Drinking water as a source of environmental DNA for the detection of terrestrial wildlife species

Andersen K, Bird KL, Rasmussen M, Haile J, Breuning-Madsen H, Kjaer KH, Orlando L, Gilbert MTP, Willerslev E (2012) Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity. Mol Ecol 21:1966–1979. doi: 10.1111/j.1365-294X.2011.05261.x

Bohmann K, Evans A, Gilbert MTP, Carvalho GR, Creer S, Knapp M, Yu DW, de Bruyn M (2014) Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol 29:358–367. doi: 10.1016/j.tree.2014.04.003

Calvignac-Spencer S, Merkel K, Kutzner N, Kuhl H, Boesch C, Kappeler PM, Metzger S, Schubert G, Leendertz FH (2013) Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity. Mol Ecol 22:915–924. doi: 10.1111/mec.12183

Chaves PB, Graeff VG, Lion MB, Oliveira LR, Eizirik E (2012) DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples. Mol Ecol Resour 12:18–35. doi: 10.1111/j.1755-0998.2011.03056.x

Coissac E, Riaz T, Puillandre N (2012) Bioinformatic challenges for DNA metabarcoding of plants and animals. Mol Ecol 21:1834–1847. doi: 10.1111/j.1365-294X.2012.05550.x

Dejean T, Valentini A, Duparc A, Pellier-Cuit S, Pompanon F, Taberlet P, Miaud C (2011) Persistence of environmental DNA in freshwater ecosystems. PLoS One. doi: 10.1371/journal.pone.0023398

Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biol Lett 4:423–425. doi: 10.1098/rsbl.2008.0118

Goldberg CS, Sepulveda A, Ray A, Baumgardt J, Waits LP (2013) Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum). Freshw Sci 32:792–800. doi: 10.1899/13-046.1

Goldberg CS, Strickler KM, Pilliod DS (2015) Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms. Biol Conserv 183:1–3. doi: 10.1016/j.biocon.2014.11.040

Hoss M, Kohn M, Paabo S, Knauer F, Schroder W (1992) Excrement analysis by PCR. Nature 359:199. doi: 10.1038/359199a0

Larsen RT, Bissonette JA, Flinders JT, Whiting JC (2012) Framework for understanding the influences of wildlife water developments in the western United States. Calif Fish Game 98:148–163

Nichols RV, Konigsson H, Danell K, Spong G (2012) Browsed twig environmental DNA: diagnostic PCR to identify ungulate species. Mol Ecol Resour 12:983–989. doi: 10.1111/j.1755-0998.2012.03172.x

Phillips S, Anderson R, Schapire R (2006) Maximum entropy modeling of species geographic distributions. Ecol Model 190:231–259. doi: 10.1016/j.ecolmodel.2005.03.026

Piaggio AJ, Engeman RM, Hopken MW, Humphrey JS, Keacher KL, Bruce WE, Avery ML (2014) Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA. Mol Ecol Resour 14:374–380. doi: 10.1111/1755-0998.12180

Pilliod DS, Goldberg CS, Arkle RS, Waits LP (2013) Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples. Can J Fish Aquat Sci 70:1123–1130. doi: 10.1139/cjfas-2013-0047

Rodgers T, Janečka J (2013) Applications and techniques for non-invasive faecal genetics research in felid conservation. Eur J Wildl Res 59:1–16. doi: 10.1007/s10344-012-0675-6

Rosenstock SS, Ballard WB, Devos JC (1999) Viewpoint: benefits and impacts of wildlife water developments. J Range Manage 52:302–311. doi: 10.2307/4003538

Schnell IB, Thomsen PF, Wilkinson N, Rasmussen M, Jensen LRD, Willerslev E, Bertelsen MF, Gilbert MTP (2012) Screening mammal biodiversity using DNA from leeches. Curr Biol 22:R262–R263. doi: 10.1016/j.cub.2012.02.058

Schubert G, Stockhausen M, Hoffmann C, Merkel K, Vigilant L, Leendertz FH, Calvignac-Spencer S (2014) Targeted detection of mammalian species using carrion fly-derived DNA. Mol Ecol Resour 15:285–294. doi: 10.1111/1755-0998.12306

Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21:1794–1805. doi: 10.1111/j.1365-294X.2012.05538.x

Strickler KM, Fremier AK, Goldberg CS (2015) Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms. Biol Conserv 183:85–92. doi: 10.1016/j.biocon.2014.11.038

Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH (2012a) Environmental DNA. Mol Ecol 21:1789–1793. doi: 10.1111/j.1365-294X.2012.05542.x

Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E (2012b) Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol 21:2045–2050. doi: 10.1111/j.1365-294X.2012.05470.x

Thomsen PF, Willerslev E (2015) Environmental DNA—an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv 183:4–18. doi: 10.1016/j.biocon.2014.11.019

Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Orlando L, Willerslev E (2012) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565–2573. doi: 10.1111/j.1365-294X.2011.05418.x

Waits LP, Paetkau D (2005) Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. J Wildl Manag 69:1419–1433. doi: 10.2193/0022-541x(2005)69[1419:ngstfw]2.0.co;2

Wilcox TM, McKelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS One. doi: 10.1371/journal.pone.0059520

Williams CL, Blejwas K, Johnston JJ, Jaeger MM (2003) A coyote in sheep’s clothing: predator identification from saliva. Wildl Soc Bull 31:926–932