Phylogeographic analysis of the Japanese wild boar (Sus scrofa leucomystax)

The Japanese wild boar (Sus scrofa leucomystax) is an indigenous subspecies of the wild boar, which is distributed inHonshu, Shikoku, Kyushu, and other smaller islands of Japan. The distribution area of the Japanese wild boar has in the last 40years expanded by 1.9-fold due to improved suitable survival conditions, such as global warming which has decreased snowfall,increased abandoned farmland, and decreased hunting pressure. As a result, the negative impacts of this population increase onhumans continue to spread. In this study, 1,251 Japanese wild boars were sampled from 32 prefectures which nearly cover theentire expanded distribution area in Japan, and phylogeographical analysis was performed using 30 Measurement of DomesticAnimal Diversity recommended microsatellite markers.Both neighbor-joining (NJ) phylogenetic trees constructed using Nei's DA genetic distance matrix and population geneticstructure analysis classified Japanese wild boar into six phylogeographical subpopulations, including northern Honshu, easternHonshu, central Honshu, western Honshu, Shikoku, and Kyushu. The six identified genetic subpopulations were speculated to formas a result of several factors, including human activity between the northern and eastern Honshu, occurrence of three mountainranges of 3,000-meter height between the eastern and central Honshu, the inland sea between western Honshu and Shikoku, and thepresence of strait between western Honshu and Kyushu. Interestingly, some individual wild boars from Gunma, Tochigi, andMiyazaki areas formed distinct and separate subpopulations, with animals within these subgroups exhibiting traits such as lowgenetic differentiation and high diversity, which likely suggested gene influx from domestic pigs or other sources.