as a Papuan genetic feature. These
haplogroups are not found in the western part of the Southeast Asia archipelago. The
analysis by Y-chromosome markers showed similar results.
Several human movements from mainland China are thought to have changed the
dynamics of most of the Pacific, especially with the presence of Polynesian motifs which

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