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Tools and Resources Environmental DNA

eDNA assays

Assays listed here are probe-based quantitative PCR (qPCR) assays from the literature. We did not include conventional PCR assays, primers for metabarcoding, or more general qPCR assays developed as positive controls. Some species have multiple assays available in the literature.

Many labs are also running currently unpublished assays. Assays for many western North American amphibians have been developed by the WSU eDNA lab: labs.wsu.edu/goldberglab. Assays for many western North American fishes have been developed by the National Genomics Center: https://www.fs.fed.us/research/genomics-center/edna/Another resource for finding out who is working on what is at http://edna.fisheries.org/.

Note: Assays designed for one area may create false negatives or false positives when applied to another part of a species range if the validation wasn’t conducted globally. Additionally, errors might occur if PCR recipe or thermoprofile are changed. All assays should be re-validated with tissue samples when using them under new conditions. Also, please note that probe melting temperature is linked to probe chemistry and often fluorophores are only available with particular chemistries (e.g., MGB). 

Published probe-based qPCR assays for species detection in eDNA samples (updated May 2019). 

Common nameLatin namePublication
Acheilognathus typusAcheilognathus typusSakata et al. 2017
Aedes mosquitosAedes spp.Schneider et al. 2016
African clawed frogXenopus laevisSecondi et al. 2016
Alligator snapping turtleMacrochelys temminckiiFeist et al. 2018
Amami Oshima Frog Odorrana splendidaIwai et al. 2019
American bullfrogLithobates catesbieanusStrickler et al. 2015
Anopheles mosquitoAnopheles gambiae sensu latoOrdero et al. 2018
Arctic charSalvelinus alpinus/malmaRodgers et al. 2017
Arctic graylingThymallus arcticusCarim et al. 2016
Arctic graylingThymallus arcticusRodgers et al. 2017
Arizona treefrogHyla wrightorumGoldberg et al. 2018
Asian clamCorbicula flumineaCowart et al. 2018
Atlantic cod Gadus morhuaKnudson et al. 2019
Atlantic herringClupea harengusThomsen et al. 2012
Atlantic herring Clupea harengusKnudson et al. 2019
Atlantic mackerel Scomber scombrusKnudson et al. 2019
Atlantic salmonSalmo salarAtkinson et al. 2017
Austropeplea tomentosaAustropeplea tomentosaRathinasamy et al. 2018
Ayu sweetfishPlecoglossus altivelisYamanaka and Minamoto 2016
BdBatrochochytrium dendrobatidisBoyle et al. 2004
Bighead carpHypophthalmichthys nobilisCoulter et al. 2013
Bighead carpHypophthalmichthys nobilisFarrington et al. 2015
Bighead carpHypophthalmichthys nobilisRoy et al. 2018
Black carpMylopharyngodon piceusRoy et al. 2018
Blanding's turtleEmydoidea blandingiiLacoursiere-Roussel et al. 2016
Bluegill sunfishLepomis macrochirusDoi et al. 2015
Boa constrictorBoa constrictorHunter et al. 2015
Brazilian waterweedEgeria densaFujiwara et al. 2016
Brook troutSalvelinus fontinalisWilcox et al. 2013
Brook trout Salvelinus fontinalisHulley et al. 2019
Brown troutSalmo truttaCarim et al. 2016
Brown troutSalmo truttaGustavson et al. 2015
Brown troutSalmo truttaGustavson et al. 2015
Brown troutSalmo truttaDeutschmann et al. 2019
BryozoanBugula neritinaKim et al. 2018
Bull troutSalvelinus confluentusWilcox et al. 2014
BurbotLota lotaRodgers et al. 2017
Burmese pythonPython molurus bivittatusHunter et al. 2015
California red-legged frogRana draytoniiHalstead et al. 2018
California red-legged frogRana draytoniiHalstead et al. 2018
Cane toadRhinella marinaTingley et al. 2019
Carpet sea squirtDidemnum vexillumSimpson et al. 2017
Carpet sea squirtDidemnum vexillumSimpson et al. 2017
Chilean devil rayMobula tarapacanaGargan et al. 2017
Chilodonella hexastichaChilodonella hexastichaGomes et al. 2017
Chinese giant salamanderAndrias davidianusFukumoto et al. 2015
Chinese sleeperPerccottus gleniiRoy et al. 2018
Chinook salmonOncorhynchus tshawytschaBrandl et al. 2015
Chinook salmonOncorhynchus tshawytschaLaramie et al. 2015
Chiricahua leopard frogRana chiricahuensisGoldberg et al. 2018
Coldwater crayfishFaxonius eupunctusRice et al. 2018
Common carpCyprinus carpioTakahara et al. 2012
Common carpCyprinus carpioEichmiller et al. 2014
Common carpCyprinus carpioUchii et al. 2017
Common gartersnakeThamnophis sirtalisLacoursiere-Roussel et al. 2016
Common snapping turtleChelydra serpentinaLacoursiere-Roussel et al. 2016
Common spadefoot toadPelobates fuscusThomsen et al. 2012
Corallivorous seastar Acanthaster cf. solarisUthicke et al. 2018
Crucian carpCarassius carassiusHarper et al. 2019
Crucian carpCarassius carassiusRoy et al. 2018
Deepwater sculpin Myoxocephalus thompsoniiHulley et al. 2019
Dolly Varden Salvelinus malmaMinamoto et al. 2018
Dolly Varden troutSalvelinus malmaRodgers et al. 2017
Eastern pondmusselLigumia nasutaCurrier et al. 2018
Eurasian otterLutra lutraThomsen et al. 2012
European eelAnguila anguilaSeymour et al. 2018
European flounderPlatichthys flesusThomsen et al. 2012
European flounder Platichthys flesusKnudson et al. 2019
European plaice Pleuronectes platessa)Knudson et al. 2019
European shadsAlosa spp.Antognazza et al. 2019
European weather loachMisgurnus fossilisThomsen et al. 2012
Fibrocapsa japonicaFibrocapsa japonicaEngesmo et al. 2018
Flathead grey mulletMugil cephalus cephalusYamanaka and Minamoto 2016
Flatwoods salamanderAmbystoma cingulatum/bishopiMcKee et al. 2015
Gizzard shadDorosoma cepedianumPerez et al. 2018
Golden tree frogPhytotriades auratusTorresdal et al. 2017
GoldfishCarassius auratusKamoroff and Goldberg 2018
Goldsinny-wrasseCtenolaburs rupestrisThomsen et al. 2012
Gopher frogLithobates capitoMcKee et al. 2015
Grass carpCtenopharyngodon idellaRoy et al. 2018
Great cormorantPhalacrocorax carboThomsen et al. 2012
Great crested newtTriturus cristatusThomsen et al. 2012
Green anacondaEunectes murinusHunter et al. 2015
Green sturgeonAcipenser medirostrisBrandl et al. 2015
Harbor porpoisePhocoena phocoenaFoote et al. 2012
HellbenderCryptobranchus alleganiensisSpear et al. 2015
Heterosigma akashiwo Heterosigma akashiwo Engesmo et al. 2018
Hula painted frogLatonia nigriventerRenan et al. 2017
Hybrid striped bassMorone saxatilis x chrysopsRoy et al. 2018
Idaho giant salamanderDicamptodon atterimusPilliod et al. 2013
IdeLeuciscus idusRoy et al. 2018
Japanese basket clamCorbicula japonicaTakahara et al. 2019
Japanese eelAnguilla japonicaWatanabe et al. 2004
Japanese giant salamanderAndrias japonicusFukumoto et al. 2015
Japanese jack mackerelTrachurus japonicusYamamoto et al. 2016
Japanese medakaOryzias sakaizumiiTsuji et al. 2018
Japanese medakaOryzias latipesTsuji et al. 2018
Japanese rice fishOryzias latipesTsuji et al. 2018
Japanese sea nettleChrysaora pacificaMinamoto et el. 2017
Karenia mikimotoi Karenia mikimotoiEngesmo et al. 2018
Karlodinium veneficumKarlodinium veneficumEngesmo et al. 2018
Kidneyshell musselPtychobranchus fasciolarisCurrier et al. 2018
Killer whaleOrcinus orcaBaker et al. 2018
Lacustrine shrimp Palaemon paucidensWu et al. 2018
Lake sturgeonAcipenser fulvescensYusishen et al. 2018
Lake troutSalvelinus namaycushLacoursiere-Roussel et al. 2015
Lake whitefish Coregonus clupeaformisHulley et al. 2019
Large white-faced darter (dragonfly)Leucorrhinia pectoralisThomsen et al. 2012
Largemouth bassMicropterus salmoidesPerez et al. 2018
Liver flukeFasciola hepaticaRathinasamy et al. 2018
Longfin smeltSpirinchus thaleichthysBrandl et al. 2015
ManateesTrichechus spp.Hunter et al. 2018
Mandarin fishSiniperca chuatsiRoy et al. 2018
Mapleleaf musselQuadrula quadrulaCurrier et al. 2018
mayflyEphemera danicaSeymour et al. 2018
Mekong giant catfishPangasianodon gigasBellemain et al. 2016
Narrow-clawed crayfish in partAstacus leptodactylus, clade IIAgersnap et al. 2017
Narrow-clawed crayfish in partAstacus leptodactylus, clade IAgersnap et al. 2017
Nepa hoffmanniNepa hoffmanniDoi et al. 2017
New Zealand mudsnailPotamopyrgus antipodarumGoldberg et al. 2013
Noble crayfishAstacus astacusAgersnap et al. 2017
North African pythonPython sebaeHunter et al. 2015
Northern anchovyEngraulis mordaxSassoubre et al. 2016
Northern leatherside chubLepidomeda copeiDysthe et al. 2018
Northern medakaOryzias sakaizumiiTsuji et al. 2018
Northern pikeEsox luciusOlsen et al. 2016 (erratum)
Northern red-legged frogRana auroraHalstead et al. 2018
Northern red-legged frogRana auroraHalstead et al. 2018
Northern snakeheadChanna argusRoy et al. 2018
Northern watersnakeNerodia sipedonLacoursiere-Roussel et al. 2016
Opossum shrimpMysis diluvianaCarim et al. 2016
Oriental weatherloachMisgurnus anguillicaudatusFurlan et al. 2016
Ornate chorus frogPseudacris ornataGoldberg et al. 2018
Pacific chub mackerelScomber japonicasSassoubre et al. 2016
Pacific coast lampreyLampetra spp. in partOstberg et al. 2018
Pacific LampreyEntosphenus tridentatusOstberg et al. 2018
Pacific sardineSardinops sagaxSassoubre et al. 2016
Painted turtleChrysemys pictaLacoursiere-Roussel et al. 2016
Patch-nosed salamanderUrspelerpes bruceiPierson et al. 2016
Pond loachMisgurnus anguillicaudatusRoy et al. 2018
Rainbow smelt Osmerus mordaxHulley et al. 2019
Rainbow trout Oncorhynchus mykissMinamoto et al. 2018
Rainbow trout/steelheadOncorhynchus mykissBrandl et al. 2015
Rainbow trout/steelheadOncorhynchus mykissWilcox et al. 2015
Red shinerCyprinella lutrensis Roy et al. 2018
Redfin perchPerca fluviatilisBylemans et al. 2016
River herringAlosa psuedoharengus and A. aestivalisPlough et al. 2018
Rocky mountain tailed frogAscaphus montanusPilliod et al. 2013
Rosette agent (parasite)Sphaerothecum destruensSana et al. 2018
Round gobyNeogobius melanostomusNathan et al. 2014
Round whitefish Prosopium cylindraceumHulley et al. 2019
Rusty crayfishOrconectes rusticusDougherty et al. 2016
Sacramento pikeminnowPtychocheilus grandisBrandl et al. 2015
Sacramento splittailPogonichthys macrolepidotusBrandl et al. 2015
Sakhalin taimenParahucho perryiMizumoto et al. 2017
Salmon flukeGyrodactylus salarisRusch et al. 2018
Salvelinus confluentusBull trout - improved assayDysthe et al. 2018
SaugerSander canadensisDysthe et al. 2017
Schistosoma mansoni Schistosoma mansoni Sato et al. 2018
SchneiderAlburnoides bipunctatusRiaz et al. 2018
Sea lampreyPetromyzon marinusGustavson et al. 2015
Sea lamprey Petromyzon marinus Gustavson et al. 2015
Sea lampreyPetromyzon marinusSchloesser et al. 2018
Sea squirtDidemnum perlucidumSimpson et al. 2017
Shorthorn sculpinMyoxocephalus scorpiusThomsen et al. 2012
Signal crayfishPacifastacus leniusculusAgersnap et al. 2017
Signal crayfish (Scotland)Pacifastacus leniusculusHarper et al. 2018
Signal crayfish in partPacifastacus leniusculusDunn et al. 2017
Silver and bighead carpHypophthalmichthys spp.Turner et al. 2014
Silver carpHypophthalmichthys molitrixCoulter et al. 2013
Silver carpHypophthalmichthys molitrixFarrington et al. 2015
Silver carpHypophthalmichthys molitrixAmberg et al. 2015
Silver carpHypophthalmichthys molitrixRoy et al. 2018
Slimy sculpinCottus cognatusRodgers et al. 2017
Smallmouth bassMicropterus dolomieuBrandl et al. 2015
Smallmouth bassMicropterus dolomieuHulley et al. 2019
Smooth newtLissotriton vulgaris vulgarisSmart et al. 2015
Sockeye salmonOncorhynchus nerkaTillotson et al. 2018
Southeast liver flukeOpisthorchis viverriniHashizume et al. 2017
Spottail shiner Notropis hudsoniusHulley et al. 2019
Spotted garLepisosteus oculatusBoothroyd et al. 2016
Striped bassMorone saxatilisBrandl et al. 2015
Striped newtNotophthalmus perstriatusMcKee et al. 2015
Sturgeon chubMacrhybopsis gelidaMason et al. 2018
Tadpole shrimpLepidurus apusThomsen et al. 2012
Temperate seabassLateolabrax japonicusYamanaka and Minamoto 2016
Tetracapsuloides bryosalmonaeTetracapsuloides bryosalmonaeHutchins et al. 2018
Threadfin shadDorosoma petenenseBrandl et al. 2015
Three-lips (fish)Opsariichthys uncirostris uncirostrisMaruyama et al. 2018
Three-spined sticklebackGasterosteus aculeatusThomsen et al. 2012
Tidewater gobyEucyclogobius newberryiSchmelzle and Kinziger 2016
Tiger salamanderAmbystoma mavortiumGoldberg et al. 2018
WalleyeSander vitreusDysthe et al. 2017
water fleaDaphnia magnaSeymour et al. 2018
Water thymeHydrilla verticillataMatsuhashi et al. 2016
Wavy-rayed lampmusselLampsilis fasciolaCurrier et al. 2018
Wels catfishSilurus glanisRoy et al. 2018
Western pearlshell musselMargaritifera falcataDysthe et al. 2018
Western toadAnaxyrus boreasFranklin et al. 2018
Westslope cutthroatOncorhynchus clarkii lewsiWilcox et al. 2015
White colonial sea squirtDidemnum perlucidumSimpson et al. 2017
White sharkCarcharodon carchariasLafferty et al. 2018
White sturgeonAcipenser transmontanusBrandl et al. 2015
Whitespotted char Salvelinus leucomaenisMinamoto et al. 2018
Wood frogRana sylvaticaSpangler et al. 2017
Wood turtleGlyptemys insculptaLacoursiere-Roussel et al. 2016
Yellow anacondaEunectes notaeusHunter et al. 2015
Yellow perchPerca flavescensHulley et al. 2019
Atlantic salmonSalmo salar, O. keta, O. tshawytscha, O. gorbuscha, O. mykiss, O. nerka, and O. kisutcRasmusson Hellberg et al. 2010
Chum salmonOncorhynchus ketaRasmusson Hellberg et al. 2010
Chinook salmonOncorhynchus tshawytschaRasmusson Hellberg et al. 2010
Pink salmonOncorhynchus gorbuschaRasmusson Hellberg et al. 2010
Rainbow troutOncorhynchus mykiss,Rasmusson Hellberg et al. 2010
Coho salmonOncorhynchus kisutchRasmusson Hellberg et al. 2010
Sockeye salmonOncorhynchus nerkaRasmusson Hellberg et al. 2010
American bullfrogRana catesbeianaLin et al. 2019
Painted turtle Chrysemys pictaAdams et al. 2019
Broad whitefishCoregonus nasus Rodgers et al. 2019
Freshwater pearl musselMargaritifera margaritifera Carlsson et al. 2017
Dwarf wedgemussel Alasmidonta heterodonSchill and Galbraith 2019
Sardine ciscoCoregonus sardinellaRodgers et al. 2019
Wood turtleGlyptemys insculptaAkre et al. 2019
Common carpCyprinus carpioMinamoto et al. 2017
Coastal tailed frogAscaphus trueiHobbs et al. 2019
Yellowstone cutthroatOncorhynchus clarkii bouvieriWilcox et al. 2015