The origin of Papuans is generally associated with the first settlement of
Australasia by a lineage dubbed 'Australasians' or 'Australo-Papuans' during the
Initial Upper Paleolithic, which is "ascribed to a population movement with uniform genetic features and material culture" (
Ancient East Eurasians), and sharing deep ancestry with modern
East Asian peoples and other Asia-Pacific groups. It is estimated that people reached
Sahul (the geological continent consisting of Australia and New Guinea) between 50,000 and 37,000 years ago. Rising sea levels separated New Guinea from Australia about 10,000 years ago. However, Aboriginal Australians and Papuans had diverged genetically much earlier, around 40,000 years BP. Papuans are more closely related to
Melanesians than to Aboriginal Australians.
Autosomal DNA The genetic makeup of Papuans is primarily derived from
Ancient East Eurasians, which relates them to other mainland Asian groups such as the "
AASI", Andamanese, as well as East/Southeast Asians, although although there is possible gene flow from an earlier Out-of-Africa group (xOoA), around 2%, next to additional archaic
Denisovan admixture in the
Sahul region. Papuans may harbor varying degrees of deep admixture from "a lineage
basal to West and East-Eurasians which occurred sometimes between 45 and 38kya", although they are generally regarded "as a simple sister group of
Tianyuan" ("Basal East Asians"). They are also closely related to
Andamanese Onge and East Asians and mainly differ due to their Denisovan admixture. It's believed that Papuans underwent a secondary admixture event with Altai-related Denisovan populations after they diverged from the ancestors of East Asians, who already mixed with Denisovans. This event was separate from the admixture event experienced by Filipino
Negritos, explaining why Papuans have relatively lower Denisovan ancestry.According to a 2025 study, Papuans are a sister group to East Asians with no genetic input from earlier Out-of-African populations. They diverged from Europeans and East Asians about 51.2 and 46.2 thousand years ago respectively and mixed with Denisovans about 31.2 thousand years ago, contributing to about 3.23% of their genetic makeup. Compared to Europeans and East Asians, Papuans also experienced severe bottlenecking.Papuans display pronounced genetic diversity, explained through isolation and drift between different subgroups after the settlement of
New Guinea. The most notable differentiation was found to be between Highlanders and Lowlanders. Papuan Highlanders fall into three clusters, but form a single clade compared against Lowlanders. The Highlanders underwent a population bottleneck around 10,000 years ago, associated with the adoption of Neolithic lifestyles. Papuan Lowlanders display increased diversity and can be broadly differentiated into a Southern Lowlander cluster and a Northern Lowlander cluster. The genetic differentiation among Papuans is suggested to date back at least 20kya, while the sub-structure among Highlanders dates back around 10kya, with higher diversity among western Highlanders than Eastern ones. The genetic diversity is paralleled by linguistic and cultural diversity. East Asian-related admixture is also observed in modern Papuans, especially coastal Papuan groups. Based on a reevaluation of mitogenomes, Gandini et al. 2025 proposed a "long chronology", which suggested an earlier settlement of Sahul by two migration routes about ~60 ka. One route came from northern Sunda via the
Philippine archipelago whilst the other came from southern Sunda via
Mainland Southeast Asia, with both routes ultimately tracing back to South Asia. The settlers that undertook these routes were ancestral to populations indigenous to Australia, New Guinea and Oceania, and related to other East Eurasians instead of belonging to a separate wave. The genetic divergence between the indigenous inhabitants of Sahul and Sunda was also believed to be ancient and rapid.
Archaic introgression Based on his genetic studies of the
Denisova hominin, an ancient human species discovered in 2010,
Svante Pääbo claims that
ancient human ancestors of the Papuans interbred in Asia with these humans. He has found that people of New Guinea share 4%–7% of their genome with the Denisovans, indicating this exchange. Denisovan introgressions may have influenced the immune system of present-day Papuans and potentially favoured "variants to immune-related phenotypes" and "adaptation to the local environment".
ASPM gene In a 2005 study of
ASPM gene variants, Mekel-Bobrov et al. found that the Papuan people have among the highest rate of the newly evolved ASPM HaplogroupD, at 59.4% occurrence of the approximately 6,000-year-old
allele. While it is not yet known exactly what selective advantage is provided by this gene variant, the haplogroupD allele is thought to be positively selected in populations and to confer some substantial advantage that has caused its frequency to rapidly increase. ==Papuan ethnic groups==