• Full Text
• PDF (1407 K)
• PDF-Plus (377 K)
• Suppl. data

Challenges for assessing vertebrate diversity in turbid Saharan water-bodies using environmental DNA

Bastian Egeter,^a Sara Peixoto,^ab José C. Brito,^ab Simon Jarman,^cd Pamela Puppo,^a Guillermo Velo-Antón^a

^aCIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal.

^bDepartamento de Biologia da Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 4169-007 Porto, Portugal.

^cTrace and Environmental DNA (TrEnD) Laboratory, Molecular and Life Sciences, Curtin University, WA, 6102, Australia.

^dEnvironomics Future Science Platform, CSIRO National Collections and Marine Infrastructure, Crawley, WA, 6009, Australia.

Corresponding editor: Xavier Pochon

Published on the web 12 October 2018.

Received April 5, 2018. Accepted September 26, 2018.

Genome, 2018, 61(11): 807-814, https://doi.org/10.1139/gen-2018-0071

References

•  
  Adrian-Kalchhauser I, Burkhardt-Holm P. 2016. An eDNA assay to monitor a globally invasive fish species from flowing freshwater. PLoS ONE 11(1): e0147558 Crossref, Medline, Google Scholar.
•  
  Alberdi A, Aizpurua O, Gilbert MTP, Bohmann K. 2018. Scrutinizing key steps for reliable metabarcoding of environmental samples. Methods Ecol. Evol. 9(1): 134-147 Crossref, Google Scholar.
•  
  Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM. 2014. Environmental conditions influence eDNA persistence in aquatic systems. Environ. Sci. Technol. 48(3): 1819-1827 Crossref, Medline, Google Scholar.
•  
  Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E. 2016. obitools: a unix-inspired software package for DNA metabarcoding. Mol. Ecol. Resour. 16(1): 176-182 Crossref, Medline, Google Scholar.
•  
  Brito JC, Godinho R, Martínez-Freiría F, Pleguezuelos JM, Rebelo H, Santos X, et al. 2014. Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel. Biol. Rev. 89(1): 215-231 Crossref, Medline, Google Scholar.
•  
  Calvignac-Spencer S, Merkel K, Kutzner N, Kühl H, Boesch C, Kappeler PM, et al. 2013. Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity. Mol. Ecol. 22(4): 915-924 Crossref, Medline, Google Scholar.
•  
  Civade R, Dejean T, Valentini A, Roset N, Raymond J-C, Bonin A, et al. 2016. Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system. PLoS ONE 11(6): e0157366 Crossref, Medline, Google Scholar.
•  
  Coey, S., Fernández, C.A., Vogler, A.P., Yu, D., Atkinson, P., and Coates, A. 2015. Survey for African freshwater fish using DNA barcoding. In The 35th Annual Conference of the International Association for Impact Assessment, Firenze Fiera Congress & Exhibition Center, Florence, Italy, 20–23 April 2015. Google Scholar
•  
  Corse E, Meglécz E, Archambaud G, Ardisson M, Martin J-F, Tougard C, et al. 2017. A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies. Mol. Ecol. Resour. 17(6): e146-e159 Crossref, Medline, Google Scholar.
•  
  De Barba M, Miquel C, Boyer F, Mercier C, Rioux D, Coissac E, et al. 2014. DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. Mol. Ecol. Resour. 14(2): 306-323 Crossref, Medline, ISI, Google Scholar.
•  
  Deagle BE, Jarman SN, Coissac E, Pompanon F, Taberlet P. 2014. DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match. Biol. Lett. 10(9): 20140562 Crossref, Medline, Google Scholar.
•  
  Djurhuus A, Pitz K, Sawaya NA, Rojas-Márquez J, Michaud B, Montes E, et al. 2018. Evaluation of marine zooplankton community structure through environmental DNA metabarcoding. Limnol. Oceanogr. Methods 16(4): 209-221 Crossref, Medline, Google Scholar.
•  
  Eichmiller JJ, Miller LM, Sorensen PW. 2016. Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish. Mol. Ecol. Resour. 16(1): 56-68 Crossref, Medline, Google Scholar.
•  
  Eva B, Harmony P, Thomas G, Francois G, Alice V, Claude M, et al. 2016. Trails of river monsters: Detecting critically endangered Mekong giant catfish Pangasianodon gigas using environmental DNA. Glob. Ecol. Conserv. 7: 148-156 Crossref, Google Scholar.
•  
  Furlan EM, Gleeson D. 2017. Improving reliability in environmental DNA detection surveys through enhanced quality control. Mar. Freshw. Res. 68(2): 388-395 Crossref, Google Scholar.
•  
  Gansauge M-T, Meyer M. 2013. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8(4): 737-748 Crossref, Medline, Google Scholar.
•  
  Goldberg CS, Strickler KM, Fremier AK. 2018. Degradation and dispersion limit environmental DNA detection of rare amphibians in wetlands: Increasing efficacy of sampling designs. Sci. Total Environ. 633: 695-703 Crossref, Medline, Google Scholar.
•  
  Green HC, Field KG. 2012. Sensitive detection of sample interference in environmental qPCR. Water Res. 46(10): 3251-3260 Crossref, Medline, Google Scholar.
•  
  Hinlo R, Gleeson D, Lintermans M, Furlan E. 2017. Methods to maximise recovery of environmental DNA from water samples. PLoS ONE 12(6): e0179251 Crossref, Medline, Google Scholar.
•  
  Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, et al. 2016. MEGAN community edition — interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12(6): e1004957 Crossref, Medline, ISI, Google Scholar.
•  
  Jerde CL, Mahon AR, Chadderton WL, Lodge DM. 2011. “Sight-unseen” detection of rare aquatic species using environmental DNA. Conserv. Lett. 4(2): 150-157 Crossref, ISI, Google Scholar.
•  
  Jerde CL, Olds BP, Shogren AJ, Andruszkiewicz EA, Mahon AR, Bolster D, et al. 2016. Influence of stream bottom substrate on retention and transport of vertebrate environmental DNA. Environ. Sci. Technol. 50(16): 8770-8779 Crossref, Medline, Google Scholar.
•  
  Kelly RP, Port JA, Yamahara KM, Crowder LB. 2014. Using environmental DNA to census marine fishes in a large mesocosm. PLoS ONE 9(1): e86175 Crossref, Medline, ISI, Google Scholar.
•  
  Kircher M, Sawyer S, Meyer M. 2011. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40(1): e3 Crossref, Medline, Google Scholar.
•  
  Kocher A, de Thoisy B, Catzeflis F, Valière S, Bañuls AL, Murienne J. 2017a. iDNA screening: Disease vectors as vertebrate samplers. Mol. Ecol. 26(22): 6478-6486 Crossref, Medline, Google Scholar.
•  
  Kocher A, de Thoisy B, Catzeflis F, Huguin M, Valière S, Zinger L, et al. 2017b. Evaluation of short mitochondrial metabarcodes for the identification of Amazonian mammals. Methods Ecol. Evol. 8(10): 1276-1283 Crossref, Google Scholar.
•  
  Kondo NI, Nakagawa M, Matsuzaki S-i, Ueno R, Takamura K, Ito H. 2016. DNA barcoding, environmental DNA and an ongoing attempt of detecting biodiversity in Lake Kasumigaura. J. Integr. Field Sci. 13: 21-29 Google Scholar.
•  
  Liang Z, Keeley A. 2013. Filtration recovery of extracellular DNA from environmental water samples. Environ. Sci. Technol. 47(16): 9324-9331 Crossref, Medline, Google Scholar.
•  
  Lopes CM, Sasso T, Valentini A, Dejean T, Martins M, Zamudio KR, et al. 2017. eDNA metabarcoding: a promising method for anuran surveys in highly diverse tropical forests. Mol. Ecol. Resour. 17(5): 904-914 Crossref, Medline, Google Scholar.
•  
  Majaneva M, Diserud OH, Eagle SH, Boström E, Hajibabaei M, Ekrem T. 2018. Environmental DNA filtration techniques affect recovered biodiversity. Sci. Rep. 8(1): 4682 Crossref, Medline, Google Scholar.
•  
  Maudet C, Luikart G, Dubray D, Von Hardenberg A, Taberlet P. 2004. Low genotyping error rates in wild ungulate faeces sampled in winter. Mol. Ecol. Resour. 4(4): 772-775 Crossref, Google Scholar.
•  
  Pääbo S, Poinar H, Serre D, Jaenicke-Després V, Hebler J, Rohland N, et al. 2004. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38(1): 645-679 Crossref, Medline, Google Scholar.
•  
  Pérez LM, Fittipaldi M, Adrados B, Morató J, Codony F. 2013. Error estimation in environmental DNA targets quantification due to PCR efficiencies differences between real samples and standards. Folia Microbiol. 58(6): 657-662 Crossref, Medline, Google Scholar.
•  
  Pilliod DS, Goldberg CS, Arkle RS, Waits LP. 2014. Factors influencing detection of eDNA from a stream-dwelling amphibian. Mol. Ecol. Resour. 14(1): 109-116 Crossref, Medline, Google Scholar.
•  
  Pimm SL, Jenkins CN, Abell R, Brooks TM, Gittleman JL, Joppa LN, et al. 2014. The biodiversity of species and their rates of extinction, distribution, and protection. Science 344(6187): 1246752 Crossref, Medline, Google Scholar.
•  
  Pochon X, Bott NJ, Smith KF, Wood SA. 2013. Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests. PLoS ONE 8(9): e73935 Crossref, Medline, Google Scholar.
•  
  Port JA, O’Donnell JL, Romero-Maraccini OC, Leary PR, Litvin SY, Nickols KJ, et al. 2016. Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA. Mol. Ecol. 25(2): 527-541 Crossref, Medline, Google Scholar.
•  
  Rees HC, Maddison BC, Middleditch DJ, Patmore JRM, Gough KC. 2014. The detection of aquatic animal species using environmental DNA — a review of eDNA as a survey tool in ecology. J. Appl. Ecol. 51(5): 1450-1459 Crossref, Google Scholar.
•  
  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(21): e145-e145 Crossref, Medline, ISI, Google Scholar.
•  
  Robson HL, Noble TH, Saunders RJ, Robson SK, Burrows DW, Jerry DR. 2016. Fine-tuning for the tropics: application of eDNA technology for invasive fish detection in tropical freshwater ecosystems. Mol. Ecol. Resour. 16(4): 922-932 Crossref, Medline, Google Scholar.
•  
  Rodgers TW, Xu CC, Giacalone J, Kapheim KM, Saltonstall K, Vargas M, et al. 2017. Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community. Mol. Ecol. Resour. 17(6): e133-e145 Crossref, Medline, Google Scholar.
•  
  Shehzad W, McCarthy TM, Pompanon F, Purevjav L, Coissac E, Riaz T, et al. 2012a. Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia. PLoS ONE 7(2): e32104 Crossref, Medline, Google Scholar.
•  
  Shehzad W, Riaz T, Nawaz MA, Miquel C, Poillot C, Shah SA, et al. 2012b. Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan. Mol. Ecol. 21(8): 1951-1965 Crossref, Medline, Google Scholar.
•  
  Shehzad W, Nawaz MA, Pompanon F, Coissac E, Riaz T, Shah SA, et al. 2015. Forest without prey: livestock sustain a leopard Panthera pardus population in Pakistan. Oryx 49(2): 248-253 Crossref, Google Scholar.
•  
  Shogren AJ, Tank JL, Andruszkiewicz EA, Olds B, Jerde C, Bolster D. 2016. Modelling the transport of environmental DNA through a porous substrate using continuous flow-through column experiments. J. R. Soc. Interface 13(119) Crossref, Medline, Google Scholar.
•  
  Spens J, Evans AR, Halfmaerten D, Knudsen SW, Sengupta ME, Mak SS, et al. 2017. Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed filter. Methods Ecol. Evol. 8(5): 635-645 Crossref, Google Scholar.
•  
  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 Crossref, Google Scholar.
•  
  Takahara T, Minamoto T, Yamanaka H, Doi H, Kawabata Zi. 2012. Estimation of fish biomass using environmental DNA. PLoS ONE 7(4): e35868 Crossref, Medline, Google Scholar.
•  
  Thomsen PF, Kielgast JOS, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, et al. 2012. Monitoring endangered freshwater biodiversity using environmental DNA. Mol. Ecol. 21(11): 2565-2573 Crossref, Medline, ISI, Google Scholar.
•  
  Trape S. 2009. Impact of climate change on the relict tropical fish fauna of Central Sahara: threat for the survival of Adrar mountains fishes, Mauritania. PLoS ONE 4(2): e4400 Crossref, Medline, Google Scholar.
•  
  Turner CR, Barnes MA, Xu CC, Jones SE, Jerde CL, Lodge DM. 2014. Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods Ecol. Evol. 5(7): 676-684 Crossref, Google Scholar.
•  
  Vale CG, Pimm SL, Brito JC. 2015. Overlooked mountain rock pools in deserts are critical local hotspots of biodiversity. PLoS ONE 10(2): e0118367 Crossref, Medline, Google Scholar.
•  
  Valentini A, Taberlet P, Miaud C, Civade R, Herder J, Thomsen PF, et al. 2016. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol. Ecol. 25(4): 929-942 Crossref, Medline, Google Scholar.
•  
  Vences M, Lyra ML, Perl RGB, Bletz MC, Stanković D, Lopes CM, et al. 2016. Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene. Conserv. Genet. Resour. 8(3): 323-327 Crossref, Google Scholar.
•  
  Verheye HM, Dumont HJ. 1984. The calanoid copepods of the Nile system. Hydrobiologia 110(1): 191-212 Crossref, Google Scholar.
•  
  Walker DM, Leys JE, Dunham KE, Oliver JC, Schiller EE, Stephenson KS, et al. 2017. Methodological considerations for detection of terrestrial small-body salamander eDNA and implications for biodiversity conservation. Mol. Ecol. Resour. 17(6): 1223-1230 Crossref, Medline, Google Scholar.
•  
  Williams KE, Huyvaert KP, Piaggio AJ. 2017. Clearing muddied waters: Capture of environmental DNA from turbid waters. PLoS ONE 12(7): e0179282 Crossref, Medline, Google Scholar.
•  
  Xiong M, Shao X, Long Y, Bu H, Zhang D, Wang D, et al. 2016. Molecular analysis of vertebrates and plants in scats of leopard cats (Prionailurus bengalensis) in southwest China. J. Mammal. 97(4): 1054-1064 Crossref, Google Scholar.
•  
  Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7(1–2): 203-214 Crossref, Medline, ISI, Google Scholar.