Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations

SIMPLE SUMMARY: Human activities have left indelible traces in the gene pool of livestock as well as recently domesticated wild animal species which are manifested by changes in their genome structure, often accompanied by the significant loss of biodiversity, especially in the case of small local populations. Despite the benefits of deer farming, intensive artificial selection associated with domestication can lead to several negative effects, including founder effects, inbreeding depression, or rapid decline in effective population size, which are also often present in traditional livestock. This study investigates the effect of human-mediated selection on the diversity of seven farmed red deer populations compared to two wild populations through the quantification of the level of genomic heterozygosity, inbreeding, admixture, and gene flow. These results will help to improve traditional breeding schemes and assist in a more sustainable utilisation of available animal genetic resources. ABSTRACT: In this study, we analysed the effect of human-mediated selection on the gene pool of wild and farmed red deer populations based on genotyping-by-sequencing data. The farmed red deer sample covered populations spread across seven countries and two continents (France, Germany, Hungary, Latvia, New Zealand, Poland, and Slovakia). The Slovak and Spain wild red deer populations (the latter one in a large game estate) were used as control outgroups. The gene flow intensity, relationship and admixture among populations were tested by the Bayesian approach and discriminant analysis of principal components (DAPC). The highest gene diversity (H(e) = 0.19) and the lowest genomic inbreeding (F(HOM) = 0.04) found in Slovak wild population confirmed our hypothesis that artificial selection accompanied by bottlenecks has led to the increase in overall genomic homozygosity. The Bayesian approach and DAPC consistently identified three separate genetic groups. As expected, the farmed populations were clustered together, while the Slovak and Spanish populations formed two separate clusters. Identified traces of genetic admixture in the gene pool of farmed populations reflected a strong contemporary migration rate between them. This study suggests that even if the history of deer farming has been shorter than traditional livestock species, it may leave significant traces in the genome structure.