NEW YORK – A new natural selection-focused analysis led by investigators at the Francis Crick Institute and the University of Pennsylvania suggests that ancient European farmers obtained immune-related genetic loci through admixture with European hunter-gatherers, while retaining variants linked to light skin pigmentation.
"When farming groups expanded from the Near East into Europe and mixed with local hunter-gatherers, the natural prediction would be that the farmers' immunity genes would be best adapted to the farming lifestyle and thus selected for," senior and co-corresponding author Pontus Skoglund, a group leader in ancient genomics at the Francis Crick Institute who is also affiliated with the University of Pennsylvania, said in a statement. "However, we see the opposite, that hunter-gatherer ancestry is enriched at the MHC immunity locus."
As they reported in Current Biology on Thursday, the researchers analyzed adaptive admixture patterns using genome-wide SNP profiles for 677 ancient Europeans reaching back some 15,000 years to the Mesolithic, Early Neolithic, and Middle Neolithic periods. With genetic data covering around 7,500 years, they retraced the effects of admixture between Neolithic European farmers and Mesolithic hunter-gatherers as farming groups migrated to Europe from the Near East some 8,000 years ago.
"This study examined a broad swath of ancient individuals, in both geographic and temporal sense," first author Tom Davy, an ancient genomics researcher at the Francis Crick Institute, said in an email.
The team's results suggested that the interactions preferentially impacted certain parts of the genome in the incoming farming populations.
In particular, the researchers found higher-than-usual levels of hunter-gatherer ancestry across the major histocompatibility complex (MHC) region in admixed individuals, Davy explained.
While more research will be needed to tease out the specific infectious diseases or other pressures that preferentially selected for the hunter-gatherer version of the MHC region, he noted that the observed pattern is unlikely to reflect exposure to a single disease.
"[I]t may be that we are instead observing selection for higher diversity at this locus in general," he said. "It's worth remembering that many of the genes in this area contribute to many other traits past immunity."
When the investigators looked at skin pigmentation-related variants in the SLC24A5 gene, meanwhile, they saw signs of selection that favored the maintenance of sequences from the incoming European farmer groups, Davy explained, suggesting that there was strong selection for lighter pigmentation variants and against hunter-gatherer skin pigmentation variants.
"One hypothesis is that lighter skin pigmentation allowed farmers to synthesize more vitamin D from ultraviolet radiation, while hunter-gatherers were able to obtain sufficient vitamin D from their diet," co-senior author Iain Mathieson, a genetics researcher with the UPenn Perelman School of Medicine, said in a statement.