Carrion fly‐derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community |
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| Authors: | Torrey W. Rodgers Charles C. Y. Xu Jacalyn Giacalone Karen M. Kapheim Kristin Saltonstall Marta Vargas Douglas W. Yu Panu Somervuo Patrick A. Jansen |
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| Affiliation: | 1. Department of Wildland Resources, Utah State University, Logan, UT, USA;2. Smithsonian Tropical Research Institute, Balboa, Panama;3. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China;4. Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands;5. Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada;6. College of Science and Mathematics, Montclair State University, Montclair, NJ, USA;7. Department of Biology, Utah State University, Logan, UT, USA;8. School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK;9. Department of Biosciences, University of Helsinki, Helsinki, Finland |
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| Abstract: | 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 8 years 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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| Keywords: | Barro Colorado Island biodiversity camera trapping environmental DNA transect counts |
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