The genetic origins of the Polynesians

The Polynesian voyagers were undoubtedly some of the greatest sailors and navigators the world has ever seen. Using star signs, trade winds, ocean currents and even signs of animals in order to detect land, they were able to traverse massive distances in a short amount of time. This article will go through the genetic profile of these ancient long-distance voyagers and their modern descendants.

Today, Polynesian languages are spoken by roughly 700 000 people. Most speakers belong to the indigenous peoples inhabiting the Polynesian islands. Polynesia was the last region on earth to be settled by humans. Polynesian languages belong to the large family of Austronesian languages. The Austronesian languages weren’t always spoken in the islands of Southeast Asia, but started spreading through the islands between 3000 BC and 1000 BC. They were spread by people from East Asia, likely from Taiwan and the northern Philipines, associated with the Lapita material culture. Before that, Papuan languages were likely spoken by the Paleolithic Melanesian tribes that had settled Near Oceania about 40,000 BC. In 3000 BC, the Austronesian speakers of the Lapita culture reached remote Oceania. It’s easy to distinguish the late-arriving Polynesian Lapita culture from the previous inhabitants in the archaeological record. This is due to the latter leaving behind a whole lot of impressive and distinct pottery as well as permanent village settlements in coastal areas.

Hawaiki: the sacred Polynesian homeland & the East Asian people of the Lapita culture

Present-day Polynesians derive most of their autosomal DNA from two ancestral populations. The first is an East Asian population that likely dispersed from what is now Taiwan. This ancestral component can be called the Austronesian component. This was a population that was adapted to farming, and had likely originated in a group from mainland China that settled Taiwan about 8000 years ago. According to Lipson et al. (2014) this ancient indigenous Taiwanese genetic component is unique to Austronesian speakers and accounts for at least a quarter of the total DNA in all Austronesian speaking populations. In Polynesians, it makes up 75% of their total DNA. In Polynesian mythology, the original homeland of the Polynesian people is known as Hawaiki. The concept of this ancient homeland exists in various forms in all Polynesian cultures. In Polynesian myth, it is often said that the spirits of Polynesian people return to this homeland after their death, and Hawaiki can be seen as a kind of underworld. One can’t help but wonder if Hawaiki may have something to do with Taiwan, the place where the ancestors of all Polynesians once set out from in order to brave the ocean and settle the islands of Southeast Asia.

DNA research has somewhat vindicated this concept of Hawaiki, the Polynesian urheimat. As mentioned earlier, it’s worth noting that all Austronesian-speakers have shared, deep autosomal ancestry from this ancient Taiwanese population. Unsurprisingly, according to Skoglund et al. (2016) this population no longer exists in an unmixed form. However, the modern populations that are genetically the most similar to this ancestral East Asian population are the indigenous Kankanaey people of the Philipines and the indigenous Atayal people of Taiwan. They can both be seen as a good proxy for what the East Asian population that contributed to Polynesian ethnogenesis was like in terms of DNA. The 2016 study by Skoglund and colleagues sequenced the DNA of 3 ancient individuals (all 3 were females) from the Lapita culture. The DNA samples were collected from skeletons found at Teouma and Talasiu. The Teouma Lapita site is located on the south coast of Efate Island, Vanuatu and the Talaisu Lapita site is located in the Fanga ‘Uta Lagoon which is roughly 10 kilometers north of Nuku’alofa, on a palaeoreef-limestone shoreline.

Unlike modern day Polynesians, these 3 Lapitan individuals did not have any Papuan DNA. Instead, they seem to represent an unmixed East Asian population, and were indeed similar to (but not exactly the same as) present-day Atayal people. They carried the typical Polynesian mtDNA haplogroup B4a1a1a. That’s helpful, because now we know where the Austronesian DNA component in Polynesians comes from. We also know that Austronesians managed to reach Oceania without mixing with the Papuan hunter-gatherers. This, of course, raises the question of where modern Polynesians get their Papuan DNA component from. Luckily, DNA research has an answer to that question as well.

Papuan hunter-gatherers: the Melanesian population ancestral to Polynesians

What the study mentioned above also found was that the Austronesian ancestry in Polynesians was somewhat female-mediated, evidenced by Polynesian mtDNA being mainly East Asian in origin. The Papuan DNA component however, shows an origin in a somewhat gender-biased admixture event. At some point, Papuan hunter-gatherer males mixed with the seafaring and farming Austronesian groups, and the result was the Polynesian genetic profile. The Papuan hunter-gatherers were genetically similar to (but not exactly the same as) modern day New Guinea Highlanders, and seem to be the source of Y-DNA haplogroups C1b2a1a (P33), K-P79, and M in Polynesian populations. It is unknown why these lineages underwent founder effects, but it’s possible that hunter-gatherer males with a lot of knowledge of local island flora and fauna had advantages over the Austronesian males and were more competitive for that reason. Another possibility is that the Austronesians simply had a shortage of males as a result of their often very dangerous journeys.

However, not all of the original Y-DNA haplogroups of the East Asian proto-Lapitans disappeared. Far from it, in fact. The frequency of Y-DNA haplogroups of Papuan origin among Polynesians varies a lot depending on what island population we look at. Tongans, for example, kept a high frequency of the original Austronesian male lines. Among Tongan males, O3a2c*(P164) reaches about 54%. This haplogroup has a high frequency among males of the indigenous Taiwanese Ami people as well, a further testament to the ancient connection between these groups. Not to mention, it’s present at relatively high frequencies in all Polynesian populations.Various other branches of haplogroup O are found in all Polynesians today, and these along with the previously mentioned O3a2c* are the lineages that would have been present among the earliest proto-Lapitans who initially set out to explore the islands of Southeast Asia, while the Melanesian Y-DNA lineages would have been assimilated later on before Polynesians went on to explore Remote Oceania.

Below is a map showing the various autosomal DNA components of Austronesian speakers in the islands of South East Asia. As you can see, the Austronesian component makes up the majority of the autosomal DNA of Polynesians, at about 75%. The remaining ~25% of Polynesian DNA consists of the Papuan/Melanesian component.

Ancestry component proportions among Austronesian speakers in ISEA, from Lipson et al. (2014)

Considering that Polynesian languages do have some distinct properties that aren’t found in other Austronesian languages, it’s quite possible that the Melanesian hunter-gatherers contributed to the Polynesian languages with some loanwords.

There are other interesting genetic variations in the region, such as Vanuatu where we can observe many indigenous Austronesian languages being spoken, despite the inhabitants remaining mainly of Papuan ancestry with a relatively small genetic input from Austronesian settlers.

While the geneflow between Papuans and Austronesians seems to have been sex-biased in the sense that Papuan male haplogroups found their way into the Austronesian genepool, this wasn’t always the case. Sometimes it was the other way around, too. For example, Kayser et al. (2002) detected a male-mediated contact between the lowland/coastal regions of New Guinea into the highlands, and the presence of Austronesian haplogroups O-M119 and O-M122 among New Guinea highlanders is evidence of this. The typical Austronesian mtDNA haplogroup B4a1a1a however, hasn’t been found among Papuan highlanders, suggesting that sometimes it was also Austronesian men that ventured further inland and mingled with Papuan populations.

Thor Heyerdahl’s hypothesis and Native American ancestry in Polynesians

The legendary Norwegian explorer Thor Heyerdahl had a theory about a South American population that settled eastern Polynesia. Heyerdahl had set out to prove that it was possible to use a primitive sea vessel to cross the Pacific, and he managed to do so by building a wooden raft and sailing it west from the South American coast. At the time, his ideas about these things were seen as very controversial and did not gain much traction. We now know that South Americans probably did not settle Polynesia. They did, however, have contacts with Polynesians.

“A sea so vast vast the human mind can scarcely grasp it”

– Chronicler of Ferdinand Magellan’s expedition, describing the Pacific Ocean

A 2014 study confirmed that people of Rapa Nui have, on average, about 8% Native American admixture from a population genetically similar to modern-day Wayuu people indigenous to Colombia and Venezuela. However, a study by Ioannidis et al. (2020) found that Native American DNA found itself into the Polynesian gene pool before Polynesians settled Easter Island. The estimated date for when this admixture event between Polynesians and South Americans took place is around 1150 AD. It is currently unknown how exactly the contacts leading to this admixture event were established, but what is likely is that it was the Polynesians that initiated the first contact. This is because the Polynesians had far more advanced maritime technology, and could have gotten to South America in order to conduct trade. Given that the Native American genetic input in Polynesians seem to be pretty much exclusively maternal, it was most likely Polynesian men taking some South American women home with them. The alternative is that South Americans ventured west and met and mixed with Polynesians somewhere on an island in Polynesia, but that is less likely. However, more ancient DNA samples are needed in order to reliably explain how Polynesians acquired Native American DNA and to really get to the bottom of this trans-Pacific geneflow.

Speaking of trans-Pacific travels. Starchy tubers native to South America such as the sweet potato and their long presence in Polynesia adds further strength to the theory that Polynesians visited South America and brought back some useful plants and possibly female companions, judging by the Native American maternal DNA input in Polynesians. The indigenous Quechua people of the Andean mountains call sweet potaotes “kumara”. That’s suspiciously close to the Polynesian word for the root vegetable, which is “kuumala”. Additionally, DNA analysis of sweet potatoes (plenty of such DNA sequencing has been carried out) has shown that the sweet potatoes found in Polynesia belong to a lineage that was introduced there from South America long before European settlers introduced younger lineages and types of sweet potatoes in the western Pacific. Captain James Cook collected a number of plants that were later kept in a herbarium during his travels. His collection included a number of sweet potatoes, and these are the historical specimens which were later used for DNA analysis and compared to modern sweet potatoes. The Polynesian sweet potatoes are distinct, and seem to be quite old. This solidifies the theory of significant contact between indigenous South Americans and Polynesians. It’s quite likely that the sweet potato was first introduced in the Pacific Islands between 1000-1100 AD, around the time of the first contact between Polynesians and South Americans.

A recent study published by Ioannidis et al., (2021) in September 2021 also suggested that the estimated date for the introduction of Native American DNA into Polynesian populations is around 1100 AD. Autosomal DNA indicates that the fascinating megalithic traditions associated with the island cultures of Raivavae, Rapa Nui and the Marquesas all sprung out of an initially small founder population that likely expanded from the Tuamotu Islands. Analysis of genetic patterns specific to this founder population found that it was probably among the Polynesian settlers of Rapa Nui, Raivavae and the Marquesas that an admixture event associated with the introduction of Native American ancestry occurred. What appears to have happened is that the founder population from Tuamotu encountered a Native American population and mingled with them just prior to founding the cultures of Raivavae, Rapa Nui and the Marquesas. This aligns well with Ioannidis‘ study from 2020 which estimated a similar date for the initial Polynesian and Native American admixture event.

Something interesting about the Native American admixture in Polynesians is that it means that Polynesians have Ancient North Eurasian (ANE) DNA. This very ancient DNA component was partly ancestral to both Europeans and Native Americans. Through the admixture of the latter with Polynesians, ANE ancestry had managed to reach even Oceania, therefore spanning the continents of Asia, Europe, the Americas and Oceania. That’s quite impressive, given that this type of ancestry was originally only present in a rather small hunter-gatherer population in Paleolithic Siberia!


So, what we see here is essentially two main populations gradually mixing. One mobile Neolithic East Asian population with advanced seafaring technology, and one Melanesian forager population. They came together and formed the population that became the Polynesians. This admixture event seems to have happened after the Lapita period, and the Melanesian genetic input seems to be mostly male-mediated. Polynesians do have a small amount of South American admixture, which is female-mediated and likely originates in trade with Native Americans somewhere along the western coastline of South America. The genetic profile of Polynesians can therefore best be described as consisting of 2 main components (Austronesian and Melanesian). In addition to that, as mentioned above, some Polynesians have DNA from a third, minor component (indigenous South American). This admixture dates back to roughly 900 years ago. However, the exact details surrounding early contact between Polynesians and South Americans are blurry, and more ancient DNA is required to get to the bottom of how and when they met and mingled.


Lipson et al (2014): Reconstructing Austronesian population history in Island Southeast Asia

Kayser, Manfred et al (2006): Melanesian and Asian Origins of Polynesians: mtDNA and Y Chromosome Gradients Across the Pacific

Hudjashov et al, (2018): Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles

Kayser, Manfred (2000): Melanesian origins of Polynesian Y chromosomes

Kayser, Manfred (2002): Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea

Roullier, Caroline (2013): Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination

Mirabal et al (2012): Increased Y-chromosome resolution of haplogroup O suggests genetic ties between the Ami aborigines of Taiwan and the Polynesian Islands of Samoa and Tonga

Ioannidis et al (2020): Native American gene flow into Polynesia predating Easter Island settlement

Skoglund, Pontus (2016): Genomic insights into the peopling of the Southwest Pacific

Ghiani et al (2006): Y-chromosome-Specific STR haplotype data on the Rapanui population (Easter Island)

Alexander G. Ioannidis et al. (2021): Paths and timings of the peopling of Polynesia inferred from genomic networks

© Genomic Atlas 2021

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5 Comments Add yours

  1. Loco says:

    Neat! Is the Papuan C haplogroup related to the C haplogroup in Mongolia??

    1. Absolutely, but only distantly so. C-M130 is a very old lineage. It’s present in populations that are very divergent from one another, such as indigenous Australians and Na-Dene speaking Native Americans. At one point however, these populations share a common paternal ancestor. Some clades of C even had a presence in Upper Paleolithic Europe.

  2. Alex-RE says:

    I found this article through Reddit. As a half Tongan, half Filipino guy living in the US I find it really interesting. Cheers.

    1. That’s great to hear!

  3. Steve Tomasi says:

    This is so helpful to my research.

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