Evaluating Ethanol-based Sample Preservation to Facilitate Use of DNA Barcoding in Routine Freshwater Biomonitoring Programs Using Benthic Macroinvertebrates

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Stein, Eric D ^a   White, Bryan P ^a   Mazor, Raphael D ^a   Miller, Peter E ^b   Pilgrim, Erik M ^c  

^a SOUTHERN CALIFORNIA COASTAL WATER RESEARCH PROJECT   (United States)

^b UNIVERSITY OF GUELPH   (Canada)

^c U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL; GLYCEROL;

ANIMAL TISSUE; ARTICLE; BEETLE; BIOLOGICAL MONITORING; COI GENE; CONTROLLED STUDY; DILUTION; DIPTERA; DNA BARCODING; DNA DETERMINATION; EPHEMEROPTERA; FRESHWATER ENVIRONMENT; GASTROPOD; GENE SEQUENCE; GENETIC VARIABILITY; LEPTOHYPHIDAE; MACROBENTHOS; MITOCHONDRIAL GENE; NONHUMAN; ORGANIC MATTER PRODUCTION; POLLUTION MONITORING; SEQUENCE HOMOLOGY; TAXONOMY; TISSUE PRESERVATION; TRICHOPTERA; WATER POLLUTION INDICATOR;

ANIMALS; AQUATIC ORGANISMS; BASE SEQUENCE; BIODIVERSITY; DNA; DNA BARCODING, TAXONOMIC; DNA PRIMERS; ELECTRON TRANSPORT COMPLEX IV; ETHANOL; GASTROPODA; INSECT PROTEINS; INSECTS; PRESERVATION, BIOLOGICAL;

EPHEMEROPTERA; LEPTOHYPHIDAE;

EID: 84871879095     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0051273     Document Type: Article

References (27)

1. Hebert PDN, Cywinska A, Ball SL, deWaard JR, (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 270: 313-321.
2. Zhou X, Adamowicz SJ, Jacobus LM, DeWalt E, Hebert PDN, (2009) Towards a Comprehensive Barcode Library for Arctic Life-Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada. Front Zool 6: 30.
3. Sweeney BW, Battle JM, Jackson JK, Dapkey T, (2011) Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? J North Am Benthol Soc 30 (1) (): 195-216.
4. Pilgrim EM, Jackson SA, Swenson S, Turcasanyi I, Friedman E, et al. (2011) Incorporation of DNA barcoding into large-scale biomonitoring program: opportunities and pitfalls. J North Am Benthol Soc 30 (1) (): 217-231.
5. Hebert PDN, Ratnasingham S, deWaard JR, (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B Biol Sci 270: S596-S599.
6. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM, (2004) Identification of Birds through DNA Barcodes. PLoS Biol 2 (10) (): e312.
7. Stoeckle MY, Hebert PDN, (2008) Barcode of Life. Scientific American 299: 82-88.
8. Borisenko AV, Sones JE, Hebert PDN, (2009) The front-end logistics of DNA barcoding: challenges and prospects. Mol Ecol Resour 9: 27-34.
9. Janzen DH, Hallwachs W, Blandin P, Burns JM, Cadiou JM, et al. (2009) Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity. Mol Ecol Resour 9: 1-26.
10. Ratnasingham S, Hebert PDN, (2007) BOLD: The Barcode of Life Data System (www.barcodinglife.org). Mol Ecol Notes 7: 355-364.
11. König U, Borcherding J, (2012) Preserving young-of-the-year Perca fluviatilis in ethanol, formalin, or in a frozen state and the consequences for measuring morphometrics. J Appl Ichthyol pp. 1-5.
12. Bainard LD, Klironomos JN, Hart MM, (2010) Differential effect of sample preservation methods on plant and arbuscular mycorrhizal fungal DNA. J Microbiol Methods Aug 82 (2) (): 124-30.
13. Szinwelski N, Fialho VS, Yotoko KSC, Seleme LR, Sperber C, (2012) Ethanol fuel improves arthropod capture in pitfall traps and preserves DNA. ZooKeys 196: 11-22.
14. Hauer FV, Resh H (1996) Benthic macroinvertebrates. In: Methods in Stream Ecology. San Diego, CA: Methods in Stream Ecology, Academic Press. pp. 339-369.
15. Merritt RW, Cummins KW, Resh VH, Batzer DP (2008) Sampling Aquatic Insects: Collection devices, statistical considerations, and rearing procedures. An Introduction to the Aquatic Insects of North America. Dubuque, Iowa. Kendall/Hunt Publishing Company. Chapter 3 pp. 15 to 37.
16. Flournoy LE, Adams RP, Pandy RN, (1996) Interim and archival preservation of plant specimens in alcohols for DNA studies. Biotechniques 20 (4) (): 657-660.
17. Nagy ZT, (2010) A hands-on overview of tissue preservation methods for molecular genetic analyses. Org Divers Evol 10 (1) (): 91-105.
18. Morris K, Johnson S, Steele N (2012) San Gabriel River 2010 State of the Watershed Report. Council for Watershed Health, Los Angeles, CA.
19. Ivanova NV, deWaard JR, Hebert PDN, (2006) An inexpensive, automation-friendly protocol for recovering high-quality DNA. Mol Ecol Notes 6: 998-1002.
20. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
21. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28 (10) (): 2731-2739.
22. Kimura M, (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
23. Gaston GR, Bartlett JHW, McAllister AP, Heard RW, (1996) Biomass variations of estuarine macrobenthos preserved in ethanol and formalin. Estuaries Coast 19 (3) (): 674-679.
24. Baird DJ, Pascoe TJ, Zhou X, Hajibabaei M, (2011) Building freshwater macroinvertebrate DNA-barcode libraries from reference collection material: formalin preservation vs specimen age. J North Am Benthol Soc 30: 125-130.
25. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R, (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotech 3 (5) (): 294-299.
26. Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN, (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proc Nat Acad Sci USA 103: 968-971.
27. Meyer CP, (2003) Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics. Biol J Linn Soc Lond 79: 401-459.