Small mammalian remains were newly discovered from the Late Quaternary sediments of the Yaeyama region (Ishigaki and Yonaguni Islands) in the southwestern-most part of Japan. We examined these materials based on taxonomical and chronological approaches, in order to reconstruct the past fauna in this region. Accelerator Mass Spectrometry radiocarbon dating indicates that the mammalian assemblages from Ishigaki and Yonaguni Islands are composed mainly of late Holocene fossils. The fossil assemblage from Ishigaki Island comprises five species of small mammals belonging to Soricomorpha (Suncus murinus), Chiroptera (Pteropus sp., Hipposideros turpis, and Rhinolophus perditus), and Rodentia (Niviventer sp.). One rodent bone, collected from the fissure sediments near Sabichi-do Cave, Ishigaki Island, is dated at 230 ± 20 yBP (ca. AD 1,700), and is considered part of the recent remain. Furthermore, the fossil assemblage from Umabana-zaki Fissure, on Yonaguni Island, is dated at 1,760 ± 20 yBP (ca. AD 300) and comprises three species of small mammals belonging to Chiroptera (Pipistrellus cf. abramus) and Rodentia (Niviventer sp. and Mus musculus). Niviventer is not currently distributed in Japan. Only domestic rats (Rattus rattus and R. norvegicus) live on Ishigaki and Yonaguni Islands at the present time. However, the fossil assemblage from Umabana-zaki Fissure is dominated completely by Niviventer sp. Most fossils of small mammals found from the late Holocene Ishigaki and Yonaguni Islands represented species that are currently endemic to the Yaeyama region. Niviventer sp. from these islands is unique because this form has never been found from neighboring regions, such as Taiwan and Miyako Islands, and because it likely existed in the late Holocene. These discoveries support the hypothesis that the Yaeyama region had been isolated zoogeographically from the continent even during the Last Glacial Maximum, when the sea level had drastically fallen.
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