Local-scale genetic structure in the Japanese wild boar (Sus scrofa leucomystax): insights from autosomal microsatellites

Abstract

The Japanese wild boar (Sus scrofa leucomystax) is one of the most widely distributed mammals in Japan. However, its population structure and pattern of gene flow at a regional level are poorly understood. In this study, we investigated the local-scale genetic structure of the Japanese wild boar. In total, 172 individuals sampled in Gifu Prefecture, central Japan, were genotyped for 29 autosomal microsatellite loci. Significant genetic differentiations (F ST = 0.020–0.128) were detected among some geographical areas. In addition, in the overall population (n = 172), all loci deviating from the Hardy–Weinberg equilibrium exhibited a significant deficit of heterozygotes. These results suggest the presence of genetic substructuring in the local population. Moreover, Bayesian cluster analysis revealed the presence of substructuring within the population, despite the relatively small study area (10,621 km2). Spatial Bayesian cluster analysis showed that the boundaries of subpopulations were generally consistent with landscape features (e.g. main rivers, urban areas and road and train networks). Our study implies that these landscape features play a significant role as a barrier to dispersal and gene flow in the local population of the Japanese wild boar.