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Many labs are also running currently unpublished assays.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 name	Latin name	Publication
Acheilognathus typus	Acheilognathus typus	Sakata et al. 2017
Aedes mosquitos	Aedes spp.	Schneider et al. 2016
African clawed frog	Xenopus laevis	Secondi et al. 2016
Alligator snapping turtle	Macrochelys temminckii	Feist et al. 2018
Amami Oshima Frog	Odorrana splendida	Iwai et al. 2019
American bullfrog	Lithobates catesbieanus	Strickler et al. 2015
Anopheles mosquito	Anopheles gambiae sensu lato	Ordero et al. 2018
Arctic char	Salvelinus alpinus/malma	Rodgers et al. 2017
Arctic grayling	Thymallus arcticus	Carim et al. 2016
Arctic grayling	Thymallus arcticus	Rodgers et al. 2017
Arizona treefrog	Hyla wrightorum	Goldberg et al. 2018
Asian clam	Corbicula fluminea	Cowart et al. 2018
Atlantic cod	Gadus morhua	Knudson et al. 2019
Atlantic herring	Clupea harengus	Thomsen et al. 2012
Atlantic herring	Clupea harengus	Knudson et al. 2019
Atlantic mackerel	Scomber scombrus	Knudson et al. 2019
Atlantic salmon	Salmo salar	Atkinson et al. 2017
Austropeplea tomentosa	Austropeplea tomentosa	Rathinasamy et al. 2018
Ayu sweetfish	Plecoglossus altivelis	Yamanaka and Minamoto 2016
Bd	Batrochochytrium dendrobatidis	Boyle et al. 2004
Bighead carp	Hypophthalmichthys nobilis	Coulter et al. 2013
Bighead carp	Hypophthalmichthys nobilis	Farrington et al. 2015
Bighead carp	Hypophthalmichthys nobilis	Roy et al. 2018
Black carp	Mylopharyngodon piceus	Roy et al. 2018
Blanding's turtle	Emydoidea blandingii	Lacoursiere-Roussel et al. 2016
Bluegill sunfish	Lepomis macrochirus	Doi et al. 2015
Boa constrictor	Boa constrictor	Hunter et al. 2015
Brazilian waterweed	Egeria densa	Fujiwara et al. 2016
Brook trout	Salvelinus fontinalis	Wilcox et al. 2013
Brook trout	Salvelinus fontinalis	Hulley et al. 2019
Brown trout	Salmo trutta	Carim et al. 2016
Brown trout	Salmo trutta	Gustavson et al. 2015
Brown trout	Salmo trutta	Gustavson et al. 2015
Brown trout	Salmo trutta	Deutschmann et al. 2019
Bryozoan	Bugula neritina	Kim et al. 2018
Bull trout	Salvelinus confluentus	Wilcox et al. 2014
Burbot	Lota lota	Rodgers et al. 2017
Burmese python	Python molurus bivittatus	Hunter et al. 2015
California red-legged frog	Rana draytonii	Halstead et al. 2018
California red-legged frog	Rana draytonii	Halstead et al. 2018
Cane toad	Rhinella marina	Tingley et al. 2019
Carpet sea squirt	Didemnum vexillum	Simpson et al. 2017
Carpet sea squirt	Didemnum vexillum	Simpson et al. 2017
Chilean devil ray	Mobula tarapacana	Gargan et al. 2017
Chilodonella hexasticha	Chilodonella hexasticha	Gomes et al. 2017
Chinese giant salamander	Andrias davidianus	Fukumoto et al. 2015
Chinese sleeper	Perccottus glenii	Roy et al. 2018
Chinook salmon	Oncorhynchus tshawytscha	Brandl et al. 2015
Chinook salmon	Oncorhynchus tshawytscha	Laramie et al. 2015
Chiricahua leopard frog	Rana chiricahuensis	Goldberg et al. 2018
Coldwater crayfish	Faxonius eupunctus	Rice et al. 2018
Common carp	Cyprinus carpio	Takahara et al. 2012
Common carp	Cyprinus carpio	Eichmiller et al. 2014
Common carp	Cyprinus carpio	Uchii et al. 2017
Common gartersnake	Thamnophis sirtalis	Lacoursiere-Roussel et al. 2016
Common snapping turtle	Chelydra serpentina	Lacoursiere-Roussel et al. 2016
Common spadefoot toad	Pelobates fuscus	Thomsen et al. 2012
Corallivorous seastar	Acanthaster cf. solaris	Uthicke et al. 2018
Crucian carp	Carassius carassius	Harper et al. 2019
Crucian carp	Carassius carassius	Roy et al. 2018
Deepwater sculpin	Myoxocephalus thompsonii	Hulley et al. 2019
Dolly Varden	Salvelinus malma	Minamoto et al. 2018
Dolly Varden trout	Salvelinus malma	Rodgers et al. 2017
Eastern pondmussel	Ligumia nasuta	Currier et al. 2018
Eurasian otter	Lutra lutra	Thomsen et al. 2012
European eel	Anguila anguila	Seymour et al. 2018
European flounder	Platichthys flesus	Thomsen et al. 2012
European flounder	Platichthys flesus	Knudson et al. 2019
European plaice	Pleuronectes platessa)	Knudson et al. 2019
European shads	Alosa spp.	Antognazza et al. 2019
European weather loach	Misgurnus fossilis	Thomsen et al. 2012
Fibrocapsa japonica	Fibrocapsa japonica	Engesmo et al. 2018
Flathead grey mullet	Mugil cephalus cephalus	Yamanaka and Minamoto 2016
Flatwoods salamander	Ambystoma cingulatum/bishopi	McKee et al. 2015
Gizzard shad	Dorosoma cepedianum	Perez et al. 2018
Golden tree frog	Phytotriades auratus	Torresdal et al. 2017
Goldfish	Carassius auratus	Kamoroff and Goldberg 2018
Goldsinny-wrasse	Ctenolaburs rupestris	Thomsen et al. 2012
Gopher frog	Lithobates capito	McKee et al. 2015
Grass carp	Ctenopharyngodon idella	Roy et al. 2018
Great cormorant	Phalacrocorax carbo	Thomsen et al. 2012
Great crested newt	Triturus cristatus	Thomsen et al. 2012
Green anaconda	Eunectes murinus	Hunter et al. 2015
Green sturgeon	Acipenser medirostris	Brandl et al. 2015
Harbor porpoise	Phocoena phocoena	Foote et al. 2012
Hellbender	Cryptobranchus alleganiensis	Spear et al. 2015
Heterosigma akashiwo	Heterosigma akashiwo	Engesmo et al. 2018
Hula painted frog	Latonia nigriventer	Renan et al. 2017
Hybrid striped bass	Morone saxatilis x chrysops	Roy et al. 2018
Idaho giant salamander	Dicamptodon atterimus	Pilliod et al. 2013
Ide	Leuciscus idus	Roy et al. 2018
Japanese basket clam	Corbicula japonica	Takahara et al. 2019
Japanese eel	Anguilla japonica	Watanabe et al. 2004
Japanese giant salamander	Andrias japonicus	Fukumoto et al. 2015
Japanese jack mackerel	Trachurus japonicus	Yamamoto et al. 2016
Japanese medaka	Oryzias sakaizumii	Tsuji et al. 2018
Japanese medaka	Oryzias latipes	Tsuji et al. 2018
Japanese rice fish	Oryzias latipes	Tsuji et al. 2018
Japanese sea nettle	Chrysaora pacifica	Minamoto et el. 2017
Karenia mikimotoi	Karenia mikimotoi	Engesmo et al. 2018
Karlodinium veneficum	Karlodinium veneficum	Engesmo et al. 2018
Kidneyshell mussel	Ptychobranchus fasciolaris	Currier et al. 2018
Killer whale	Orcinus orca	Baker et al. 2018
Lacustrine shrimp	Palaemon paucidens	Wu et al. 2018
Lake sturgeon	Acipenser fulvescens	Yusishen et al. 2018
Lake trout	Salvelinus namaycush	Lacoursiere-Roussel et al. 2015
Lake whitefish	Coregonus clupeaformis	Hulley et al. 2019
Large white-faced darter (dragonfly)	Leucorrhinia pectoralis	Thomsen et al. 2012
Largemouth bass	Micropterus salmoides	Perez et al. 2018
Liver fluke	Fasciola hepatica	Rathinasamy et al. 2018
Longfin smelt	Spirinchus thaleichthys	Brandl et al. 2015
Manatees	Trichechus spp.	Hunter et al. 2018
Mandarin fish	Siniperca chuatsi	Roy et al. 2018
Mapleleaf mussel	Quadrula quadrula	Currier et al. 2018
mayfly	Ephemera danica	Seymour et al. 2018
Mekong giant catfish	Pangasianodon gigas	Bellemain et al. 2016
Narrow-clawed crayfish in part	Astacus leptodactylus, clade II	Agersnap et al. 2017
Narrow-clawed crayfish in part	Astacus leptodactylus, clade I	Agersnap et al. 2017
Nepa hoffmanni	Nepa hoffmanni	Doi et al. 2017
New Zealand mudsnail	Potamopyrgus antipodarum	Goldberg et al. 2013
Noble crayfish	Astacus astacus	Agersnap et al. 2017
North African python	Python sebae	Hunter et al. 2015
Northern anchovy	Engraulis mordax	Sassoubre et al. 2016
Northern leatherside chub	Lepidomeda copei	Dysthe et al. 2018
Northern medaka	Oryzias sakaizumii	Tsuji et al. 2018
Northern pike	Esox lucius	Olsen et al. 2016 (erratum)
Northern red-legged frog	Rana aurora	Halstead et al. 2018
Northern red-legged frog	Rana aurora	Halstead et al. 2018
Northern snakehead	Channa argus	Roy et al. 2018
Northern watersnake	Nerodia sipedon	Lacoursiere-Roussel et al. 2016
Opossum shrimp	Mysis diluviana	Carim et al. 2016
Oriental weatherloach	Misgurnus anguillicaudatus	Furlan et al. 2016
Ornate chorus frog	Pseudacris ornata	Goldberg et al. 2018
Pacific chub mackerel	Scomber japonicas	Sassoubre et al. 2016
Pacific coast lamprey	Lampetra spp. in part	Ostberg et al. 2018
Pacific Lamprey	Entosphenus tridentatus	Ostberg et al. 2018
Pacific sardine	Sardinops sagax	Sassoubre et al. 2016
Painted turtle	Chrysemys picta	Lacoursiere-Roussel et al. 2016
Patch-nosed salamander	Urspelerpes brucei	Pierson et al. 2016
Pond loach	Misgurnus anguillicaudatus	Roy et al. 2018
Rainbow smelt	Osmerus mordax	Hulley et al. 2019
Rainbow trout	Oncorhynchus mykiss	Minamoto et al. 2018
Rainbow trout/steelhead	Oncorhynchus mykiss	Brandl et al. 2015
Rainbow trout/steelhead	Oncorhynchus mykiss	Wilcox et al. 2015
Red shiner	Cyprinella lutrensis	Roy et al. 2018
Redfin perch	Perca fluviatilis	Bylemans et al. 2016
River herring	Alosa psuedoharengus and A. aestivalis	Plough et al. 2018
Rocky mountain tailed frog	Ascaphus montanus	Pilliod et al. 2013
Rosette agent (parasite)	Sphaerothecum destruens	Sana et al. 2018
Round goby	Neogobius melanostomus	Nathan et al. 2014
Round whitefish	Prosopium cylindraceum	Hulley et al. 2019
Rusty crayfish	Orconectes rusticus	Dougherty et al. 2016
Sacramento pikeminnow	Ptychocheilus grandis	Brandl et al. 2015
Sacramento splittail	Pogonichthys macrolepidotus	Brandl et al. 2015
Sakhalin taimen	Parahucho perryi	Mizumoto et al. 2017
Salmon fluke	Gyrodactylus salaris	Rusch et al. 2018
Salvelinus confluentus	Bull trout - improved assay	Dysthe et al. 2018
Sauger	Sander canadensis	Dysthe et al. 2017
Schistosoma mansoni	Schistosoma mansoni	Sato et al. 2018
Schneider	Alburnoides bipunctatus	Riaz et al. 2018
Sea lamprey	Petromyzon marinus	Gustavson et al. 2015
Sea lamprey	Petromyzon marinus	Gustavson et al. 2015
Sea lamprey	Petromyzon marinus	Schloesser et al. 2018
Sea squirt	Didemnum perlucidum	Simpson et al. 2017
Shorthorn sculpin	Myoxocephalus scorpius	Thomsen et al. 2012
Signal crayfish	Pacifastacus leniusculus	Agersnap et al. 2017
Signal crayfish (Scotland)	Pacifastacus leniusculus	Harper et al. 2018
Signal crayfish in part	Pacifastacus leniusculus	Dunn et al. 2017
Silver and bighead carp	Hypophthalmichthys spp.	Turner et al. 2014
Silver carp	Hypophthalmichthys molitrix	Coulter et al. 2013
Silver carp	Hypophthalmichthys molitrix	Farrington et al. 2015
Silver carp	Hypophthalmichthys molitrix	Amberg et al. 2015
Silver carp	Hypophthalmichthys molitrix	Roy et al. 2018
Slimy sculpin	Cottus cognatus	Rodgers et al. 2017
Smallmouth bass	Micropterus dolomieu	Brandl et al. 2015
Smallmouth bass	Micropterus dolomieu	Hulley et al. 2019
Smooth newt	Lissotriton vulgaris vulgaris	Smart et al. 2015
Sockeye salmon	Oncorhynchus nerka	Tillotson et al. 2018
Southeast liver fluke	Opisthorchis viverrini	Hashizume et al. 2017
Spottail shiner	Notropis hudsonius	Hulley et al. 2019
Spotted gar	Lepisosteus oculatus	Boothroyd et al. 2016
Striped bass	Morone saxatilis	Brandl et al. 2015
Striped newt	Notophthalmus perstriatus	McKee et al. 2015
Sturgeon chub	Macrhybopsis gelida	Mason et al. 2018
Tadpole shrimp	Lepidurus apus	Thomsen et al. 2012
Temperate seabass	Lateolabrax japonicus	Yamanaka and Minamoto 2016
Tetracapsuloides bryosalmonae	Tetracapsuloides bryosalmonae	Hutchins et al. 2018
Threadfin shad	Dorosoma petenense	Brandl et al. 2015
Three-lips (fish)	Opsariichthys uncirostris uncirostris	Maruyama et al. 2018
Three-spined stickleback	Gasterosteus aculeatus	Thomsen et al. 2012
Tidewater goby	Eucyclogobius newberryi	Schmelzle and Kinziger 2016
Tiger salamander	Ambystoma mavortium	Goldberg et al. 2018
Walleye	Sander vitreus	Dysthe et al. 2017
water flea	Daphnia magna	Seymour et al. 2018
Water thyme	Hydrilla verticillata	Matsuhashi et al. 2016
Wavy-rayed lampmussel	Lampsilis fasciola	Currier et al. 2018
Wels catfish	Silurus glanis	Roy et al. 2018
Western pearlshell mussel	Margaritifera falcata	Dysthe et al. 2018
Western toad	Anaxyrus boreas	Franklin et al. 2018
Westslope cutthroat	Oncorhynchus clarkii lewsi	Wilcox et al. 2015
White colonial sea squirt	Didemnum perlucidum	Simpson et al. 2017
White shark	Carcharodon carcharias	Lafferty et al. 2018
White sturgeon	Acipenser transmontanus	Brandl et al. 2015
Whitespotted char	Salvelinus leucomaenis	Minamoto et al. 2018
Wood frog	Rana sylvatica	Spangler et al. 2017
Wood turtle	Glyptemys insculpta	Lacoursiere-Roussel et al. 2016
Yellow anaconda	Eunectes notaeus	Hunter et al. 2015
Yellow perch	Perca flavescens	Hulley et al. 2019
Atlantic salmon	Salmo salar, O. keta, O. tshawytscha, O. gorbuscha, O. mykiss, O. nerka, and O. kisutc	Rasmusson Hellberg et al. 2010
Chum salmon	Oncorhynchus keta	Rasmusson Hellberg et al. 2010
Chinook salmon	Oncorhynchus tshawytscha	Rasmusson Hellberg et al. 2010
Pink salmon	Oncorhynchus gorbuscha	Rasmusson Hellberg et al. 2010
Rainbow trout	Oncorhynchus mykiss,	Rasmusson Hellberg et al. 2010
Coho salmon	Oncorhynchus kisutch	Rasmusson Hellberg et al. 2010
Sockeye salmon	Oncorhynchus nerka	Rasmusson Hellberg et al. 2010
American bullfrog	Rana catesbeiana	Lin et al. 2019
Painted turtle	Chrysemys picta	Adams et al. 2019
Broad whitefish	Coregonus nasus	Rodgers et al. 2019
Freshwater pearl mussel	Margaritifera margaritifera	Carlsson et al. 2017
Dwarf wedgemussel	Alasmidonta heterodon	Schill and Galbraith 2019
Sardine cisco	Coregonus sardinella	Rodgers et al. 2019
Wood turtle	Glyptemys insculpta	Akre et al. 2019
Common carp	Cyprinus carpio	Minamoto et al. 2017
Coastal tailed frog	Ascaphus truei	Hobbs et al. 2019
Striped jack	Pseudocaranx dentex	Murakami et al. 2019
Yellowstone cutthroat	Oncorhynchus clarkii bouvieri	Wilcox et al. 2015