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

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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.

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Acknowledgments

The authors thank the members of hunting clubs in Gifu Prefecture and Mr. Takahiro Yokota (Gifu Prefectural Government) for providing wild boar samples. We thank Shobudani Farm (Ibigawa, Gifu, Japan) for providing pig samples. We are also grateful to Mr. Satoshi Wada (Gifu Prefectural Government) for assistance in making the figures. Helpful comments from two anonymous reviewers improved the manuscript. This work was supported in part by the 2015 grant from Gifu University to R. Tadano.

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Authors and Affiliations

  1. Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan

    Ryo Tadano & Aya Nagai

  2. Research Center for Wildlife Management, Gifu University, Gifu, 501-1193, Japan

    Junji Moribe

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  1. Ryo Tadano
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  2. Aya Nagai
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  3. Junji Moribe
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Correspondence to Ryo Tadano.

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Tadano, R., Nagai, A. & Moribe, J. Local-scale genetic structure in the Japanese wild boar (Sus scrofa leucomystax): insights from autosomal microsatellites. Conserv Genet 17, 1125–1135 (2016). https://doi.org/10.1007/s10592-016-0848-z

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