A DNA Barcode Library for North American Ephemeroptera: Progress and Prospects

PLOS ONE, Dec 2019

DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for water quality assessment programs. A prerequisite for identification using barcodes is a reliable reference library. We gathered 4165 sequences from the barcode region of the mitochondrial cytochrome c oxidase subunit I gene representing 264 nominal and 90 provisional species of mayflies (Insecta: Ephemeroptera) from Canada, Mexico, and the United States. No species shared barcode sequences and all can be identified with barcodes with the possible exception of some Caenis. Minimum interspecific distances ranged from 0.3–24.7% (mean: 12.5%), while the average intraspecific divergence was 1.97%. The latter value was inflated by the presence of very high divergences in some taxa. In fact, nearly 20% of the species included two or three haplotype clusters showing greater than 5.0% sequence divergence and some values are as high as 26.7%. Many of the species with high divergences are polyphyletic and likely represent species complexes. Indeed, many of these polyphyletic species have numerous synonyms and individuals in some barcode clusters show morphological attributes characteristic of the synonymized species. In light of our findings, it is imperative that type or topotype specimens be sequenced to correctly associate barcode clusters with morphological species concepts and to determine the status of currently synonymized species.

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A DNA Barcode Library for North American Ephemeroptera: Progress and Prospects

et al. (2012) A DNA Barcode Library for North American Ephemeroptera: Progress and Prospects. PLoS ONE 7(5): e38063. doi:10.1371/journal.pone.0038063 A DNA Barcode Library for North American Ephemeroptera: Progress and Prospects Jeffrey M. Webb 0 Luke M. Jacobus 0 David H. Funk 0 Xin Zhou 0 Boris Kondratieff 0 Christy J. Geraci 0 R. 0 Edward DeWalt 0 Donald J. Baird 0 Barton Richard 0 Iain Phillips 0 Paul D. N. Hebert 0 Brock Fenton, University of Western Ontario, Canada 0 1 Biodiversity Institute of Ontario, University of Guelph , Guelph, Ontario , Canada , 2 Division of Science, Indiana University Purdue University Columbus, Columbus, Indiana, United States of America, 3 Stroud Water Research Center, Avondale, Pennsylvania, United States of America , 4 BGI, Shenzhen, Guangdong Province , China , 5 Department of Bioagricultural Sciences and Pest Management, Colorado State University , Fort Collins , Colorado, United States of America, 6 Department of Entomology , National Museum of Natural History , Smithsonian Institution , Washington, D. C. , United States of America, 7 Prairie Research Institute , Illinois Natural History Survey , University of Illinois, Champaign, Illinois, United States of America, 8 Environment Canada, Canadian Rivers Institute, Department of Biology, University of New Brunswick , Fredericton, New Brunswick , Canada , 9 Laboratory of Aquatic Entomology, Florida A&M University , Tallahassee , Florida, United States of America , 10 Saskatchewan Watershed Authority, Saskatoon, Saskatchewan , Canada DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for water quality assessment programs. A prerequisite for identification using barcodes is a reliable reference library. We gathered 4165 sequences from the barcode region of the mitochondrial cytochrome c oxidase subunit I gene representing 264 nominal and 90 provisional species of mayflies (Insecta: Ephemeroptera) from Canada, Mexico, and the United States. No species shared barcode sequences and all can be identified with barcodes with the possible exception of some Caenis. Minimum interspecific distances ranged from 0.3-24.7% (mean: 12.5%), while the average intraspecific divergence was 1.97%. The latter value was inflated by the presence of very high divergences in some taxa. In fact, nearly 20% of the species included two or three haplotype clusters showing greater than 5.0% sequence divergence and some values are as high as 26.7%. Many of the species with high divergences are polyphyletic and likely represent species complexes. Indeed, many of these polyphyletic species have numerous synonyms and individuals in some barcode clusters show morphological attributes characteristic of the synonymized species. In light of our findings, it is imperative that type or topotype specimens be sequenced to correctly associate barcode clusters with morphological species concepts and to determine the status of currently synonymized species. - Funding: This project was funded by the Government of Canada through Genome Canada and the Ontario Genomics Institute (2008-OGI-ICI-03), and Environment Canadas Competitiveness and Environmental Sustainability Indicators (CESI) Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. DNA barcoding [1] of animals, the analysis of a standardized segment of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene, has rapidly become an important tool for the identification, delimitation, and discovery of species [13]. DNA barcoding has the further advantage that identification success extends across all life stages, allowing the association of immatures with adults [4,5]. Its capacity to identify all life stages is particularly important for aquatic ecology and biological monitoring (biomonitoring) of water quality because the aquatic larvae are usually the life stage studied [6]. Unfortunately, this is the life stage that is the most poorly known taxonomically because most species concepts in aquatic insects are based on the morphology of adult males. The identification of larvae is further hindered by the fact that many are rather delicate, especially mayflies (Ephemeroptera), and the structures critical for confident identifications such as gills, legs, and caudal filaments are commonly damaged or missing. The application of DNA barcoding to freshwater biomonitoring has recently generated much interest for several reasons [712]. In addition to allowing the identification of difficult specimens, barcoding provides a level of data standardization that has been previously lacking in environmental assessments [13], aiding broader comparisons of results gathered through monitoring programs. Furthermore, barcoding reliably produces species-level (or even (...truncated)


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Jeffrey M. Webb, Luke M. Jacobus, David H. Funk, Xin Zhou, Boris Kondratieff, Christy J. Geraci, R. Edward DeWalt, Donald J. Baird, Barton Richard, Iain Phillips, Paul D. N. Hebert. A DNA Barcode Library for North American Ephemeroptera: Progress and Prospects, PLOS ONE, 2012, Volume 7, Issue 5, DOI: 10.1371/journal.pone.0038063