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Polynesian Island Population History Revealed From Present-Day Human Genomes

NEW YORK – An international team led by investigators at Stanford University has teased out historical settlement patterns in Polynesia based on genome sequence data in present-day humans.

"[I]nstead of ancient genomes, which are rare and often have missing pieces of DNA, we can use modern genomes, for which we have much more data, permitting finer-scale analyses and employing modern big data techniques," co-first author Alexander Ioannidis, a researcher affiliated with Stanford University and Mexico's Center for Research and Advanced Studies of the National Polytechnic Institute, noted in an email.

As they reported in Nature on Wednesday, he and his colleagues relied on ancestry-specific computational strategies to analyze historical population patterns based on array-based SNP data for 430 individuals from 21 present-day Pacific Island populations. By computationally teasing apart Polynesian ancestry tracts and stretches of DNA that was identical-by-descent in the modern genomes, they were able to retrace early movement between islands in the region based on rare variants that were lost along the way.

"We perform the reconstruction in part by analyzing the bottlenecking (founder effects) that dominate the genetics of each island, settled by a small number of individuals who voyaged from a previous island across thousands of kilometers of open ocean," Ioannidis explained. "We show that each island is a founder population with its own unique genetics."

The analyses traced Polynesian island settlement to around the Middle Ages, while uncovering genetic connections between distant islands where populations became known for their megalithic statue building, including Easter Island, Raivavae, and North and South Marquesas.

Using clues from the rare variants lost en route as people moved from one island to the next and experienced genetic bottlenecks, for example, the team saw signs that settlers first migrated from Samoa to the Rarotonga in the Cook Islands in the year 830 or so, along a path shared with populations that ultimately landed in Fiji and Tonga.

From Rarotonga, meanwhile, settlers subsequently moved on to the Society Islands to the northeast in roughly 1050. Not long after, in 1109, migrants from Rarotonga moved on to Rapa Iti in the south and small Cook Islands such as Mauke and Atiu to the northeast. Still other Rarotonga settlers spread into the Austral Islands and the Tuamotu Archipelago in the west, and, as recently as the 1300s, to the islands that are marked by megalithic statues, such as North Marquesas.

"The modern peoples of Polynesia harbor strong genetic evidence for a range expansion beginning in Samoa and propagating across eastern Polynesia through a series of telescoping founder events from the 11th and 12th centuries," the authors reported.

The investigators noted that rare variants that made it through genetic bottlenecks along the way were more apt to became enriched in founder populations on each island, including variants with potential ties to human health or disease susceptibility.

"[I]slands, particularly those near the end of the settlement sequences, will have some variants at high frequency that are very rare in everyone else in the world," Ioannidis noted. "Some of these will have important implications for health, and we map which populations these are that should be the focus of future studies."

Moreover, he noted that the methods used to assess Polynesian settlement patterns for the study resembled those used to come up with genetic risk prediction across populations and to find parts of the human genome with potential ties to COVID-19 severity in Pacific Islanders or individuals from other global populations.

"We have introduced ancestry-specific computational methods for detailed characterization of Polynesian variant frequencies within admixed, modern samples, so potential admixture within future cohorts from such diverse populations should not be considered a barrier to designing these studies," the authors concluded. "Continued partnerships with these communities will be crucial, since such studies will benefit both the personalized health understandings of these populations, as well as the global genetic understandings of all of us."