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Sci Rep. 2018 Mar 14;8(1):4493. doi: 10.1038/s41598-018-22817-5.

Demonstration of the potential of environmental DNA as a tool for the detection of avian species.

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PRESTO, Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan.
Center for Ecological Research, Kyoto University, Otsu, 520-2113, Japan.
Yokohama Zoological Gardens ZOORASIA, Kanagawa, 241-0001, Japan.
College of Bioresource Sciences, Nihon University, Kanagawa, 252-0880, Japan.
Natural History Museum and Institute, Chiba, 260-8682, Japan.
Department of Zoology, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan.
Department of Biological Sciences, The University of Tokyo, Tokyo, 113-0032, Japan.
Natural History Museum and Institute, Chiba, 260-8682, Japan.


Birds play unique functional roles in the maintenance of ecosystems, such as pollination and seed dispersal, and thus monitoring bird species diversity is a first step towards avoiding undesirable consequences of anthropogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have frequent contact with water and that tissues that contain their DNA that persists in the environment (environmental DNA; eDNA) could be used to detect the presence of avian species. To this end, we applied a set of universal PCR primers (MiBird, a modified version of fish/mammal universal primers) for metabarcoding avian eDNA. We confirmed the versatility of MiBird primers by performing in silico analyses and by amplifying DNAs extracted from bird tissues. Analyses of water samples from zoo cages of birds with known species composition suggested that the use of MiBird primers combined with Illumina MiSeq could successfully detect avian species from water samples. Additionally, analysis of water samples collected from a natural pond detected five avian species common to the sampling areas. The present findings suggest that avian eDNA metabarcoding would be a complementary detection/identification tool in cases where visual census of bird species is difficult.

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