Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

Population bottlenecks, inbreeding, and artificial selection can all, in
principle, influence levels of deleterious genetic variation. However, the
relative importance of each of these effects on genome-wide patterns of
deleterious variation remains controversial. Domestic and wild canids
offer a powerful system to address the role of these factors in
influencing deleterious variation because their history is dominated by
known bottlenecks and intense artificial selection. Here, we assess
genome-wide patterns of deleterious variation in 90 whole-genome sequences
from breed dogs, village dogs, and gray wolves. We find that the ratio of
amino acid changing heterozygosity to silent heterozygosity is higher in
dogs than in wolves and, on average, dogs have 2–3% higher genetic load
than gray wolves. Multiple lines of evidence indicate this pattern is
driven by less efficient natural selection due to bottlenecks associated
with domestication and breed formation, rather than recent inbreeding.
Further, we find regions of the genome implicated in selective sweeps are
enriched for amino acid changing variants and Mendelian disease genes. To
our knowledge, these results provide the first quantitative estimates of
the increased burden of deleterious variants directly associated with
domestication and have important implications for selective breeding
programs and the conservation of rare and endangered species.
Specifically, they highlight the costs associated with selective breeding
and question the practice favoring the breeding of individuals that best
fit breed standards. Our results also suggest that maintaining a large
population size, rather than just avoiding inbreeding, is a critical
factor for preventing the accumulation of deleterious variants.