Development of a quantitative polymerase chain reaction assay and environmental DNA sampling methods for Giant Gartersnake (Thamnophis gigas)

English version

Autoři: Gregg Schumer ^aff001; Eric C. Hansen ^aff002; Paul J. Anders ^aff003; Scott M. Blankenship ^aff001
Působiště autorů: Cramer Fish Sciences-Genidaqs, West Sacramento, CA, United States of America ^aff001; Eric Hansen Consulting, Sacramento, CA, United States of America ^aff002; Cramer Fish Sciences, Moscow, ID, United States of America ^aff003
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pone.0222493

Souhrn

The Giant Gartersnake (Thamnophis gigas) is a low density visually evasive species with a low detection probability based on standard field survey methods (e.g., traps, visual census). Habitat loss has resulted in extirpations or serious declines for T. gigas populations throughout the southern two thirds of its historic range. Uncertainty regarding its current distribution and occupancy present management challenges for the species. Enhancing survey sensitivity through development of environmental DNA sampling (eDNA) methods would improve compliance monitoring under the Endangered Species Act, recovery planning for T. gigas, and evaluation of California’s Central Valley tule marsh habitat on which this species depends. To address these needs, we designed and validated diagnostic quantitative Polymerase Chain Reaction (qPCR) assays for identifying portions of the Cytochrome B (CytB) and the Nicotinamide adenine dinucleotide (NADH) dehydrogenase subunit 4 (ND4) genes of the T. gigas mitochondrial genome. The designed ND4 qPCR assay was not specific to T. gigas DNA and amplified DNA from a closely related and spatially co-occurring Thamnophis species (T.s. fitchi). The CytB T. gigas qPCR assay proved specific to a species level with a sensitivity that reliably detected T. gigas DNA at a concentration of 2.0x10^-5 ng μL^-1. To assess detection range, coordinated field sampling was conducted at aquatic sites with an observed and documented population of T. gigas. The T. gigas qPCR assay reliably detected DNA from samples taken 300m downstream from the known source. We then used environmental eDNA sampling and qPCR analysis to augment unsuccessful trap surveys in the southern range of T. gigas and detected DNA in 28 of the 52 locations sampled, confirming that T. gigas was still present at some sites where physical trapping failed to identify presence. QPCR-based DNA detection coupled with eDNA sampling methods provides an effective means to obtain critical population metrics from this otherwise cryptic, federally protected and hard to study organism, offering great promise for elucidating patterns of occupancy with greater efficiency and at far less cost than trapping methods, particularly where detection probabilities are low.

Klíčová slova:

Biology and life sciences – Cell biology – Biochemistry – Research and analysis methods – Molecular biology – Evolutionary biology – Database and informatics methods – Bioinformatics – Sequence analysis – Sequence alignment – People and places – Molecular biology techniques – Computer and information sciences – Evolutionary systematics – Taxonomy – Data management – Geographical locations – Cellular structures and organelles – Artificial gene amplification and extension – Polymerase chain reaction – Earth sciences – Geomorphology – Topography – Landforms – Extraction techniques – Bioenergetics – Energy-producing organelles – Mitochondria – Valleys – North America – United States – BLAST algorithm – DNA extraction – DNA barcoding – Molecular systematics – California

Zdroje

1. Fitch HS. A biogeographical study of the ordinoides artenkreis of garter snakes (genus Thamnophis). Univ Calif Press. 1940;44: 1–150.

2. Hansen GE. Hansen G.E. 1998. Cherokee Canal sediment removal project post-construction giant garter snake (Thamnophis gigas) surveys. California Department of Water Resources; 1998 p. 9. Report No.: Contract No. B-81535.

3. Hanson GE, Brode JM. Status of the giant garter snake, Thamnophis couchi gigas (Fitch). State of California, the Resources Agency, Department of Fish and Game; 1980.

4. U.S. Fish and Wildlife Service. Endangered and threatened wildlife and plants; determination of threatened status for the giant garter snake. Federal Register 58:54053–54066; 1993.

5. U.S. Fish and Wildlife Service. Draft recovery plan for the giant garter snake (Thamnophis gigas). U.S. Fish and Wildlife Service, Portland, Oregon; 1999.

6. Brode J. Natural history of the giant garter snake (Thamnophis couchi gigas). Proceedings of the conference on California herpetology, HF DeListe, PR Brown, B Kaufman, and BM McGurty (eds) Southwestern Herpetologists Society, Special Publication. 1988. pp. 25–28.

7. Hansen EC. Year 2003 investigations of the giant garter snake (Thamnophis gigas) in the Middle American Basin: Sutter County, California. Prep Sacram Area Flood Control Agency. 2004;

8. Hansen GE, Brode JM. Results of relocating canal habitat of the giant garter snake (Thamnophis gigas) during widening of State Route 99/70 in Sacramento and Sutter counties, California. Caltrans; 1993 p. 36. Report No.: Interagency Agreement 03E325 (FG7550) (FY 87/88-91-92).

9. Wylie GD, Casazza ML, Daughety JK. 1996 progress report for the giant garter snake study. Dixon Research Station, California Science Center: USGS Biological Resources Division; 1997.

10. Dahl TE. Wetlands losses in the United States, 1780’s to 1980’s. Report to the Congress [Internet]. National Wetlands Inventory, St. Petersburg, FL (USA); 1990. Available: http://www.osti.gov/scitech/biblio/5527872

11. Frayer WE, Peters DD, Pywell Hr. Wetlands of the California Central Valley: status and trends: 1939-mid-1980’s. U Fish Wildl Serv Reg 1 Portland USAnp Jun 1989. 1989;

12. U.S. Fish and Wildlife Service. Giant garter snake (Thamnophis gigas) 5-year review: summary and evaluation. Sacram Fish Wildl Off Sacram. 2006;46.

13. Dickert C. Progress Report for the San Joaquin Valley Giant Garter Snake Conservation Project. Los Banos CA Los Banos Wildl Complex Calif Dep Fish Game. 2003;

14. Hansen EC. Implementation of Priority 1, Priority 2, and Priority 3 Recovery Tasks for Giant Garter Snake (Thamnophis gigas)–continuing Surveys in Merced County, California, with an Expansion to Northern Fresno County. U.S. Fish and Wildlife Service; 2008. Report No.: FWS Agreement No. 802707G112.

15. Wylie GD. Results of the 1998 survey for giant garter snakes in and around the Grasslands area of the San Joaquin Valley [Internet]. US Geological Survey, Dixon Field Station; 1999. Available: https://pubs.er.usgs.gov/publication/96799

16. Wylie GD, Amarello M. Surveys for the current distribution and abundance of Giant Gartersnakes (Thamnophis gigas) in the southtern San Joaquin Valley. US Geological Survey, Dixon Field Station; 2008 p. 24.

17. Halstead BJ, Wylie GD, Coates PS, Casazza ML. Bayesian adaptive survey protocols for resource management. J Wildl Manag. 2011;75: 450–457.

18. Halstead BJ, Wylie GD, Coates PS, Casazza ML. The U.S. Geological Survey Quantitative Adaptive Survey Protocol for the Giant Gartersnake (Thamnophis gigas). 2009. Report No.: U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, 6924 Tremont Road, Dixon, CA 95620, USA.

19. Hansen EC, Scherer RD. Distribution of the Giant Gartersnake (Thamnophis gigas) in the Volta Area of the San Joaquin Valley. Report prepared for the U.S. Fish and Wildlife Service pursuant to FWS Agreement No. F15AP00275; 2017.

20. Casazza ML, Wylie GD, Gregory CJ. A funnel trap modification for surface collection of aquatic amphibians and reptiles. Herpetol Rev. 2000;31: 91–92.

21. Jerde CL, Mahon AR, Chadderton WL, Lodge DM. “Sight‐unseen” detection of rare aquatic species using environmental DNA. Conserv Lett. 2011;4: 150–157. doi: 10.1111/j.1755-263X.2010.00158.x

22. Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, et al. Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol. 2011;21: 2565–2573. doi: 10.1111/j.1365-294X.2011.05418.x 22151771

23. Bergman PS, Schumer G, Blankenship S, Campbell E. Detection of Adult Green Sturgeon Using Environmental DNA Analysis. PLOS ONE. 2016;11: e0153500. doi: 10.1371/journal.pone.0153500 27096433

24. Turner CR, Barnes MA, Xu CC, Jones SE, Jerde CL, Lodge DM. Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods Ecol Evol. 2014;5: 676–684.

25. Vernooy R, Haribabu E, Muller MR, Vogel JH, Hebert PDN, Schindel DE, et al. Barcoding Life to Conserve Biological Diversity: Beyond the Taxonomic Imperative. PLOS Biol. 2010;8: e1000417. doi: 10.1371/journal.pbio.1000417 20644709

26. Johns GC, Avise JC. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Mol Biol Evol. 1998;15: 1481–1490. doi: 10.1093/oxfordjournals.molbev.a025875 12572611

27. Moritz C, Schneider CJ, Wake DB. Evolutionary Relationships Within the Ensatina Eschscholtzii Complex Confirm the Ring Species Interpretation. Syst Biol. 1992;41: 273–291. doi: 10.1093/sysbio/41.3.273

28. Goebel AM, Donnelly JM, Atz ME. PCR Primers and Amplification Methods for 12S Ribosomal DNA, the Control Region, Cytochrome Oxidase I, and Cytochromebin Bufonids and Other Frogs, and an Overview of PCR Primers which Have Amplified DNA in Amphibians Successfully. Mol Phylogenet Evol. 1999;11: 163–199. doi: 10.1006/mpev.1998.0538 10082619

29. Hansen EC. Status, Distribution, and Demography of San Joaquin Valley Giant Garter Snake (Thamnophis gigas) Populations: Implications for Species-specific Management and Recovery. Completed as partial fulfillment of a Master of Science degree in Biological Sciences, College of Natural Sciences, California State University, Chico; 2008.

30. Hansen EC, Wack R, Poppenga R, Strohm K, Johnson C, Bunn D, et al. Comparative pathology, health, and contaminant exposure within San Joaquin Valley and Sacramento Valley giant garter snake (Thamnophis gigas) populations. 2011;Bureau of Reclamation (BOR) pursuant to BOR Agreement No. 08FG200042.

31. U.S. Fish and Wildlife Service. Giant garter snake (Thamnophis gigas) 5-year review: summary and evaluation. Sacram Fish Wildl Off Sacram. 2012;

32. Fish U.S. and Wildlife Service. 2015 Revised draft recovery plan for the giant garter snake (Thamnophis gigas). 2015. Report No.: U.S. Fish and Wildlife Service, Pacific Southwest Region, USA.

33. Sloan J. Progress report for the San Joaquin Valley giant garter snake conservation project. 2004 p. 18. Report No.: Los Banos Wildlife Complex, California Department of Fish and Game, Los Banos, CA.

34. California Natural Diversity Database. Computer printout of sensitive species records in California. Updated version as of December 2016. California Department of Fish and Wildlife, Natural Heritage Division, Sacramento, CA; 2016.

35. Dickert C. Giant garter snake surveys at some areas of historical occupation in the Grassland Ecological Area, Merced Co. and Mendota Wildlife Area, Fresno Co., California. Calif Fish Game. 2005;91: 255–269.

36. Hansen GE. Status of the giant garter snake (Thamnophis gigas) in the San Joaquin Valley in 1995. California Department of Fish and Game; 1996 p. 9. Report No.: Standard Agreement no. FG4052IF.

37. Halstead BJ, Wood DA, Bowen L, Waters SC, Vandergast AG, Ersan JS, et al. An evaluation of the efficacy of using environmental DNA (eDNA) to detect giant gartersnakes (Thamnophis gigas). U.S. Department of Interior U.S. Geologic Survey; 2017.

Development of a quantitative polymerase chain reaction assay and environmental DNA sampling methods for Giant Gartersnake (Thamnophis gigas)

Souhrn

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Zdroje

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