Journal
MOLECULAR ECOLOGY RESOURCES
Volume 17, Issue 6, Pages e133-e145Publisher
WILEY
DOI: 10.1111/1755-0998.12701
Keywords
Barro Colorado Island; biodiversity; camera trapping; environmental DNA; transect counts
Funding
- Smithsonian Tropical Research Institute
- STRI Terrestrial Environmental Studies Project
- U.S. Department of Education Math-Science Partnerships Project
- National Natural Science Foundation of China [31400470, 41661144002, 31670536, 31500305, GYHZ1754]
- Ministry of Science and Technology of China [2012FY110800]
- University of East Anglia
- State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology [GREKF13-13, GREKF14-13, GREKF16-09]
- Natural Environment Research Council [NE/M021696/1] Funding Source: researchfish
- NERC [NE/M021696/1] Funding Source: UKRI
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Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera trapping. We collected 1,084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared blast with the new program protax, and we found that protax improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by 8years of transect counts and camera trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys and has the potential to detect a broader range of species than more commonly used methods.
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