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Papua (also known as Irian Jaya, West Irian/Irian Barat, West Papua/Papua Barat and Indonesian New Guinea) is the Indonesian half of the Island of New Guinea. Roughly located between 0 and 9 degrees S latitude and 130 E and 141 E degrees longitude and encompassing some 421,981 square kilometers with high mountains, swamps and both high and lowland jungles it is a treasure of the world.
There are two native people groups to be found in Papua. Melanesians (generally your islanders such as Biak and Sorong) and Papuans (formerly known as Negritos) with two distinct Papuan and Austronesian language groups. While estimates vary (depending on how one defines language and dialect) on how many languages can be found in Papua most suggest around 250 distinct languages. Some place the number as high as 600. Some of these languages consist of only a handful of speakers
Between 60,000 and 40,000 years ago the first Papuans arrived by boat/raft in West New Guinea. The later arrival of the Austronesians pushed the Papuans eastward resulting in the occupation of the highlands about 30,000 years ago. In some cases, such as the islands areas (Biak etc) it resulted in intermingling leading to the development of the Melanesian populations.
Successive migrations from China and mainland Asia gradually pushed the Papuan ancestors eastwards till they hit New Guinea, Australia and the Pacific islands beyond. Small-related populations used to be found and in some cases still remain in other parts of Asia. Indeed, in Biak one used to be able to find a distinct people group who dominated the interior of the island and whose genetics and appearance suggest a "pure" Papuan ancestry. They were known as Arfak or Faksi but any linguistic proof of their Papuan ancestry has been lost as a result of the domination of the Biak language.
Archeology and linguistics indicate an essentially eastward migration throughout Papua with the Melanesians dominating the islands and a few coastal areas. In some places, such as Sentani, there is evidence of intermingling. Given the Biak peoples love of slave trading one can also find evidence of long term intermingling within the Melanesian populations. The Papuans went on to populate the mountain areas and most of the lowland areas.
The ending of the major migrations into the New Guinea area did not of course mean an end to cultural, racial and linguistic interactions with the neighbors. Eastern New Guineans (PNG) in particular maintained trade throughout the local islands there though that is not relevant to our discussion here. Of course most of that interaction involved the island peoples and only rarely other people groups.
Blood (genetic) research confirms the above. An H. C. Bos found genetic conformity between Biak, Halmahera, Seram, Kai islands and Alor. Migrations, war, slave trading and rescued castaways all contributed to this conformity. Certainly the Biak people and their related neighbors were not quietly sitting at home! Records indicate slave raids to the Moluccas, Timor and to East Java. They also engaged in regular trading but for the most part it seems their visits to parts foreign were hostile. Indeed, for the Kisar Timorese the word Papuan mean pirate! They also were often in Makassar for trade and in particular for trees for the Biak long distance outrigger prahus.
Not all these visits were made on their own. The evidence suggests that sometime in the 15th century the Biak area fell under the control of the Tidore Empire. They paid tribute to Tidore which was handled through mediators from Halmahere. Whether as part of their tribute obligations or whether they participated for their own profit (alliance) Biak people often took part in Tidore raids westwards (Java, Timor etc) as well.
Other evidence of East-West contact dates even further back. In Borobudur, which dates from the 8th century, can be found friezes depicting frizzy/curly hair peoples. The Negarakertagama, a poem from the 14th century dedicated to the east Javanese king of Majapahit, refers to Papua as well. Specifically, it names two areas called Onin and Seran on the southwestern side of the Bird's Head Peninsula. Of course for many centuries there has also been trade items such as Birds of Paradise feathers and massoi bark found throughout Indonesia. Clearly contact was ongoing between Papua and the rest of Indonesia.
Not until 1511 did Papua meet the Western world when Spanish sailors sighted New Guinea but did not come ashore. In 1527 the Spanish visited and landed in Papua. However, not until the late 1600's does Papua come under Dutch control. In 1855 missionaries began their work in Papua but it was not until 1908 that a permanent presence was established. Dutch control was briefly upset during World War Two but was reestablished thereafter. However, on May 1st 1963 Indonesia assumed full administrative control of West Papua and in 1969 Papua became a full member province of Republik Indonesia.