The positions of the rostral opening of the pterygoid canal and the foramen of the zygomatic nerve in dogs and wolves were observed using samples taken from the crania of 144 contemporary Japanese dogs, 45 European dogs, and 36 grey wolves. The rostral opening of the pterygoid canal was located in the pterygopalatine fossa in 85–100% of the European dog and grey wolf individuals examined in this study; however, in 35% of the Japanese dogs, the opening was found in the medial wall of the orbital fissure, at a relatively high incidence rate compared with European dogs and wolves. This trait of the Japanese dogs is considered to be a variant, and to learn about its origin the crania of 45 Jomon dogs (5th millennium–10th century BC), 1 Jomon Japanese wolf (c. 6000 BP14C), 13 Yayoi dogs (5th–4thcenturies BC), 14 dogs from China (5th millennium–20th century BC), and 108 dogs from Susuya site, Sakhalin (4th century BC–6th century AD) were examined. The rostral opening of the pterygoid canal in the orbital fissure of the Neolithic period dogs from Japan and China had an occurrence rate of 73–100%, higher than that of contemporary Japanese dogs, giving rise to the possibility that this variant of the contemporary Japanese dogs is an inherited trait. It should be noted that in the modern 8 Japanese wolves (c. 17th century AD), 75% were of the orbital fissure type, and the Jomon Japanese wolf also had a pterygoid canal which opened into the orbital fissure, a trend differing from that of the grey wolf elsewhere in the world. The foramen for the zygomatic nerve was present in Jomon dogs at a relatively high occurrence rate. However, it was rarely observed overall among the dog specimens examined, and none were observed in the wolf samples.
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