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Volumn 25, Issue 4, 2016, Pages 929-942

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

(27)  Valentini, Alice a   Taberlet, Pierre b,c   Miaud, Claude d   Civade, Raphaël e   Herder, Jelger f   Thomsen, Philip Francis g   Bellemain, Eva a   Besnard, Aurélien d   Coissac, Eric b   Boyer, Frédéric b   Gaboriaud, Coline a   Jean, Pauline a   Poulet, Nicolas h   Roset, Nicolas i   Copp, Gordon H j,k   Geniez, Philippe d   Pont, Didier e   Argillier, Christine l   Baudoin, Jean Marc l   Peroux, Tiphaine l   more..

a Spygen   (France)
b CNRS   (France)
h ONEMA   (France)
i ONEMA *  (France)

Author keywords

amphibian; detection probability; environmental DNA; fish; monitoring; wildlife management

Indexed keywords

FRESH WATER; MITOCHONDRIAL DNA; PRIMER DNA;

EID: 84958280498     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.13428     Document Type: Article
Times cited : (841)

References (56)
  • 1
    • 84900328028 scopus 로고    scopus 로고
    • Electrofishing efficiency in low conductivity neotropical streams: Towards a non-destructive fish sampling method
    • Allard L, Grenouillet G, Khazraie K, et al,. (2014) Electrofishing efficiency in low conductivity neotropical streams: towards a non-destructive fish sampling method. Fisheries Management and Ecology, 21, 234-243.
    • (2014) Fisheries Management and Ecology , vol.21 , pp. 234-243
    • Allard, L.1    Grenouillet, G.2    Khazraie, K.3
  • 2
    • 84873738235 scopus 로고    scopus 로고
    • Development of a fish-based index to assess the eutrophication status of European lakes
    • Argillier C, Caussé S, Gevrey M, et al,. (2013) Development of a fish-based index to assess the eutrophication status of European lakes. Hydrobiologia, 704, 193-211.
    • (2013) Hydrobiologia , vol.704 , pp. 193-211
    • Argillier, C.1    Caussé, S.2    Gevrey, M.3
  • 3
    • 79952259978 scopus 로고    scopus 로고
    • Has the Earth's sixth mass extinction already arrived?
    • Barnosky AD, Matzke N, Tomiya S, et al,. (2011) Has the Earth's sixth mass extinction already arrived? Nature, 471, 51-57.
    • (2011) Nature , vol.471 , pp. 51-57
    • Barnosky, A.D.1    Matzke, N.2    Tomiya, S.3
  • 4
    • 77954336858 scopus 로고    scopus 로고
    • ITS as an environmental DNA barcode for fungi: An in silico approach reveals potential PCR biases
    • Bellemain E, Carlsen T, Brochmann C, et al,. (2010) ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology, 10, 189.
    • (2010) BMC Microbiology , vol.10 , pp. 189
    • Bellemain, E.1    Carlsen, T.2    Brochmann, C.3
  • 5
    • 84888305715 scopus 로고    scopus 로고
    • IUCN and perspectives on biodiversity conservation in a changing world
    • Beumer C, Martens P, (2013) IUCN and perspectives on biodiversity conservation in a changing world. Biodiversity and Conservation, 22, 3105-3120.
    • (2013) Biodiversity and Conservation , vol.22 , pp. 3105-3120
    • Beumer, C.1    Martens, P.2
  • 6
    • 85028161389 scopus 로고    scopus 로고
    • Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus)
    • Biggs J, Ewald N, Valentini A, et al,. (2015) Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus). Biological Conservation, 183, 19-28.
    • (2015) Biological Conservation , vol.183 , pp. 19-28
    • Biggs, J.1    Ewald, N.2    Valentini, A.3
  • 7
    • 84955199272 scopus 로고    scopus 로고
    • Obitools: A unix-inspired software package for DNA metabarcoding
    • Boyer F, Mercier C, Bonin A, et al,. (2015) obitools: a unix-inspired software package for DNA metabarcoding. Molecular Ecology Resources, doi: 10.1111/1755-0998.12428.
    • (2015) Molecular Ecology Resources
    • Boyer, F.1    Mercier, C.2    Bonin, A.3
  • 8
    • 8744307994 scopus 로고    scopus 로고
    • Multimodel inference understanding AIC and BIC in model selection
    • Burnham KP, Anderson DR, (2004) Multimodel inference understanding AIC and BIC in model selection. Sociological Methods & Research, 33, 261-304.
    • (2004) Sociological Methods & Research , vol.33 , pp. 261-304
    • Burnham, K.P.1    Anderson, D.R.2
  • 9
    • 84859574767 scopus 로고    scopus 로고
    • Bioinformatic challenges for DNA metabarcoding of plants and animals
    • Coissac E, Riaz T, Puillandre N, (2012) Bioinformatic challenges for DNA metabarcoding of plants and animals. Molecular Ecology, 21, 1834-1847.
    • (2012) Molecular Ecology , vol.21 , pp. 1834-1847
    • Coissac, E.1    Riaz, T.2    Puillandre, N.3
  • 10
    • 0034682945 scopus 로고    scopus 로고
    • Ancient DNA: Do it right or not at all
    • Cooper A, Poinar HN, (2000) Ancient DNA: do it right or not at all. Science, 289, 1139.
    • (2000) Science , vol.289 , pp. 1139
    • Cooper, A.1    Poinar, H.N.2
  • 11
    • 0026313879 scopus 로고
    • Juvenile fishes as functional describers of fluvial ecosystem dynamics: Applications on the river Rhône, France
    • Copp GH, Oliver JM, Peňáz M, Roux AL, (1991) Juvenile fishes as functional describers of fluvial ecosystem dynamics: applications on the river Rhône, France. Regulated Rivers: Research & Management, 6, 135-145.
    • (1991) Regulated Rivers: Research & Management , vol.6 , pp. 135-145
    • Copp, G.H.1    Oliver, J.M.2    Peňáz, M.3    Roux, A.L.4
  • 13
    • 44649181189 scopus 로고    scopus 로고
    • The IBTS database: A plea for quality control
    • Daan N, (2001) The IBTS database: a plea for quality control. ICES CM, 3, 1-5.
    • (2001) ICES CM , vol.3 , pp. 1-5
    • Daan, N.1
  • 14
    • 80053275663 scopus 로고    scopus 로고
    • From molecules to management: Adopting DNA-based methods for monitoring biological invasions in aquatic environments
    • Darling JA, Mahon AR, (2011) From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environmental Research, 111, 978-988.
    • (2011) Environmental Research , vol.111 , pp. 978-988
    • Darling, J.A.1    Mahon, A.R.2
  • 15
    • 84894242220 scopus 로고    scopus 로고
    • DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: Application to omnivorous diet
    • De Barba M, Miquel C, Boyer F, et al,. (2014) DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. Molecular Ecology Resources, 14, 306-323.
    • (2014) Molecular Ecology Resources , vol.14 , pp. 306-323
    • De Barba, M.1    Miquel, C.2    Boyer, F.3
  • 16
    • 84919648788 scopus 로고    scopus 로고
    • DNA metabarcoding and the cytochrome c oxidase subunit i marker: Not a perfect match
    • Deagle BE, Jarman SN, Coissac E, Pompanon F, Taberlet P, (2014) DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match. Biology Letters, 10, 20140562.
    • (2014) Biology Letters , vol.10 , pp. 20140562
    • Deagle, B.E.1    Jarman, S.N.2    Coissac, E.3    Pompanon, F.4    Taberlet, P.5
  • 17
    • 84921929059 scopus 로고    scopus 로고
    • Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
    • Deiner K, Walser J-C, Mächler E, Altermatt F, (2015) Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biological Conservation, 183, 53-63.
    • (2015) Biological Conservation , vol.183 , pp. 53-63
    • Deiner, K.1    Walser, J.-C.2    Mächler, E.3    Altermatt, F.4
  • 18
    • 84863997760 scopus 로고    scopus 로고
    • Improved detection of an alien invasive species through environmental DNA barcoding: The example of the American bullfrog Lithobates catesbeianus
    • Dejean T, Valentini A, Miquel C, et al,. (2012) Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus. Journal of Applied Ecology, 49, 953-959.
    • (2012) Journal of Applied Ecology , vol.49 , pp. 953-959
    • Dejean, T.1    Valentini, A.2    Miquel, C.3
  • 20
    • 84955198010 scopus 로고    scopus 로고
    • Quantification of mesocosm fish and amphibian species diversity via eDNA metabarcoding
    • Evans NT, Olds BP, Turner CR, et al,. (2015) Quantification of mesocosm fish and amphibian species diversity via eDNA metabarcoding. Molecular Ecology Resources, doi: 10.1111/1755-0998.12433.
    • (2015) Molecular Ecology Resources
    • Evans, N.T.1    Olds, B.P.2    Turner, C.R.3
  • 21
    • 77954554269 scopus 로고    scopus 로고
    • An in silico approach for the evaluation of DNA barcodes
    • Ficetola GT, Coissac E, Zundel S, et al,. (2010) An in silico approach for the evaluation of DNA barcodes. BMC Genomics, 11, 434.
    • (2010) BMC Genomics , vol.11 , pp. 434
    • Ficetola, G.T.1    Coissac, E.2    Zundel, S.3
  • 22
    • 80052983206 scopus 로고    scopus 로고
    • Unmarked: An R package for fitting hierarchical models of wildlife occurrence and Abundance
    • Fiske I, Chandler R, (2011) Unmarked: an R package for fitting hierarchical models of wildlife occurrence and Abundance. Journal of Statistical Software, 43, 1-23.
    • (2011) Journal of Statistical Software , vol.43 , pp. 1-23
    • Fiske, I.1    Chandler, R.2
  • 26
    • 84888440953 scopus 로고    scopus 로고
    • Passive capture techniques
    • (eds Zale A.V. Parrish D.L. Sutton T.M.), American Fisheries Society, Bethesda, Maryland
    • Hubert WA, Pope KL, Dettmers JM, (2012) Passive capture techniques. In: Fisheries Techniques (eds, Zale AV, Parrish DL, Sutton TM,), pp. 223-265. American Fisheries Society, Bethesda, Maryland.
    • (2012) Fisheries Techniques , pp. 223-265
    • Hubert, W.A.1    Pope, K.L.2    Dettmers, J.M.3
  • 27
    • 0003110488 scopus 로고
    • Rainbow trout and brook trout mortality from high voltage AC electrofishing in a controlled environment
    • Hudy M, (1985) Rainbow trout and brook trout mortality from high voltage AC electrofishing in a controlled environment. North American Journal of Fisheries Management, 5, 475-479.
    • (1985) North American Journal of Fisheries Management , vol.5 , pp. 475-479
    • Hudy, M.1
  • 28
    • 84903287030 scopus 로고    scopus 로고
    • Harnessing DNA to improve environmental management
    • Kelly RP, Port JA, Yamahara KM, et al,. (2014a) Harnessing DNA to improve environmental management. Science, 344, 1455-1456.
    • (2014) Science , vol.344 , pp. 1455-1456
    • Kelly, R.P.1    Port, J.A.2    Yamahara, K.M.3
  • 29
    • 84898618580 scopus 로고    scopus 로고
    • Using environmental DNA to census marine fishes in a large mesocosm
    • Kelly RP, Port JA, Yamahara KM, Crowder LB, (2014b) Using environmental DNA to census marine fishes in a large mesocosm. PLoS ONE, 9, e86175.
    • (2014) PLoS ONE , vol.9 , pp. e86175
    • Kelly, R.P.1    Port, J.A.2    Yamahara, K.M.3    Crowder, L.B.4
  • 30
    • 57649115641 scopus 로고    scopus 로고
    • Imperfect detection and its consequences for monitoring for conservation
    • Kéry M, Schmidt BR, (2008) Imperfect detection and its consequences for monitoring for conservation. Community Ecology, 9, 207-216.
    • (2008) Community Ecology , vol.9 , pp. 207-216
    • Kéry, M.1    Schmidt, B.R.2
  • 31
    • 84921917001 scopus 로고    scopus 로고
    • Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix
    • Klymus KE, Richter CA, Chapman DC, Paukert C, (2015) Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix. Biological Conservation, 183, 77-84.
    • (2015) Biological Conservation , vol.183 , pp. 77-84
    • Klymus, K.E.1    Richter, C.A.2    Chapman, D.C.3    Paukert, C.4
  • 32
    • 0000989596 scopus 로고    scopus 로고
    • Estimating site occupancy rates when detection probabilities are less than one
    • MacKenzie DI, Nichols JD, Lachman GB, et al,. (2002) Estimating site occupancy rates when detection probabilities are less than one. Ecology, 83, 2248-2255.
    • (2002) Ecology , vol.83 , pp. 2248-2255
    • MacKenzie, D.I.1    Nichols, J.D.2    Lachman, G.B.3
  • 34
    • 0005529424 scopus 로고    scopus 로고
    • Selecting gear for monitoring fish assemblages
    • (ed. Cowx I.G.), Blackwell Science Ltd., Oxford
    • Miranda LE, Schramm HL, (2000) Selecting gear for monitoring fish assemblages. In: Management and Ecology of River Fisheries (ed., Cowx IG,), pp. 3-13. Blackwell Science Ltd., Oxford.
    • (2000) Management and Ecology of River Fisheries , pp. 3-13
    • Miranda, L.E.1    Schramm, H.L.2
  • 35
    • 84957454676 scopus 로고    scopus 로고
    • MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than 230 subtropical marine species
    • Miya M, Sato Y, Fukunaga T, et al,. (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society Open Science, 2, 150088.
    • (2015) Royal Society Open Science , vol.2 , pp. 150088
    • Miya, M.1    Sato, Y.2    Fukunaga, T.3
  • 36
    • 84922480438 scopus 로고    scopus 로고
    • Biodiversity: Life - A status report
    • Monastersky R, (2014) Biodiversity: life-a status report. Nature, 516, 158-161.
    • (2014) Nature , vol.516 , pp. 158-161
    • Monastersky, R.1
  • 37
    • 84901642271 scopus 로고    scopus 로고
    • The biodiversity of species and their rates of extinction, distribution, and protection
    • Pimm SL, Jenkins CN, Abell R, et al,. (2014) The biodiversity of species and their rates of extinction, distribution, and protection. Science, 344, 1246752.
    • (2014) Science , vol.344 , pp. 1246752
    • Pimm, S.L.1    Jenkins, C.N.2    Abell, R.3
  • 38
    • 42049112560 scopus 로고    scopus 로고
    • Widespread unidirectional transfer of mitochondrial DNA: A case in western Palaearctic water frogs
    • Plötner J, Uzzell T, Beerli P, et al,. (2008) Widespread unidirectional transfer of mitochondrial DNA: a case in western Palaearctic water frogs. Journal of Evolutionary Biology, 21, 668-681.
    • (2008) Journal of Evolutionary Biology , vol.21 , pp. 668-681
    • Plötner, J.1    Uzzell, T.2    Beerli, P.3
  • 39
    • 84859602598 scopus 로고    scopus 로고
    • Who is eating what: Diet assessment using next generation sequencing
    • Pompanon F, Deagle BE, Symondson WOC, et al,. (2012) Who is eating what: diet assessment using next generation sequencing. Molecular Ecology, 21, 1931-1950.
    • (2012) Molecular Ecology , vol.21 , pp. 1931-1950
    • Pompanon, F.1    Deagle, B.E.2    Symondson, W.O.C.3
  • 40
  • 41
    • 82255164364 scopus 로고    scopus 로고
    • EcoPrimers: Inference of new DNA barcode markers from whole genome sequence analysis
    • Riaz T, Shehzad W, Viari A, et al,. (2011) ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Research, 39, e145.
    • (2011) Nucleic Acids Research , vol.39 , pp. e145
    • Riaz, T.1    Shehzad, W.2    Viari, A.3
  • 43
    • 84455196041 scopus 로고    scopus 로고
    • The quality of name-based species records in databases
    • Santos AM, Branco M, (2012) The quality of name-based species records in databases. Trends in Ecology & Evolution, 27, 6-7.
    • (2012) Trends in Ecology & Evolution , vol.27 , pp. 6-7
    • Santos, A.M.1    Branco, M.2
  • 44
    • 84943579883 scopus 로고    scopus 로고
    • Tag jumps illuminated - Reducing sequence-to-sample misidentifications in metabarcoding studies
    • Schnell IB, Bohmann K, Gilbert MTP, (2015) Tag jumps illuminated-reducing sequence-to-sample misidentifications in metabarcoding studies. Molecular Ecology Resources, 15, 1289-1303.
    • (2015) Molecular Ecology Resources , vol.15 , pp. 1289-1303
    • Schnell, I.B.1    Bohmann, K.2    Gilbert, M.T.P.3
  • 45
    • 10044220678 scopus 로고    scopus 로고
    • Status and trends of amphibian declines and extinctions worldwide
    • Stuart SN, Chanson JS, Cox NA, et al,. (2004) Status and trends of amphibian declines and extinctions worldwide. Science, 306, 1783-1786.
    • (2004) Science , vol.306 , pp. 1783-1786
    • Stuart, S.N.1    Chanson, J.S.2    Cox, N.A.3
  • 46
    • 33847371187 scopus 로고    scopus 로고
    • Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding
    • Taberlet P, Coissac E, Pompanon F, et al,. (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research, 35, e14.
    • (2007) Nucleic Acids Research , vol.35 , pp. e14
    • Taberlet, P.1    Coissac, E.2    Pompanon, F.3
  • 49
    • 82555175820 scopus 로고    scopus 로고
    • Population size influences amphibian detection probability: Implications for biodiversity monitoring programs
    • Tanadini LG, Schmidt BR, (2011) Population size influences amphibian detection probability: implications for biodiversity monitoring programs. PLoS ONE, 6, e28244.
    • (2011) PLoS ONE , vol.6 , pp. e28244
    • Tanadini, L.G.1    Schmidt, B.R.2
  • 50
    • 85028163034 scopus 로고    scopus 로고
    • Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity
    • Thomsen PF, Willerslev E, (2015) Environmental DNA-an emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation, 183, 4-18.
    • (2015) Biological Conservation , vol.183 , pp. 4-18
    • Thomsen, P.F.1    Willerslev, E.2
  • 51
    • 84861563592 scopus 로고    scopus 로고
    • Monitoring endangered freshwater biodiversity using environmental DNA
    • Thomsen PF, Kielgast J, Iversen LL, et al,. (2012a) Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 21, 2565-2573.
    • (2012) Molecular Ecology , vol.21 , pp. 2565-2573
    • Thomsen, P.F.1    Kielgast, J.2    Iversen, L.L.3
  • 52
    • 84865580050 scopus 로고    scopus 로고
    • Detection of a diverse marine fish fauna using environmental DNA from seawater samples
    • Thomsen PF, Kielgast J, Iversen LL, et al,. (2012b) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE, 7, e41732.
    • (2012) PLoS ONE , vol.7 , pp. e41732
    • Thomsen, P.F.1    Kielgast, J.2    Iversen, L.L.3
  • 53
    • 84904401917 scopus 로고    scopus 로고
    • Environmental DNA surveillance for invertebrate species: Advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds
    • Tréguier A, Paillisson J-M, Dejean T, et al,. (2014) Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds. Journal of Applied Ecology, 51, 871-879.
    • (2014) Journal of Applied Ecology , vol.51 , pp. 871-879
    • Tréguier, A.1    Paillisson, J.-M.2    Dejean, T.3
  • 55
    • 84922359193 scopus 로고    scopus 로고
    • WWF. (eds McLellan R. Iyengar L. Jeffries B. Oerlemans N.), WWF, Gland, Switzerland
    • WWF (2014) Living Planet Report 2014: Summary. (eds, McLellan R, Iyengar L, Jeffries B, Oerlemans N,), WWF, Gland, Switzerland.
    • (2014) Living Planet Report 2014: Summary
  • 56
    • 84864289492 scopus 로고    scopus 로고
    • DNA from soil mirrors plant taxonomic and growth form diversity
    • Yoccoz NG, Bråthen KA, Gielly L, et al,. (2012) DNA from soil mirrors plant taxonomic and growth form diversity. Molecular Ecology, 21, 3647-3655.
    • (2012) Molecular Ecology , vol.21 , pp. 3647-3655
    • Yoccoz, N.G.1    Bråthen, K.A.2    Gielly, L.3


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