Selection trajectories of genetic variants underlying domestic animal traits

The study of animal domestication is an important model system for understanding adaptive responses to changes in environmental conditions, demography and selective pressures over time. Despite decades of genetic research into traits associated with domestication, our understanding of the underlying genetic basis of adaptation to the domestic niche remains poor. Using genome-wide modern DNA, previous studies have contrasted populations of wild and domestic animals to scan for segregating signatures of selection in their respective genomes. Due to the intensive nature of modern breeding practices, it is unclear which candidate genes identified by these methods were under selection during the initial process of domestication, and which represent more recent improvement traits. Time series data, obtained from ancient DNA, can resolve these questions by directly observing changes in allele frequencies over time. Here, we reconstruct the allelic trajectory of >100,000 GWAS variants linked to quantitative traits, in four key domestic species (cattle, pigs, horses and goats). Using a novel dataset of >400 ancient nuclear genomes, spanning >12,000 years of evolutionary history, we are able to quantify the temporal origins and strength of selection for genetic variants associated with health, reproductive, performance, production, aesthetic and behavioural traits in domestic animal populations.

This is an ongoing project and we hope to publish early 2019.