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Environmental DNA metabarcoding reveals the presence of a small, quick-moving, nocturnal water shrew in a forest stream

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Chimarrogale platycephala (Japanese water shrew) is an endangered, semi-aquatic mammal species in Japan, and understanding the C. platycephala habitat is vital for conservation planning. However, the species is difficult to locate using conventional methods, like visual observations and camera/video traps, due to its small size, nocturnal behavior, and low population densities in semi-aquatic environments. Environmental DNA (eDNA) analysis has been used to survey distributions of macro-organisms, with the advantage of non-invasiveness, high sensitivity, and cost-effectiveness. In this study, we analyzed the eDNA in flowing water from possible C. platycephala habitats, using a metabarcoding approach that allows simultaneous multi-species detection. The eDNA of this species was detected at 2 of the 16 study sites. Based on eDNA screening data, camera trap surveys confirmed the presence of shrews at both locations. This study successfully discovered a previously unknown habitat of an endangered semi-aquatic mammal, using eDNA metabarcoding and camera traps. Wide ranging use of eDNA surveys will facilitate detection and appropriate conservation of C. platycephala, and can be applied to other critically endangered semi-aquatic mammals.

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Fig. 1
Fig. 2

Data availability

DDBJ accession numbers of the present DNA sequences are as follows: DRA Submission ID = DRA009286, BioProject ID = PRJDB4990, and BioSample ID = SAMD00194191–SAMD00194229. DNA sequences can be viewed directly at


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We would like to thank World Freshwater Aquarium Aquatotto Gifu for providing information on C. platycephala.

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Correspondence to Masayuki Ushio or Yuji Isagi.

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Yonezawa, S., Ushio, M., Yamanaka, H. et al. Environmental DNA metabarcoding reveals the presence of a small, quick-moving, nocturnal water shrew in a forest stream. Conserv Genet 21, 1079–1084 (2020).

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