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This study described the detailed osteological features of the Setouchi salamander Hynobius setouchi. H. setouchi, which is endemic to central Japan, was recently delineated from the wide range of H. nebulosus species based on molecular and external morphological characteristics. However, the osteological features of the species belonging to the genus Hynobius have not been examined, which has hindered the detailed understanding of morphological diversity in the genus. To address this problem, this study elucidated the osteological features of the salamander using micro-computed tomography scanning and whole-mount double staining methods. The articular, a part of the hypobranchial I, a part of coracoid, pubis, carpus, and tarsus were cartilaginous in small-sized individuals and were partially or completely ossified in large-sized individuals. The degree of ossification varied in the operculum, basibranchial II, and ascending process of the palatoquadrate. However, ossification was not associated with body size. The lacrimal, ossified manus, and ossified pes exhibited varying degrees of articulation or fusion irrespective of body size. Moreover, the cranium and tarsus of H. setouchi exhibited several unique characteristics. These osteological characteristics will aid in revising the taxonomy and phylogeny of the Hynobius species.

Taxonomic identification of two Taiwanese salamanders, Hynobius sonani (Maki, 1922), and H. formosanus Maki, 1922, was clarified. Based on the descriptions and measurement data in the original description, we confirmed that H. sonani has been treated as H. formosanus and vice versa, which might have been caused by confusion of sampling localities of the two species. Because we could not find the holotypes of the two species and concluded these were lost, we herein assign neotypes for these species for precluding future taxonomic confusion.