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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Many labs are also running currently unpublished assays.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 qPCR assays for species detection in eDNA samples (updated June 2018). Full citations can be found through our References page or in our Mendeley database. 

Common nameLatin namePublication
Acheilognathus typusAcheilognathus typusSakata et al. 2017
Aedes mosquitosAedes spp.Schneider et al. 2016
African clawed frogXenopus laevisSecondi et al. 2016
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 herringClupea harengusThomsen et al. 2012
Atlantic salmonSalmo salarAtkinson et al. 2017
Ayu sweetfishPlecoglossus altivelisYamanaka and Minamoto 2016
Bighead carpHypophthalmichthys nobilisCoulter et al. 2013
Bighead carpHypophthalmichthys nobilisFarrington et al. 2015
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
Brown troutSalmo truttaCarim et al. 2016
Brown troutSalmo truttaGustavson et al. 2015
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
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
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
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 weather loachMisgurnus fossilisThomsen et al. 2012
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
Goldsinny-wrasseCtenolaburs rupestrisThomsen et al. 2012
Gopher frogLithobates capitoMcKee et al. 2015
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
Hula painted frogLatonia nigriventerRenan et al. 2017
Idaho giant salamanderDicamptodon atterimusPilliod et al. 2013
Japanese giant salamanderAndrias japonicusFukumoto et al. 2015
Japanese jack mackerelTrachurus japonicusYamamoto et al. 2016
Japanese rice fishOryzias latipesTsuji et al. 2018
Japanese sea nettleChrysaora pacificaMinamoto et el. 2017
Kidneyshell musselPtychobranchus fasciolarisCurrier et al. 2018
Killer whaleOrcinus orcaBaker et al. 2018
Lacustrine shrimp Palaemon paucidensWu et al. 2018
Lake troutSalvelinus namaycushLacoursiere-Roussel et al. 2015
Large white-faced darter (dragonfly)Leucorrhinia pectoralisThomsen et al. 2012
Largemouth bassMicropterus salmoidesPerez et al. 2018
Longfin smeltSpirinchus thaleichthysBrandl et al. 2015
ManateesTrichechus spp.Hunter 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 IAgersnap et al. 2017
Narrow-clawed crayfish in partAstacus leptodactylus, clade IIAgersnap 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 medakaOryzias sakaizumiiTsuji et al. 2018
Northern pikeEsox luciusOlsen et al. 2016 (erratum)
Northern red-legged frogRana auroraHalstead 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
Rainbow trout/steelheadOncorhynchus mykissBrandl et al. 2015
Rainbow trout/steelheadOncorhynchus mykissWilcox et al. 2015
Redfin perchPerca fluviatilisBylemans et al. 2016
Rocky mountain tailed frogAscaphus montanusPilliod et al. 2013
Rosette agent (parasite)Sphaerothecum destruensSana et al. 2018
Round gobyNeogobius melanostomusNathan et al. 2014
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
SaugerSander canadensisDysthe et al. 2017
Sea lampreyPetromyzon marinusGustavson et al. 2015
Sea squirtDidemnum perlucidumSimpson et al. 2017
Shorthorn sculpinMyoxocephalus scorpiusThomsen et al. 2012
Signal crayfishPacifastacus leniusculusAgersnap et al. 2017
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
Slimy sculpinCottus cognatusRodgers et al. 2017
Smallmouth bassMicropterus dolomieuBrandl et al. 2015
Smooth newtLissotriton vulgaris vulgarisSmart et al. 2015
Sockeye salmonOncorhynchus nerkaTillotson et al. 2018
Southeast liver flukeOpisthorchis viverriniHashizume et al. 2017
Spotted garLepisosteus oculatusBoothroyd et al. 2016
Striped bassMorone saxatilisBrandl et al. 2015
Striped newtNotophthalmus perstriatusMcKee et al. 2015
Tadpole shrimpLepidurus apusThomsen et al. 2012
Temperate seabassLateolabrax japonicusYamanaka and Minamoto 2016
Threadfin shadDorosoma petenenseBrandl et al. 2015
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
Western pearlshell musselMargaritifera falcataDysthe et al. 2018
Westslope cutthroatOncorhynchus clarkii lewsiWilcox et al. 2015
White colonial sea squirtDidemnum perlucidumSimpson et al. 2017
White sturgeonAcipenser transmontanusBrandl et al. 2015
Wood frogRana sylvaticaSpangler et al. 2017
Wood turtleGlyptemys insculptaLacoursiere-Roussel et al. 2016
Yellow anacondaEunectes notaeusHunter et al. 2015
Yellowstone cutthroatOncorhynchus clarkii bouvieriWilcox et al. 2015