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Biological Identifications of Mayflies (Ephemeroptera)

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Biological Identifications of Mayflies (Ephemeroptera) J. N. Am. Benthol. Soc., 2005, 24(3):508±524 q 2005 by The North American Benthological Society Biological identi®cations of may¯ies (Ephemeroptera) using DNA barcodes SHELLEY L. BALL1 AND PAUL D. N. HEBERT2 Department of Zoology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 STEVEN K. BURIAN3 Department of Biology, Southern Connecticut State University, New Haven, Connecticut 06515 USA JEFFREY M. WEBB4 Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089 USA Abstract. We tested the ef®cacy of DNA barcodes in identifying may¯y species primarily from the northeastern United States and central Canada. We sequenced a 630-base-pair segment of the mitochondrial gene, cytochrome c oxidase 1 (COI), from 1 individual of each of 80 species to create a reference sequence pro®le. We used these reference sequences to identify 70 additional specimens representing 32 of the species that were in the pro®le. DNA barcodes correctly identi®ed 69 of the 70 test specimens. The sole exception was an individual identi®ed morphologically as Maccaffertium modestum that showed deep genetic divergence from other M. modestum specimens. Mean sequence divergence within species was 1%, whereas mean divergence among congeneric species was an order of magnitude greater (18%). We conclude that DNA barcoding can provide a powerful tool for may¯y species identi®cation. Key words: aquatic invertebrates, may¯y, species identi®cation, mtDNA, COI. Accurate identi®cation of species is funda- notypic variation in taxonomically important mental to both basic and applied aquatic re- traits can pose signi®cant challenges during search. Studies of community structure, food- species identi®cation. Such variation can lead to web dynamics, biodiversity, and biomonitoring misidenti®cation of specimens (Kondratieff and depend critically on the accuracy of species dis- Voshell 1984, Wolf and Mort 1986, Burian 2001), crimination and identi®cation. Despite an in- regardless of whether the variation is environ- creasing demand for taxonomic expertise in the mentally or genetically based. In other cases, aquatic sciences, the number of taxonomists con- different species exhibit extremely limited mor- tinues to dwindle (New 1996, Stribling et al. phological variation despite reproductive isola- 2003). Furthermore, morphology-based identi®- tion and large genetic divergence between them; cation of many aquatic invertebrate species is such cryptic species can be detected only particularly challenging. Taxonomic keys often through genetic analysis (Funk et al. 1988, Hogg exist only for a certain life stage or gender. Thus, et al. 1998, Witt and Hebert 2000). assigning species names to specimens is often A DNA-based species identi®cation system impossible in studies where immatures make (DNA barcoding, Hebert et al. 2003a) offers a up a large proportion of the sample (as in bio- promising supplemental technique for the iden- monitoring). Years of experience also may be re- ti®cation of taxa for which morphology-based quired before investigators can effectively use identi®cations are problematic, for associating the taxonomic keys that are available. Last, phe- different life stages, and for enabling those in- vestigators lacking the morphology-based skills to identify taxa reliably. DNA barcodes consist 1 Present address: Molecular Diagnostics Laborato- of short DNA sequences that function as unique ry, National Centre for Advanced Bio-protection Tech- nologies, PO Box 84, Lincoln University, Canterbury, species identi®ers. Species in a variety of animal New Zealand. E-mail: [email protected] groups have been discriminated reliably using ; 2 E-mail addresses: [email protected] an 650-base-pair fragment of the mitochon- 3 [email protected] drial gene, cytochrome c oxidase 1 (COI) (He- 4 [email protected] bert et al. 2003a, 2004a, b, Hogg and Hebert 508 2005] DNA BARCODES FOR MAYFLY IDENTIFICATION 509 2004). For example, Hebert et al. (2003b) showed sequencing, but also ensured the preservation of that 13,000 closely related species pairs from a a voucher specimen (housed at the University of range of animal phyla regularly showed deep Guelph) for further morphological examination. genetic divergences, enabling reliable species We extracted total DNA in 50 mL of Proteinase identi®cations. Thus, DNA barcoding holds the K for 24 to 36 h at 558C. We used the primer potential to serve as a species identi®cation sys- pair LC01490 (5'-GGTCAACAAATCATAAAGA tem for all animal life, an approach that will be TATTGG-3') and HC02198 (5'-TAAACTTCAG particularly valuable when morphology-based GGTGACCAAAAAATCA-3') to amplify a 658- identi®cations are dif®cult or access to taxonom- base-pair fragment of COI (Folmer et al. 1994). ic expertise is limited. DNA was ampli®ed using the following PCR We tested the ef®cacy of DNA barcodes for reaction: 5 mLof103 PCR buffer pH 8.3 (10 mM the identi®cation of may¯ies collected primarily Tris-HCl pH 8.3, 1.5 mM MgCl2,50mMKCl, from the northeastern United States and central 0.01% NP-40), 38.8 mL of distilled water, 200 Canada. We targeted may¯ies because of their mM of each dNTP, 1 unit of Taq polymerase, 0.3 importance in aquatic research, particularly in mMofeachprimer,and1to3mL of DNA tem- biomonitoring studies where samples regularly plate. The polymerase chain reaction (PCR) ther- consist of immatures. Moreover, the identi®ca- mal regime consisted of 1 cycle of 948C for 1 tion of many may¯y species through morphol- min,5cyclesof948C for 5 min, 458C for 1.5 min, ogy remains problematic (Kondratieff and Vosh- and 728C for 1.5 min. We followed this cycle ell 1984, McCafferty and Pereira 1984, Waltz et with 35 cycles of 948C for 1 min, 508C for 1 min, al. 1996, 1998, Baumgardner and McCafferty and 728C for 1 min, and a ®nal cycle of 728C for 2000, Jacobus and McCafferty 2000, 2002, Burian 5 min. We visualized all PCR products on 1% 2001) despite the importance of may¯ies in agarose gels using ethidium bromide. We gel- aquatic research. The speci®c aim of our study puri®ed PCR products using the Qiaex II kit was to test the ability of COI to correctly iden- (Qiagen, Mississauga, Ontario) and sequenced tify may¯y species by comparing their sequence them on an ABI 377 automated sequencer (Ap- similarity to a pool of reference sequences from plied Biosystems, Foster City, California) using individuals of known taxonomic identity. the Big Dye v.3 dye termination kit. We aligned sequences using Sequence Editor 1.9 (Applied Biosystems). Alignment was Methods straightforward because of the absence of in- Sequences dels. We pruned the sequences to 630 base pairs before further analysis. We have provided a list We sequenced COI from 150 may¯y speci- of may¯y taxa, their locations of collection, and mens, including representatives from 80 species GenBank accession numbers in Appendix 1. (;15% of the North American species), 30 gen- ; era ( 30% of the North American genera) and COI pro®les 12 of the 21 families known from North Amer- ica. We obtained most of our samples from the We tested the ability of COI to identify species northeastern United States and central Canada, correctly by creating a COI pro®le or reference but we sequenced additional specimens from data set based upon a single sequence from each geographic locations across North America and of the 80 may¯y species. We created a pro®le a single leptohyphid specimen that was collect- neighbour-joining (NJ) tree of Kimura-2-param- ed in Costa Rica, Central America. We focused eter (K2P) distances, using MEGA2.1 (available on species that are relatively common and for from: www.megasoftware.net). The K2P model which taxonomic keys are available. provides the best metric when genetic distances All specimens used in our study had been are low (Nei and Kumar 2000). We used a sim- preserved in 75 to 95% ethanol for periods rang- ple NJ algorithm because the goal of barcoding ing from 1 to 20 y. When whole nymphs or is to provide species identi®cation based on se- adults were obtained, we removed a single leg quence similarity rather than to reconstruct or a very small tissue piece from the thorax or deeper phylogenetic relationships accurately. leg and preserved the remainder of the speci- Furthermore, NJ provides the necessary speed men. This approach provided ample DNA for of analysis for the large data sets that are typical 510 S. L. BALL ET AL. [Volume 24 of DNA barcoding studies. We used a jumping When we had sequences for several individuals bristletail (Machiloides sp.) sequence obtained of a species, we used one randomly chosen in- from GenBank as the outgroup. dividual to represent that species. We calculated K2P divergences for all congeneric species pairs Test taxa and plotted them as a frequency histogram. We calculated mean intra- and interspeci®c K2P di- We tested the ability of the COI pro®le to gen- vergences as the overall mean of all pairwise erate correct species identi®cations for 70 test comparisons within each species and the mean specimens representing 32 of the 80 species in- of all pairwise comparisons within each genus, cluded in the pro®le by determining the se- respectively. quence congruence between the 80 pro®le spec- imens and the 70 test specimens. These test Results specimens were mock unknowns because their species identi®cations were known from prior Pro®le sequences morphological examination by 2 of us (SKB and JMW) who are taxonomists of North American Eleven of the 12 families in our NJ pro®le . may¯ies. We used these mock unknowns to as- were represented by 1 species. Nine of these sess the congruence between morphological and families formed cohesive groups in the NJ pro- COI-based species identi®cation.
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