Population Bottlenecks Led to the Accumulation of Deleterious Variants in Domestic and Wild Canids

Domesticated dogs have undergone dramatic population bottlenecks associated with domestication and breed formation as well as recent inbreeding. To investigate the role of population history in shaping the patterns of deleterious mutations in canids, we analyzed 131 whole genome sequences, including 60 genomes from 43 breeds of domestic dogs, 43 village dogs, and 21 genomes from 15 grey wolf populations. We find that the ratio of amino-acid changing to silent variants increases with decreasing neutral genetic diversity, suggesting a decrease in the efficacy of selection in smaller populations as predicted by the nearly neutral theory. Overall, breed dogs have the highest ratio of amino-acid changing to silent variants, wolves have the lowest ratio and village dogs are intermediate. Interestingly however, certain wolf populations, like high altitude Tibetan wolves and the Isle Royale island population, which have a small population size, also show an unusually high ratio of amino acid changing to silent variants. In principle, the reduced efficacy of selection in domestic dogs could be due to either bottlenecks or recent inbreeding. We find the same overall patterns when computing heterozygosity by sampling sequencing reads from distinct individuals within a population, suggesting that the observed increase in the ratio of amino acid changing variants in dogs was likely driven by population bottlenecks, rather than recent inbreeding. This result has important implications for conservation efforts as it suggests that population size may be more important than inbreeding for influencing the accumulation of deleterious variants.