Selection trajectories of genetic variants underlying domestic animal traits
E. K. Irving-Pease, L. A. F. Frantz, G. Larson, J. G. Schraiber
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 speculation surrounding the existence of "domestication genes", the underlying genetic basis of traits differentiating domestic animals them from their wild counterparts remains poorly understood. 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 hundreds of variants associated with quantitative trait loci (QTLs) in four key domestic species (cattle, pigs, horses and goats). Using a novel dataset of >300 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. The resulting timelines allow direct correlation between changes in ecological conditions within the domestic niche and selection for specific adaptive traits. Our results demonstrate the critical importance of time series data in resolving the underlying evolutionary process of animal domestication.