Environmental DNA detection of spot-tailed quoll from soil is unlikely to be useful for routine monitoring
Lauren C. White
A * , Jenny L. Nelson A , Maria Cardoso B and Carlo Pacioni A C
A
B
C
Abstract
Accurate monitoring data on species presence and distribution are crucial for effective conservation management. Environmental DNA (eDNA)-based techniques, in which species are detected from trace amounts of DNA found throughout the environment, are promising tools that may complement traditional monitoring methods and improve detection. However, imperfect detection is a feature of all survey methods that should be properly assessed so that the probability of detecting a target species’ DNA at a site where it is present (i.e. the sensitivity of the method) can be determined. The spot-tailed quoll (Dasyurus maculatus), a carnivorous marsupial found in eastern Australia, is a difficult species to detect as it is rare and has large home ranges, often in remote and difficult to access habitat.
In this study, we aimed to evaluate the feasibility of using eDNA soil analysis as a viable alternative or complement to traditional monitoring techniques for detecting spot-tailed quoll.
We developed a species-specific assay and validated it using synthetic oligos, tissue samples and soil collected from a captive quoll enclosure. We then assessed the assay on natural environment soil samples taken from the Snowy River region from communal quoll defecation sites (latrines) and from broader quoll habitat. We used amplification success data to model the concentration of quoll DNA in soil from different site types and calculate the sensitivity of our assay.
Sensitivity was highest at latrine sites, but decreased sharply when sampling just 1 m away. In non-latrine habitat, the positive amplification rate was too low to allow for meaningful statistical analyses, suggesting that a prohibitively large number of samples would need to be analysed for detection probabilities to be adequate for routine monitoring programs.
Overall, we found that low sensitivity was driven by the low concentration of spot-tailed quoll DNA at many of the surveyed sites.
Given that quoll latrines can usually be identified from the accumulation of scats, and scats themselves can be sampled for DNA, we suggest that eDNA analysis of soil is unlikely to offer improvements over current spot-tailed quoll monitoring methods.
Keywords: Dasyurus maculatus, eDNA, qPCR, rare species, sedaDNA, sediment, sensitivity, targeted detection.
References
Aylward ML, Sullivan AP, Perry GH, Johnson SE, Louis EE, Jr (2018) An environmental DNA sampling method for aye-ayes from their feeding traces. Ecology and Evolution 8(18), 9229-9240.
| Crossref | Google Scholar | PubMed |
Bani A, De Brauwer M, Creer S, Dumbrell AJ, Limmon G, Jompa J, von der Heyden S, Beger M (2020) Informing marine spatial planning decisions with environmental DNA. Advances in Ecological Research 62, 375-407.
| Crossref | Google Scholar |
Belbin L, Wallis E, Hobern D, Zerger A (2021) The Atlas of Living Australia: history, current state and future directions. Biodiversity Data Journal 9, e65023.
| Crossref | Google Scholar | PubMed |
Belcher CA, Darrant JP (2004) Home range and spatial organization of the marsupial carnivore, Dasyurus maculatus maculatus (Marsupialia: Dasyuridae) in south-eastern Australia. Journal of Zoology 262, 271-280.
| Crossref | Google Scholar |
Belcher CA, Darrant JP (2006) Habitat use by tiger quoll (Dasyurus maculatus) (Marsupialia: Dasyuridae) in south-eastern Australia. Journal of Zoology 269(2), 183-190.
| Crossref | Google Scholar |
Bohmann K, Evans A, Gilbert MTP, Carvalho GR, Creer S, Knapp M, Douglas WY, De Bruyn M (2014) Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution 29(6), 358-367.
| Crossref | Google Scholar | PubMed |
Burk A, Springer MS (2000) Intergeneric relationships among Macropodoidea (Metatheria: Diprotodontia) and the chronicle of kangaroo evolution. Journal of Mammalian Evolution 7, 213-237.
| Crossref | Google Scholar |
Cairns KM, Wilton AN (2016) New insights on the history of canids in Oceania based on mitochondrial and nuclear data. Genetica 144, 553-565.
| Crossref | Google Scholar | PubMed |
Camaclang AE, Maron M, Martin TG, Possingham HP (2015) Current practices in the identification of critical habitat for threatened species. Conservation Biology 29(2), 482-492.
| Crossref | Google Scholar | PubMed |
Claridge AW, Mifsud G, Dawson J, Saxon MJ (2004) Use of infrared digital cameras to investigate the behaviour of cryptic species. Wildlife Research 31(6), 645-650.
| Crossref | Google Scholar |
Claridge AW, Paull D, Dawson J, Mifsud G, Murray AJ, Poore R, Saxon MJ (2005) Home range of the spotted-tailed quoll (Dasyurus maculatus), a marsupial carnivore, in a rainshadow woodland. Wildlife Research 32(1), 7-14.
| Crossref | Google Scholar |
Darling JA, Mahon AR (2011) From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environmental Research 111(7), 978-988.
| Crossref | Google Scholar | PubMed |
De Brauwer M, Chariton A, Clarke LJ, Cooper MK, DiBattista J, Furlan E, Giblot-Ducray D, Gleeson D, Harford A, Herbert S, MacDonald AJ, Miller A, Montgomery K, Mooney T, Noble LM, Rourke M, Sherman CDH, Stat M, Suter L, West KM, White N, Villacorta-Rath C, Zaiko A, Trujillo-Gonzalez A (2022a) Environmental DNA protocol development guide for biomonitoring. (National eDNA Reference Centre: Canberra)
De Brauwer M, Chariton A, Clarke LJ, Cooper MK, DiBattista J, Furlan E, Giblot-Ducray D, Gleeson D, Harford A, Herbert S, MacDonald AJ, Miller A, Montgomery K, Mooney T, Noble LM, Rourke M, Sherman CDH, Stat M, Suter L, West KM, White N, Villacorta-Rath C, Zaiko A, Trujillo-Gonzalez A (2022b) Environmental DNA Test Validation Guidelines. (National eDNA Reference Centre, Canberra, ACT, Australia)
De Brauwer M, Clarke LJ, Chariton A, Cooper MK, De Bruyn M, Furlan E, MacDonald AJ, Rourke ML, Sherman CD, Suter L, Villacorta-Rath C (2023) Best practice guidelines for environmental DNA biomonitoring in Australia and New Zealand. Environmental DNA 5, 417-423.
| Crossref | Google Scholar |
Fediajevaite J, Priestley V, Arnold R, Savolainen V (2021) Meta-analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards. Ecology and Evolution 11(9), 4803-4815.
| Crossref | Google Scholar | PubMed |
Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biology Letters 4(4), 423-425.
| Crossref | Google Scholar | PubMed |
Ficetola GF, Taberlet P, Coissac E (2016) How to limit false positives in environmental DNA and metabarcoding? Molecular Ecology Resources 16, 604-607.
| Crossref | Google Scholar | PubMed |
Frankham GJ, Handasyde KA, Eldridge MDB (2012) Novel insights into the phylogenetic relationships of the endangered marsupial genus Potorous. Molecular Phylogenetics and Evolution 64(3), 592-602.
| Crossref | Google Scholar | PubMed |
Furlan EM, Gleeson D, Hardy CM, Duncan RP (2016) A framework for estimating the sensitivity of eDNA surveys. Molecular Ecology Resources 16(3), 641-654.
| Crossref | Google Scholar | PubMed |
Gogarten JF, Hoffmann C, Arandjelovic M, Sachse A, Merkel K, Dieguez P, Agbor A, Angedakin S, Brazzola G, Jones S, Langergraber KE, Lee K, Marrocoli S, Murai M, Sommer V, Kühl H, Leendertz FH, Calvignac-Spencer S (2020) Fly-derived DNA and camera traps are complementary tools for assessing mammalian biodiversity. Environmental DNA 2(1), 63-76.
| Crossref | Google Scholar |
Gu W, Swihart RK (2004) Absent or undetected? Effects of non-detection of species occurrence on wildlife–habitat models. Biological Conservation 116(2), 195-203.
| Crossref | Google Scholar |
Gutiérrez-Cacciabue D, Cid AG, Rajal VB (2016) How long can culturable bacteria and total DNA persist in environmental waters? The role of sunlight and solid particles. The Science of the Total Environment 539, 494-502.
| Crossref | Google Scholar | PubMed |
Ishige T, Miya M, Ushio M, Sado T, Ushioda M, Maebashi K, Yonechi R, Lagan P, Matsubayashi H (2017) Tropical-forest mammals as detected by environmental DNA at natural saltlicks in Borneo. Biological Conservation 210, 281-285.
| Crossref | Google Scholar |
Kellner K, Meredith M, Kellner MK (2019) Package ‘jagsUI’ (version 1.5.2). Available at https://cran.r-project.org/web/packages/jagsUI/index.html [accessed 8 June 2023]
Klymus KE, Merkes CM, Allison MJ, Goldberg CS, Helbing CC, Hunter ME, Jackson CA, Lance RF, Mangan AM, Monroe EM, Piaggio AJ, Stokdyk JP, Wilson CC, Richter CA (2020) Reporting the limits of detection and quantification for environmental DNA assays. Environmental DNA 2(3), 271-282.
| Crossref | Google Scholar |
Krajewski C, Young J, Buckley L, Woolley PA, Westerman M (1997) Reconstructing the evolutionary radiation of dasyurine marsupials with cytochrome b, 12S rRNA, and protamine P1 gene trees. Journal of Mammalian Evolution 4, 217-236.
| Crossref | Google Scholar |
Kyle KE, Allen MC, Dragon J, Bunnell JF, Reinert HK, Zappalorti R, Jaffe BD, Angle JC, Lockwood JL (2022) Combining surface and soil environmental DNA with artificial cover objects to improve terrestrial reptile survey detection. Conservation Biology 36(6), e13939.
| Crossref | Google Scholar | PubMed |
Massilani D, Morley MW, Mentzer SM, Aldeias V, Vernot B, Miller C, Stahlschmidt M, Kozlikin MB, Shunkov MV, Derevianko AP, Conard NJ, Wurz S, Henshilwood CS, Vasquez J, Essel E, Nagel S, Richter J, Nickel B, Roberts RG, Pääbo S, Slon V, Goldberg P, Meyer M (2022) Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments. Proceedings of the National Academy of Sciences 119(1), e2113666118.
| Crossref | Google Scholar | PubMed |
Matsumura S, Inoshima Y, Ishiguro N (2014) Reconstructing the colonization history of lost wolf lineages by the analysis of the mitochondrial genome. Molecular Phylogenetics and Evolution 80, 105-112.
| Crossref | Google Scholar | PubMed |
Mitchell KJ, Pratt RC, Watson LN, Gibb GC, Llamas B, Kasper M, Edson J, Hopwood B, Male D, Armstrong KN, Meyer M, Hofreiter M, Austin J, Donnellan SC, Lee MS, Phillips MJ, Cooper A (2014) Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular Biology and Evolution 31(9), 2322-2330.
| Crossref | Google Scholar | PubMed |
Modave E, MacDonald AJ, Sarre SD (2017) A single mini-barcode test to screen for Australian mammalian predators from environmental samples. GigaScience 6(8), gix052.
| Crossref | Google Scholar |
Morant J, González-Oreja JA, Martínez JE, López-López P, Zuberogoitia I (2020) Applying economic and ecological criteria to design cost-effective monitoring for elusive species. Ecological Indicators 115, 106366.
| Crossref | Google Scholar |
Murray DC, Coghlan ML, Bunce M (2015) From benchtop to desktop: important considerations when designing amplicon sequencing workflows. PloS one 10(4), p. e0124671.
| Google Scholar |
Neice AA, McRae SB (2021) An eDNA diagnostic test to detect a rare, secretive marsh bird. Global Ecology and Conservation 27, e01529.
| Crossref | Google Scholar |
Nelson JL, Scroggie MP, Belcher CA (2014) Developing a camera trap survey protocol to detect a rare marsupial carnivore, the spotted-tailed quoll (Dasyurus maculatus). In ‘Camera trapping: wildlife management and research’. (Eds P Meek, P Fleming, G Ballard, P Banks, A Claridge, J Sanderson, D Swann) pp. 271–279. (CSIRO publishing: Canberra, ACT, Australia)
Nilsson MA, Arnason U, Spencer PB, Janke A (2004) Marsupial relationships and a timeline for marsupial radiation in South Gondwana. Gene 340(2), 189-196.
| Crossref | Google Scholar | PubMed |
Nilsson MA, Zheng Y, Kumar V, Phillips MJ, Janke A (2018) Speciation generates mosaic genomes in kangaroos. Genome Biology and Evolution 10(1), 33-44.
| Crossref | Google Scholar | PubMed |
Norros V, Laamanen T, Meissner K, Iso-Touru T, Kahilainen A, Lehtinen S, Lohtander-Buckbee K, Nygård H, Pennanen T, Ruohonen-Lehto M, Sirkiä P, Suikkanen S, Tolkkinen M, Vainio E, Velmala S, Vuorio K, Vihervaara P (2022) Roadmap for implementing environmental DNA (eDNA) and other molecular monitoring methods in Finland—Vision and action plan for 2022–2025. Reports of the Finnish Environment Institute 20, Finnish Environment Institute, pp. 3–67.
Phillips MJ, Haouchar D, Pratt RC, Gibb GC, Bunce M (2013) Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes. PLoS ONE 8(2), e57745.
| Crossref | Google Scholar | PubMed |
Priestley V, Allen R, Binstead M, Arnold R, Savolainen V (2021) Quick detection of a rare species: Forensic swabs of survey tubes for hazel dormouse Muscardinus avellanarius urine. Methods in Ecology and Evolution 12(5), 818-827.
| Crossref | Google Scholar |
Prosser CM, Hedgpeth BM (2018) Effects of bioturbation on environmental DNA migration through soil media. PLoS ONE 13(4), e0196430.
| Crossref | Google Scholar | PubMed |
Ramón-Laca A, Gleeson D, Yockney I, Perry M, Nugent G, Forsyth DM (2014) Reliable discrimination of 10 ungulate species using high resolution melting analysis of faecal DNA. PLoS ONE 9(3), e92043.
| Crossref | Google Scholar | PubMed |
Roussel JM, Paillisson JM, Treguier A, Petit E (2015) The downside of eDNA as a survey tool in water bodies. Journal of Applied Ecology 52, 823-826.
| Crossref | Google Scholar |
Ruibal M, Peakall R, Claridge A, Firestone K (2009) Field-based evaluation of scat DNA methods to estimate population abundance of the spotted-tailed quoll (Dasyurus maculatus), a rare Australian marsupial. Wildlife Research 36(8), 721-736.
| Crossref | Google Scholar |
Ruibal M, Peakall R, Claridge A (2010) Socio-seasonal changes in scent-marking habits in the carnivorous marsupial Dasyurus maculatus at communal latrines. Australian Journal of Zoology 58(5), 317-322.
| Crossref | Google Scholar |
Ryan E, Bateman P, Fernandes K, van der Heyde M, Nevill P (2022) eDNA metabarcoding of log hollow sediments and soils highlights the importance of substrate type, frequency of sampling and animal size, for vertebrate species detection. Environmental DNA 4(4), 940-953.
| Crossref | Google Scholar |
Sirois SH, Buckley DH (2019) Factors governing extracellular DNA degradation dynamics in soil. Environmental Microbiology Reports 11(2), 173-184.
| Crossref | Google Scholar | PubMed |
Song JW, Schultz MT, Casman EA, Bockrath KD, Mize E, Monroe EM, Tuttle-Lau M, Small MJ (2020) A probabilistic model for designing and assessing the performance of eDNA sampling protocols. Molecular Ecology Resources 20(2), 404-414.
| Crossref | Google Scholar | PubMed |
Springer MS, Douzery E (1996) Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. Journal of Molecular Evolution 43, 357-373.
| Crossref | Google Scholar | PubMed |
Takahashi M, Saccò M, Kestel JH, Nester G, Campbell MA, van der Heyde M, Heydenrych MJ, Juszkiewicz DJ, Nevill P, Dawkins KL, Bessey C, Fernandes K, Miller H, Power M, Mousavi-Derazmahalleh M, Newton JP, White NE, Richards ZT, Allentoft ME (2023) Aquatic environmental DNA: a review of the macro-organismal biomonitoring revolution. Science of the Total Environment 873, 162322.
| Crossref | Google Scholar | PubMed |
Tsuji S, Ushio M, Sakurai S, Minamoto T, Yamanaka H (2017) Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance. PLoS ONE 12(4), e0176608.
| Crossref | Google Scholar | PubMed |
Wang H, Qi J, Xiao D, Wang Z, Tian K (2017) A re-evaluation of dilution for eliminating PCR inhibition in soil DNA samples. Soil Biology and Biochemistry 106, 109-118.
| Crossref | Google Scholar |
Webb KM, Allard MW (2009) Mitochondrial genome DNA analysis of the domestic dog: identifying informative SNPs outside of the control region. Journal of Forensic Sciences 54(2), 275-288.
| Google Scholar |
Westerman M, Springer MS, Dixon J, Krajewski C (1999) Molecular relationships of the extinct pig-footed bandicoot Chaeropus ecaudatus (Marsupialia: Perameloidea) using 12S rRNA sequences. Journal of Mammalian Evolution 6, 271-288.
| Crossref | Google Scholar |
Westerman M, Loke S, Springer MS (2004) Molecular phylogenetic relationships of two extinct potoroid marsupials, Potorous platyops and Caloprymnus campestris (Potoroinae: Marsupialia). Molecular Phylogenetics and Evolution 31(2), 476-485.
| Crossref | Google Scholar | PubMed |
Westerman M, Kear BP, Aplin K, Meredith RW, Emerling C, Springer MS (2012) Phylogenetic relationships of living and recently extinct bandicoots based on nuclear and mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 62(1), 97-108.
| Crossref | Google Scholar | PubMed |
Wilson KA, Lulow M, Burger J, Fang YC, Andersen C, Olson D, O’Connell M, McBride MF (2011) Optimal restoration: accounting for space, time and uncertainty. Journal of Applied Ecology 48(3), 715-725.
| Crossref | Google Scholar |
Xia Z, Zhan A, Johansson ML, DeRoy E, Haffner GD, MacIsaac HJ (2021) Screening marker sensitivity: optimizing eDNA-based rare species detection. Diversity and Distributions 27(10), 1981-1988.
| Crossref | Google Scholar |
