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Vanuatu Population Structure, History Drawn From Contemporary Genetic Data

NEW YORK – Using a combination of SNP genotyping and genome sequencing data, a team from France, Sweden, Peru, the UK, and Germany has characterized genetic patterns and ancestral histories for ni-Vanuatu Indigenous populations found on more than two dozen western Remote Oceanic islands.

"[O]ur study emphasizes the need to include diverse populations in genetic studies, not only to address key anthropological and evolutionary questions that are important for specific geographic regions, but also to identify factors shaping the genetic diversity of human populations as a whole," first and co-corresponding author Lara Arauna, a human evolutionary genetics researcher at the Pasteur Institute, and her colleagues wrote in Current Biology on Wednesday.

The researchers brought together thousands of blood samples collected from ni-Vanuatu individuals from 2003 to 2005, ultimately performing array-based profiling across nearly 2.4 million SNPs in 1,433 participants, including almost 300 couples. They noted that 173 samples were removed during a quality control step, while another 179 whole-genome sequences were added in subsequent analyses.

Together with published sequence and SNP data for contemporary and ancient individuals in Oceania, Eurasia, and beyond, the team's new data offered a look at ancestry patterns and population dynamics in the Vanuatu archipelago in the past 3,000 or so years.

"Ancient DNA studies suggest an initial settlement by East Asian-related peoples that was quickly followed by the arrival of Papuan-related populations, leading to a major population turnover," the authors explained. "Yet there is uncertainty over the population processes and the sociocultural factors that have shaped the genomic diversity of ni-Vanuatu, who present nowadays among the world's highest linguistic and cultural diversity."

In each of the island populations considered, the team traced East Asian ancestry and Papuan ancestry back to similar source populations: a group with ties to East Asia that was genetically similar to present-day populations in Taiwan and the Philippines, and a Papuan population-related group resembling contemporary groups on the Bismarck Archipelago islands.

Admixture between the populations occurred some 1,700 to 2,300 years ago and appeared to be "relatively synchronous across islands, in agreement with a peopling history common to all the archipelagoes," the authors explained, noting that "the high cultural diversity of ni-Vanuatu results from a rapid cultural diversification that developed in situ, as suggested by linguistic, archaeological, and archaeogenetic studies."

Similarly, the researchers noted that an influx of Polynesian ancestry — going back around 600 to 1,000 years ago — has left its mark on the genomes of both Polynesian-speaking and non-Polynesian-speaking populations in central and southern regions of Vanuatu.

Even so, they found that proportional contributions of different ancestry groups varied from one population and place to the next, particularly when it came to East Asian ancestry. That ancestry was pronounced on an island called Ambae, where levels of Polynesian ancestry were relatively low, but showed more modest contributions to populations on northern Vanuatu islands such as Malekula, Ambrym, and Epi.

Together, the authors suggested, the results "indicate that ni-Vanuatu are descended from relatively synchronous admixture events between the same sources of Papuan- and East Asian-related ancestry, yet their proportions differ markedly across islands, suggesting that the Papuan-related ancestry shift that started [approximately 2,500 years ago] was geographically uneven."

The team also started to tease apart still other contributions to present-day population genetics, including patterns of assortative mating — mating between individuals with similar genotypes — in the couples profiled. Because the authors did not see between-couple overlap at specific genomic loci or polygenic trait contributors, they suggested that assortative mating in the region stemmed from social factors rather than physical similarities between spouses.

"[W]e found no statistical evidence that genotypes at trait-associated variants are more similar or dissimilar between spouses than expected," they wrote, adding that the results point to "assortative mating driven by social structure as the cause of ancestry-based assortments among ni-Vanuatu."