A DNA barcode library for North American ephemeroptera: Progress and prospects

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Webb, Jeffrey M ^a   Jacobus, Luke M ^b   Funk, David H ^c   Zhou, Xin ^d   Kondratieff, Boris ^e   Geraci, Christy J ^f   DeWalt, R Edward ^g   Baird, Donald J ^h   Richard, Barton ⁱ   Phillips, Iain ^j   Hebert, Paul D N ^a  

^a UNIVERSITY OF GUELPH   (Canada)

^b INDIANA UNIVERSITY PURDUE UNIVERSITY COLUMBUS   (United States)

^c STROUD WATER RESEARCH CENTER   (United States)

^d BGI SHENZHEN   (China)

^e Veterinary Dentistry and Oral Surgery   (United States)

^f DEPARTMENT OF PALEOBIOLOGY   (United States)

^g UNIVERSITY OF ILLINOIS   (United States)

^h UNIVERSITY OF NEW BRUNSWICK   (Canada)

ⁱ FLORIDA A AND M UNIVERSITY   (United States)

^j Saskatchewan Watershed Authority   (Canada)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; MITOCHONDRIAL CYTOCHROME C OXIDASE SUBUNIT I; UNCLASSIFIED DRUG;

ARTICLE; CAENIS; CANADA; DNA BARCODING; EPHEMEROPTERA; INSECT; MEXICO; MITOCHONDRIAL CYTOCHROME C OXIDASE SUBUNIT I GENE; NONHUMAN; POLYPHYLY; SPECIES DIFFERENCE; SPECIES DISTRIBUTION; UNITED STATES; ANIMAL; CLASSIFICATION; FEMALE; GROWTH, DEVELOPMENT AND AGING; LIFE CYCLE STAGE; MALE; METHODOLOGY; NORTH AMERICA;

CAENIS; EPHEMEROPTERA; INSECTA;

ANIMALS; DNA BARCODING, TAXONOMIC; FEMALE; INSECTS; LIFE CYCLE STAGES; MALE; NORTH AMERICA; SPECIES SPECIFICITY;

EID: 84861589148     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038063     Document Type: Article

References (38)

1. Hebert PDN, Cywinska A, Ball SL, DeWaard JR, (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B-Biological Sciences 270: 313-321 doi:10.1098/rspb.2002.2218.
2. Ball SL, Hebert PDN, Burian SK, Webb JM, (2005) Biological identifications of mayflies (Ephemeroptera) using DNA barcodes. Journal of the North American Benthological Society 24: 508-524.
3. Zhou X, Robinson JL, Geraci CJ, Parker R, Flint OS, et al. (2011) Accelerated construction of a regional DNA-barcode reference library: caddisflies (Trichoptera) in the Great Smoky Mountains National Park. Journal of the North American Benthological Society 30: 131-162 doi:10.1899/10-010.1.
4. Mynott JH, Webb JM, Suter PJ, (2011) Adult and larval associations of the alpine stonefly genus Riekoperla McLellan (Plecoptera: Gripopterygidae) using mitochondrial DNA. Invertebrate Systematics 25: 11-21.
5. Zhou X, Kjer KM, Morse JC, (2007) Associating larvae and adults of Chinese Hydropsychidae caddisflies (Insecta:Trichoptera) using DNA sequences. Journal of the North American Benthological Society 26: 719-742 doi:10.1899/06-089.1.
6. Rosenberg D, Resh VH, (1993) An introduction to freshwater biomonitoring and benthic invertebrates. In: Rosenberg DM, Resh VH, editors. Freshwater Biomonitoring and Benthic Macroinvertebrates New York Chapman and Hall pp. 1-9.
7. Pfrender ME, Hawkins CP, Bagley M, Courtney GW, Creutzburg BR, et al. (2010) Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches. The Quarterly Review of Biology 85: 319-340.
8. Baird DJ, Sweeney BW, (2011) Applying DNA barcoding in benthology: the state of the science. Journal of the North American Benthological Society 30: 122-124 doi:10.1899/10-154.1.
9. Baird DJ, Pascoe TJ, Zhou X, Hajibabaei M, (2011) Building freshwater macroinvertebrate DNA-barcode libraries from reference collection material: formalin preservation vs specimen age. Journal of the North American Benthological Society 30: 125-130 doi:10.1899/10-013.1.
10. Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ, (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6: e17497 doi:10.1371/journal.pone.0017497.
11. Pilgrim EM, Jackson S, Swenson S, Turcsanyi I, Friedman E, et al. (2011) Incorporation of DNA barcoding into a large-scale biomonitoring program: opportunities and pitfalls. Journal of the North American Benthological Society 30: 217-231 doi:10.1899/10-012.1.
12. Sweeney BW, Battle JM, Jackson JK, Dapkey T, (2011) Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? Journal of the North American Benthological Society 30: 195-216 doi:10.1899/10-016.1.
13. Cao Y, Hawkins CP, (2011) The comparability of bioassessments: a review of conceptual and methodological issues 1. Journal of the North American Benthological Society 30: 680-701 doi:10.1899/10-067.1.
14. Lenat DR, Resh VH, (2001) Taxonomy and stream ecology: the benefits of genus- and species-level identifications. Journal of the North American Benthological Society 20: 287 doi:10.2307/1468323.
15. Feio MJ, Reynoldson TB, Graça MAS, (2006) The influence of taxonomic level on the performance of a predictive model for water quality assessment. Water Research 376: 367-376 doi:10.1139/F05-221.
16. Poff NL, Olden JD, Vieira NKM, Finn DS, Simmons MP, et al. (2006) Functional trait niches of North American lotic insects: traits-based ecological applications in light of phylogenetic relationships. Journal of the North American Benthological Society 25: 730-755.
17. Lenat DR, (1993) A biotic index for the southeastern United States: derivation and list of tolerance values, with criteria for assigning water-quality ratings. Journal of the North American Benthological Society 12: 279-290.
18. Lenat DR, Penrose DL, (1996) History of the EPT taxa richness metric. Bulletin of the North American Benthological Society 13: 305-306.
19. Webb JM, Sun L, McCafferty WP, Ferris VR, (2007) A new species and new synonym in Heptagenia Walsh (Ephemeroptera: Heptageniidae: Heptageniinae) based on molecular and morphological evidence. Journal of Insect Science 7: 63 doi:10.1673/031.007.6301.
20. Zhou X, Adamowicz SJ, Jacobus LM, DeWalt RE, Hebert PDN, (2009) Towards a comprehensive barcode library for arctic life- Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada. Frontiers in Zoology 6: 30 doi:10.1186/1742-9994-6-30.
21. Zhou X, Jacobus LM, DeWalt RE, Adamowicz SJ, Hebert PDN, (2010) Ephemeroptera, Plecoptera, and Trichoptera fauna of Churchill (Manitoba, Canada): insights into biodiversity patterns from DNA barcoding. Journal of the North American Benthological Society 29: 814-837 doi:10.1899/09-121.1.
22. Alexander LC, Delion M, Hawthorne DJ, Lamp WO, Funk DH, (2009) Mitochondrial lineages and DNA barcoding of closely related species in the mayfly genus Ephemerella (Ephemeroptera: Ephemerellidae). Journal of the North American Benthological Society 28: 584-595 doi:10.1899/08-150.1.
23. Hebert PDN, DeWaard JR, Landry J-F, (2010) DNA barcodes for 1/1000 of the animal kingdom. Biology letters 6: 359-362 doi:10.1098/rsbl.2009.0848.
24. Hausmann A, Haszprunar G, Segerer AH, Speidel W, Behounek G, et al. (2011) Now DNA-barcoded: the butterflies and larger moths of Germany. Spixiana 34: 47-58.
25. Jacobus LM, McCafferty WP, (2004) Revisionary contributions to the genus Drunella (Ephemeroptera: Ephemerellidae). Journal of the New York Entomological Society 112: 127-147. doi:10.1664/0028-7199(2004)112[0127:RCTTGD]2.0.CO; 2.
26. Funk DH, Sweeney BW, Jackson JK, (2008) A taxonomic reassessment of the Drunella lata (Morgan) species complex (Ephemeroptera:Ephemerellidae) in northeastern North America. Journal of the North American Benthological Society 27: 647-663 doi:10.1899/08-026.1.
27. Hajibabaei M, Smith MA, Janzen DH, Rodriguez JJ, Whitfield JB, et al. (2006) A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes 6: 959-964 doi:10.1111/j.1471-8286.2006.01470.x.
28. Shokralla S, Zhou X, Janzen DH, Hallwachs W, Landry J-F, et al. (2011) Pyrosequencing for mini-barcoding of fresh and old museum specimens. PLoS ONE 6: e21252 doi:10.1371/journal.pone.0021252.
29. James SW, Porco D, Decaëns T, Richard B, Rougerie R, et al. (2010) DNA barcoding reveals cryptic diversity in Lumbricus terrestris L., 1758 (Clitellata): resurrection of L. herculeus (Savigny, 1826). PloS one 5: e15629 doi:10.1371/journal.pone.0015629.
30. Favret C, Miller GL, (2011) The neotype of the cotton aphid (Hemiptera: Aphididae: Aphis gossypii Glover 1877). Proceedings of the Entomological Society of Washington 113: 119-126.
31. Hausmann A, Hebert PDN, Mitchell A, Rougerie R, Sommerer M, et al. (2009) Revision of the Australian Oenochroma vinaria Guenée, 1858 species-complex (Lepidoptera: Geometridae, Oenochrominae): DNA barcoding reveals cryptic diversity and assesses status of type specimen without dissection. Zootaxa 2239: 1-21.
32. Yeates DK, Seago A, Nelson L, Cameron SL, Joseph L, et al. (2011) Integrative taxonomy, or iterative taxonomy? Systematic Entomology 36: 209-217 doi:10.1111/j.1365-3113.2010.00558.x.
33. DeWalt RE, (2011) DNA barcoding: a taxonomic point of view. Journal of the North American Benthological Society 30: 174-181 doi:10.1899/10-021.1.
34. Ogden TH, Whiting MF, (2005) Phylogeny of Ephemeroptera (mayflies) based on molecular evidence. Molecular Phylogenetics and Evolution 37: 625-643 doi:10.1016/j.ympev.2005.08.008.
35. Ogden TH, Gattolliat JL, Sartori M, Staniczek AH, Soldán T, et al. (2009) Towards a new paradigm in mayfly phylogeny (Ephemeroptera): combined analysis of morphological and molecular data. Systematic Entomology 34: 616-634 doi:10.1111/j.1365-3113.2009.00488.x.
36. Ivanova NV, DeWaard JR, Hebert PDN, (2006) An inexpensive, automation-friendly protocol for recovering high-quality DNA. Molecular Ecology Notes 6: 998-1002 doi:10.1111/j.1471-8286.2006.01428.x.
37. DeWaard JR, Ivanova NV, Hajibabaei M, Hebert PDN, (2008) Assembling DNA barcodes: analytical protocols. In: Martin CC, editors. Methods in Molecular Biology Volume 410 Environmental Genomics. Totowa, New Jersey: Humana Press pp. 275-283.
38. 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. Molecular Biology and Evolution 28: 2731-2739 doi:10.1093/molbev/msr121.