Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years

Abstract

Ancient DNA is reshaping our understanding of the evolutionary history of dogs. Technical constraints, however, limit its applicability, such as inferring changes in inbreeding through time. Genotype imputation, a statistical methodology for inferring missing genotypes, presents a promising, yet unexplored, solution. We show that the imputation of ancient dogs and wolves is highly accurate. By imputing ancient dogs, we study inbreeding patterns over the past 10,000 y and find that a significant increase has occurred only in recent times and uncover that genomic regions resistant to homozygosity are significantly enriched for immunity and chemosensory receptor genes. We demonstrate the accuracy of imputation for ancient canids, paving the way for future studies to leverage the greater information content of phased haplotypes.