Abstract
The DNA detection of wildlife from environmental samples has the potential to contribute significantly to wildlife management and ecological research. In terrestrial ecosystems, much work has focused on the identification of mammal predators from faecal (scat) samples. However, the relatively high time and financial costs of collecting and analysing scat DNA remain barriers to more widespread implementation of such DNA detection methods, especially for high-throughput surveys. Here, we evaluate methods used for DNA extraction from scats, as applied to detection of the Australian red fox, an introduced predator. We compare the relative costs of two approaches: the method previously used to screen thousands of scat samples in surveys over several years, and a modified version which involves swabbing scats at the time of collection and using a mechanised liquid handling platform to extract DNA from the swabs. We demonstrate that mechanised DNA extraction from swabs is more efficient than manual DNA extraction from whole scats, in terms of both time and resources. This provides a means for rapid, high-throughput screening of scats for the presence of mammal predators, enabling time-effective management responses to non-invasive surveys.
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Berry O, Sarre SD, Farrington L, Aitken N (2007) Faecal DNA detection of invasive species: the case of feral foxes in Tasmania. Wildl Res 34:1–7. https://doi.org/10.1071/WR06082
Bohmann K, Evans A, Gilbert MTP et al (2014) Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol 29:358–367. https://doi.org/10.1016/j.tree.2014.04.003
Brown WE, Ramsey DSL, Gaffney R (2014) Degradation and detection of fox (Vulpes vulpes) scats in Tasmania: evidence from field trials. Wildl Res 41:681–690
Caley P, Ramsey DSL, Barry SC (2015) Inferring the distribution and demography of an invasive species from sighting data: the red fox incursion into Tasmania. PLoS One 10:1–18. https://doi.org/10.1371/journal.pone.0116631
Champlot S, Berthelot C, Pruvost M, Bennett EA, Grange T, Geigl EM (2010) An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications. PLoS One 5:e13042. https://doi.org/10.1371/journal.pone.0013042
Davison A, Birks JDS, Brookes RC, Braithwaite TC, Messenger JE (2002) On the origin of faeces: morphological versus molecular methods for surveying rare carnivores from their scats. J Zool 257:141–143
Fernandes CA, Ginja C, Pereira I, Tenreiro R, Bruford MW, Santos-Reis M (2008) Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula. Conserv Genet 9:681–690. https://doi.org/10.1007/s10592-007-9364-5
Furlan EM, Gleeson D, Hardy CM, Duncan RP (2015) A framework for estimating the sensitivity of eDNA surveys. Mol Ecol Resour 16:641–654. https://doi.org/10.1111/1755-0998.12483
Gastón A, Blázquez-Cabrera S, Garrote G, Mateo-Sánchez MC, Beier P, Simón MA, Saura S (2016) Response to agriculture by a woodland species depends on cover type and behavioural state: insights from resident and dispersing Iberian lynx. J Appl Ecol 53:814–824. https://doi.org/10.1111/1365-2664.12629
Goldberg CS, Turner CR, Deiner K, Klymus KE, Thomsen PF, Murphy MA, Spear SF, McKee A, Oyler-McCance SJ, Cornman RS, Laramie MB, Mahon AR, Lance RF, Pilliod DS, Strickler KM, Waits LP, Fremier AK, Takahara T, Herder JE, Taberlet P (2016) Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods Ecol Evol 7:1299–1307. https://doi.org/10.1111/2041-210X.12595
Hänfling B, Handley LL, Read DS et al (2016) Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Mol Ecol 25:3101–3119. https://doi.org/10.1111/mec.13660
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649
Kwok S, Higuchi R (1989) Avoiding false positives with PCR. Nature 339:237–238
Linchant J, Lisein J, Semeki J, Lejeune P, Vermeulen C (2015) Are unmanned aircraft systems (UASs) the future of wildlife monitoring? A review of accomplishments and challenges. Mamm Rev 45:239–252. https://doi.org/10.1111/mam.12046
MacDonald AJ, Sarre SD (2015) Species assignment from trace DNA sequences: an in silico assessment of the test used to survey for foxes in Tasmania. J Appl Ecol 52:1649–1655. https://doi.org/10.1111/1365-2664.12506
MacDonald AJ, Sarre SD (2017) A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA. Mol Ecol Resour 17:708–720. https://doi.org/10.1111/1755-0998.12618
Meek PD, Ballard GA, Vernes K, Fleming PJS (2015) The history of wildlife camera trapping as a survey tool in Australia. Aust Mammal 37:1–12. https://doi.org/10.1071/AM14021
Miles KA, Holtz MN, Lounsberry ZT, Sacks BN (2015) A paired comparison of scat-collecting versus scat-swabbing methods for noninvasive recovery of mesocarnivore DNA from an arid environment. Wildl Soc Bull 39:797–803. https://doi.org/10.1002/wsb.600
Modave E, MacDonald AJ, Sarre SD (2017) A single mini-barcode test to screen for Australian mammalian predators from environmental samples. Gigascience gix052. https://doi.org/10.1093/gigascience/gix052
Mumma MA, Adams JR, Zieminski C, Fuller TK, Mahoney SP, Waits LP (2016) A comparison of morphological and molecular diet analyses of predator scats. J Mammal 97:112–120. https://doi.org/10.1093/jmammal/gyv160
Piggott MP, Taylor AC (2003a) Remote collection of animal DNA and its applications in conservation management and understanding the population biology of rare and cryptic species. Wildl Res 30(1):13
Piggott MP, Taylor AC (2003b) Extensive evaluation of faecal preservation and DNA extraction methods in Australian native and introduced species. Aust J Zool 51:341–355. https://doi.org/10.1071/ZO03012
Pires AE, Fernandes ML (2003) Last lynxes in Portugal? Molecular approaches in a pre-extinction scenario. Conserv Genet 4:525–532. https://doi.org/10.1023/A:1024762013876
Pirie TJ, Thomas RL, Fellowes MDE (2015) Limitations to recording larger mammalian predators in savannah using camera traps and spoor. Wildl Biol 22:13–21. https://doi.org/10.2981/wlb.00129
Pompanon F, Deagle BE, Symondson WOC et al (2012) Who is eating what: diet assessment using next generation sequencing. Mol Ecol 21:1931–1950. https://doi.org/10.1111/j.1365-294X.2011.05403.x
Ramón-Laca A, Soriano L, Gleeson D, Godoy JA (2015) A simple and effective method for obtaining mammal DNA from faeces. Wildl Biol 21:195–203. https://doi.org/10.2981/wlb.00096
Ramsey DSL, Barclay C, Campbell CD, Dewar E, MacDonald AJ, Modave E, Quasim S, Sarre SD (2018) Detecting rare carnivores using scats: implications for monitoring a fox incursion into Tasmania. Ecol Evol 8: 732-743. https://doi.org/10.1002/ece3.3694
Ramsey DSL, MacDonald AJ, Quasim S, Barclay C, Sarre SD (2015) An examination of the accuracy of a sequential PCR and sequencing test used to detect the incursion of an invasive species: the case of the red fox in Tasmania. J Appl Ecol 52:562–570
Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E (2011) ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res 39:e145. https://doi.org/10.1093/nar/gkr732
Roy P, Upadhyay RK (2015) Conserving Iberian lynx in Europe: issues and challenges. Ecol Complex 22:16–31. https://doi.org/10.1016/j.ecocom.2014.12.007
Rutledge LY, Holloway JJ, Patterson BR, White BN (2009) An improved field method to obtain DNA for individual identification from wolf scat. J Wildl Manag 73:1430–1435. https://doi.org/10.2193/2008-492
Salas A, Prieto L, Montesino M, Albarrán C, Arroyo E, Paredes-Herrera MR, di Lonardo AM, Doutremepuich C, Fernández-Fernández I, de la Vega AG, Alves Ć, López CM, López-Soto M, Lorente JA, Picornell A, Espinheira RM, Hernández A, Palacio AM, Espinoza M, Yunis JJ, Pérez-Lezaun A, Pestano JJ, Carril JC, Corach D, Vide MC, Álvarez-Iglesias V, Pinheiro MF, Whittle ḾR, Brehm A, Gómez J (2005) Mitochondrial DNA error prophylaxis: assessing the causes of errors in the GEP’02-03 proficiency testing trial. Forensic Sci Int 148:191–198. https://doi.org/10.1016/j.forsciint.2004.06.008
Sarmento P, Carrapato C, Eira C, Silva JP (2017) Spatial organization and social relations in a reintroduced population of endangered Iberian lynx Lynx pardinus. Oryx:1–12. https://doi.org/10.1017/S0030605317000370
Sarre SD, MacDonald AJ, Barclay C et al (2013) Foxes are now widespread in Tasmania: DNA detection defines the distribution of this rare but invasive carnivore. J Appl Ecol 50:459–468. https://doi.org/10.1111/1365-2664.12011
Sarre SD, MacDonald AJ, Berry OF et al (2014) Defining specificity in DNA detection of wildlife: Response to Goncalves et al. “‘The risks of using “‘species-specific’” PCR assays in wildlife research: the case of red fox (Vulpes vulpes) identification in Tasmania.’”. Forensic Sci Int Genet 13:206–207. https://doi.org/10.1016/j.fsigen.2014.08.006
Sarre SD, Walsh R, Aitken N, et al (2007) DNA detection of foxes to prevent establishment in Tasmania. In: Witmer GW, Pitt WC, Fagerstone KA (eds) Managing vertebrate invasive species: Proceedings of an International Symposium. USDA/APHIS/WS, National Wildlife Research Center, Fort Collins, CO. 2007., pp 454–459
Stokeld D, Frank ASK, Hill B, Choy JL, Mahney T, Stevens A, Young S, Rangers D, Rangers W, Gillespie GR (2015) Multiple cameras required to reliably detect feral cats in northern Australian tropical savanna: an evaluation of sampling design when using camera traps. Wildl Res 42:642–649. https://doi.org/10.1071/WR15083
Wultsch C, Waits LP, Hallerman EM, Kelly MJ (2015) Optimizing collection methods for noninvasive genetic sampling of neotropical felids. Wildl Soc Bull 39:403–412. https://doi.org/10.1002/wsb.540
Acknowledgements
Thanks to Elise Dewar, Catriona Campbell, Elodie Modave, and staff and volunteers from the Department of Primary Industries, Parks, Water and Environment, Tasmania, for help with sample collection. Sam Ryan assisted with laboratory analyses and Aaron Adamack assisted with data analysis. Thanks to two anonymous reviewers for their useful suggestions.
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The authors declare that they have no conflict of interest.
Funding
This study was partly funded by the Invasive Animals Cooperative Research Centre project 1.L.21.
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Communicated by: Joanna Stojak
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Quasim, S., MacDonald, A.J. & Sarre, S.D. Towards more efficient large-scale DNA-based detection of terrestrial mammal predators from scats. Mamm Res 63, 387–393 (2018). https://doi.org/10.1007/s13364-018-0369-x
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DOI: https://doi.org/10.1007/s13364-018-0369-x