November 8, 2012

Hawaiian genetic study shows 2-1 Asian-Melanesian admixture in Polynesians

Queen Liliuokalani of Hawaii in her youth
Native Hawaiians still make up some 38% of the population of Hawaii but most of them have mixed ancestry nowadays. This new study may help to understand them better and also includes some interesting findings about the overall origins of Polynesians, whose Melanesian ancestry is revealed as very significant.

Sung K. Kim et al., Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0047881]


The population genetic structure of Native Hawaiians has yet to be comprehensively studied, and the ancestral origins of Polynesians remain in question. In this study, we utilized high-resolution genome-wide SNP data and mitochondrial genomes of 148 and 160 Native Hawaiians, respectively, to characterize their population structure of the nuclear and mitochondrial genomes, ancestral origins, and population expansion. Native Hawaiians, who self-reported full Native Hawaiian heritage, demonstrated 78% Native Hawaiian, 11.5% European, and 7.8% Asian ancestry with 99% belonging to the B4 mitochondrial haplogroup. The estimated proportions of Native Hawaiian ancestry for those who reported mixed ancestry (i.e. 75% and 50% Native Hawaiian heritage) were found to be consistent with their self-reported heritage. A significant proportion of Melanesian ancestry (mean = 32%) was estimated in 100% self-reported Native Hawaiians in an ADMIXTURE analysis of Asian, Melanesian, and Native Hawaiian populations of K = 2, where K denotes the number of ancestral populations. This notable proportion of Melanesian admixture supports the “Slow-Boat” model of migration of ancestral Polynesian populations from East Asia to the Pacific Islands. In addition, approximately 1,300 years ago a single, strong expansion of the Native Hawaiian population was estimated. By providing important insight into the underlying population structure of Native Hawaiians, this study lays the foundation for future genetic association studies of this U.S. minority population.

In my understanding, the most interesting elements from this study are the ADMIXTURE analyses:

Figure 1. ADMIXTURE clustering of Native Hawaiians for K = 5 (A) and K = 6 (B). Figures 1A and 1B illustrate the clustering of Native Hawaiians and HGDP samples based on GWAS data.

As the general Admixture analysis was not really conclusive about the Melanesian and Asian affinities of Native Hawaiians, the authors also performed a supervised K=2 analysis:

Figure 4. Supervised ADMIXTURE results for K = 2...

This appears to show rather unmistakably that Hawaiians (and by extension surely also other Polynesians, very close in genetics and history across the Pacific Ocean) have an important amount of Melanesian genetics, consistent with the "Slow Boat" model and the relevance of Melanesian Y-DNA haplogroup C2a among all Polynesian populations.


  1. IIRC, 20-25% Melanesian ancestry in Eastern Polynesians has been the conventional assumption. But 32% is certainly within the error bars. Hawai'i might be shifted a bit due to founder effect. I am thinking that this was a US funded researcher limited by geography and funding, as Hawai'i is not the best site to sample. In particular, the current gene pool is mixed with massive post WWII admixture with Samoans, who are regarded as "locals" by native Hawaiians.

    A better population study of Eastern Polynesians would use people from less cosmopolitan places, the Tuamotus, the Marquesas, and the outer Cook Islands. But these are all hard places to reach, you pretty much would have to use a research vessel, or be very adventurous with local transportation options.

    1. In truth I would rather lower the figure a bit but did not want to make things too complicated in the main entry, so I chose to shut up.

      The reason I say this is because the main East Asian references are not from SE Asia but "middle" East Asia, which is clearly not the origin of Austronesians. And Cambodians, the only SE Asian, reference appear as slightly mixed with Melanesians in the K=2 supervised analysis but this component appears (roughly) as "Polynesian" in the K=6 unsupervised run. It's likely that the fractions mask a cline or even the lack of identification of the true SE Asian component.

      It's plausible that taking Papuans, Han and Japanese out of the equation (keeping only SE Asians and Island Melanesians, as well as Hawaiians themselves) would produce a more accurate picture.

      Another element of confusion may be the European admixture that even some of the 100% Hawaiian Natives do sport, which may show as "non-Han/non-Japanese" for many SNPs, aggrandizing incorrectly the Melanesian component.

      So 20-25%, rather the latter, can still be a correct estimate because neither Han nor Japanese represent properly the genetic pool of SE Asia.

  2. "In addition, approximately 1,300 years ago a single, strong expansion of the Native Hawaiian population was estimated".

    Makes complete sense. That's almost certainly the period when they first arrived.

  3. So I'll post information on the deeper origin of the Hawaiians here:

    "500-600 years. The difference between the beginning and the end".

    Yes. And that is a rapid expansion. Unless you're suffering from some 'Exodus syndrome' where every migration consists of thousands of people crossing some imaginary 'Red Sea'. The population had to grow on each unoccupied island it reached until enough people had been born to make it necessary to find a new unoccupied island. It is extremely doubtful that anyone born in the Admiralty Islands made it all the way to Samoa. Especially as the dates given in the Ricaut paper you referenced give the following dates:

    Bismark Archipelago: 3450-3350.
    Reefs - Santa Cruz: 3200.
    Vanuatu, New Caledonia, Fiji, Tonga and Samoa: 3200-2800.

    The back movement to the Solomons is given as 2800-2600, so there is no overlap between the back movement to the Solomons and the arrival in Samoa. And a few Wiki links:

    "Seafarers associated with the Lapita diaspora first settled the islands making up the Kingdom of Tonga about 1500 BC.[1] The area served (along with Fiji and Samoa) as a gateway into the rest of the Pacific region known as Polynesia".

    "The oldest date so far from pre-historic remains in Samoa has been calculated by New Zealand scientists to a likely true age of circa 3,000 BP (Before Present) from a Lapita site at Mulifanua during the 1970s".

    So the time taken to bridge the gap between the Admiralty Islands and Fiji/Tonga/Samoa could be as little as 350 years. And the evidence is universally accepted (except by you) that no major population movement from further west was involved in the expansion from Samoa into Polynesia proper.

  4. another short comment. The continued reference in the links both you and I provided at the 'Oceania' post consistently maintained that the Lapita expansion had leapfrogged the Solomon Islands. So the fact that Solomon Island haplotypes now form the majority through Remote Oceania except for Polynesia itself surely should have alerted you to the fact that the Lapita/Austronesian migration into Remote Oceania must have been more complicated than you envisaged.


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