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BoG Presentation Highlights Polygenic Adaptation in Recent British Population History

COLD SPRING HARBOR, NY (GenomeWeb) – Polygenic adaptation appears to have played a more pronounced and pervasive role in the adaptation of complex human traits than previously appreciated, according to a study presented this week at the Biology of Genomes meeting by Stanford University genetics researcher Yair Field.

During a session on population genomics, Field described efforts to untangle human genetic adaptation over relatively recent genetic history — within the past 2,000 years or so — in the ancestors of modern-day Britons.

Using an approach called the singleton density score (SDS), which teases out recent allele frequency changes in the past using singleton mutation information from present-day genome sequences, he and colleagues from the US, UK, and France searched for signs of recent natural selection with allele frequency data for nearly 3,200 individuals in the UK10K dataset with British ancestry.

"SDS focuses on patterns of variation around each SNP to infer recent changes in the relative frequencies of the two alleles," Field and co-authors explained in a preprint manuscript of the paper appearing on BioRxiv. "[R]ecent selection distorts the ancestral genealogy of sampled haplotypes at a selected site."

Whereas many past studies have focused on selection consequences involving small numbers of variants with large effects on a given trait, Field explained, the new analysis explored the contributions that multiple, small-effect alleles make to human adaptation and phenotypic variation.

For example, he noted that height has been established as a highly polygenic trait in Europeans. With the help of the SDS approach, which uncovered so-called "trait-increasing SDS" patterns, the team saw what Field called a "huge" signal of selection for increased height, with allele frequency alterations stretching across most of the genome as British population statures swelled.

Similarly, when they turned their attention to almost four dozen other complex traits considered in past genome-wide association studies, the researchers uncovered signals of selection affecting polygenic alleles associated with traits such lactase persistence — ongoing lactase enzyme activity that enables milk digestion by adults — and immune features mediated by the human leukocyte antigen system.

Likewise, the British population appears to have undergone recent polygenic adaptations leading to ballooning infant birth weights and head circumferences and hip size increases in females, coupled with lighter pigmentation features such as blue eyes and blonde hair.

Overall, Field and his co-authors found that the SDS-centered approach made it possible to scan for polygenic adaptions more precisely than anticipated, though they cautioned that their findings may not all stem from direct selection on the specific traits being considered, since alleles involved in polygenic adaptation may impact more than one aspect of human biology.