In many ways, dogs are an ideal model for the study of genetic erosion and populationrecovery, problems of major concern in the field of conservation genetics. Genetic diversity in many dog breeds has been declining systematically since the beginning ofthe 1800s, when modern breeding practices came into fashion. As such, inbreedingin domestic dog breeds is substantial and widespread and has led to an increase in recessive deleterious mutations of high effect as well as general inbreeding depression.Pedigrees can in theory be used to guide breeding decisions, though are often incomplete and do not reflect the full history of inbreeding. Small microsatellite panelsare also used in some cases to choose mating pairs to produce litters with low levelsof inbreeding. However, the long-term impact of such practices has not been thoroughly evaluated. Here, we use forward simulation on a model of the dog genometo examine the impact of using limited marker panels to guide pairwise mating decisions on genome-wide population-level genetic diversity. Our results suggest that inunmanaged populations, where breeding decisions are made at the pairwise—ratherthan population-level, such panels can lead to accelerated loss of genetic diversity atgenome regions unlinked to panel markers, compared to random mating. These results demonstrate the importance of genome-wide genetic panels for managing andconserving genetic diversity in dogs and other companion animals.
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