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Team Seeks Signs of Early Agricultural Adaptation in Hundreds of Ancient Genomes

NEW YORK (GenomeWeb) – A large-scale analysis of ancient DNA samples from Eurasia is providing a look at the genomic adaptations that followed migration to the region by Neolithic farming populations.

As they reported online today in Nature, researchers at Harvard Medical School, University College Dublin, the University of Adelaide, and elsewhere searched for signs of admixture and selection using genome-wide SNP patterns in hundreds of Eurasian samples stretching back between around 2,300 to 8,500 years. With these data, they uncovered parts of the genome that appeared prone to selection during the advent of European farming.

"Our results … directly document selection on loci related to pigmentation, diet, and immunity," they wrote, "painting a picture of populations adapting to settled agricultural life at high latitudes."

The team's results support the notion that a Neolithic population from Anatolia made up the first farming groups in Europe. It also pointed to previously unappreciated population mixing in the steppe region in the Near East.

"The Neolithic revolution is perhaps the most important transition in human prehistory," co-senior author Ron Pinhasi, an archaeology researcher at University College Dublin, said in a statement. "We now have proof that people did actually go from Anatolia into Europe and brought farming with them."

Rather than solely extrapolating back from patterns in present-day genomes, the researchers reasoned that access to ancient DNA might offer a more refined window on human adaptations to new environments — in this case, the arrival of farming populations in Europe.

By tapping into relatively well-preserved DNA from inner ear, petrous bone samples and using increasingly well-established, in-solution hybridization methods for ancient DNA enrichment, the study's authors genotyped 26 ancient Neolithic Anatolian individuals not tested previously, marking "the first genome-wide ancient DNA data from the eastern Mediterranean."

To that, the team added new or improved genotyping data for more than 100 other ancient samples tested by targeted enrichment and sequencing as well as existing SNP data for 67 ancient samples.

All told, the collection provided a look at more than a million SNPs in 230 ancient samples from western Eurasia.

Consistent with the role of the Neolithic Anatolians in early European farming, the researchers found that these ancient samples clustered more closely with samples from farmers in Germany, Hungary, and Spain than they did with samples from present-day near-Eastern populations. Likewise, they found that nearly half of the Neolithic Anatolians belonged to a Y chromosome haplogroup common to early European farmers.

Using data from more than three-dozen samples at 1,500 and 5,600 years BCE from the so-called Samara steppe region, the team also assessed relationships between the Yamnaya, eastern hunter-gatherer populations, and other populations in the Near East.

Along with evidence of admixture between steppe populations and eastern hunter-gatherer populations going thousands of years BCE, for example, the group saw an influx of Anatolian Neolithic and/or early European farmer ancestry into the steppe populations before the late Bronze Age.

Moreover, the researchers' results hint that taller populations in northern Europe may owe some of their height gain to higher proportions of ancestry from steppe populations compared with southern Europeans, who tend to have higher ancestry from populations that lived in the Iberian peninsula during Neolithic and Copper Age times.

To search for signs of selection affecting the western Eurasian populations, meanwhile, the researchers assessed almost 1.1 million autosomal SNPs in the ancient samples and in samples from four European populations included in the 1000 Genomes Project, identifying a dozen loci with signals of selection spanning three or more SNPs apiece.

The strongest association fell in and around an allele that arose in Europeans in the last few thousand years that's linked to lactase persistence, the ongoing production of an enzyme needed to digest milk into adulthood.

But the team also saw patterns consistent with selection at sites in the genome coding for enzymes involved in fatty acid metabolism, an allele associated with light skin pigmentation, and loci linked to celiac disease.