Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys

Evidence from a known tropical mammal community

Torrey W. Rodgers, Charles C.Y. Xu, Jacalyn Giacalone Willis, Karen M. Kapheim, Kristin Saltonstall, Marta Vargas, Douglas W. Yu, Panu Somervuo, W. Owen McMillan, Patrick A. Jansen

Research output: Contribution to journalArticleResearchpeer-review

10 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)e133-e145
JournalMolecular Ecology Resources
Volume17
Issue number6
DOIs
StatePublished - 1 Nov 2017

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carrion insects
carrion
Diptera
Mammals
mammal
mammals
DNA
trapping
Biodiversity
transect
Islands
Vertebrates
vertebrates
biodiversity
sampling
vertebrate
Panama
Lizards
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Keywords

  • Barro Colorado Island
  • biodiversity
  • camera trapping
  • environmental DNA
  • transect counts

Cite this

Rodgers, Torrey W. ; Xu, Charles C.Y. ; Giacalone Willis, Jacalyn ; Kapheim, Karen M. ; Saltonstall, Kristin ; Vargas, Marta ; Yu, Douglas W. ; Somervuo, Panu ; McMillan, W. Owen ; Jansen, Patrick A. / Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys : Evidence from a known tropical mammal community. In: Molecular Ecology Resources. 2017 ; Vol. 17, No. 6. pp. e133-e145.
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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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Rodgers, TW, Xu, CCY, Giacalone Willis, J, Kapheim, KM, Saltonstall, K, Vargas, M, Yu, DW, Somervuo, P, McMillan, WO & Jansen, PA 2017, 'Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community', Molecular Ecology Resources, vol. 17, no. 6, pp. e133-e145. https://doi.org/10.1111/1755-0998.12701

Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys : Evidence from a known tropical mammal community. / Rodgers, Torrey W.; Xu, Charles C.Y.; Giacalone Willis, Jacalyn; Kapheim, Karen M.; Saltonstall, Kristin; Vargas, Marta; Yu, Douglas W.; Somervuo, Panu; McMillan, W. Owen; Jansen, Patrick A.

In: Molecular Ecology Resources, Vol. 17, No. 6, 01.11.2017, p. e133-e145.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Xu, Charles C.Y.

AU - Giacalone Willis, Jacalyn

AU - Kapheim, Karen M.

AU - Saltonstall, Kristin

AU - Vargas, Marta

AU - Yu, Douglas W.

AU - Somervuo, Panu

AU - McMillan, W. Owen

AU - Jansen, Patrick A.

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KW - biodiversity

KW - camera trapping

KW - environmental DNA

KW - transect counts

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