Environmental DNA (eDNA) detection and habitat occupancy of threatened spotted gar (Lepisosteus oculatus)

Aquatic Conservation: Marine and Freshwater Ecosystems

Volumn 26, Issue 6, 2016, Pages 1107-1119

  Boothroyd, Margaret ^a,b   Mandrak, Nicholas E ^c   Fox, Michael ^a   Wilson, Chris C ^b  

^a TRENT UNIVERSITY   (Canada)

^b ONTARIO MINISTRY OF NATURAL RESOURCES   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

endangered species; fish; genetics; lake; littoral; new techniques

Indexed keywords

CONSERVATION STATUS; DETECTION METHOD; DNA; FINFISH; HABITAT SELECTION; HABITAT USE; LITTORAL ENVIRONMENT; POLYMERASE CHAIN REACTION; RARE SPECIES; SITE SELECTION; SPECIES OCCURRENCE;

CANADA; ONTARIO [CANADA];

LEPISOSTEUS OCULATUS;

EID: 84954350021     PISSN: 10527613     EISSN: 10990755     Source Type: Journal    
DOI: 10.1002/aqc.2617     Document Type: Article

References (60)

1. Abell R. 2002. Conservation for the biodiversity crisis. Conservation Biology 16: 1435–1437.
2. Anchordoquy TJ, Molina MC. 2007. Preservation of DNA. Cell Preservation Technology 5: 180–188.
3. Biggs J, Ewald N, Valentini A, Garboriaud C, Dejean T, Griffiths RA, Foster J, Wilkinson JW, Arnell A, Brotherton P, et al. 2015. Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus). Biological Conservation 183: 19–28.
4. Bouvier LD. Mandrak NE. 2010. Information in support of a Recovery Potential Assessment of Spotted Gar (Lepisosteus oculatus) in Canada. DFO Canadian Science Advisory Secretariat Research Document 2010/079.
5. Bronnenhuber JE, Wilson CC. 2013. Combining species-specific COI primers with environmental DNA analysis for targeted detection of rare freshwater species. Conservation Genetics Resources 5: 971–975.
6. Butchart SHM, Walpole M, Collen B, van Strien A, Scharlemann JPW, Almond REA, Baillie JEM, Bomhard B, Brown C, Bruno J, et al. 2010. Global biodiversity: indicators of recent declines. Science 328: 1164–1168.
7. Burns M, Valdivia H. 2008. Modelling the limit of detection in real-time quantitative PCR. European Food Research Technology 226: 1513–1524.
8. COSEWIC. 2005. COSEWIC Assessment and update status report on the spotted gar Lepisosteus oculatus in Canada. Committee on the Status of Endangered Species in Canada, Ottawa, ON. Available: http://publications.gc.ca/collections/Collection/CW69-14-67-2005E.pdf. (Accessed: 5 December 2014)
9. Darling JA, Mahon AR. 2011. From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environmental Research 7: 978–988.
10. Deiner K, Altermatt F. 2014. Transport distance of invertebrate environmental DNA in a natural river. PLoS One 9: e88786.
11. 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 6: e23398.
12. Dejean T, Valentini A, Miquel C, Taberlet P, Bellemain E, Miaud C. 2012. Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus. Journal of Applied Ecology 49: 953–959.
13. Department of Fisheries and Oceans (DFO). 2010. Recovery potential assessment of Spotted gar (Lepisosteus oculatus) in Canada. Department of Fisheries and Oceans, Burlington, ON. Canadian Science Advisory Secretariat Science Advisory Report 047. Available: http://www.dfo-mpo.gc.ca/CSAS/Csas/publications/sar-as/2010/2010_047_e.pdf. (accessed 23 January 2013)
14. Dissing J, Rudbeck L, Marcher H. 1996. A five minute procedure for extraction of genomic DNA from whole blood, semen and forensic stains for PCR. Advances in Forensic Haemogenetics 6: 269–271.
15. Eichmiller JJ, Bajer PG, Sorenson PW. 2014. The relationship between the distribution of common carp and their environmental DNA in a small lake. PLoS One 9: e112611.
16. ECALS (Environmental DNA Calibration Study). 2013. Environmental DNA Calibration Study Interim Technical Review Report February 2013. United States. Available at: http://www.asiancarp.us/documents/ECALS_INTERIM.pdf. (accessed 8 December 2012)
17. Ficetola G, Miaud C, Pompanon F, Taberlet P. 2008. Species detection using environmental DNA from water samples. Biology Letters 4: 423–425.
18. Ficetola GF, Pansu J, Bonin A, Coissac E, Giguet-Covex C, De Barba M, Gielly L, Lopes CM, Boyer F, Pompanon F, et al. 2015. Replication levels, false presences and the estimation of the presence/ absence from eDNA metabarcoding data. Molecular Ecology Resources 15: 543–556.
19. Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Klyn LA, Salling AB, Galatius A, Orlando L, Gilbert MTP. 2012. Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS One 7: e41781.
20. Foy CA, Parkes HC. 2001. Emerging homogeneous DNA-based technologies in the clinical laboratory. Clinical Chemistry 47: 990–1000.
21. Glass WR, Mandrak NE. 2014. Distribution of Spotted Gar (Lepisosteus oculatus) adults and juveniles in the Rondeau Bay, Long Point Bay, and Hamilton Harbour watersheds. Canadian Manuscript Report of Fisheries and Aquatic Sciences 3048.
22. Glass WR, Corkum LD, Mandrak NE. 2012. Spring and summer distribution and habitat use by adult threatened spotted gar in Rondeau Bay, Ontario, using radiotelemetry. Transactions of American Fisheries Society 141: 1026–1035.
23. Goldberg C, Pilliod D, Arkle R, Waits L. 2011. Molecular detection of vertebrates in stream water: a demonstration using rocky mountain tailed frogs and Idaho giant salamanders. PLoS One 6: e22746.
24. Gray SM, Chapman LJ, Mandrak NE. 2012. Turbidity reduces hatching success in threatened spotted gar (Lepisosteus oculatus). Environmental Biology of Fishes 94: 689–694.
25. Hebert PDN, Cywinska A, Ball SL, DeWaard JR. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society (Biological Sciences) 270: 313–322.
26. Herrington SJ, Hettiger KN, Heist EJ, Keeney DB. 2008. Hybridization between longnose and alligator gars in captivity with comments on possible gar hybridization in nature. Proceedings of the American Fisheries Society 137: 158–164.
27. Invasive Species Advisory Committee (ISAC). 2012. Validation of PCR-based asssays and laboratory accreditation for environmental detection of aquatic species. US Department of the Interior. Washington, DC 20240. Available: http://www.invasivespecies.gov/ISAC/White%20Papers/ISAC_PCR_WHITEPAPER_FINAL.pdf. (accessed 3 March 2013).
28. Jane SF, Wilcox TM, McKelvey KS, Young MK, Schwartz MK, Lowe WH, Letcher BH, Whiteley AR. 2015. Distance, flow and PCR inhibition, eDNA dynamics in two headwater streams. Molecular Ecology Resources 15: 216–227.
29. Janosik AM, Johnston CE. 2015. Environmental DNA as an effective tool for detection of imperiled fishes. Environmental Biology of Fishes. 98: 1889–1893.
30. Jelks HL, McCormick F, Walsh SJ, Nelson JS, Burkhead NM, Contreras-Balderas S, Diaz-Pardo E, Hendrikson DA, Lyons J, Mandrak NE, et al. 2008. Conservation status of imperiled North American freshwater and diadromous fishes. Fisheries 33: 372–407.
31. Jerde CL, Mahon AR, Chadderton WL, Lodge DM. 2011. ‘Sight-unseen’ detection of rare aquatic species using environmental DNA. Conservation Letters 4: 150–157.
32. Klymus KE, Richter CA, Chapman DC, Paukert C. 2015. Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix. Biological Conservation 183: 77–84.
33. Laramie MB, Pilliod DS, Goldberg CS. 2015. Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biological Conservation 183: 29–37.
34. Mahon AR, Rohly A, Budney M, Elgin E, Jerde W, Chadderton WL, Lodge DM. 2010. Environmental DNA monitoring and surveillance: standard operation procedures. Report to the United States Army Corps of Engineers, Environmental Laboratories, Cooperative Environmental Studies Unit, Vicksburg, Mississippi. Available: http://edna.nd.edu/Environmental_DNA_at_ND/Publications_and_Reports.html (accessed 3 March 2013).
35. Mahon AR, Jerde CL, Galaska M, Bergner JL, Chadderton L, Lodge DM, Hunter ME, Nico LG. 2013. Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments. PLoS One 8: e58316.
36. Marson D, Gertzen E, Cudmore B. 2014. Results of the Burlington 2013 Asian carp early detection field monitoring program. Canadian Manuscript Report of Fisheries and Aquatic Sciences 3054.
37. Merkes CM, McCalla SG, Jensen NR, Gailkowski MP, Amberg JJ. 2014. Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data. PLoS One 9: e113346.
38. Moyer GR, Díaz-Ferguson E, Hill JE, Shea C. 2014. Assessing environmental DNA detection in controlled lentic systems. PLoS One 9: e103767.
39. Olson ZH, Briggler JT, Williams RN. 2012. An eDNA approach to detect eastern hellbenders (Cryotibranchus a. alleganiensis) using samples of water. Wildlife Research 39: 629–636.
40. Ostrand KB, Braeutigam B, Wahl D. 2004. Consequences of vegetation density and prey species on spotted gar foraging. Transactions of the American Fisheries Society 133: 794–800.
41. Page LM, Burr BM. 1991. A Field Guide to Freshwater Fishes: North America North of Mexico, Boston, MA: Houghton Mifflin.
42. Pilliod DS, Goldberg CS, Arkle RS, Waits LP. 2013. Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples. Canadian Journal of Fisheries and Aquatic Science 70: 1123–1130.
43. Putman RJ. 1995. Ethical considerations and animal welfare in ecological field studies. Biodiversity Conservation 4: 903–915.
44. Ratnasingham S, Hebert PDN. 2007. BOLD: The Barcode of Life Data System (www.barcodinglife.org). Molecular Ecology Notes 7: 355–364.
45. Rosenfeld JS, Hatfield T. 2006. Information needs for assessing critical habitat of freshwater fish. Canadian Journal of Fisheries and Aquatic Sciences 63: 683–698.
46. Ros-García A, Nicolás A, García-Pérez AL, Juste RA, Hurtado A. 2012. Development and evaluation of a real-time PCR assay for the quantitative detection of Theileria annulata in cattle. Parasites and Vectors 5: 171.
47. Schmidt BR, Kéry M, Ursenbacher S, Hyman OJ, Collins JP. 2013. Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen. Methods in Ecology and Evolution 4: 646–653.
48. Sigsgaard EE, Carl H, Møller PR, Thomsen PF. 2015. Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples. Biological Conservation 183: 46–52.
49. Singh J. 2002. The biodiversity crisis: a multifaceted review. Current Science 82: 638–647.
50. Snedden GA, Kelso WE, Rutherford DA. 1999. Diel and seasonal patterns of spotted gar movement and habitat use in the Lower Atchafalaya River Basin, Louisiana. Transactions of the American Fisheries Society 128: 144–154.
51. Staton SK, Boyko AL, Dunn SE, Burridge M. 2012. Recovery strategy for the Spotted Gar (Lepisosteus oculatus) in Canada. Species at Risk Act Recovery Strategy Series. Fisheries and Oceans Canada. Available at: http://www.sararegistry.gc.ca/virtual_sara/files/plans/rs_lepisoste_tachete_sp_gar_1012_e.pdf (accessed 26 July 2015).
52. Strayer DL, Dudgeon D. 2010. Freshwater biodiversity conservation: recent progress and future challenges. Journal of the North American Benthological Society 20: 344–358.
53. Strickler KM, Fremier AK, Goldberg CS. 2015. Quantifying effects of UV, temperature, and pH on degradation rates of eDNA in aquatic microcosms. Biological Conservation 183: 85–92.
54. Takahara T, Minamoto T, Yamanaka H, Doi H, Kawabata Z. 2012. Estimation of fish biomass using environmental DNA. PLoS One 7: e35868.
55. Takahara T, Minamoto T, Doi H. 2013. Using environmental DNA to estimate the distribution of invasive fish species in ponds. PLoS One 8: e56584.
56. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731–2739.
57. Thompson WL. 2004. Sampling Rare or Elusive Species, Island Press: Washington DC.
58. Thomsen P, Kielgast J, Iversen L, Wiuf C, Rasmussen M, Gilbert MT, Orlando L, Willerslev E. 2012. Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology 21: 2565–2573.
59. Tyler JD, Granger MN. 1984. Notes on food habitats, size, and spawning behavior of spotted gar in Lake Lawtonka, Oklahoma. Proceedings of the Oklahoma Academy of Science 64: 8–10.
60. Williams JE, Williams RN, Thurow RF, Elwell L, Phillip DP, Harris FA, Kershner JL, Martinez PJ, Miller D, Reeves GH. 2011. Native fish conservation areas: a vision for large-scale conservation of native fish communities. Fisheries 36: 267–277.