Jun 13, 2017

Environmental DNA enables detection of terrestrial mammals from forest pond water

Molecular Ecology Resources
Masayuki UshioMasaki Miya

Abstract

Terrestrial animals must have frequent contact with water to survive, implying that environmental DNA (eDNA) originating from those animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. The versatility of MiMammal primers was tested in silico and by amplifying DNAs extracted from tissues. The results suggested that MiMammal primers are capable of amplifying and distinguishing a diverse group of mammalian species. In addition, analyses of water samples from zoo cages of mammals with known species composition suggested that MiMammal primers could successfully detect mammalian species from water samples in the field. Then, we performed an experiment to detect mammals from natural ecosystems by collecting five 500-ml water samples from ponds in two cool-temperate forests in Hokkaido, northern Japan. MiMammal amplicon libraries were constructed using eDNA extracted from water samples, and sequences generated by Illumina MiSeq were subjected to data processing and taxonomic assignment. We ther...Continue Reading

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  • Citations18

References

Mentioned in this Paper

Procyon lotor
Deer (mammal)
House mice
Shrews
Sorex unguiculatus
Extraction
Oligonucleotide Primers
Zebrafish
DNA Binding Domain
Clethrionomys rufocanus

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