| paper ID | Authors | Year | Journal | DOI | Title | Type of eDNA | Study System | Organism Focus | Target Species | Aim |
| 1 |
Adrian-Kalchhauser, I. & Burkhardt-Holm, P.
|
2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.0147558 | An eDNA assay to monitor a globally invasive fish species from flowing freshwater | water | river | fish | round goby (Neogobius melanostomus) | assay design, validation and development |
| 2 |
Agersnap, S., Brenner Larsen, W., Knudsen, S. W., Strand, D., Thomsen, P. F., Hesselsøe, M., Mortensen, P. B., Vrålstad, T. & Møller, P. R.
|
2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0179261 | Monitoring of noble, signal and narrow clawed crayfish using environmental DNA from freshwater samples | water | river, lake | crustacean | noble crayfish (Astacus astacus), signal crayfish (Pacifastacus leniusculus), narrow-clawed crayfish (Astacus leptodactylus) | assay design, validation and development – focus on LOD/LOQ |
| 3 | Amberg, J. J., McCalla, S. G., Monroe, E., Lance, R., Baerwaldt, K. & Gaikowski, M. P. | 2015 | Journal of Great Lakes Research | https://doi.org/10.1016/j.jglr.2015.02.009 | Improving efficiency and reliability of environmental DNA analysis for silver carp | water | river, lake | fish | Silver carp (Hypophthalmichthys molitrix) | assay development – PCR Vs qPCR, inhibition |
| 4 | Amberg, J. J., Merkes, C. M., Stott, W., Rees, C. B. & Erickson, R. A. | 2019 | Management of Biological Invasions | https://doi.org/10.3391/mbi.2019.10.1.06 | Environmental DNA as a tool to help inform zebra mussel, Dreissena polymorpha, management in inland lakes | water | lake | mussel | zebra mussel (Dreissena polymorpha) | eDNA assay development, testing |
| 5 | Anderson, J. T., Schumer, G., Anders, P. J., Horvath, K. & Merz, J. E. | 2018 | Journal of Fish and Wildlife Management | https://doi.org/10.3996/012018-JFWM-006 | Confirmed observation: a North American Green Sturgeon Acipenser medirostris recorded in the Stanislaus River, California | water | river | fish | North American green sturgeon (Acipenser medirostris) | confirmation record of North American green sturgeon through gridded eDNA sampling regime and snorkel survey |
| 6 | Antognazza, C. M., Britton, J. R., Potter, C., Franklin, E., Hardouin, E. A., Gutmann Roberts, C., Aprahamian, M. & Andreou, D. | 2019 | Aquatic Conservation: Marine and Freshwater Ecosystems | https://doi.org/10.1002/aqc.3010 | Environmental DNA as a non-invasive sampling tool to detect the spawning distribution of European anadromous shads (Alosa spp.) | water | river | fish | allis shad (Alosa alosa), twaite shad (Alosa fallax), hybrids | assay development and validation |
| 7 | Ardura, A., Zaiko, A., Martinez, J. L., Samulioviene, A., Semenova, A. & Garcia-Vazquez, E. | 2015 | Marine Environmental Research | https://doi.org/10.1016/j.marenvres.2015.09.013 | eDNA and specific primers for early detection of invasive species – A case study on the bivalve Rangia cuneata, currently spreading in Europe | water | mesocosm, lagoon, Baltic Sea | mollusc | North American wedge clam (Rangia cuneata) | assay design and validation |
| 8 | Atkinson, S., Carlsson, J. E. L., Ball, B., Egan, D., Kelly-Quinn, M., Whelan, K. & Carlsson, J. | 2018 | Aquatic Conservation: Marine and Freshwater Ecosystems | https://doi.org/10.1002/aqc.2931 | A quantitative PCR based environmental DNA assay for detecting Atlantic salmon (Salmo salar L.) | water | river | fish | Atlantic salmon (Salmo salar) | assay design, validation and field study |
| 9 | Baker, C. S., Steel, D., Nieukirk, S. & Klinck, H. | 2018 | Freshwater Science | https://doi.org/10.3389/fmars.2018.00133 | Environmental DNA (eDNA) from the wake of the whales: droplet digital PCR for detection and species identification | water | ocean | mammal | killer whale (Orcinus orca) | assay design, validation and development – persistence/degradation |
| 10 | Baker, S. J., Niemiller, M. L., Stites, A. J., Ash, K. T., Davis, M. A., Dreslik, M. J. & Phillips, C. A. | 2018 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-018-1053-9 | Evaluation of environmental DNA to detect Sistrurus catenatus and Ophidiomyces ophiodiicola in crayfish burrows | water | crayfish burrows | microorganism, reptile | eastern massasauga rattlesnake (Sistrurus catenatus), keratinophilic fungus (Ophidiomyces ophiodiicola) | assay design and validation |
| 11 | Balasingham, K. D., Walter, R. P. & Heath, D. D. | 2017 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12598 | Residual eDNA detection sensitivity assessed by quantitative real-time PCR in a river ecosystem | water | river | fish | Atlantic salmon (Salmo salar) | previously designed assay |
| 12 | Baldigo, B. P., Sporn, L. A., George, S. D. & Ball, J. A. | 2017 | Transactions of the American Fisheries Society | https://doi.org/10.1080/00028487.2016.1243578 | Efficacy of environmental DNA to detect and quantify brook trout populations in headwater streams of the Adirondack Mountains, New York | water | stream | fish | brook trout (Salvelinus fontinalis) | previously designed assay, field study |
| 13 | Baque, R. H., Gilliam, A. O., Robles, L. D., Jakubowski, W. & Slifko, T. R. | 2011 | water Research | https://doi.org/10.1016/j.watres.2011.03.032 | A real-time RT-PCR method to detect viable Giardia lamblia cysts in environmental waters | water | effluent | microorganism | parasitic microorganism (Giardia lamblia) | assay design and validation and field study |
| 14 | Barnes, M. A., Turner, C. R., Jerde, C. L., Renshaw, M. A., Chadderton, W. L. & Lodge, D. M. | 2014 | Environmental Science & Technology | https://doi.org/10.1021/es404734p | Environmental conditions influence eDNA persistence in aquatic systems | water | mesocosm | fish | common carp (Cyprinus carpio) | eDNA degradation in the lab |
| 16 | Beauclerc, K., Wozney, K., Smith, C. & Wilson, C. | 2018 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-017-0962-3 | Development of quantitative PCR primers and probes for environmental DNA detection of amphibians in Ontario | NA – tissue sample | NA | amphibian | 24 amphibian species native to Ontario | assay design and validation |
| 17 | Bellemain, E., Patricio, H., Gray, T., Guegan, F., Valentini, A., Miaud, C. & Dejean, T. | 2016 | Global Ecology and Conservation | https://doi.org/10.1016/j.gecco.2016.06.007 | Trails of river monsters: detecting critically endangered Mekong giant catfish Pangasianodon gigas using environmental DNA | water | experimental pond, pool | fish | Mekong giant catfish (Pangasianodon gigas) | assay design and validation |
| 18 | Berger, C. S. & Aubin-Horth, N. | 2018 | Journal of Experimental Biology | https://doi.org/10.1242/jeb.178137 | An eDNA-qPCR assay to detect the presence of the parasite Schistocephalus solidus inside its threespine stickleback host | water | lake, marsh | tapeworm | tapeworm (Schistocephalus solidus) | assay design and validation |
| 19 | Bergman, P. S., Schumer, G., Blankenship, S. & Campbell, E. | 2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.0153500 | Detection of adult green sturgeon using environmental DNA analysis | water | river | fish | green sturgeon (Acipenser medirostris) | assay design and validation |
| 20 | Biggs, J., Ewald, N., Valentini, A., Gaboriaud, C., Dejean, T., Griffiths, R. A., Foster, J., Wilkinson, J. W., Arnell, A., Brotherton, P., Williams, P. & Dunn, F. | 2015 | Biological Conservation | https://doi.org/10.1016/j.biocon.2014.11.029 | Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus) | water | pond | amphibian | great crested newt (Triturus cristatus) | previously designed assay, modified assay and validation, field study |
| 21 | Boothroyd, M., Mandrak, N. E., Fox, M. & Wilson, C. C. | 2016 | Aquatic Conservation: Marine and Freshwater Ecosystems | https://doi.org/10.1002/aqc.2617 | Environmental DNA (eDNA) detection and habitat occupancy of threatened spotted gar (Lepisosteus oculatus) | water | lake, river | fish | spotted gar (Lepisosteus oculatus) | assay design, validation and field study |
| 22 | Bracken, F. S. A., Rooney, S. M., Kelly-Quinn, M., King, J. J. & Carlsson, J. | 2019 | Ecology and Evolution | https://doi.org/10.1002/ece3.4777 | Identifying spawning sites and other critical habitat in lotic systems using eDNA “snapshots”: a case study using the sea lamprey Petromyzon marinus L. | water | river | fish | sea lamprey (Petromyzon marinus) | assay design, field study |
| 23 | Brandl, S., Schumer, G., Schreiner, B. M., Conrad, J. L., May, B. & Baerwald, M. R. | 2015 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12305 | Ten real-time PCR assays for detection of fish predation at the community level in the San Francisco Estuary–Delta | NA – tissue sample | estuary | fish | 53 fish species (salmon, sturgeon, smelt, etc.) | assay design and validation |
| 24 | Bronnenhuber, J. E. & Wilson, C. C. | 2013 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-013-9946-0 | Combining species-specific COI primers with environmental DNA analysis for targeted detection of rare freshwater species | NA – tissue sample | NA | crustacean, mollusc, fish | rare and invasive freshwater species | assay design and validation |
| 25 | Buxton, A. S., Groombridge, J. J. & Griffiths, R. A. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0183371 | Is the detection of aquatic environmental DNA influenced by substrate type? | water | mesocosm | amphibian | great crested newt (Triturus cristatus) | influence of substrate type |
| 26 | Buxton, A. S., Groombridge, J. J. & Griffiths, R. A. | 2018 | PLoS ONE | https://doi.org/10.1371/journal.pone.0191737 | Seasonal variation in environmental DNA detection in sediment and water samples | water, sediment | pond | amphibian | great crested newt (Triturus cristatus) | detection in sediment vs. detection in water |
| 27 | Buxton, A. S., Groombridge, J. J., Zakaria, N. B. & Griffiths, R. A. | 2017 | Scientific Reports | https://doi.org/10.1038/srep46294 | Seasonal variation in environmental DNA in relation to population size and environmental factors | water | pond | amphibian | great crested newt (Triturus cristatus) | detection and population density |
| 28 | Bylemans, J., Furlan, E. M., Hardy, C. M., McGuffie, P., Lintermans, M. & Gleeson, D. M. | 2017 | Methods in Ecology and Evolution | https://doi.org/10.1111/2041-210X.12709 | An environmental DNA-based method for monitoring spawning activity: a case study, using the endangered Macquarie perch (Macquaria australasica) | water | mesocosm, river | fish | Macquarie perch (Macquaria australasica) | assay design, validation and ecological investigation – spawning activity |
| 29 | Bylemans, J., Furlan, E. M., Pearce, L., Daly, T. & Gleeson, D. M. | 2016 | Biological Invasions | https://doi.org/10.1007/s10530-016-1203-5 | Improving the containment of a freshwater invader using environmental DNA (eDNA) based monitoring | water | river | fish | redfin perch (Perca fluviatilis) | field application of Furlan & Gleeson 2016 |
| 30 | Cai, W., Ma, Z., Yang, C., Wang, L., Wang, W., Zhao, G., Geng, Y. & Yu, D. W. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0177724 | Using eDNA to detect the distribution and density of invasive crayfish in the Honghe-Hani rice terrace World Heritage site | water | rice field | crustacean | red swamp crayfish (Procambarus clarkii) | assay design and validation |
| 32 | Carim, K. J., Dysthe, J. C., Young, M. K., McKelvey, K. S. & Schwartz, M. K. | 2016 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-016-0531-1 | An environmental DNA assay for detecting Arctic grayling in the upper Missouri River basin, North America | water | river | fish | Arctic grayling (Thymallus arcticus) | assay design and validation |
| 33 | Carim, K. J., Wilcox, T. M., Anderson, M., Lawrence, D. J., Young, M. K., McKelvey, K. S. & Schwartz, M. K. | 2016 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-016-0548-5 | An environmental DNA marker for detecting non native brown trout (Salmo trutta) | water | river | fish | Brown trout (Salmo trutta) | assay development and validation, field study |
| 34 | Carim, K. J., Christianson, K. R., McKelvey, K. M., Pate, W. M., Silver, D. B., Johnson, B. M., Galloway, B. T., Young, M. K. & Schwartz, M. K. | 2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.0161664 | Environmental DNA marker development with sparse biological information: a case study on opossum shrimp (Mysis diluviana) | water | lake | crustacean | opossum shrimp (Mysis diluviana) | assay design and validation |
| 35 | Carim, K. J., Dysthe, J. C., Young, M. K., McKelvey, K. S. & Schwartz, M. K. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0169334 | A noninvasive tool to assess the distribution of Pacific lamprey (Entosphenus tridentatus) in the Columbia River basin | water | river | fish | Pacific lamprey (Entosphenus tridentatus) | eDNA assay design to detect Pacific lamprey |
| 36 | Carlsson, J. E. L., Egan, D., Collins, P. C. Farrell, E. D., Igoe, F. & Carlsson, J. | 2017 | Aquatic Conservation: Marine and Freshwater Ecosystems | https://doi.org/10.1002/aqc.2788 | A qPCR MGB probe based eDNA assay for European freshwater pearl mussel (Margaritifera margaritifera L.) | water | river | mussel | European freshwater pearl mussel (Margaritifera margaritifera L.) | assay development and validation |
| 37 | Carraro, L., Bertuzzo, E., Mari, L., Fontes, I., Hartikainen, H., Strepparava, N., Schmidt-Posthaus, H., Wahli, T., Jokela, J., Gatto, M. & Rinaldo, A. | 2017 | Proceedings of the National Academy of Sciences of the United States of America | https://doi.org/10.1073/pnas.1713691114 | Integrated field, laboratory, and theoretical study of PKD spread in a Swiss prealpine river | water | river | myxozoan | myxozoan parasite (Tetracapsuloides bryosalmonae) | assay and info is in Supplementary Information / Appendix |
| 38 | Carraro, L., Hartikainen, H., Jokela, J., Bertuzzo, E. & Rinaldo, A. | 2018 | Proceedings of the National Academy of Sciences of the United States of America | https://doi.org/10.1073/pnas.1813843115 | Estimating species distribution and abundance in river networks using environmental DNA | water | river | bryozoan & myxozoan | parasite host (Fredericella sultana), myxozoan parasite (Tetracapsuloides bryosalmonae) | assay and info is in Supplementary Information / Appendix |
| 39 | Cho, A., Morris, T., Wilson, C. & Freeland, J. | 2016 | Genome | https://doi.org/10.1139/gen-2015-0196 | Development of species-specific primers with potential for amplifying eDNA from imperilled freshwater unionid mussels | water | mesocosm | mussel | 8 unionid species Ontario | assay design and validation |
| 40 | Clusa, L. & García‐Vázquez, E. | 2018 | Aquatic Conservation: Marine and Freshwater Ecosystems | https://doi.org/10.1002/aqc.2890 | A simple, rapid method for detecting seven common invasive fish species in Europe from environmental DNA | water | aquarium, river | fish | bullheads (Ameiurus melas, Ameiurus nebulosus), western mosquitofish (Gambusia affinis), eastern mosquitofish (Gambusia holbrooki), pumpkinseed (Lepomis gibbosus), largemouth bass (Micropterus salmoides), stone moroko (Pseudorasbora parva) | assay design and validation |
| 41 | Clusa, L., Ardura, A., Fernández, S., Roca, A. A. & García-Vázquez, E. | 2017 | PeerJ | https://doi.org/10.7717/peerj.3045 | An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples | water | river, reservoir | fish | rainbow trout (Oncorhynchus mykiss), Atlantic salmon (Salmo salar), brown trout (Salmo trutta), brook trout (Salvelinus fontinalis), lake trout (Salvelinus namaycush) | assay design and validation |
| 42 | Clusa, L., Ardura, A., Gower, F., Miralles, L., Tsartsianidou, V., Zaiko, A. & Garcia-Vazquez, E. | 2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.0162899 | An easy phylogenetically informative method to trace the globally invasive Potamopyrgus mud snail from river’s eDNA | water | river | mollusc | New Zealand mud snail (Potamopyrgus antipodarum) | assay design and validation |
| 43 | Clusa, L., Miralles, L., Basanta, A., Escot, C. & Garcia-Vazquez, E. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0188126 | eDNA for detection of five highly invasive molluscs. A case study in urban rivers from the Iberian Peninsula | water | river | mollusc | Asian clam (Corbicula fluminea), red-rimmed melania (Melanoides tuberculata), Conrad’s false mussel (Mytilopsis leucophaeata), Chinese pond mussel (Sinanodonta woodiana) | assay design and validation |
| 44 | Collins, R. A., Armstrong, K. F., Holyoake, A. J. & Keeling, S. | 2013 | Biological Invasions | https://doi.org/10.1007/s10530-012-0376-9 | Something in the water: biosecurity monitoring of ornamental fish imports using environmental DNA | water | aquarium | fish | zebrafish (Danio rerio) | assay design and validation; not easily accessible |
| 45 | Collins, R. A., Wangensteen, O. S., O’Gorman, E. J., Mariani, S., Sims, D. W. & Genner, M. J. | 2018 | Communications Biology | https://doi.org/10.1038/s42003-018-0192-6 | Persistence of environmental DNA in marine systems | water | marine | crustacean, fish | shanny (Lipophrys pholis), common shore crab (Carcinus maenas) | assay design and validation |
| 46 | Costas, B. A., McManus, G., Doherty, M. & Katz, L. A. | 2007 | Limnology and Oceanography: Methods | https://doi.org/10.4319/lom.2007.5.163 | Use of species-specific primers and PCR to measure the distributions of planktonic ciliates in coastal waters | water | sea | microorganism | planktonic ciliates | assay design and validation |
| 47 | Coulter, A. A., Keller, D., Amberg, J. J., Bailey, E. J. & Goforth, R. R. | 2013 | Freshwater Biology | https://doi.org/10.1111/fwb.12106 | Phenotypic plasticity in the spawning traits of bigheaded carp (Hypophthalmichthys spp.) in novel ecosystems | fish eggs in water | river | fish | bigheaded carp (Hypophthalmichthys spp.) | assay development: identification of drifting eggs qPCR |
| 48 | Cowart, D. A., Breedveld, K. G. H., Ellis, M. J., Hull, J. M. & Larson, E. R. | 2018 | Journal of Crustacean Biology | https://doi.org/10.1093/jcbiol/ruy007/4925914 | Environmental DNA (eDNA) applications for the conservation of imperiled crayfish (Decapoda: Astacidea) through monitoring of invasive species barriers and relocated populations | water | creek, lake, river | crustacean | Shasta crayfish (Pacifastacus fortis), American signal crayfish (Pacifastacus leniusculus) | assay design and validation |
| 49 | Cowart, D. A., Renshaw, M. A., Gantz, C. A., Umek, J., Chandra, S., Egan, S. P., Lodge, D. M. & Larson, E. R. | 2018 | Management of Biological Invasions | https://doi.org/10.3391/mbi.2018.9.1.03 | Development and field validation of an environmental DNA (eDNA) assay for invasive clams of the genus Corbicula | water | lake, reservoir | mollusc | Asian clam (Corbicula fluminea) | assay design and validation |
| 50 | Currier, C. A., Morris, T. J., Wilson, C. C. & Freeland, J. R. | 2018 | Aquatic Conservation: Marine and Freshwater Ecosystems | https://doi.org/10.1002/aqc.2869 | New Zealand mud snail (Potamopyrgus antipodaru) | water | river | mollusc | 4 unionid species Ontario | assay design and validation |
| 51 | Davis, A. J., Williams, K. E., Snow, N. P., Pepin, K. M. & Piaggio, A. J. | 2018 | Ecology and Evolution | https://doi.org/10.1002/ece3.4552 | Accounting for observation processes across multiple levels of uncertainty improves inference of species distributions and guides adaptive sampling of environmental DNA | water | mud pond | mammal | wild boar (Sus scrofa) | based on Williams et al 2017; wild boar |
| 52 | Davison, P. I., Créach, V., Liang, W. J., Andreou, D., Britton, J. R. & Copp, G. H. | 2016 | Journal of Fish Biology | https://doi.org/10.1111/jfb.13086 | Laboratory and field validation of a simple method for detecting four species of non-native freshwater fish using eDNA | water | aquarium, experimental & natural pond | fish | pumpkinseed (Lepomis gibbosus), sunbleak (Leucaspius delineatus), fathead minnow (Pimephales promelas), topmouth gudgeon (Pseudorasbora parva) | assay design, validation and development – persistence, spatial distribution |
| 53 | Davison, P. I., Copp, G. H., Créach, V., Vilizzi, L. & Britton, J. R. | 2017 | Science of Nature | https://doi.org/10.1007/s00114-017-1453-9 | Application of environmental DNA analysis to inform invasive fish eradication operations | water | pond | fish | topmouth gudgeon (Pseudorasbora parva) | assay design and validation |
| 54 | Davy, C. M., Kidd, A. G. & Wilson, C. C. | 2015 | PLoS ONE | https://doi.org/10.1371/journal.pone.0130965 | Development and validation of environmental DNA (eDNA) markers for detection of freshwater turtles | water | aquarium, experimental pond | reptile | multiple freshwater turtles | assay design, validation and development – PCR Vs qPCR, inhibition, cost comparison |
| 55 | de Souza, L. S., Godwin, J. C., Renshaw, M. A. & Larson, E. | 2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.0165273 | Environmental DNA (eDNA) detection probability is influenced by seasonal activity of organisms | water | river, stream reaches | amphibian, reptile | Black Warrior waterdog (Necturus alabamensis), flattened musk turtle (Sternotherus depressus) | assay design, validation and development – occupancy modeling, seasonality |
| 56 | De Ventura, L., Kopp, K., Seppaelae, K. & Jokela, J. | 2017 | Management of Biological Invasions | https://doi.org/10.3391/mbi.2017.8.1.10 | Tracing the quagga mussel invasion along the Rhine river system using eDNA markers: early detection and surveillance of invasive zebra and quagga mussels | water | river | mussel | zebra mussel (Dreissena polymorpha), quagga mussel (Dreissena bugensis) | development of Bronnenhuber et al. 2013 |
| 57 | Deagle, B. E., Bax, N., Hewitt, C. L. & Patil, J. G. | 2003 | Marine and Freshwater Research | https://doi.org/10.1071/MF03031 | Development and evaluation of a PCR-based test for detection of Asterias (Echinodermata: Asteroidea) larvae in Australian plankton samples from ballast water | plankton sample, water | ballast water | echinoderm | sea stars (Echinodermata: Asteroidea) | assay design and validation |
| 58 | Deiner, K. & Altermatt, F. | 2014 | PLoS ONE | https://doi.org/10.1371/journal.pone.0088786 | Transport distance of invertebrate environmental DNA in a natural river | water | river | crustacean, mollusc | freshwater water flea (Daphnia longispina), swollen river mussel (Unio tumidus) | assay design, validation and development – eDNA transport |
| 59 | Dejean, T., Valentini, A., Duparc, A., Pellier-Cuit, S., Pompanon, F., Taberlet, P. & Miaud, C. | 2011 | PLoS ONE | https://doi.org/10.1371/journal.pone.0023398 | Persistence of environmental DNA in freshwater ecosystems | water | mesocosm, experimental pond | amphibian, fish | American bullfrog (Lithobates catesbeianus), Siberian sturgeon (Acipenser baerii) | assay design, validation and development – persistence, density |
| 60 | Dejean, T., Valentini, A., Miquel, C., Taberlet, P., Bellemain, E. & Miaud, C. | 2012 | Journal of Applied Ecology | https://doi.org/10.1111/j.1365-2664.2012.02171.x | Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus | water | pond | amphibian | American bullfrog (Rana catesbeiana = Lithobates catesbeianus) | not sure if development from Ficetola et al. 2008 |
| 61 | Díaz-Ferguson, E., Herod, J., Galvez, J. & Moyer, G. | 2014 | Management of Biological Invasions | https://doi.org/10.3391/mbi.2014.5.2.05 | Development of molecular markers for eDNA detection of the invasive African jewelfish (Hemichromis letourneuxi): a new tool for monitoring aquatic invasive species in National Wildlife Refuges | water | aquarium, canal | fish | African jewelfish (Hemichromis letourneuxi) | assay design, validation and development – PCR Vs qPCR, detection probability |
| 62 | Doi, H., Inui, R., Akamatsu, Y., Kanno, K., Yamanaka, H., Takahara, T. & Minamoto, T. | 2017 | Freshwater Biology | https://doi.org/10.1111/fwb.12846 | Environmental DNA analysis for estimating the abundance and biomass of stream fish | water | stream | fish | sweetfish (Plecoglossus altivelis) | previously designed assay, field study |
| 63 | Doi, H., Katano, I., Sakata, Y., Souma, R., Kosuge, T., Nagano, M., Ikeda, K., Yano, K. & Tojo, K. | 2017 | Royal Society of Open Science | https://doi.org/10.1098/rsos.170568 | Detection of an endangered aquatic heteropteran using environmental DNA in a wetland ecosystem | water | swamp | insect | aquatic hemipteran (Nepa hoffmanni) | assay design and validation |
| 64 | Doi, H., Takahara, T., Minamoto, T., Matsuhashi, S., Uchii, K. & Yamanaka, H. | 2015 | Environmental Science & Technology | https://doi.org/10.1021/acs.est.5b00253 | Droplet digital polymerase chain reaction (PCR) outperforms real-time PCR in the detection of environmental DNA from an invasive fish species | water | pond | fish | bluegill sunfish (Lepomis macrochirus) | assay development – qPCR vs. ddPCR, inhibition, LOD |
| 65 | Doi, H., Uchii, K., Takahara, T., Matsuhashi, S., Yamanaka, H. & Minamoto, T. | 2015 | PLoS ONE | https://doi.org/10.1371/journal.pone.0122763 | Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys | water | mesocosm | fish | common carp (Cyprinus carpio) | assay development – qPCR Vs ddPCR, abundance/biomass estimation |
| 66 | Doi, H., Akamatsu, Y., Watanabe, Y., Goto, M., Inui, R., Katano, I., Nagano, M., Takahara, T. & Minamoto, T. | 2017 | Limnology and Oceanography: Methods | https://doi.org/10.1002/lom3.10214 | Water sampling for environmental DNA surveys by using an unmanned aerial vehicle | water | lake (dam) | fish | bluegill sunfish (Lepomis macrochirus), largemouth bass (Micropterus salmoides) | development of Takahara et al. 2013 and Yamanaka et al. 2016 |
| 67 | Doi, H., Uchii, K., Matsuhashi, S., Takahara, T., Yamanaka, H. & Minamoto, T. | 2017 | Limnology and Oceanography: Methods | https://doi.org/10.1002/lom3.10161 | Isopropanol precipitation method for collecting fish environmental DNA | water | lake, mesocosm | fish | common carp (Cyprinus carpio L.) | development of Takahara et al. 2012 |
| 68 | Dougherty, M. M., Larson, E. R., Renshaw, M. A., Gantz, C. A., Egan, S. P., Erickson, D. M. & Lodge, D. M. | 2016 | Journal of Applied Ecology | https://doi.org/10.1111/1365-2664.12621 | Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances | water | lake | crustacean | rusty crayfish (Orconectes rusticus) | assay design, validation and development – detection probability, abundance estimation |
| 69 | Doyle, J. R., McKinnon, A. D. & Uthicke, S. | 2017 | Marine Biology | https://doi.org/10.1007/s00227-017-3206-x | Quantifying larvae of the coralivorous seastar Acanthaster cf. solaris on the Great Barrier Reef using qPCR | water | sea | echinoderm | crown-of-thorns sea star (Acanthaster cf. solaris) | assay design and validation, field sampling |
| 70 | Dunker, K. J., Sepulveda, A. J., Massengill, R. L., Olsen, J. B., Russ, O. L., Wenburg, J. K. & Antonovich, A. | 2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.0162277 | Potential of environmental DNA to evaluate northern pike (Esox lucius) eradication efforts: an experimental test and case study | water | lake | fish | northern pike (Esox lucius) | based on Olsen et al. 2015 and Olsen et al. 2016; the primer paper and the Erratum |
| 71 | Dunn, N., Priestley, V., Herraiz, A., Arnold, R. & Savolainen, V. | 2017 | Ecology and Evolution | https://doi.org/10.1002/ece3.3316 | Behavior and season affect crayfish detection and density inference using environmental DNA | water | mesocosm | crustacean | American signal crayfish (Pacifastacus leniusculus) | assay design, validation and development – behaviour, seasonality |
| 72 | Dysthe, J. C., Carim, K. J., Ruggles, M., McKelvey, K. S., Young, M. K. & Schwartz, M. K. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0176459 | Environmental DNA assays for the sister taxa sauger (Sander canadensis) and walleye (Sander vitreus) | water | river | fish | sauger (Sander canadensis), walleye (Sander vitreus) | assay design, validation and field study |
| 73 | Dysthe, J. C., Rodgers, T., Franklin, T. W., Carim, K. J., Young, M. K., McKelvey, K. S., Mock, K. E. & Schwartz, M. K. | 2018 | Ecology and Evolution | https://doi.org/10.1002/ece3.3898 | Repurposing environmental DNA samples—detecting the western pearlshell (Margaritifera falcata) as a proof of concept | water | creek, river, stream | mollusc | western pearlshell (Margaritifera falcata) | assay design and validation |
| 74 | Dysthe, J. C., Carim, K. J., Paroz, Y. M., McKelvey, K. S., Young, M. K. & Schwartz, M. K. | 2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.0162200 | Quantitative PCR assays for detecting loach minnow (Rhinichthys cobitis) and spikedace (Meda fulgida) in the southwestern United States | water | river | fish | loach minnow (Rhinichthys cobitis), spikedace (Meda fulgida) | assay design and validation |
| 75 | Dysthe, J. C., Franklin, T. W., McKelvey, K. S., Young, M. K. & Schwartz, M. K. | 2018 | PLoS ONE | https://doi.org/10.1371/journal.pone.0206851 | An improved environmental DNA assay for bull trout (Salvelinus confluentus) based on the ribosomal internal transcribed spacer I | water | river | fish | bull trout (Salvelinus confluentus) | assay design and validation |
| 76 | Egan, S. P., Barnes, M. A., Hwang, C. T., Mahon, A. R., Feder, J. L., Ruggiero, S. T., Tanner, C. E. & Lodge, D. M. | 2013 | Conservation Letters | https://doi.org/10.1111/conl.12017 | Rapid invasive species detection by combining environmental DNA with light transmission spectroscopy | water | lake | mussel, crustacean | quagga mussel (Dreissena bugensis), zebra mussel (Dreissena polymorpha), Chinese mitten crab (Eriocheir sinensis), golden mussel (Limnoperna fortunei), green crab (Carcinus maenas) | development of Pie et al. 2006, Mahon et al. 2011 and Senapati et al. 2009 |
| 77 | Egan, S. P., Grey, E., Olds, B., Feder, J. L., Ruggiero, S. T., Tanner, C. E. & Lodge, D. M. | 2015 | Environmental Science & Technology | https://doi.org/10.1021/es5058659 | Rapid molecular detection of invasive species in ballast and harbor water by integrating environmental DNA and light transmission spectroscopy | water | ballast & harbour water | mussel | quagga mussel (Dreissena bugensis), zebra mussel (Dreissena polymorpha) | Quantifying larvae of the coralivorous seastar Acanthaster cf. solaris on the Great Barrier Reef using qPCR |
| 78 | Eichmiller, J. J., Bajer, P. G. & Sorensen, P. W. | 2014 | PLoS ONE | https://doi.org/10.1371/journal.pone.0112611 | The relationship between the distribution of common carp and their environmental DNA in a small lake | water | lake | fish | common carp (Cyprinus carpio) | assay design, validation and development – sampling strategy, spatial distribution |
| 79 | Eichmiller, J. J., Best, S. E. & Sorensen, P. W. | 2016 | Environmental Science & Technology | https://doi.org/10.1021/acs.est.5b05672 | Effects of temperature and trophic state on degradation of environmental DNA in lake water | water | lakewater in microcosm | fish | common carp (Cyprinus carpio) | development of Eichmiller et al. 2014 – at least new extraction |
| 80 | Eichmiller, J. J., Miller, L. M. & Sorensen, P. W. | 2016 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12421 | Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish | water | controlled laboratory experiment | fish | common carp (Cyprinus carpio) | not sure if development of Eichmiller et al. 2014 – contains assay of Oncorhynchus keta in Supporting Info |
| 81 | Eiler, A., Löfgren, A., Hjerne, O., Nordén, S. & Saetre, P. | 2018 | Scientific Reports | https://doi.org/10.1038/s41598-018-23740-5 | Environmental DNA (eDNA) detects the pool frog (Pelophylax lessonae) at times when traditional monitoring methods are insensitive | water | pond | amphibian | pool frog (Pelophylax lessonae) | assay design, validation and development – occupancy modeling, seasonality, life history |
| 82 | Emenyeonu, L. C., Croxford, A. E. & Wilkinson, M. J. | 2018 | PLoS ONE | https://doi.org/10.1371/journal.pone.0201617 | The potential of aerosol eDNA sampling for the characterisation of commercial seed lots | air | seed dust | plant | maize (Zea mays), cowpea (Vigna unguiculata) | contains a new qPCR protocol |
| 83 | Erickson, R. A., Merkes, C. M., Jackson, C. A., Goforth, R. R. & Amberg, J. J. | 2017 | Journal of Great Lakes Research | https://doi.org/10.1016/j.jglr.2017.06.003 | Seasonal trends in eDNA detection and occupancy of bigheaded carps | water | river | fish | bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix) | assay design and validation |
| 84 | Evans, N. T., Shirey, P. D., Wieringa, J. G., Mahon, A. R. & Lamberti, G. A. | 2017 | Fisheries | https://doi.org/10.1080/03632415.2017.1276329 | Comparative cost and effort of fish distribution detection via environmental DNA analysis and electrofishing | water | river | fish | brook trout (Salvelinus fontinalis) | development of Wilcox et al. 2013 |
| 85 | Farley, N. J., Vasquez, A. A., Kik, R., David, S. R., Katailiha, A. S., Walker, X. N. & Ram, J. L. | 2018 | Transactions of the American Fisheries Society | https://doi.org/10.1002/tafs.10043 | Primer designs for identification and environmental DNA (eDNA) detection of gars | water | aquarium | fish | gars (Lepisosteidae) | assay design and validation |
| 86 | Farrington, H. L., Edwards, C. E., Guan, X., Carr, M. R., Baerwaldt, K. & Lance, R. F. | 2015 | PLoS ONE | https://doi.org/10.1371/journal.pone.0117803 | Mitochondrial genome sequencing and development of genetic markers for the detection of DNA of invasive bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) in environmental water samples from the United States | water | bayou, creek | fish | bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix) | assay design and validation |
| 87 | Feist, S. M., Jones, R. L., Copley, J. L., Pearson, L. S., Berry, G. A. & Qualls, C. P. | 2018 | Chelonian Conservation and Biology | https://doi.org/10.2744/CCB-1315.1 | Development and validation of an environmental DNA method for detection of the alligator snapping turtle (Macrochelys temminckii) | water | river, lake | turtle | alligator snapping turtle (Macrochelys temminckii) | assay design and validation |
| 88 | Fernandez, S., Sandin, M. M., Beaulieu, P. G., Clusa, L., Martinez, J. L., Ardura, A. & Garcia-Vazquez, E. | 2018 | PEERJ | https://doi.org/10.7717/peerj.4486 | Environmental DNA for freshwater fish monitoring: insights for conservation within a protected area | water | stream | fish | rainbow trout (Oncorhynchus mykiss), brown trout (Salmo trutta) | development of Gustavson et al. 2015 and Wilcox et al. 2015 |
| 89 | Ficetola, G. F., Miaud, C., Pompanon, F. & Taberlet, P. | 2008 | Biology Letters | https://doi.org/10.1098/rsbl.2008.0118 | Species detection using environmental DNA from water samples | water | pond | amphibian | American bullfrog (Lithobates catesbeianus) | assay design and validation |
| 90 | Fontes, I., Hartikainen, H., Holland, J. W., Secombes, C. J. & Okamura, B. | 2017 | Diseases of Aquatic Organisms | https://doi.org/10.3354/dao03116 | Tetracapsuloides bryosalmonae abundance in river water | water | river | myxozoan | myxozoan parasite (Tetracapsuloides bryosalmonae) | assay design and validation |
| 91 | Foote, A. D., Thomsen, P. F., Sveegaard, S., Wahlberg, M., Kielgast, J., Kyhn, L. A., Salling, A. B., Galatius, A., Orlando, L. & Gilbert, M. T. P. | 2012 | PLoS ONE | https://doi.org/10.1371/journal.pone.0041781 | Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals | water | sea pen, Baltic sea | mammal | harbor porpoise (Phocoena phocoena) | assay design and validation |
| 92 | Forsström, T. & Vasemägi, A. | 2016 | Marine Pollution Bulletin | https://doi.org/10.1016/j.marpolbul.2016.05.054 | Can environmental DNA (eDNA) be used for detection and monitoring of introduced crab species in the Baltic Sea? | water | aquarium, bay, Archipelago Sea | crustacean | mud crab (Rhithropanopeus harrisii) | assay design, validation and development – persistence/degradation |
| 93 | Franklin, T. W., Dysthe, J. C., Golden, M., McKelvey, K. S., Hossack, B. R., Carim, K. J., Tait, C., Young, M. K. & Schwartz, M. K. | 2018 | Global Ecology and Conservation | https://doi.org/10.1016/j.gecco.2018.e00438 | Inferring presence of the western toad (Anaxyrus boreas) species complex using environmental DNA | water | pond | amphibian | western toad (Anaxyrus boreas) | assay design and validation |
| 94 | Franklin, T. W., Dysthe, J. C., Rubenson, E. S., Carim, K. J., Olden, J. D., McKelvey, K. S., Young, M. K. & Schwartz, M. K. | 2018 | Northwest Science | https://doi.org/10.3955/046.092.0207 | A non-invasive sampling method for detecting non-native smallmouth bass (Micropterus dolomieu) | water | stream | fish | smallmouth bass (Micropterus dolomieu) | assay design and validation |
| 95 | Franklin, T. W., McKelvey, K. S., Golding, J. D., Mason, D. H., Dysthe, J. C., Pilgrim, K. L., Squires, J. R., Aubry, K. B., Long, R. A., Greaves, S. E., Raley, C. M., Jackson, S., MacKay, P., Lisbon, J., Sauder, J. D., Pruss, M. T., Heffington, D. & Schwartz, M. K. | 2019 | Biological Conservation | https://doi.org/10.1016/j.biocon.2018.11.006 | Using environmental DNA methods to improve winter surveys for rare carnivores: DNA from snow and improved noninvasive techniques | snow, hair | forest | mammal | Canada lynx (Lynx canadensis), fisher (Pekania pennanti), wolverine (Gulo gulo) | assay design and validation |
| 96 | Fujiwara, A., Matsuhashi, S., Doi, H., Yamamoto, S. & Minamoto, T. | 2016 | Freshwater Science | https://doi.org/10.1086/685882 | Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds | water | aquarium, pond | plant | invasive plant (Egeria densa) | assay design, validation and development – persistence/degradation |
| 97 | Fukumoto, S., Ushimaru, A. & Minamoto, T. | 2015 | Journal of Applied Ecology | https://doi.org/10.1111/1365-2664.12392 | A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan | water | river | amphibian | Japanese giant salamander (Andrias japonicus), Chinese giant salamander (Andrias davidianus) | assay design, validation and field study |
| 98 | Furlan, E. M., Gleeson, D., Hardy, C. M. & Duncan, R. P. | 2016 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12483 | A framework for estimating the sensitivity of eDNA surveys | water | river, stream | fish | oriental weatherloach (Misgurnus anguillicaudatus) | assay design, validation and development – occupancy modeling, abundance estimation |
| 99 | Furlan, E. M. & Gleeson, D. | 2016 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-016-0523-1# | Environmental DNA detection of redfin perch, Perca fluviatilis | water | river | fish | redfin perch (Perca fluviatilis) | assay development and validation, field study |
| 100 | Furlan, E. M. & Gleeson, D. | 2017 | Marine and Freshwater Research | https://doi.org/10.1071/MF15349 | Improving reliability in environmental DNA detection surveys through enhanced quality control | water | stream | fish | common carp (Cyprinus carpio) | assay design and validation |
| 101 | Gantz, C. A., Renshaw, M. A., Erickson, D., Lodge, D. M. & Egan, S. P. | 2018 | Biological Invasions | https://doi.org/10.1007/s10530-018-1718-z | Environmental DNA detection of aquatic invasive plants in lab mesocosm and natural field conditions | water | mesocosm, river, watershed | plant | Canadian pondweed (Elodea canadensis), western waterweed (Elodea nuttallii), water thyme (Hydrilla verticillata) | assay design, validation and development – persistence/degradation |
| 102 | Gargan, L. M., Morato, T., Pham, C. K., Finarelli, J. A., Carlsson, J. E. L. & Carlsson, J. | 2017 | Marine Biology | https://doi.org/10.1007/s00227-017-3141-x | Development of a sensitive detection method to survey pelagic biodiversity using eDNA and quantitative PCR: a case study of devil ray at seamounts | water | seamount | fish | Chilean devil ray (Mobula tarapacana) | assay design and validation |
| 103 | Gaynor, J. J., Bologna, P. A. X., Restaino, D. J. & Barry, C. L. | 2017 | Journal of Coastal Research | https://doi.org/10.2112/SI78-014.1 | qPCR detection of early life history stage Chrysaora quinquecirrha (sea nettles) in Barnegat Bay, New Jersey | water | marine | jellyfish | sea nettles (Chrysaora quinquecirrha) | assay design and validation |
| 104 | Geerts, A. N., Boets, P., Van den Heede, S., Goethals, P. & Van der Heyden, C. | 2018 | Ecological Indicators | https://doi.org/10.1016/j.ecolind.2017.08.068 | A search for standardized protocols to detect alien invasive crayfish based on environmental DNA (eDNA): a lab and field evaluation | water | aquarium, pond, rampart | crustacean | red swamp crayfish (Procambarus clarkii) | assay design, validation and development – sampling/extraction/primer comparison |
| 105 | Ghosal, R., Eichmiller, J. J., Witthuhn, B. A. & Sorensen, P. W. | 2018 | Ecology and Evolution | https://doi.org/10.1002/ece3.4169 | Attracting common carp to a bait site with food reveals strong positive relationships between fish density, feeding activity, environmental DNA, and sex pheromone release that could be used in invasive fish management | water | lake | fish | common carp (Cyprinus carpio) | based on Eichmiller et al. 2016 |
| 106 | Gingera, T. D., Steeves, T. B., Boguski, D. A., Whyard, S., Li, W. & Docker, M. F. | 2016 | Journal of Great Lakes Research | https://doi.org/10.1016/j.jglr.2016.02.017 | Detection and identification of lampreys in Great Lakes streams using environmental DNA | water | river, stream | fish | sea lamprey (Petromyzon marinus), American brook lamprey (Lethenteron appendix), chestnut lamprey (Ichthyomyzon castaneus), silver lamprey (Ichthyomyzon unicuspis), northern brook lamprey (Ichthyomyzon fossor) | assay design, validation and development – spawning, density estimation |
| 107 | Gingera, T. D., Bajno, R., Docker, M. F. & Reist, J. D. | 2017 | Management of Biological Invasions | https://doi.org/10.3391/mbi.2017.8.3.03 | Environmental DNA as a detection tool for zebra mussels Dreissena polymorpha (Pallas, 1771) at the forefront of an invasion event in Lake Winnipeg, Manitoba, Canada | water | lake | mussel | zebra mussel (Dreissena polymorpha) | assay design and validation |
| 108 | Goldberg, C. S., Pilliod, D. S., Arkle, R. S. & Waits, L. P. | 2011 | PLoS ONE | https://doi.org/10.1371/journal.pone.0022746 | Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders | water | stream | amphibian | Rocky Mountain tailed frog (Ascaphus montanus), Idaho giant salamander (Dicamptodon aterrimus) | assay design and validation |
| 109 | Goldberg, C. S., Sepulveda, A., Ray, A., Baumgardt, J. & Waits, L. P. | 2013 | Freshwater Science | https://doi.org/10.1899/13-046.1 | Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum) | water | aquarium, river | mollusc | New Zealand mudsnail (Potamopyrgus antipodarum) | assay design and validation |
| 110 | Goldberg, C. S., Strickler, K. M. & Fremier, A. K. | 2018 | Science of the Total Environment | https://doi.org/10.1016/j.scitotenv.2018.02.295 | Degradation and dispersion limit environmental DNA detection of rare amphibians in wetlands: increasing efficacy of sampling designs | water | wetland | amphibian | Chiricahua leopard frogs (Rana chiricahuensis), Sonoran tiger salamanders (Ambystoma mavortium stebbinsi), American bullfrog (Rana catesbeiana), Arizona tree frogs (Hyla wrightorum), reticulated flatwoods salamanders (Ambystoma bishopi), ornate chorus frogs (Pseudacris ornata) | assay design, validation and development – sampling strategy, spatial distribution, abiotic factors |
| 111 | Gomes, G. B., Hutson, K. S., Domingos, J. A., Chung, C., Hayward, S., Miller, T. L. & Jerry, D. R. | 2017 | Aquaculture | https://doi.org/10.1016/j.aquaculture.2017.06.021 | Use of environmental DNA (eDNA) and water quality data to predict protozoan parasites outbreaks in fish farms | water | pond | microorganism | ciliate protozoan (Chilodonella hexasticha) | assay design and validation |
| 112 | Goricki, S., Stankovic, D., Snoj, A., Kuntner, M., Jeffery, W. R., Trontelj, P., Pavicevic, M., Grizelj, Z., Naparus-Aljancic, M. & Aljancic, G. | 2017 | Scientific Reports | https://doi.org/10.1038/srep45054 | Environmental DNA in subterranean biology: range extension and taxonomic implications for Proteus | water | cavewater, spring | amphibian | olm (Proteus anguinus) | assay design and validation |
| 113 | Goto, K., Min, Y. Y., Sato, E. & Toyota, K. | 2011 | Nematology | https://doi.org/10.1163/138855410X543175 | A multiplex real-time PCR assay for the simultaneous quantification of the major plant-parasitic nematodes in Japan | soil | farmer’s field | nematode | southern root-nematode (Meloidogyne incognita), type of nematode (Pratylenchus penetrans), golden nematode (Globodera rostochiensis), soybean cyst nematode (Heterodera glycines) | assay design and validation |
| 114 | Guillera-Arroita, G., Lahoz-Monfort, J. J., van Rooyen, A. R., Weeks, A. R. & Tingley, R. | 2017 | Methods in Ecology and Evolution | https://doi.org/10.1111/2041-210X.12743 | Dealing with false-positive and false-negative errors about species occurrence at multiple levels | water | drain | amphibian | striped marsh frog (Limnodynastes peronii), spotted marsh frog (Limnodynastes tasmaniensis), southern brown tree frog (Litoria ewingii), common froglet (Crinia signifera) | new assays described in Supplementary Information |
| 115 | Gustavson, M. S., Collins, P. C., Finarelli, J. A., Egan, D., Conchúir, R. Ó., Wightman, G. D., King, J. J., Gauthier, D. T., Whelan, K., Carlsson, J. E. L. & Carlsson, J. | 2015 | Journal of Fish Biology | https://doi.org/10.1111/jfb.12781 | An eDNA assay for Irish Petromyzon marinus and Salmo trutta and field validation in running water | water | river | fish | sea lamprey (Petromyzon marinus), brown trout (Salmo trutta) | assay design, validation and development – abundance estimation |
| 116 | Halstead, B. J., Kleeman, P. M., Goldberg, C. S., Bedwell, M., Douglas, R. B. & Ulrich, D. W. | 2018 | Northwestern Naturalist | https://doi.org/10.1898/NWN17-17.1 | Occurrence of California red-Legged (Rana draytonii) and northern red-Legged (Rana aurora) frogs in timberlands of Mendocino County, California, examined with environmental DNA | water | stream | amphibian | California red-legged frog (Rana draytonii), northern red-legged frog (Rana aurora) | occupancy modeling |
| 117 | Hamaguchi, M., Shimabukuro, H., Hori, M., Yoshida, G., Terada, T. & Miyajima, T. | 2018 | Limnology and Oceanography: Methods | https://doi.org/10.1002/lom3.10242 | Quantitative real-time polymerase chain reaction (PCR) and droplet digital PCR duplex assays for detecting Zostera marina DNA in coastal sediments | sediment | Seto Inland Sea | plant | common eelgrass (Zostera marina) | assay design, validation and development – qPCR vs. ddPCR |
| 118 | Harper, K. J., Anucha, N. P., Turnbull, J. F., Bean, C. W. & Leaver, M. J. | 2018 | Management of Biological Invasions | https://doi.org/10.3391/mbi.2018.9.2.07 | Searching for a signal: environmental DNA (eDNA) for the detection of invasive signal crayfish, Pacifastacus leniusculus (Dana, 1852) | water | aquarium, loch, river | crustacean | signal crayfish (Pacifastacus leniusculus) | assay design, validation and development – persistence, density, seasonality |
| 119 | Harper, L. R., Griffiths, N. P., Lawson Handley, L., Sayer, C. D., Read, D. S., Harper, K. J., Blackman, R. C., Li, J. & Hanfling, B. | 2019 | Freshwater Biology | https://doi.org/10.1111/fwb.13197 | Development and application of environmental DNA surveillance for the threatened crucian carp (Carassius carassius) | water | lake | fish | crucian carp (Carassius carassius) | assay design and validation |
| 120 | Harrer, L. E. F. & Levi, T. | 2018 | Ecosphere | https://doi.org/10.1002/ecs2.2076 | The primacy of bears as seed dispersers in salmon-bearing ecosystems | saliva on vegetation | forest | mammal | black bear (Ursus americanus), brown bear (Ursus arctos) | old assays used for new eDNA approaches |
| 121 | Hashizume, H. H., Sato, M., Sato, M. O., Ikeda, S., Yoonuan, T., Sanguankiat, S., Pongvongsa, T., Moji, K. & Minamoto, T. | 2017 | Acta Tropica | https://doi.org/10.1016/j.actatropica.2017.01.008 | Application of environmental DNA analysis for the detection of Opisthorchis viverrini DNA in water samples | water | pond, river, rice field | microorganism | trematode (Opisthorchis viverrini) | assay design, validation and field study |
| 122 | Hinlo, R., Furlan, E., Suitor, L. & Gleeson, D. | 2017 | Management of Biological Invasion | https://doi.org/10.3391/mbi.2017.8.1.09 | Environmental DNA monitoring and management of invasive fish: comparison of eDNA and fyke netting | water | river | fish | common carp (Cyprinus carpio), redfin perch (Perca fluviatilis), oriental weatherloach (Misgurnus anguillicaudatus) | previously designed assay, field study |
| 123 | Hinlo, R., Gleeson, D., Lintermans, M. & Furlan, E. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0179251 | Methods to maximise recovery of environmental DNA from water samples | water | mesocosm | fish | oriental weatherloach (Misgurnus anguillicaudatus) | also based on Furlan et al. 2015 |
| 124 | Hinlo, R., Lintermans, M., Gleeson, D., Broadhurst, B. & Furlan, E. | 2018 | Biological Invasions | https://doi.org/10.1007/s10530-018-1760-x | Performance of eDNA assays to detect and quantify an elusive benthic fish in upland streams | water | stream | fish | oriental weatherloach (Misgurnus anguillicaudatus) | development of Furlan et al. 2015 |
| 125 | Hobbs, J., Round, J. M., Allison, M. J. & Helbing, C. C. | 2019 | PLoS ONE | https://doi.org/10.1371/journal.pone.0213849 | Expansion of the known distribution of the coastal tailed frog, Ascaphus truei, in British Columbia, Canada, using robust eDNA detection methods | water | stream | amphibian | coastal tailed frog (Ascaphus truei) | assay design and validation |
| 127 | Hunter, M. E., Dorazio, R. M., Butterfield, J. S. S., Meigs-Friend, G., Nico, L. G. & Ferrante, J. A. | 2017 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12619 | Detection limits of quantitative and digital PCR assays and their influence in presence–absence surveys of environmental DNA | water | pond | fish | grass carp (Ctenopharyngodon idella) | assay design, validation and development – LOD, occupancy modeling |
| 128 | Hunter, M. E., Meigs-Friend, G., Ferrante, J. A., Kamla, A. T., Dorazio, R. M., Diagne, L. K., Luna, F., Lanyon, J. M. & Reid, J. P. | 2018 | Endangered Species Research | https://doi.org/10.3354/esr00880 | Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in vulnerable manatee populations | water | bayou, lake, river | mammal | manatee (Trichechus spp.), dugong (Dugong dugon) | assay design, validation and development – occupancy modeling, qPCR vs. ddPCR |
| 129 | Hunter, M. E., Oyler-McCance, S. J., Dorazio, R. M., Fike, J. A., Smith, B. J., Hunter, C. T., Reed, R. N. & Hart, K. M. | 2015 | PLoS ONE | https://doi.org/10.1371/journal.pone.0121655 | Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese pythons | water | mesocosm, pond, pool | reptile | Burmese python (Python molurus bivittatus), Northern African python (Python sebae), boa constrictor (Boa constrictor), green (Eunectes murinus), yellow anaconda (Eunectes notaeus) | assay design, validation and development – occupancy modeling |
| 130 | Hunter, M. E., Ferrante, J. A., Meigs-Friend, G. & Ulmer, A. | 2019 | Scientific Reports | https://doi.org/10.1038/s41598-019-40977-w | Improving eDNA yield and inhibitor reduction through increased water volumes and multi-filter isolation techniques | water | stream | fish | grass carp (Ctenopharyngodon idella) | development from Hunter et al. 2017 |
| 131 | Hutchins, P. R., Sepulveda, A. J., Martin, R. M. & Hopper, L. R. | 2018 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-017-0812-3 | A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples | water | river | myxozoan | myxozoan parasite (Tetracapsuloides bryosalmonae) | assay design and validation |
| 132 | Huver, J. R., Koprivnikar, J., Johnson, P. T. J. & Whyard, S. | 2015 | Ecological Applications | https://doi.org/10.1890/14-1530.1 | Development and application of an eDNA method to detect and quantify a pathogenic parasite in aquatic ecosystems | water | pond | trematode | parasite (Ribeiroia ondatrae) | assay design and validation |
| 133 | Ikeda, K., Doi, H., Tanaka, K., Kawai, T. & Negishi, J. N. | 2016 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-016-0541-z | Using environmental DNA to detect an endangered crayfish Cambaroides japonicus in streams | water | stream | crustacean | Japanese crayfish (Cambaroides japonicus) | assay design and validation |
| 134 | Itakura, H., Wakiya, R., Yamamoto, S., Kaifu, K., Sato, T. & Minamoto, T. | 2019 | Aquatic Conservation: Marine and Freshwater Ecosystems | https://doi.org/10.1002/aqc.3058 | Environmental DNA analysis reveals the spatial distribution, abundance, and biomass of Japanese eels at the river-basin scale | water | river | fish | Japanese eel (Anguilla japonica) | based on old assay, but now entirely new eDNA application |
| 136 | Jane, S. F., Wilcox, T. M., McKelvey, K. S., Young, M. K., Schwartz, M. K., Lowe, W. H., Letcher, B. H. & Whiteley, A. R. | 2015 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12285 | Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams | water | stream | fish | brook trout (Salvelinus fontinalis) | assay development – biomass, eDNA transport, inhibition |
| 137 | Janosik, A. M. & Johnston, C. E. | 2015 | Environmental Biology of Fishes | https://doi.org/10.1007/s10641-015-0405-5 | Environmental DNA as an effective tool for detection of imperiled fishes | water | stream | fish | slackwater darter (Etheostoma boschungi) | assay design and validation |
| 138 | Jerde, C. L., Mahon, A. R., Chadderton, W. L. & Lodge, D. M. | 2011 | Conservation Letters | https://doi.org/10.1111/j.1755-263X.2010.00158.x | “Sight-unseen” detection of rare aquatic species using environmental DNA | water | river-canal complex | fish | silver carp (Hypophthalmichthys molitrix), bighead carp (Hypophthalmichthys nobilis) | assay design and validation |
| 139 | Jerde, C. L., Olds, B. P., Shogren, A. J ., Andruszkiewicz, E. A., Mahon, A. R., Bolster, D. & Tank, J. L. | 2016 | Environmental Science & Technology | https://doi.org/10.1021/acs.est.6b01761 | Influence of stream bottom substrate on retention and transport of vertebrate environmental DNA | water | stream | fish | largemouth bass (Micropterus salmoides), bluegill sunfish (Lepomis macrochirus) | assay design, validation and development – qPCR Vs ddPCR, substrate type, eDNA transport |
| 140 | Jerde, C. L., Miller, D. J., Mahon, A. R., Chadderton, W. L. & Lodge, D. M. | 2012 | Conservation Letters | https://doi.org/10.1111/j.1755-263X.2012.00231.x | Response to Casey et al.’s sensitivity of detecting environmental DNA comment | water | river-canal complex | fish | silver carp (Hypophthalmichthys molitrix), bighead carp (Hypophthalmichthys nobilis) | additional info on the carp assays in there |
| 141 | Jo, T., Murakami, H., Masuda, R., Sakata, M. K., Yamamoto, S. & Minamoto, T. | 2017 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12685 | Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA | water | experimental tank, Maizuru Bay | fish | Japanese jack mackerel (Trachurus japonicus) | assay design, validation and development – fragment size, degradation |
| 142 | Jo, T., Murakami, H., Yamamoto, S., Masuda, R. & Minamoto, T. | 2019 | Ecology and Evolution | https://doi.org/10.1002/ece3.4802 | Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution | water | mesocosm | fish | Japanese jack mackerel (Trachurus japonicus) | development of Yamamoto et al. 2016 |
| 143 | Jones, R. A., Brophy, P. M., Davis, C. N., Davies, T. E., Emberson, H., Stevens, P. R. & Williams, H. W. | 2018 | Parasites and Vectors | https://doi.org/10.1186/s13071-018-2928-z | Detection of Galba truncatula, Fasciola hepatica and Calicophoron daubneyi environmental DNA within water sources on pasture land, a future tool for fluke control? | water | grazing pasture | snail, trematode | freshwater snail (Galba truncatula), common liver fluke (Fasciola hepatica), digenetic trematode (Calicophoron daubneyi) | assay design and validation |
| 144 | Kamoroff, C. & Goldberg, C. S. | 2018 | Freshwater Science | https://doi.org/10.1086/699203 | An issue of life or death: using eDNA to detect viable individuals in wilderness restoration | water | field, mesocosm | fish | comet goldfish (Carassius auratus) | assay design and validation |
| 145 | Kamoroff, C. & Goldberg, C. S. | 2018 | Limnology | https://doi.org/10.1007/s10201-018-0551-5 | Environmental DNA quantification in a spatial and temporal context: a case study examining the removal of brook trout from a high alpine basin | water | lake | fish | brook trout (Salvelinus fontinalis) | development of Wilcox et al. 2013 |
| 146 | Katano, I., Harada, K., Doi, H., Souma, R. & Minamoto, T. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0176541 | Environmental DNA method for estimating salamander distribution in headwater streams, and a comparison of water sampling methods | water | stream | amphibian | Japanese clawed salamander (Onychodactylus japonicus) | assay design, validation and development – sampling strategy, spatial distribution |
| 147 | Keskin, E. | 2014 | Biochemical Systematics and Ecology | https://doi.org/10.1016/j.bse.2014.05.003 | Detection of invasive freshwater fish species using environmental DNA survey | water | river basin | fish | Prussian carp (Carassius gibelio), North African catfish (Clarias gariepinus), Nile tilapia (Oreochromis niloticus), topmouth gudgeon (Pseudorasbora parva) | assay design and validation |
| 148 | Kim, P., Kim, D.,Yoon, T. J. & Shin, S. | 2018 | Marine Environmental Research | https://doi.org/10.1016/j.marenvres.2018.04.015 | Early detection of marine invasive species, Bugula neritina (Bryozoa: Cheilostomatida), using species-specific primers and environmental DNA analysis in Korea | water | marine | bryozoan | brown bryozoan (Bugula neritina) | assay development and validation |
| 149 | Kirshtein, J. D., Anderson, C. W., Wood, J. S., Longcore, J. E. & Voytek, M. A. | 2007 | Diseases of Aquatic Organisms | https://doi.org/10.3354/dao01831 | Quantitative PCR detection of Batrachochytrium dendrobatidis DNA from sediments and water | water, sediment | lake, pond | microorganism | chytrid fungus (Batrachochytrium dendrobatidis) | assay validation and development – in situ validation, assay comparison |
| 150 | Klobucar, S. L., Rodgers, T. W. & Budy, P. | 2017 | Canadian Journal of Fisheries and Aquatic Sciences | https://doi.org/10.1139/cjfas-2017-0114 | At the forefront: evidence of the applicability of using environmental DNA to quantify the abundance of fish populations in natural lentic waters with additional sampling considerations | water | lake | fish | Arctic char (Salvelinus alpinus) | development of Rodgers et al. 2017 |
| 151 | Klymus, K. E., Richter, C. A., Chapman, D. C. & Paukert, C. | 2015 | Biological Conservation | https://doi.org/10.1016/j.biocon.2014.11.020 | Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix | water | aquarium | fish | silver carp (Hypophthalmichthys molitrix), bighead carp (Hypophthalmichthys nobilis) | assay validation and development – biomass estimation, temperature, diet |
| 152 | Knudsen, S. W., Ebert, R. B., Hesselsoe, M., Kuntke, F., Hassingboe, J., Mortensen, P. B., Thomsen, P. F., Sigsgaard, E. E., Hansen, B. K., Nielsen, E. E. & Moller, P. R. | 2019 | Journal of Experimental Marine Biology and Ecology | https://doi.org/10.1016/j.jembe.2018.09.004 | Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea | water | marine | fish | Atlantic herring (Clupea harengus), Atlantic cod (Gadus morhua), European flounder (Platichthys flesus), European plaice (Pleuronectes platessa), Atlantic mackerel (Scomber scombrus), European eel (Anguilla anguilla) | assay design and validation |
| 153 | Kucherenko, A., Herman, J. E., Everham, E. M., III & Urakawa, H. | 2018 | Herpetologica | https://doi.org/10.1655/Herpetologica-D-16-00088 | Terrestrial snake environmental DNA accumulation and degradation dynamics and its environmental application | soil | field, mesocosm | reptile | red cornsnakes (Pantherophis guttatus), Burmese pythons (Python bivittatus) | assay design and validation |
| 154 | Lacoursière-Roussel, A., Cote, G., Leclerc, V. & Bernatchez, L. | 2016 | Journal of Applied Ecology | https://doi.org/10.1111/1365-2664.12598 | Quantifying relative fish abundance with eDNA: a promising tool for fisheries management | water | lake | fish | lake trout (Salvelinus namaycush) | assay design and validation – comparison of gillnet catches and DNA quantities |
| 155 | Lacoursière-Roussel, A., Dubois, Y., Normandeau, E.& Bernatchez, L. | 2016 | Genome | https://doi.org/10.1139/gen-2015-0218 | Improving herpetological surveys in eastern North America using the environmental DNA method | water | river | reptile | wood turtle (Glyptemys insculpta) | assay development |
| 156 | Lafferty, K. D., Benesh, K. C., Mahon, A. R., Jerde, C. L. & Lowe, C. G. | 2018 | Freshwater Science | https://doi.org/10.3389/fmars.2018.00355 | Detecting southern California’s white sharks with environmental DNA | water | marine | fish | white shark (Carcharodon carcharias) | assay design and validation |
| 157 | Laramie, M. B., Pilliod, D. S. & Goldberg, C. S. | 2015 | Biological Conservation | https://doi.org/10.1016/j.biocon.2014.11.025 | Characterizing the distribution of an endangered salmonid using environmental DNA analysis | water | river | fish | Chinook salmon (Oncorhynchus tshawytscha) | assay design, validation and field study |
| 158 | Larson, E. R., Renshaw, M. A., Gantz, C. A., Umek, J., Chandra, S., Lodge, D. & Egan, S. P. | 2017 | Hydrobiologia | https://doi.org/10.1007/s10750-017-3210-7 | Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America | water | lake | crustacean | rusty crayfish (Orconectes rusticus), signal crayfish (Pacifastacus leniusculus) | Orconectes rusticus previously designed primers, Pacifastacus leniusculus assay design and development |
| 159 | Lugg, W. H., Griffiths, J., van Rooyen, A. R., Weeks, A. R. & Tingley, R. | 2017 | Methods in Ecology and Evolution | https://doi.org/10.1111/2041-210X.12951 | Optimal survey designs for environmental DNA sampling | water | river | mammal | Platypus (Ornithorhynchus anatinus) | assay design and validation (see Appendix S1) |
| 160 | Ma, H., Stewart, K., Lougheed, S., Zheng, J., Wang, Y. & Zhao, J. | 2016 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-016-0597-9 | Characterization, optimization, and validation of environmental DNA (eDNA) markers to detect an endangered aquatic mammal | water | river | mammal | Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) | assay design and validation, testing amplicon length – 13 primer pairs designed |
| 161 | MacDonald, A. J., Young., M. J., Lintermans, M. & Sarre, S. D. | 2014 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-014-0196-6 | Primers for detection of Macquarie perch from environmental and trace DNA samples | water | river | fish | Macquarie perch (Macquaria australasica) | assay design |
| 162 | Mächler, E., Deiner, K., Spahn, F. & Altermatt, F. | 2015 | Environmental Science & Technology | https://doi.org/10.1021/acs.est.5b04188 | Fishing in the water: effect of sampled water volume on environmental DNA-based detection of macroinvertebrates | water | river | crustacean, insect, mollusc | river limpet (Ancylus fluviatilis), nymph (Baetis buceratus), amphipod (Gammarus pulex) | previously designed assay, validation and field study |
| 163 | Mächler, E., Deiner, K., Steinmann, P. & Altermatt, F. | 2015 | Freshwater Science | https://doi.org/10.1086/678128 | Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species | water | lake, river | crustacean, insect, mollusc | river limpet (Ancylus fluviatilis), waterlouse (Asellus aquaticus), minnow mayfly (Baetis buceratus), northern river crangonyctid (Crangonyx pseudogracilis), common freshwater shrimp (Gammarus pulex) | assay design and validation |
| 164 | Mächler, E., Osathanunkul, M. & Altermatt, F. | 2018 | PLoS ONE | https://doi.org/10.1371/journal.pone.0195529 | Shedding light on eDNA: neither natural levels of UV radiation nor the presence of a filter feeder affect eDNA-based detection of aquatic organisms | water | mesocosm | crustacean, mollusc | common freshwater shrimp (Gammarus pulex), waterlouse (Asellus aquaticus), New Zealand mud snail (Potamopyrgus antipodarum) | assay design and used previously published P. antipodarum assay – UV on eDNA |
| 165 | Mahon, A. R., Barnes, M. A., Li, F., Egan, S. P., Tanner, C. E., Ruggiero, S. T., Feder, J. L. & Lodge, D. M. | 2013 | Journal of the Royal Society Interface | https://doi.org/10.1098/rsif.2012.0637 | DNA-based species detection capabilities using laser transmission spectroscopy | water | mesocosm | mussel | quagga mussel (Dreissena bugensis) | development of Mahon et al. 2011 |
| 166 | Mahon, A. M., Jerde, C. L., Galaska, M., Bergner, J. L., Lindsay Chadderton, W., Lodge, D. M., Hunter, M. E. & Nico, L. G. | 2013 | PLoS ONE | https://doi.org/10.1371/journal.pone.0058316 | Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments | water | canal system | fish | black carp (Mylpharyngodon piceus), grass carp (Ctenopharyngodon idella), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), common carp (Cyprinus carpio), goldfish (Carassius auratus) | previously published assays |
| 167 | Mahon, A. R., Barnes, M. A., Senapati, S., Feder, J. L., Darling, J. A., Chang, H. C & Lodge, D. M. | 2011 | PLoS ONE | https://doi.org/10.1371/journal.pone.0017280 | Molecular detection of invasive species in heterogeneous mixtures using a microfluidic carbon nanotube platform | water | artificial ballast water | mussel | quagga mussel (Dreissena bugensis), Chinese mitten crab (Eriocheir sinensis), golden mussel (Limnoperna fortunei) | development of Pie et al. (2006) and basis for a lot more papers |
| 168 | Malekian, M., Sadeghi, P. & Goudarzi, F. | 2018 | Herpetological Conservation and Biology | NA | Assessment of environmental DNA for detection of an imperiled amphibian, the Luristan newt (Neurergus kaiseri, Schmidt 1952) | water | pond | amphibian | Luristan newt (Neurergus kaiseri) | development of old assay |
| 169 | Maruyama, A., Nakamura, K., Yamanaka, H., Kondoh, M. & Minamoto, T. | 2014 | PLoS ONE | https://doi.org/10.1371/journal.pone.0114639 | The release rate of environmental DNA from juvenile and adult fish | water | mesocosm | fish | bluegill sunfish (Lepomis macrochirus) | previously designed assay – further development |
| 170 | Maruyama, A., Sugatani, K., Watanabe, K., Yamanaka, H. & Imamura, A. | 2018 | Ecology and Evolution | https://doi.org/10.1002/ece3.4653 | Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers | water | river | fish | three-lips (Opsariichthys uncirostris) | assay design and validation |
| 171 | Mason, D. H., Dysthe, J. C., Franklin, T. W., Skorupski, J. A., Young, M. K., McKelvey, K. S. & Schwartz, M. K. | 2018 | PLoS ONE | https://doi.org/10.1371/journal.pone.0209601 | qPCR detection of sturgeon chub (Macrhybopsis gelida) DNA in environmental samples | water | river | fish | sturgeon chub (Macrhybopsis gelida) | assay design and validation |
| 172 | Matsuhashi, S., Doi, H., Fujiwara, A., Watanabe, S. & Minamoto, T. | 2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.015621 | Evaluation of the environmental DNA method for estimating distribution and biomass of submerged aquatic plants | water | pond | plant | water thyme (Hydrilla verticillata) | assay design and validation |
| 173 | Matter, A. N., Falke, J. A., Lopez, J. A. & Savereide, J. W. | 2018 | North American Journal of Fisheries Management | https://doi.org/10.1002/nafm.10014 | A rapid-assessment method to estimate the distribution of juvenile Chinook salmon in tributary habitats using eDNA and occupancy estimation | water | river | fish | Chinook salmon (Oncorhynchus tshawytscha) | development of Takahara et al 2012 and Laramie et al 2015 |
| 174 | Mauvisseau, Q., Coignet, Q., Delaunay, C., Pinet, F., Bouchon, D. & Souty-Grosset, C. | 2018 | Hydrobiologia | https://doi.org/10.1007/s10750-017-3288-y | Environmental DNA as an efficient tool for detecting invasive crayfishes in freshwater ponds | water | mesocosm, pond | crustacean | Louisiana crayfish (Procambarus clarkii), spinycheek crayfish (Orconectes limosus), signal crayfish (Pacifastacus leniusculus) | assay design and validation |
| 175 | Mauvisseau, Q., Parrondoa, M., Fernández, M. P., García, L., Martínezc, J. L., García-Vázquez, E. & Borrell, Y. | 2017 | Fisheries Research | https://doi.org/10.1016/j.fishres.2017.02.023 | On the way for detecting and quantifying elusive species in the sea: the Octopus vulgaris case study | water | aquarium, marine | mollusc | common octopus (Octopus vulgaris) | assay design and validation |
| 176 | Mauvisseau, Q., Burian, A., Gibson, C., Brys, R., Ramsey, A. & Sweet, M. | 2019 | Scientific Reports | https://doi.org/10.1038/s41598-018-37001-y | Influence of accuracy, repeatability and detection probability in the reliability of species-specific eDNA based approaches | water | mesocosm | mussel | pearl mussel (Margaritifera margaritifera) | development of Stoeckle et al. 2017 and Carlsson et al. 2017 |
| 177 | McKee, A. M., Calhoun, D. L., Barichivich, W. J., Spear, S. F., Goldberg, C. S. & Glenn, T. C. | 2015 | Journal of Fish and Wildlife Management | https://doi.org/10.3996/042014-JFWM-034 | Assessment of environmental DNA for detecting presence of imperiled aquatic amphibian species in isolated wetlands | water | wetland | amphibian | frosted salamander (Ambystoma cingulatum), reticulated flatwoods salamanders (Ambystoma bishopi), striped newt (Notophthalmus perstriatus), gopher frog (Lithobates capito) | assay design and validation |
| 178 | McKelvey, K. S., Young, M. K., Knotek, W. L., Carim, K. J., Wilcox, T. M., Padgett-Stewart, T. M. & Schwartz, M. K. | 2016 | Journal of Fish Biology | https://doi.org/10.1111/jfb.12863 | Sampling large geographic areas for rare species using environmental DNA: a study of bull trout Salvelinus confluentus occupancy in western Montana | water | stream | fish | bull trout (Salvelinus confluentus) | application of Wilcox et al. 2013 |
| 179 | Merkes, C. M., McCalla, G. S., Jensen, N. R., Gaikowski, M. P. & Amberg, J. J. | 2014 | PLoS ONE | https://doi.org/10.1371/journal.pone.0113346 | Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data | water | river | fish | bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix) | previously designed assay |
| 180 | Minamoto, T., Fukuda, M., Katsuhara, K. R., Fujiwara, A., Hidaka, S., Yamamoto, S., Takahashi, K. & Masuda, R. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0173073 | Environmental DNA reflects spatial and temporal jellyfish distribution | water | bay, mesocosm | jellyfish | Japanese sea nettle (Chrysaora pacifica) | assay design and validation |
| 181 | Minamoto, T., Hayami, K., Sakata, M. K. & Imamura, A. | 2019 | Ecological Research | https://doi.org/10.1111/1440-1703.1018 | Real-time polymerase chain reaction assays for environmental DNA detection of three salmonid fish in Hokkaido, Japan: application to winter surveys | water | river | fish | quagga mussel (Dreissena bugensis), Chinese mitten crab (Eriocheir sinensis), golden mussel (Limnoperna fortuneii) | assay design and validation |
| 182 | Minamoto, T., Naka, T., Moji, K. & Maruyama, A. | 2016 | Limnology | https://doi.org/10.1007/s10201-015-0457-4 | Techniques for the practical collection of environmental DNA: filter selection, preservation, and extraction | water | aquarium | fish | common carp (Cyprinus carpio) | development of Takahara et al. 2012 |
| 183 | Miralles, L., Dopico, E., Devlo-Devla, F. & Garcia-Vazquex, E. | 2016 | Marine Pollution Bulletin | https://doi.org/10.1016/j.marpolbul.2016.06.072 | Controlling populations of invasive pygmy mussel (Xenostrobus securis) through citizen science and environmental DNA | water | coastal water, ports | mollusc | pygmy mussel (Xenostrobus securis) | previously designed primers, field study, eradication |
| 184 | Mizumoto, H., Urabe, H., Kanbe, T., Fukushima, M. & Araki, H. | 2017 | Limnology | https://doi.org/10.1007/s10201-017-0535-x | Establishing an environmental DNA method to detect and estimate the biomass of Sakhalin taimen, a critically endangered Asian salmonid | water | mesocosm | fish | Sakhalin taimen (Parahucho perryi) | assay design and validation, biomass |
| 185 | Moyer, G. R., Diaz-Ferguson, E., Hill, J. E. & Shea, C. | 2014 | PLoS ONE | https://doi.org/10.1371/journal.pone.0103767 | Assessing environmental DNA detection in controlled lentic systems | water | mesocosm | fish | African jewelfish (Hemichromis bimaculatus) | development of Diaz-Fergusson et al. 2014 |
| 186 | Munoz-Colmenero, M., Ardura, A., Clusa, L., Miralles, L., Gower, F., Zaiko, A. & Garcia-Vazquez, E. | 2018 | Journal for Nature Conservation | https://doi.org/10.1016/j.jnc.2017.12.004 | New specific molecular marker detects Ficopomatus enigmaticus from water eDNA before positive results of conventional sampling | water | marine | polychaeta | tubeworm (Ficopomatus enigmaticus) | assay design and validation |
| 188 | Nathan, L. R., Jerde, C. L., Budny, M. L. & Mahon, A. R. | 2014 | Conservation Biology | https://doi.org/10.1111/cobi.12381 | The use of environmental DNA in invasive species surveillance of the Great Lakes commercial bait trade | water | aquarium | fish | bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), round goby (Neogobius melanostomus), tubenose goby (Proterorhinus semilunaris), Eurasian rudd (Scardinius erythrophthalmus), goldfish (Carassius auratus) | assay design and validation plus assay from previous publications |
| 189 | Nathan, L. R., Simmons, M., Wegleitner, B. L., Jerde, C. L & Mahon, A. R. | 2014 | Environmental Science & Technology | https://doi.org/10.1021/es5034052 | Quantifying environmental DNA signals for aquatic invasive species across multiple detection platforms | water | mesocosm | fish | round goby (Neogobius melanostomus) | assay design and validation, ddPCR, standard PCR vs. qPCR |
| 190 | Nevers, M. B., Byappanahalli, M. N., Morris, C. C., Shively, D., Przybyla-Kelly, K., Spoljaric, A. M., Dickey, J. & Roseman, E. F. | 2018 | PLoS ONE | https://doi.org/10.1371/journal.pone.0191720 | Environmental DNA (eDNA): a tool for quantifying the abundant but elusive round goby (Neogobius melanostomus) | water | lake, mesocosm | fish | round goby (Neogobius melanostomus) | development of Nathan et al. 2014 |
| 191 | Newton, J., Sepulveda, A., Sylvester, K. & Thum, R. A. | 2016 | Journal of Aquatic Plant Management | NA | Potential utility of environmental DNA for early detection of Eurasian watermilfoil (Myriophyllum spicatum) | water | lake, river | plant | Eurasian watermilfoil (Myriophyllum spicatum) | assay design and validation |
| 192 | Nichols, R. V., Konigsson, H., Danell, K. & Spong, G. | 2012 | Molecular Ecology Resources | https://doi.org/10.1111/j.1755-0998.2012.03172.x | Browsed twig environmental DNA: diagnostic PCR to identify ungulate species | plant surface samples | experimental & field sample | mammals | moose (Alces alces), roe deer (Capreolus capreolus), fallow deer (Cervus dama), red deer (Cervus elaphus) | assay design and validation |
| 194 | Niemiller, M. L., Porter, M. L., Keany, J., Gilbert, H., Fong, D. W., Culver, D. C., Hobson, C. S., Kendall, K. D., Davis, M. A. & Taylor, S. J. | 2018 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-017-0785-2 | Evaluation of eDNA for groundwater invertebrate detection and monitoring: a case study with endangered Stygobromus (Amphipoda: Crangonyctidae) | water | spring | crustacean | Hay’s spring amphipod (Stygobromus hayi), potomac stygobromid (Stygobromus tenuis potomacus) | assay design and validation |
| 195 | Nukazawa, K., Hamasuna, Y. & Suzuki, Y. | 2018 | Environmental Science & Technology | https://doi.org/10.1021/acs.est.8b02293 | Simulating the advection and degradation of the environmental DNA of common carp along a river | water | river | fish | common carp (Cyprinus carpio) | development of Eichmiller et al. 2014 – see Supporting Information |
| 196 | Odero, J., Gomes, B., Fillinger, U. & Weetman, D. | 2018 | Wellcome Open Research | https://doi.org/10.12688/wellcomeopenres.14193.1 | Detection and quantification of Anopheles gambiae sensu lato mosquito larvae in experimental aquatic habitats using environmental DNA (eDNA) | water | mesocosm | insect | Anopheles gambiae complex (Anopheles gambiae sensu lato) | assay design and validation |
| 197 | Olajos, F., Bokma, F., Bartels, P., Myrstener, E., Rydberg, J., Ohlund, G., Bindler, R., Wang, X. R., Zale, R. & Englund, G. | 2018 | Methods in Ecology and Evolution | https://doi.org/10.1111/2041-210X.12890 | Estimating species colonization dates using DNA in lake sediment | sediment | lake | fish | whitefish (Coregonus lavaretus L.) | assay design and validation |
| 198 | Olsen, J. B., Lewis, C. J., Massengill, R. L., Dunker, K. J. & Wenburg, J. K. | 2015 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-015-0459-x | An evaluation of target specificity and sensitivity of three qPCR assays for detecting environmental DNA from northern pike (Esox lucius) | NA – tissue sample | NA | fish | northern pike (Esox lucius) | assay design and validation |
| 199 | Olsen, J. B., Lewis, C. J., Massengill, R. L., Dunker, K. J. & Wenburg, J. K. | 2016 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-016-0526-y | Erratum to: an evaluation of target specificity and sensitivity of three qPCR assay for detecting environmental DNA from northern pike (Esox lucius) | NA – tissue sample | NA | fish | northern pike (Esox lucius) | correct primers |
| 200 | Olson, Z. H., Briggler, J. T. & Williams, R. N. | 2012 | Wildlife Research | https://doi.org/10.1071/WR12114 | An eDNA approach to detect eastern hellbenders (Cryptobranchus a. alleganiensis) using samples of water | water | pond | amphibian | eastern hellbenders (Cryptobranchus a. alleganiensis) | assay design and validation |
| 201 | Ostberg, C. O., Chase, D. M., Hayes, M. C. & Duda, J. J. | 2018 | PeerJ | https://doi.org/10.7717/peerj.4496 | Distribution and seasonal differences in Pacific lamprey and Lampetra spp. eDNA across 18 Puget Sound watersheds | water | river | fish | Pacific lamprey (Entosphenus tridentatus), various lamprey species (Lampetra spp.) | assay design, validation and field study |
| 202 | Padgett-Stewart, T. M., Wilcox, T. M., Carim, K. J., McKelvey, K. S., Young, M. K. & Schwartz, M. K. | 2015 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-015-0511-x | An eDNA assay for river otter detection: a tool for surveying a semi-aquatic mammal | water | pool, tissue | mammal | North American river otters (Lontra canadensis) | assay design and validation |
| 203 | Parrondo, M., Clusa, L., Mauvisseau, Q. & Borrell, Y. J. | 2018 | Journal for Nature Conservation | https://doi.org/10.1016/j.jnc.2018.02.006 | Citizen warnings and post checkout molecular conformations using eDNA as a combined strategy for updating invasive species distributions | water | reservoir | fish | Wels catfish (Silurus glanis) | assay design and validation |
| 204 | Peñarrubia, L., Alcaraz, C., bij deVaate, A., Sanz, N., Pla, C., Vida, O. & Viñas, J. | 2016 | Scientific Reports | https://doi.org/10.1038/srep39067 | Validated methodology for quantifying infestation levels of dreissenid mussels in environmental DNA (eDNA) samples | water | river | mollusc | zebra mussel (Dreissena polymorpha), quagga mussel (Dreissena bugensis) | assay design and validation |
| 205 | Perez, C. R., Bonar, S. A., Amberg, J. J., Ladell, B., Rees, C., Stewart, W. T., Gill, C. J., Cantrell, C. & Robinson, A. T. | 2017 | North American Journal of Fisheries Management | https://doi.org/10.1080/02755947.2017.1342721 | Comparison of American Fisheries Society (AFS) standard fish sampling techniques and environmental DNA for characterizing fish communities in a large reservoir | water | lake | fish | largemouth bass (Micropterus salmoides), gizzard shad (Dorosoma cepedianum) | assay design, validation and field study – comparison with biomass and relative abundance |
| 206 | Pfleger, M. O., Rider, S. J., Johnston, C. E. & Janosik, A. M. | 2016 | Global Ecology and Conservation | https://doi.org/10.1016/j.gecco.2016.08.008 | Saving the doomed: Using eDNA to aid in detection of rare sturgeon for conservation (Acipenseridae) | water | river | fish | Alabama sturgeon (Scaphirhynchus suttkusi), Gulf sturgeon (Acipenser oxyrinchus desotoi) | assay design and validation |
| 207 | Piaggio, A. J., Engeman, E. M., Hopken, M. W., Humphrey, J. S., Keacher, K. L., Bruce, W. E. & Avery, M. L. | 2014 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12180 | Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA | water | everglades | reptile | Burmese python (Python bivittatus) | assay design and validation |
| 208 | Pie, M. R., Boeger, W. A., Patella, L. & Falleiros, R. M. | 2006 | Journal of Molluscan Studies | https://doi.org/10.1093/mollus/eyi070 | A fast and accurate molecular method for the detection of larvae of the golden mussel Limnoperna fortunei (Mollusca: Mytilidae) in plankton samples | water | reservoir | mollusc | golden mussel (Limnoperna fortunei) | assay design and validation |
| 209 | Pie, M. R., Stroher, P. R., Agostinis, A. O., Belmonte-Lopes, R., Tadra-Sfeir, M. Z. & Ostrensky, A. | 2017 | Anais da Academia Brasileira de Ciencias | https://doi.org/10.1590/0001-3765201720160723 | Development of a real-time PCR assay for the detection of the golden mussel (Limnoperna fortunei, Mytilidae) in environmental samples | water | water samples from reservoirs of electric power plants | mussel | golden mussel (Limnoperna fortunei) | assay design and validation |
| 210 | Pierson, T. W., McKee, A. M., Spear, S. F., Maerz, J. C., Camp, C. D. & Glenn, T. C. | 2016 | Copeia | https://doi.org/10.1643/CH-14-202 | Detection of an enigmatic plethodontid salamander using environmental DNA | water | stream | amphibian | patch-nosed salamander (Urspelerpes brucei) | assay design and validation, field testing |
| 211 | Piggot, M. P. | 2016 | Ecology and Evolution | https://doi.org/10.1002/ece3.2083 | Evaluating the effects of laboratory protocols on eDNA detection probability for an endangered freshwater fish | water | river | fish | Macquarie perch (Macquaria australasica) | previously designed assay, sample, extraction and PCR strategy |
| 212 | Piggott, M. P. | 2017 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-016-0666-0 | An environmental DNA assay for detecting Macquarie perch, Macquaria australasica | water | waterway | fish | Macquarie perch (Macquaria australasica) | assay design |
| 213 | Pilliod, D. S., Goldberg, C. S., Arkle, R. S. & Waits, L. P. | 2013 | Canadian Journal of Fisheries and Aquatic Sciences | https://doi.org/10.1139/cjfas-2013-0047 | Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples | water | stream | amphibian | Idaho giant salamander (Dicamptodon aterrimus), Rocky Mountain tailed frog (Ascaphus montanus) | further tests with assays from Goldberg et al. 2011 – DNA quantity vs. abundance |
| 214 | Pilliod, D. S., Goldberg, C. S., Arkle, R. S. & Waits, L. P. | 2014 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12159 | Factors influencing detection of eDNA from a stream-dwelling amphibian | water | stream | amphibian | Idaho giant salamander (Dicamptodon aterrimus) | previously designed assay, validation |
| 215 | Pitt, A. L., Shinskie, J. L., Tavano, J. J., Hartzell, S. M., Delahunty, T. & Spear, S. F. | 2017 | Freshwater Biology | https://doi.org/10.1111/fwb.12917 | Decline of a giant salamander assessed with historical records, environmental DNA and multi-scale habitat data | water | pond | amphibian | eastern hellbender (Cryptobranchus alleganiensis alleganiensis) | development of Spear et al. 2015 using McKee et al. 2015 |
| 216 | Prosser, C. M. & Hedgpeth, B. M. | 2018 | PLoS ONE | https://doi.org/10.1371/journal.pone.0196430 | Effects of bioturbation on environmental DNA migration through soil media | soil | mesocosm | fish | zebrafish (Danio rerio) | development of Tang et al. 2006 |
| 217 | Raemy, M. & Ursenbacher, S. | 2018 | Amphibia-Reptilia | https://doi.org/10.1163/15685381-17000025 | Detection of the European pond turtle (Emys orbicularis) by environmental DNA: is eDNA adequate for reptiles? | water | pond | reptile | European pond turtle (Emys orbicularis) | assay design and validation |
| 218 | Rathinasamy, V., Hosking, C., Tran, L., Kelley, J., Williamson, G., Swan, J., Elliott, T., Rawlin, G., Beddoe, T. & Spithill, T. W. | 2018 | Veterinary Parasitology | https://doi.org/10.1016/j.vetpar.2018.06.018 | Development of a multiplex quantitative PCR assay for detection and quantification of DNA from Fasciola hepatica and the intermediate snail host, Austropeplea tomentosa, in water samples | water | mesocosm | snail, trematode | common liver fuke (Fasciola hepatica), aquatic gastropod mollusc (Austropeplea tomentosa) | assay design and validation |
| 219 | Rees, H. C., Bishop, K., Middleditch, D. J., Patmore, J. R. M., Maddison, B. C. & Gough, K. C. | 2014 | Ecology and Evolution | https://doi.org/10.1002/ece3.1272 | The application of eDNA for monitoring of the great crested newt in the UK | water | pond | amphibian | great crested newt (Triturus cristatus) | previously designed assay and field study |
| 220 | Reinhardt, T., van Schingen, M., Windisch, H. S., Nguyen, T. Q., Ziegler, T. & Fink, P. | 2019 | Aquatic Conservation: Marine and Freshwater Ecosystems | https://doi.org/10.1002/aqc.3038 | Monitoring a loss: detection of the semi-aquatic crocodile lizard (Shinisaurus crocodilurus) in inaccessible habitats via environmental DNA | water | mesocosm, pond | reptile | crocodile lizard (Shinisaurus crocodilurus) | assay design and validation |
| 221 | Renan, S., Gafny, S., Perl, R. G. B., Roll, U., Malka, Y., Vences, M. & Geffen, E. | 2017 | Molecular Ecology | https://doi.org/10.1111/mec.14420 | Living quarters of a living fossil—Uncovering the current distribution pattern of the rediscovered Hula painted frog (Latonia nigriventer) using environmental DNA | water | wetland | amphibian | Hula painted frog (Latonia nigriventer) | assay design and validation, testing in the field |
| 222 | Riascos, L., Geerts, A. N., Ona, T., Goethals, P., Cevallos-Cevallos, J., Vanden Berghe, W., Volckaert, F. A. M., Bonilla, J., Muylaert, K., Velarde, E., Boets, P. & Van der Heyden, C. | 2018 | Limnologica | https://doi.org/10.1016/j.limno.2018.02.002 | DNA-based monitoring of the alien invasive North American crayfish Procambarus clarkii in Andean lakes (Ecuador) | water | lake | crustacean | Louisiana crayfish (Procambarus clarkii) | assay design and validation |
| 223 | Rice, C. J., Larson, E. R. & Taylor, C. A. | 2018 | Freshwater Biology | https://doi.org/10.1111/fwb.13081 | Environmental DNA detects a rare large river crayfish but with little relation to local abundance | water | river | crustacean | coldwater crayfish (Faxonius eupunctus) | assay design and validation, qPCR vs. conventional sampling |
| 224 | Robinson, C. V., Webster, T. M. U., Cable, J., James, J. & Consuegra, S. | 2018 | Biological Conservation | https://doi.org/10.1016/j.biocon.2018.04.009 | Simultaneous detection of invasive signal crayfish, endangered white clawed crayfish and the crayfish plague pathogen using environmental DNA | water | river | crustacean, microorganism | white clawed crayfish (Austropotamobius pallipes), signal crayfish (Pacifastacus leniusculus), pathogen (Aphanomyces astaci) | assay design and validation |
| 225 | Robson, H. L. A., Noble, T. H., Saunders, R. J., Robson, S. K. A., Burrows, D. W. & Jerry, D. R. | 2016 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12505 | Fine-tuning for the tropics: application of eDNA technology for invasive fish detection in tropical freshwater ecosystems | water | river | fish | Mozambique tilapia (Oreochromis mossambicus) | assay design and validation, effects of filter size and degradation rates of eDNA |
| 226 | Rodgers, T. W., Olson, J. R., Klobucar, S. L. & Mock, K. E. | 2017 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-017-0883-1 | Quantitative PCR assays for detection of five arctic fish species: Lota lota, Cottus cognatus, Salvelinus alpinus, Salvelinus malma, and Thymallus arcticus from environmental DNA | water | river | fish | burbot (Lota lota), arctic char (Salvelinus alpinus), Dolly Varden trout (Salvelinus malma), arctic grayling (Thymallus arcticus), slimy sculpin (Cottus cognatus) | assay design and validation |
| 227 | Rodgers, T. W. & Mock, K. E. | 2015 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-015-0478-7 | Drinking water as a source of environmental DNA for the detection of terrestrial wildlife species | water | drinking station | mammal | coyote (Canis latrans) | assay design and validation |
| 228 | Rojahn, J., Gleeson, D. & Furlan, E. M. | 2018 | Wildlife Research | https://doi.org/10.1071/WR17179 | Monitoring post-release survival of the northern corroboree frog, Pseudophryne pengilleyi, using environmental DNA | water | pond | amphibian | northern corroboree frog (Pseudophryne corroboree), southern corroboree frog (Pseudophryne pengilleyi) | assay design and validation |
| 229 | Roy, M., Belliveau, V., Mandrak, N. E. & Gagne, N. | 2017 | Biological Invasions | https://doi.org/10.1007/s10530-017-1532-z | Development of environmental DNA (eDNA) methods for detecting high-risk freshwater fishes in live trade in Canada | water | aquarium | fish | crucian carp (Carassius carassius), northern snakehead (Channa argus), grass carp (Ctenopharyngodon idella), red shiner (Cyprinella lutrensis), silver carp (Hypophthalmichthys molitrix), bighead carp (Hypophthalmichthys nobilis), Ide (Leuciscus idus), Oriental weatherfish (Misgurnus anguillicaudatus), wiper (Morone chrysops x Morone saxatilis), black carp (Mylopharyngodon piceus), Amur sleeper (Perccottus glenii), Wels catfish (Silurus glanis), Chinese perch (Siniperca chuatsi) | assay design and validation |
| 231 | Rusch, J. C., Hansen, H., Strand, D. A., Markussen, T., Hytterod, S. & Vralstad, T. | 2018 | Parasites and Vectors | https://doi.org/10.1186/s13071-018-2916-3 | Catching the fish with the worm: a case study on eDNA detection of the monogenean parasite Gyrodactylus salaris and two of its hosts, Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) | water | river | microorganism | fish parasite (Gyrodactylus salaris) | Idaho giant salamander (Dicamptodon atterimus), Rocky Mountain tailed frog (Ascaphus montanus) |
| 232 | Sakata, M. K., Maki, N., Sugiyama, H. & Minamoto, T. | 2017 | The Science of Nature | https://doi.org/10.1007/s00114-017-1521-1 | Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan | water | river | fish | ray-finned fish (Acheilognathus typus) | assay design and validation |
| 233 | Sana, S., Williams, C., Hardouin, E. A., Blake, A., Davison, P., Pegg, J., Paley, R., Zhang, T. & Andreou, D. | 2018 | International Journal for Parasitology | https://doi.org/10.1016/j.ijpara.2017.11.002 | Phylogenetic and environmental DNA insights into emerging aquatic parasites: implications for risk management | water | reservoir, river, fishery | microorganism | fish parasite (Sphaerothecum destruens) | assay design and validation |
| 234 | Sansom, B. J. & Sassoubre, L. M. | 2017 | Environmental Science & Technology | https://doi.org/10.1021/acs.est.7b05199 | Environmental DNA (eDNA) shedding and decay rates to model freshwater mussel eDNA transport in a river | water | river | mollusc | freshwater mussel (Lampsilis siliquoidea) | assay design and validation (genus specific), eDNA detection downstream |
| 235 | Sassoubre, L. M., Yamahara, K. M., Gardner, L. D., Block., B. A. & Boehm, A. B. | 2016 | Environmental Science & Technology | https://doi.org/10.1021/acs.est.6b03114 | Quantification of environmental DNA (eDNA) shedding and decay rates for three marine fish | water | seawater mesocosm | fish | northern anchovy (Engraulis mordax), Pacific sardine (Sardinops sagax), Pacific chub mackerel (Scomber japonicus) | assay design and validation, shedding and decay rates of eDNA in mesocosm |
| 236 | Sato, M. O., Rafalimanantsoa, A., Ramarokoto, C., Rahetilahy, A. M., Ravoniarimbinina, P., Kawai, S., Minamoto, T., Sato, M., Kirinoki, M., Rasolofo, V., De Calan, M. & Chigusa, Y. | 2018 | International Journal for Infectious Diseases | https://doi.org/10.1016/j.ijid.2018.08.018 | Usefulness of environmental DNA for detecting Schistosoma mansoni occurrence sites in Madagascar | water | stagnant water | parasite | human water-borne parasite (Schistosoma mansoni) | assay design and validation |
| 237 | Schloesser, N. A., Merkes, C. M., Rees, C. B., Amberg, J. J., Steeves, T. B. & Docker, M. F. | 2018 | Management of Biological Invasions | https://doi.org/10.3391/mbi.2018.9.4.11 | Correlating sea lamprey density with environmental DNA detections in the lab | water | mesocosm | fish | sea lamprey (Petromyzon marinus) | assay design and validation |
| 238 | Schmelzle, M. C. & Kinziger, A. P | 2016 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12501 | Using occupancy modelling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species | water | tidewater | fish | goby (Eucyclogobius newberryi) | assay design and development, eDNA vs. seine netting (see Supporting Information for assay) |
| 239 | Schmidt, B. R., Kery, M., Ursenbacher, S., Hyman, O. & Collins, J. P. | 2013 | Methods in Ecology and Evolution | https://doi.org/10.1111/2041-210X.12052 | Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen | water | pond | microorganism | chytrid fungus (Batrachochytrium dendrobatidis) | previously designed assay, site occupancy |
| 240 | Schneider, J., Valentini, A., Dejean, T., Montarsi, F., Taberlet, P., Glaizot, O. & Fumagalli, L. | 2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.0162493 | Detection of invasive mosquito vectors using environmental DNA (eDNA) from water samples | water | pond, pool | insect | Tiger mosquito (Aedes albopictus), Asian bush mosquito (Aedes japonicus japonicus), invasive mosquito from Korea (Aedes koreicus) | assay development – single-species vs. metabarcoding |
| 241 | Scriver, M., Marinich, A., Wilson, C. & Freeland, J. | 2015 | Aquatic Botany | https://doi.org/10.1016/j.aquabot.2015.01.003 | Development of species-specific environmental DNA (eDNA) markers for invasive aquatic plants | water | mason jar filled with water | plant | water soldier (Stratiotes aloides), parrotfeather (Myriophyllum aquaticum), water hyacinth (Eichhornia crassipes), fanwort (Cabomba caroliniana), Brazilian waterweed (Egeria densa), European frogbit (Hydrocharis morsus-ranae), giant salvinia (Salvinia molesta), yellow floating heart (Nymphoides peltata), water lettuce (Pistia stratiotes), water chestnut (Trapa natans) | assay design and validation |
| 242 | Secondi, J., Dejean, T., Valentini, A., Audebaud, B. & Miaud, C. | 2016 | Amphibia-Reptilia | https://doi.org/10.1163/15685381-00003036 | Detection of a global aquatic invasive amphibian, Xenopus laevis, using environmental DNA | water | pond | amphibian | African clawed frog (Xenopus laevis) | assay design and field application – population density and DNA quantity |
| 243 | Seymour, M., Durance, I., Cosby, B. J., Ransom-Jones, E., Deiner, K., Ormerod, S. J., Colbourne, J. K., Wilgar, G., Carvalho, G. R., de Bruyn, M., Edwards, F., Emmett, B. A., Bik, H. M & Creer, S. | 2018 | Communications Biology | https://doi.org/10.1038/s42003-017-0005-3 | Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms | water | stream mesocosm | crustacean, fish, insect | planktonic crustacean (Daphnia magna), mayfly (Ephemera danica), European eel (Anguilla anguilla) | previously designed assays, effects of acidity on eDNA |
| 244 | Sigsgaard, E. E., Henrik, C., Moller, P.R. & Thomsen, P. F. | 2015 | Biological Conservation | https://doi.org/10.1016/j.biocon.2014.11.023 | Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples | water | freshwater system | fish | European weather loach (Misgurnus fossilis) | previously designed assay, field study |
| 245 | Simmons, M., Tucker, A., Chadderton, W. L., Jerde, C. L. & Mahon, A. R. | 2016 | Canadian Journal of Fisheries and Aquatic Sciences | https://doi.org/10.1139/cjfas-2015-0262 | Active and passive environmental DNA surveillance of aquatic invasive species | water | river | fish | bighead carp (Hypophthalmichthys nobilis) | previously designed assay, field study, ddPCR |
| 246 | Simpfendorfer, C. A., Kyne, P. M., Noble, T. H., Goldsbury, J., Basiita, R. K., Lindsay, R., Shields, A., Perry, C. & Jerry, D. J. | 2016 | Endangered Species Research | https://doi.org/10.3354/esr00731 | Environmental DNA detects critically endangered largetooth sawfish in the wild | water | mesocosm, river, waterhole | fish | largetooth sawfish (Pristis pristis) | assay design and validation |
| 247 | Simpson T. J. S., Dias, P. J., Snow, M., Munoz, J. & Berry, T. | 2017 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12581 | Real-time PCR detection of Didemnum perlucidum (Monniot, 1983) and Didemnum vexillum (Kott, 2002) in an applied routine marine biosecurity context | water | marine | tunicate | white colonial sea squirt (Didemnum perlucidum), carpet sea squirt (Didemnum vexillum) | assay design, validation and field study |
| 248 | Smart, A. S., Tingley, R., Weeks, A. R., van Rooyen, A .R. & McCarthy, M. A. | 2015 | Ecological Applications | https://doi.org/10.1890/14-1751.1 | Environmental DNA sampling is more sensitive than a traditional survey technique for detecting an aquatic invader | water | pond | amphibian | smooth newt (Lissotriton vulgaris vulgaris) | assay design and validation |
| 249 | Smith, K. F., Wood, S. A., Mountfort, D. O. & Cary, S. C. | 2012 | Journal of Experimental Marine Biology and Ecology | https://doi.org/10.1016/j.jembe.2011.10.021 | Development of a real-time PCR assay for the detection of the invasive clam, Corbula amurensis, in environmental samples | plankton samples | marine | mollusc | Asian clam (Corbula amurensis) | assay design and validation |
| 250 | Spangler, M. A., Huettmann, F., Herriott, I. C. & Lopez, J. A. | 2017 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-017-0916-9. | Development, validation, and evaluation of an assay for the detection of wood frogs (Rana sylvatica) in environmental DNA | water | wetland | amphibian | wood frogs (Rana sylvatica) | assay design and validation |
| 251 | Spear, S. F., Groves, J. D., Williams, L. A. & Waits, L. P. | 2015 | Biological Conservation | https://doi.org/10.1016/j.biocon.2014.11.016 | Using environmental DNA methods to improve detectability in a hellbender (Cryptobranchus alleganiensis) monitoring program | water | river | amphibian | eastern hellbender (Cryptobranchus alleganiensis alleganiensis) | assay design and validation, testing in the field |
| 252 | Stewart, K., Ma, H., Zheng, J. & Zhao, J. | 2017 | Conservation Biology | https://doi.org/10.1111/cobi.12910 | Using environmental DNA to assess population-wide spatiotemporal reserve use | water | river | mammal | Yangtze finless porpoise (Neophocaena phocaenoides) | assay design and validation – further development of first porpoise paper |
| 253 | Stoeckle, B., Beggel, S., Cerwenka, A. F., Motivans, E., Kuehn, R. & Geist, J. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0189119 | A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems | water | mesocosm | fish | round goby (Neogobius melanostomus) | assay design and validation, testing abiotic influences, inhibition |
| 254 | Stoeckle, B. C., Kuehn, R. & Geist, J. | 2016 | Aquatic Conservation: Marine and Freshwater Ecosystems | https://doi.org/10.1002/aqc.2611 | Environmental DNA as a monitoring tool for the endangered freshwater pearl mussel (Margaritifera margaritifera L.): a substitute for classical monitoring approaches? | water | stream | mollusc | freshwater pearl mussel (Margaritifera margaritifera L.) | assay development, field samples |
| 255 | Strand, D. S., Jussila, J., Johnsen, S. I., Viljamaa-Dirks, S., Edsman, L., Wiik-Nielsen, J., Viljugrein, H., Engdahl, F. & Vralstad, T. | 2014 | Journal of Applied Ecology | https://doi.org/10.1111/1365-2664.12218 | Detection of crayfish plague spores in large freshwater systems | water | lake | microorganism | crayfish plague (Aphanomyces astaci) | previously designed assay, validation in the field |
| 256 | Strickland, G. J. & Roberts, J. H. | 2019 | Hydrobiologia | https://doi.org/10.1007/s10750-018-3723-8 | Utility of eDNA and occupancy models for monitoring an endangered fish across diverse riverine habitats | water | river, stream | fish | Roanoke logperch (Percina rex) | assay design and validation |
| 257 | Strickler, K.M., Fremier, A.K. & Goldberg, C. S. | 2015 | Biological Conservation | https://doi.org/10.1016/j.biocon.2014.11.038 | Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms | water | mesocosm | amphibian | American bullfrog (Lithobates catesbeianus) | assay design and validation, abiotic influences |
| 258 | Strobel, B., Laramie, M. B. & Pilliod, D. S. | 2017 | North American Journal of Fisheries Management | https://doi.org/10.1080/02755947.2017.1335254 | Exploring the use of environmental DNA to determine the species of salmon redds | water | river | fish | Chinook salmon (Oncorhynchus tshawytscha), Coho salmon (Oncorhynchus kisutch) | development of other salmon primer papers |
| 259 | Takahara, T., Minamoto, T. & Doi, H. | 2013 | PLoS ONE | https://doi.org/10.1371/journal.pone.0056584 | Using environmental DNA to estimate the distribution of an invasive fish species in ponds | water | pond | fish | bluegill sunfish (Lepomis macrochirus) | assay validation vs. visual surveys |
| 260 | Takahara, T., Minamoto, T. & Doi, H. | 2015 | Biological Conservation | https://doi.org/10.1016/j.biocon.2014.11.014 | Effects of sample processing on the detection rate of environmental DNA from the common carp (Cyprinus carpio) | water | pond | fish | common carp (Cyprinus carpio) | previously designed assay and field validation |
| 261 | Takahara, T., Minamoto, T., Yamanaka, H., Doi, H. & Kawabata, Z. | 2012 | PLoS ONE | https://doi.org/10.1371/journal.pone.0035868 | Estimation of fish biomass using environmental DNA | water | mesocosm, pond | fish | common carp (Cyprinus carpio) | assay design and validation, biomass vs. qPCR |
| 262 | Takahashi, M. K., Meyer, M. J., Mcphee, C., Gaston, J. R., Venesky, M. D. & Case, B. F. | 2017 | The Journal of Wildlife Management | https://doi.org/10.1002/jwmg.21349 | Seasonal and diel signature of eastern hellbender environmental DNA | water | river | amphibian | eastern hellbender (Cryptobranchus alleganiensis alleganiensis) | seasonal fluctuations assay by Spear et al. 2015 |
| 263 | Takeuchi, A., Watanabe, S., Yamamoto, S., Miller, M. J., Fukuba, T., Miwa, T., Okino, T., Minamoto, T. & Tsukamoto, K. | 2019 | Marine Ecology Progress Series | https://doi.org/10.3354/meps12828 | First use of oceanic environmental DNA to study the spawning ecology of the Japanese eel Anguilla japonica | water | marine | fish | Japanese eel (Anguilla japonica) | assay design and validation |
| 264 | Thomsen, P. F., Kielgast, J., Iversen, L. L., Moller, P. R., Rasmussen, M. & Willerslev, E. | 2012 | PLoS ONE | https://doi.org/10.1371/journal.pone.0041732 | Detection of a diverse marine fish fauna using environmental DNA from seawater samples | water | marine | fish | three-spined stickleback (Gasterosteus aculeatus), European flounder (Platichthys flesus) | assay design, validation and field study |
| 265 | Thomsen, P. F., Kielgast, J., Iversen, L. L., Wiuf, C., Rasmussen, M., Gilbert, M. T., Orlando, L. & Willerslev, E. | 2012 | Molecular Ecology | https://doi.org/10.1111/j.1365-294X.2011.05418.x | Monitoring endangered freshwater biodiversity using environmental DNA | water | mesocosm, pond | amphibian, crustacean, fish, insect, mammal | great crested newt (Triturus cristatus), common spadefoot toad (Pelobates fuscus), large white-faced darter (Leucorrhinia pectoralis), Eurasian otter (Lutra lutra), European weatherloach (Misgurnus fossilis), tadpole shrimp (Lepidurus apus) | assay design and validation |
| 266 | Tillotson, M. D., Kelly, R. P., Duda, J .J., Hoy, M., Kralj, J. & Quinn, T. P. | 2018 | Biological Conservation | https://doi.org/10.1016/j.biocon.2018.01.030 | Concentrations of environmental DNA (eDNA) reflect spawning salmon abundance at fine spatial and temporal scales | water | river | fish | sockeye salmon (Oncorhynchus nerka) | previously established assay further used, improved (SECO3_861-930) |
| 267 | Tingley, R., Greenlees, M., Oertel, S., van Rooyen, A. R. & Weeks, A. R. | 2019 | Biological Invasions | https://doi.org/10.1007/s10530-018-1810-4 | Environmental DNA sampling as a surveillance tool for cane toad Rhinella marina introductions on offshore islands | water | pond | amphibian | cane toad (Rhinella marina) | assay design and validation |
| 268 | Torresdal, J. D., Farrell, A. D. & Goldberg, C. S. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0168787 | Environmental DNA detection of the golden tree frog (Phytotriades auratus) in bromeliads | water | pool | amphibian | golden tree frog (Phytotriades auratus) | assay design and validation |
| 269 | Treguier, A., Paillisson, J., Dejean, T., Valentini, A., Schlaepfer, M.A. & Roussel, J. | 2014 | Journal of Applied Ecology | https://doi.org/10.1111/1365-2664.12262 | Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds | water | pond | crustacean | red swamp crayfish (Procambarus clarkii) | assay design and validation |
| 270 | Trujillo-Gonzalez, A., Edmunds, R. C., Becker, J. A. & Hutson, K. S. | 2019 | Scientific Reports | https://doi.org/10.1038/s41598-019-41517-2 | Parasite detection in the ornamental fish trade using environmental DNA | water | mesocosm | parasite | fish parasite (Dactylogyrus spp.) | assay design and validation |
| 271 | Tsuji, S., Iguchi, Y., Shibata, N., Teramura, I., Kitagawa, T. & Yamanaka, H. | 2018 | Scientific Reports | https://doi.org/10.1038/s41598-018-27434-w | Real-time multiplex PCR for simultaneous detection of multiple species from environmental DNA: an application on two Japanese medaka species | water | aquarium, river | fish | Japanese rice fish (Oryzias latipes), northern medaka (Oryzias sakaizumii) | assay design, validation and field study |
| 272 | Tsuji, S., Ushio, M., Sakurai, S., Minamoto, T. & Yamanaka, H. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0176608 | Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance | water | aquarium | fish | ayu sweetfish (Plecoglossus altivelis altivelis), common carp (Cyprinus carpio) | eDNA degradation testing with existing primer/probe set |
| 273 | Tucker, A. J., Chadderton, W. L., Jerde, C. L., Renshaw, M. A., Uy, K., Gantz, C., Mahon, A. R., Bowen, A., Strakosh, T., Bossenbroek, J. M., Sieracki, J. L., Beletsky, D., Bergner, J. & Lodge, D. M. | 2016 | Biological Invasions | https://doi.org/10.1007/s10530-016-1209-z | A sensitive environmental DNA (eDNA) assay leads to new insights on ruffe (Gymnocephalus cernua) spread in North America | water | lake | fish | ruffe (Gymnocephalus cernua) | assay development and validation, field study |
| 274 | Turner, C. R., Barnes, M. A., Xu, C. C. Y., Jones, S. E. & Jerde, C. L. | 2014 | Methods in Ecology and Evolution | https://doi.org/10.1111/2041-210X.12206 | Particle size distribution and optimal capture of aqueous macrobial eDNA | water | lake, pond | fish | common carp (Cyprinus carpio) | eDNA particle size paper |
| 275 | Turner, C. R., Miller, D. J., Coyne, K. J. & Corush, J. | 2014 | PLoS ONE | https://doi.org/10.1371/journal.pone.0114329 | Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian big headed carp (Hypophthalmichthys spp.) | water | experimental pond, mesocosm | fish | bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix) | qPCR assay design and validation |
| 276 | Turner, C. R., Uy, K. L. & Everhart, R. C. | 2015 | Biological Conservation | https://doi.org/10.1016/j.biocon.2014.11.017 | Fish environmental DNA is more concentrated in aquatic sediments than surface water | water | pond | fish | big headed Asian carp (Hypophthalmichthys spp.) | previously designed assay and field validation |
| 277 | Uchii, K., Doi, H. & Minamoto, T. | 2016 | Molecular Ecology Resources | https://doi.org/10.1111/1755-0998.12460 | A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes | water | mesocosm, river | fish | common carp (Cyprinus carpio) | assay design and validation |
| 278 | Uchii, K., Doi, H., Yamanaka, H. & Minamoto T. | 2017 | Ecology and Evolution | https://doi.org/10.1002/ece3.3346 | Distinct seasonal migration patterns of Japanese native and non-native genotypes of common carp estimated by environmental DNA | water | lake, lagoon | fish | Japanese native and introduced non-native genotypes of common carp (Cyprinus carpio) | assay design, validation and field study |
| 279 | Ulibarri, R. M., Bonar, S. A., Rees, C., Amberg, J., Ladell, B. & Jackson, C. | 2017 | North American Journal of Fisheries Management | https://doi.org/10.1080/02755947.2017.1306005 | Comparing efficiency of American Fisheries Society standard snorkeling techniques to environmental DNA sampling techniques | water | stream | fish | bluehead sucker (Catostomus discobolus), Zuni bluehead sucker (Catostomus discobolus yarrowi) | assay design and validation |
| 280 | Uthicke, S., Lamare, M. & Doyle, J. R. | 2018 | Coral Reefs | https://doi.org/10.1007/s00338-018-1734-6 | eDNA detection of corallivorous seastar (Acanthaster cf. solaris) outbreaks on the Great Barrier Reef using digital droplet PCR | water | marine | echinoderm | crown-of-thorns sea star (Acanthaster cf. solaris) | develop a ddPCR-based method to detect eDNA |
| 281 | Valentin, R. E., Fonseca, D. M., Nielsen, A. L., Leskey, T. C. & Lockwood, J. L. | 2018 | Frontiers in Ecology and the Environment | https://doi.org/10.1002/fee.1811 | Early detection of invasive exotic insect infestations using eDNA from crop surfaces | surface | terrestrial (plant surface) | insect | brown marmorated stink bug (Halyomorpha halys) | qPCR assay to develop a protocol |
| 282 | Valentin, R. E., Maslo, B., Lockwood, J. L., Pote, J. & Fonseca, D. M. | 2016 | Pest Management Science | https://doi.org/10.1002/ps.4217 | Real-time PCR assay to detect brown marmorated stink bug, Halyomorpha halys (Stål), in environmental DNA | terrestrial | faeces, paper surface | insect | brown marmorated stink bug (Halyomorpha halys) | assay design and validation |
| 283 | Veldhoen, N., Hobbs, J., Ikonomou, G., Hii. M., Lesperence, M. & Helbing, C. C. | 2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.0164907 | Implementation of novel design features for qPCR-based eDNA assessment | water | thalweg of lotic systems | amphibian | American bullfrog (Lithobates catesbeiana), Rocky Mountain tailed frog (Ascaphus montanus) | previously designed assay and new primers developed, field study |
| 284 | Vörös, J., Márton, O., Schmidt, B.R., Gál, T. J. & Jelić, D. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0170945 | Surveying Europe’s only cave-dwelling chordate species (Proteus anguinus) using environmental DNA | water | cave systems | amphibian | olm (Proteus anguinus) | assay design and validation |
| 285 | Walsh, J. R., Spear, M. J., Shannon, T. P., Krysan, P. J. & Vander Zanden, M. J. | 2019 | Biological Invasions | https://doi.org/10.1007/s10530-018-1862-5 | Using eDNA, sediment subfossils, and zooplankton nets to detect invasive spiny water flea (Bythotrephes longimanus) | water, sediment | lake | crustacean | spiny water flea (Bythotrephes longimanus) | explore detection of Blythotrephes using three monitoring methods: zooplankton net tows, eDNA, and sampling of Blythotrephes tail spine subfossils in sediments |
| 286 | Wegleitner, B. J., Jerde, C. L., Tucker, A., Chadderton, W. L. & Mahon, A. R. | 2015 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-015-0483-x | Long duration, room temperature preservation of filtered eDNA samples | water | mesocosm | fish | round goby (Neogobius melanostomus) | test for significant loss of DNA yield from storage of polycarbonate etched filters |
| 287 | Wei, N., Nakajima, F. & Tobino, T. | 2018 | Environmental Science & Technology | https://doi.org/10.1021/acs.est.8b04956 | A microcosm study of surface sediment environmental DNA: decay observation, abundance estimation, and fragment length comparison | sediment | mesocosm | crustacean | estuarine amphipod (Grandidierella japonica) | investigate the persistence of surface sediment eDNA, the quantitative relationship between organism abundance and eDNA, and the comparison of different lengths of DNA fragments |
| 288 | Wei, N., Nakajima, F. & Tobino, T. | 2018 | Ecological Indicators | https://doi.org/10.1016/j.ecolind.2018.04.063 | Effects of treated sample weight and DNA marker length on sediment eDNA based detection of a benthic invertebrate | sediment | aquarium, marine | crustacean | estuarine amphipod (Grandidierella japonica) | developed two DNA marker sequences to analyze mitochondrial DNA from sediment samples |
| 289 | Weltz K., Lyle J. M., Ovenden J., Morgan J. A. T., Moreno D. A. & Semmens J. M. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0178124 | Application of environmental DNA to detect an endangered marine skate species in the wild | water | sea | fish | maugean skate (Zearaja maugeana) | assay design and validation |
| 290 | Wilcox, T. M., Carim, K. J., McKelvey, K. S., Young, M. K. & Schwartz, M. K. | 2015 | PLoS ONE | https://doi.org/10.1371/journal.pone.0142008 | The dual challenges of generality and specificity when developing environmental DNA markers for species and subspecies of Oncorhynchus | water | tissue samples | fish | westslope cutthroat trout (Oncorhynchus clarkii lewisi), Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri), rainbow trout (Oncorhynchus mykiss) | assay design and validation |
| 291 | Wilcox, T. M., McKelvey, K. S., Young, M. K., Jane, S. F., Lowe, W. H., Whiteley, A. R. & Schwartz, M. K. | 2013 | PLoS ONE | https://doi.org/10.1371/journal.pone.0059520 | Robust detection of rare species using environmental DNA: the importance of primer specificity | water | river | fish | brook trout (Salvelinus fontinalis), bull trout (Salvelinus confluentus) | assay design, validation and development – PCR vs. qPCR, detection probability |
| 292 | Wilcox, T. M., McKelvey, K. S., Young, M. K., Lowe, W. H. & Schwartz, M. K. | 2015 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-015-0465-z | Environmental DNA particle size distribution from brook trout (Salvelinus fontinalis) | water | old primers from Wilcox 2013 | fish | brown trout (Salvelinus fontinalis) | further assay tests |
| 293 | Wilcox, T. M., Schwartz, M. K., McKelvey, K. S., Young, M. K. & Lowe, W. H. | 2014 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-013-0113-4 | A blocking primer increases specificity in environmental DNA detection of bull trout (Salvelinus confluentus) | water | tissue sample | fish | bull trout (Salvelinus confluentus) | assay design and laboratory validation |
| 294 | Wilcox, T. M., McKelvey, K. S., Young, M. K., Sepulveda, A. J., Shepard, B. B., Jane, S. F., Whiteley, A. R., Lowe, W. H. & Schwartz, M. K. | 2016 | Biological Conservation | https://doi.org/10.1016/j.biocon.2015.12.023 | Understanding environmental DNA detection probabilities: a case study using a stream-dwelling char Salvelinus fontinalis | water | stream | fish | brook trout (Salvelinus fontinalis) | previously designed assay, case study/field study |
| 295 | Wilcox, T. M., Young, M. K., McKelvey, K. S., Isaak, D. J., Horan, D. L. & Schwartz, M. K. | 2018 | Ecosphere | https://doi.org/10.1002/ecs2.2500 | Fine-scale environmental DNA sampling reveals climate-mediated interactions between native and invasive trout species | water | river | fish | brook trout (Salvelinus fontinalis), bull trout (Salvelinus confluentus) | use eDNA sampling and high-resolution habitat covariates to build an accurate species distribution model |
| 296 | Williams, K. E., Huyvaert, K. P. & Piaggio, A. J. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0179282 | Clearing muddied waters: capture of environmental DNA from turbid waters | water | intermittent waterbody | mammal | wild boar (Sus scrofa) | assay design, validation, sampling method development |
| 297 | Williams, K. E., Huyvaert K. P., Vercauteren, K. C., Davis, A. J. & Piaggio, A. J. | 2018 | Ecology and Evolution | https://doi.org/10.1002/ece3.3698 | Detection and persistence of environmental DNA from an invasive, terrestrial mammal | water, mud | mesocosm | mammal | wild boar (Sus scrofa) | assay sensitivity, LOD etc. based on Williams et al. 2017 |
| 298 | Williams, K. E., Stedtfeld, R. D., Engle, C., Salach, P., Fakher, U., Stedtfeld, T., Dreelin, E., Stevenson, R. J., Latimore, J. & Hashsham, S. A. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0186462 | Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp. | water | lake | mussel | zebra mussel (Dreissena polymorpha), quagga mussel (Dreissena bugensis) | LAMP assay design and validation |
| 299 | Williams, K. E., Huyvaert, K. P. & Piaggio, A. J. | 2016 | BMC Research Notes | https://doi.org/10.1186/s13104-016-2104-5 | No filters, no fridges: a method for preservation of water samples for eDNA analysis | water | tank in pig enclosure | mammal | wild boar (Sus scrofa) | tested utility of Longmire’s solution as an additive to freshwater samples for preservation of eDNA |
| 300 | Willis, J. E., Stewart-Clark, S., Greenwood, S. J., Davidson, J. & Quijon, P. | 2011 | Aquatic Invasions | https://doi.org/10.3391/ai.2011.6.1.02 | A PCR-based assay to facilitate early detection of Diplosoma listerianum in Atlantic Canada | water | bay, river | tunicate | colonial tunicate (Diplosoma listerianum) | assay design and validation |
| 301 | Wilson, C., Wright, E., Bronnenhuber, J., MacDonald, F., Belore, M. & Locke, B. | 2014 | Management of Biological Invasions | https://doi.org/10.3391/mbi.2014.5.3.05 | Tracking ghosts: combined electrofishing and environmental DNA surveillance efforts for Asian carps in Ontario waters of Lake Erie | water | lake | fish | bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), grass carp (Ctenopharyngodon idella) | assay design and field study |
| 302 | Wilson, J. J., Sing, K. W., Chen, P. N. & Zieritz, A. | 2017 | Mitochondrial DNA Part A | https://doi.org/10.1080/24701394.2017.1373109 | Tracking the southern river terrapin (Batagur affinis) through environmental DNA: prospects and challenges | water | mesocosm, river | turtle | river terrapin (Batagur affinis) | assay design and validation with aquarium and field samples |
| 303 | Wineland, S. M., Welch, S. M., Pauley, T. K., Apodaca, J. J., Olszack, M., Mosher, J. J., Holmes, J. N. & Waldron, J. L. | 2019 | Freshwater Biology | https://doi.org/10.1111/fwb.13210 | Using environmental DNA and occupancy modelling to identify drivers of eastern hellbender (Cryptobranchus alleganiensis alleganiensis) extirpation | water | pond | amphibian | eastern hellbender (Cryptobranchus alleganiensis alleganiensis) | assay design and field study |
| 304 | Wood, S. A., Zaiko, A., Richter, I., Inglis, G. & Pochon, X. | 2017 | Environmental Science and Pollution Research | https://doi.org/10.1007/s11356-017.9357-y | Development of a real-time polymerase chain reaction assay for the detection of the invasive Mediterranean fanworm, Sabella spallanzanii, in environmental samples | water | marine | annelid | tube-building polychaete worm (Sabella spallanzanii) | assay design and validation |
| 305 | Wozney, K. M. & Wilson, C. C. | 2017 | Journal of Great Lakes Research | https://doi.org/10.1016/j.jglr.2017.05.001 | Quantitative PCR multiplexes for simultaneous multispecies detection of Asian carp eDNA | water | river | fish | bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), grass carp (Ctenopharyngodon idella), black carp (Mylopharyngodon piceus) | multiplex assay development |
| 306 | Wu, Q., Kawano, K., Uehara, Y., Okuda, N., Hongo, M., Tsuji, S., Yamanaka, H. & Minamoto, T. | 2018 | Freshwater Science | https://doi.org/10.1086/697542 | Environmental DNA reveals nonmigratory individuals of Palaemon paucidens overwintering in Lake Biwa shallow waters | water | lake | crustacean | lacustrine shrimp (Palaemon paucidens) | assay design, validation and field study |
| 307 | Xia, Z., Zhan, A., Gao, Y., Zhang, L., Haffner, G. D. & MacIsaac, H. J. | 2017 | Biological Invasions | https://doi.org10.1007/s10530-017-1545-7 | Early detection of a highly invasive bivalve based on environmental DNA (eDNA) | water | lake, mesocosm, reservoir, river | mollusc | golden mussel (Limnoperna fortunei) | assay design and validation |
| 308 | Xia, Z., Johansson, M. L., Gao, Y., Zhang, L., Haffner, G. D., MacIsaac, H. J. & Zhan, A. | 2018 | Ecology and Evolution | https://doi.org/10.1002/ece3.4636 | Conventional versus real-time quantitative PCR for rare species detection | water | aquarium, field | mussel | golden mussel (Limnoperna fortunei) | compare cPCR and qPCR to detect invasive golden mussel (Limnoperna fortunei) |
| 309 | Xu, N., Zhu, B., Shi, F., Shao, K., Que, Y., Li, W., Li, W., Jiao, W., Tian, H., Xu, D. & Chang, J. | 2018 | Science of Nature | https://doi.org/10.1007/s00114-018-1587-4 | Monitoring seasonal distribution of an endangered anadromous sturgeon in a large river using environmental DNA | water | river | fish | Chinese sturgeon (Acipenser sinensis) | establish a protocol for the use of eDNA to monitor distribution of Chinese sturgeon |
| 310 | Yamamoto S., Minami K., Fukaya K., Yamamoto S, Minami K, Fukaya K, Hidaka, S., Suzuki, K. W., Miya, M., Araki, H., Yamanaka, H., Maruyama, A., Miyashita, K., Masuda, R., Minamoto, T. & Kondoh, M. | 2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.0149786 | Environmental DNA as a ‘snapshot’ of fish distribution: a case study of Japanese jack mackerel in Maizuru Bay, Sea of Japan | water | marine | fish | Japanese jack mackerel (Trachurus japonicus) | assay application (Minamoto et al. unpublished data at the time of publication) |
| 311 | Yamanaka, H., Takao, D., Maruyama, A. & Imamura, A. | 2018 | Ecological Research | https://doi.org/10.1007/s11284-018-1612-2 | Species-specific detection of the endangered piscivorous cyprinid fish Opsariichthys uncirostris uncirostris, three-lips, using environmental DNA analysis | water | lake, river | fish | Amur three-lips (Opsariichthys uncirostris) | assay design and validation |
| 312 | Yamanaka, H., Minamoto, T., Matsuura, J., Sakurai, S., Tsuji, S., Motozawa, H., Hongo, M., Sogo, Y., Kakimi, N., Teramura, I., Sugita, M., Baba, M. & Kondo, A. | 2017 | Limnology | https://doi.org/10.1007/s10201-016-0508-5 | A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant | water | lake | fish | bluegill sunfish (Lepomis macrochirus) | examine effectiveness of cationic surfactants as preservatives for eDNA water samples |
| 313 | Yamanaka, H., Motozawa, H., Tsuji, S., Miyazawa, R. C., Takahara, T. & Minamoto, T. | 2016 | Ecological Research | https://doi.org/10.1007/s11284-016-1400-9 | On-site filtration of water samples for environmental DNA analysis to avoid DNA degradation during transportation | water | pond | fish | largemouth bass (Micropterus salmoides), bluegill sunfish (Lepomis macrochirus) | describe an on-site filtration system that allows the immediate filtration of water samples to minimize eDNA degradation |
| 314 | Yamanaka, Y. & Minamoto, T. | 2016 | Ecological Indicators | https://doi.org/10.1016/j.ecolind.2015.11.022 | The use of environmental DNA of fishes as an efficient method of determining habitat connectivity | water | river, marine | fish | temperate sea bass (Lateolabrax japonicus), flathead grey mullet (Mugil cephalus), ayu (Plecoglossus altivelis altivelis) | assay design and validation |
| 315 | Carim, K. J., McKelvey, K. S., Young, M. K., Wilcox, T. M. & Schwartz, M. K. | 2016 | US Department of Agriculture, Forest Service, Rocky Mountain Research Station, Fort Collins, CO. | NA | A protocol for collecting eDNA samples from streams. General Technical Report RMRS-GTR-355. | water | river, stream | aquatic | bull trout (Salvelinus confluentus), brook trout (Salvelinus fontinalis), westslope cutthroat trout (Oncorhynchus clarkii lewisi), Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri), rainbow trout (Oncorhynchus mykiss), brown trout (Salmo trutta), Arctic grayling (Thymallus arcticus), American river otters (Lontra canadensis), Rocky Mountain Tailed frogs (Ascaphus montanus), Idaho giant salamanders (Dicamptodon aterrimus) | technical report for field sampling |
| 316 | Watanabe, S., Minegishi, Y., Yoshinaga, T., Aoyama, J. & Tsukamoto, K. | 2004 | Marine Biotechnology | https://doi.org/10.1007/s10126-004-1000-5 | A quick method for species identification of Japanese eel (Anguilla japonica) using real-time PCR: an onboard application for use during sampling surveys | eggs, larvae | marine | fish | Japanese eel (Anguilla japonica) | assay design and validation – base for other Japanese eel paper |
| 317 | Dunker, K. J., Sepulveda, A. J., Massengill, R. L., Olsen, J. B., Russ, O. L., Wenburg, J. K. & Antonovich, A. | 2016 | PLoS ONE | https://doi.org/10.1371/journal.pone.0173837 | Correction: potential of environmental DNA to evaluate northern pike (Esox lucius) eradication efforts: an experimental test and case study. | water | lake | fish | northern pike (Esox lucius) | correction |
| 318 | Tang, R., Dodd, A., Lai, D., McNabb, W. C. & Love, D. R. | 2007 | Acta Biochimica et Biophysica Sinica | https://doi.org/10.1111/j.1745-7270.2007.00283.x | Validation of zebrafish (Danio rerio) reference genes for quantitative real-time RT-PCR normalization | gene expression study | aquarium | fish | zebrafish (Danio rerio) | contains primers later used |
| 319 | Vrålstad, T., Knutsen, A. K., Tengs, T. & Holst-Jensen, A. | 2009 | Veterinary Microbiology | https://doi.org/10.1016/j.vetmic.2008.12.022 | A quantitative TaqMan MGB real-time polymerase chain reaction based assay for detection of the causative agent of crayfish plague Aphanomyces astaci | NA – tissue sample | freshwater crayfish | pathogen (Oomycota) | crayfish plague (Aphanomyces astaci) | assay design and validation |
| 320 | Vrålstad, T., Knutsen, A. K., Tengs, T. & Holst-Jensen, A. | 2015 | U.S.D.A. Forest Service, National Genomics Center for Wildlife and Fish Conservation. | NA | Protocol for collecting eDNA samples from streams. V2.3 (July 2015) | water | river, stream | aquatic | NA | technical report for field sampling |
| 321 | Jensen, M. R., Knudsen, S. W., Munk, P., Thomsen, P. F. & Møller, P. R. | 2018 | Marine Biology | https://doi.org/10.1007/s00227-018-3390-3 | Tracing European eel in the diet of mesopelagic fishes from the Sargasso Sea using DNA from fish stomachs | stomach samples | marine | fish | European eel (Anguilla anguilla) | dietary study |
| 322 | Ushio, M., Murakami, H., Masuda, R., Sado, T., Miya, M., Sakurai, S., Yamanaka, H., Minamoto, T. & Kondoh, M. | 2018 | Metabarcoding and Metagenomics | https://doi.org/10.3897/mbmg.2.23297 | Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing | water | marine | fish | Japanese sardine (Sardinops melanostictus), round herring (Etrumeus teres) | comparative study metabarcoding qPCR |
| 323 | Utiger, U., Helfenberger, N., Schatti, B., Schmidt, C., Ruf, M. & Ziswiler, V. | 2002 | Russian Journal of Herpetology | NA | Molecular systematics and phylogeny of old and new world ratsnakes, Elaphe auct., and related genera (Reptilia, Squamata, Colubridae) | water | freshwater | reptiles | various rat snake species (Elaphe auct.) | infer phylogenetic relationships among Elaphe auct. using mitochondrial DNA |
| 324 | Pilliod, D. S. & Laramie, M. B. | 2016 | USGS Open File Report 2016-1091 | https://doi.org/10.3133/ofr20161091 | Salmon redd identification using environmental DNA (eDNA) | water | river | fish | Chinook salmon (Oncorhynchus tshawytscha), Coho salmon (Oncorhynchus kisutch) | develop a technique to use eDNA to distinguish between redds made by different species of salmon |
| 325 | Hyatt, A. D., Boyle, D. G., Olsen, V., Boyle, D. B., Berger, L., Obendorf, D., Dalton, A., Kriger, K., Hero, M., Hines, H., Phillott, R., Campbell, R., Marantelli, G., Gleason, F. & Colling, A. | 2007 | Diseases of Aquatic Organisms | https://doi.org/10.3354/dao073175 | Diagnostic assays and sampling protocols for the detection of Batrachochytrium dendrobatidis | NA – toe clip from frog | freshwater | pathogen (Oomycota) | amphibian chytrid fungus (Batrachochytrium dendrobatidis) | develop sample methods from toe clips of frogs, included more specificity testing from Boyle 2004 |
| 326 | Hyman, O. J. & Collins, J. P. | 2012 | Diseases of Aquatic Organisms | https://doi.org/10.3354/dao02423 | Evaluation of a filtration-based method for detecting Batrachochytrium dendrobatidis in natural bodies of water | water | pond | pathogen (Oomycota) | amphibian chytrid fungus (Batrachochytrium dendrobatidis) | develop water filtration method for detection of bd |
| 327 | Walker, S. F., Baldi Salas, M., Jenkins D., Garner, T. W. J., Cunningham A. A., Hyatt, A. D., Bosch J., & Fisher, M. C. | 2007 | Diseases of Aquatic Organisms | https://doi.org/10.3354/dao01850 | Environmental detection of Batrachochytrium dendrobatidis in a temperate climate | water, sediment | pond | pathogen (Oomycota) | amphibian chytrid fungus (Batrachochytrium dendrobatidis) | develop water and sediment detection assay |
| 328 | Chaves, P. B., Graeff, V. G., Lion, M., Oliveira, L. R. & Eizirik, E. | 2012 | Molecular Ecology Resources | https://doi.org/10.1111/j.1755-0998.2011.03056.x | DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples | scats | field, forest, zoo | carnivore | serval (Leptailurus serval), ocelot (Leopardus pardalis), jaguar (Panthera onca), leopard (Panthera pardus), tiger (Panthera tigris), puma (Puma concolor), maned wolf (Chrysocyon brachyurus), forest fox (Cerdocyon thous), pampas fox (Lycalopex gymnocercus), South American coati (Nasua nasua), South American raccoon (Procyon cancrivorus), tayra (Eira barbara) | evaluate the potential of two short mitochondrial DNA fragments and cytochrome oxidase I gene to serve as standard markers for the Carnivora |
| 329 | Wasser, S. K., Houston, C. S., Koehler, G. M., Cadd, G. G. & Fain, S. R. | 1997 | Molecular Ecology | https://doi.org/10.1046/j.1365-294X.1997.00281.x | Techniques for application of faecal DNA methods to field studies of Ursids | saliva swabs | tree | bear | American black bear (Ursus americanus), Malayan sun bear (Helarctos malayanus) | identify seed dispersers |
| 330 | Andruszkiewicz, E. A., Sassoubre, L. M. & Boehm, A. B. | 2017 | PLoS ONE | https://doi.org/10.1371/journal.pone.0185043 | Persistence of marine fish environmental DNA and the influence of sunlight | water | mesocosm, tank containing seawater | fish | Pacific chub mackerel (Scomber japonicus) | investigate the persistence of eDNA in marine waters and explore the role of sunlight in modulating eDNA persistence |
| 331 | Li, F., Mahon, A. R., Barnes, M. A., Feder, J., Lodge, D. M., Hwang, C. T., Schafer, R., Ruggiero, S. T. & Tanner, C. E. | 2011 | PLoS ONE | https://doi.org/10.1371/journal.pone.0029224 | Quantitative and rapid DNA detection by laser transmission spectroscopy | water | ballast water | mollusc | quagga mussel (Dreissena bugensis) | monitoring of ballast water with LTS |
| 332 | Boyle, D. G., Boyle, D. B., Olsen, V., Morgan, J. A. T. & Hyatt, A. D. | 2004 | Diseases of Aquatic Organisms | https://doi.org/10.3354/dao060141 | Rapid quantitative detection of chytridiomycosis (Batrachochytrium dendrobatidis) in amphibian samples using real-time TaqMan PCR assay | NA – toe clip from frog | freshwater | pathogen (Oomycota) | amphibian chytrid fungus (Batrachochytrium dendrobatidis) | develop qPCR assay for detection of bd |
| 333 | Karlsson, S., Hagen, M., Eriksen, L., Hindar, K., Jensen, A. J., Garcia de Leaniz, C., Cotter, D., Guobergsson, G., Kahilainen, K., Guojonsson, S., Romakkaniemi, A. & Ryman, N. | 2012 | Conservation Genetics Resources | https://doi.org/10.1007/s12686-012-9730-6 | A genetic marker for the maternal identification of Atlantic salmon x brown trout hybrids | water | river | fish | Atlantic salmon (Salmo salar), brown trout (Salmo trutta), Atlantic salmon x brown trout hybrid | presents a species-specific mitochondrial DNA marker for the identification of the maternal origin of hybrids |
| 334 | Vasquez, A. A., Hudson, P. L., Fujimoto, M., Keeler, K., Armenio, P. M. & Ram, J. L. | 2016 | Journal of Great Lakes Research | https://doi.org/10.1016/j.jglr.2016.04.001 | Eurytemora carolleeae in the Laurentian Great Lakes revealed by phylogenetic and morphological analysis | NA – tissue sample | lake, river | crustacean | estuarine calanoid copepod (Eurytemora carolleeae) | contains PCR conditions for paper no. 85 |
Literature databaseEDNA Validation