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Genomic Analysis of Present-Day Sardinians Shows Significant Influence From Neolithic Sources

This article has been updated to reflect how long ago Sardinians split from other European groups.

NEW YORK (GenomeWeb) – A genomic analysis of present-day Sardinians reflected the island's isolation from Europe and showed that the population's Neolithic ancestry had a significant influence on its modern structure.

Three populations are currently thought to have contributed ancestry to modern Europeans: pre-Neolithic hunter-gatherers, Neolithic farmers from the Near East and Anatolia, and Bronze Age steppe pastoralists. Some previous studies have suggested that the people of Sardinia — who have an archaeological, cultural, and linguistic history distinct from that of mainland Europe — may have higher levels of ancestry that can be traced to Neolithic farmers.

Researchers led by the University of Chicago's John Novembre analyzed whole-genome sequencing data from more than 3,500 Sardinians. As they reported yesterday in Nature Genetics, the researchers found that Sardinians became isolated from mainland Europeans about 4,300 years to 7,000 years ago, and uncovered population structure among Sardinians that seems to reflect differing levels of ancestral contributions from pre-Neolithic hunter-gatherers and Neolithic farmers.

"[T]he results suggest that while Sardinia has clearly had influence from pre-Neolithic sources and contact with steppe ancestry populations, the demographic history is one of substantial isolation and abundant Neolithic ancestry relative to the mainland," Novembre and his colleagues wrote in their paper.

They analyzed the whole-genome sequences of 3,514 individuals that were generated as part of the SardiNIA project, but particularly focused on a set of unrelated 1,577 individuals who had at least three grandparents from the same region.

By comparing these individuals' genomes with respect to their geographic origins, the researchers found the greatest axis of variation between people from Ogliastra in eastern Sardinia and those outside Ogliastra, with the exception of the new port town of Tortolì. They further noted low migration rates between eastern and western Sardinia, separated by the mountainous Gennargentu region.

The researchers also examined their Sardinian samples in light of other Mediterranean population samples to find that the Mediterranean Sea appeared to isolate Sardinia from both mainland Europe and North African populations. They estimated that Sardinians and northern European diverged about 232 generations, or about 7,000 years, ago, while Sardinians and Tuscans diverged about 143 generations, or about 4,300 years, ago.

The researchers found the Basques to be the most similar to the Sardinians, even more similar than the mainland Tuscan and Bergamasque populations. The Basque populations of Spain and France are also thought to harbor higher levels of early Neolithic farmer ancestry, and the researchers noted that the similarity between the two populations did not appear to be mediated by the influence of modern Spanish ancestry.

The investigators also confirmed that Sardinian individuals share higher levels of drift with early Neolithic farmer cultures and lower levels of shared drift with hunter-gatherer cultures, as compared to the mainland. In particular, they reported that Sardinians from the isolated, interior Gennargentu region have a higher pre-Neolithic and Neolithic ancestry than Sardinians from outside that region.

At the same time, the researchers examined whether there was gene flow from North Africa to Sardinia and found evidence of admixture that dates back between 1,800 years to 3,000 years ago. The best proxy for this gene flow was sub-Saharan African populations rather than North African populations, the researchers found. They suggested that this could be due to the ancestry of modern North Africans reflecting gene flow from the Arab expansion that occurred about 1,400 years ago, after this Sardinia admixture event.

While Sardinians have greater Neolithic ancestry on their autosomes, the common Y-chromosome haplotypes there are not associated with Neolithic ancestry, indicating sex-biased demographic changes. By analyzing the X chromosome, the investigators found a smaller effective male population size and found that genetic ancestry enriched in Sardinia is more prevalent on the X chromosome than the autosome, showing that the male lineages can be traced back to the mainland faster.