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DNA Barcodes

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Extending DNA barcoding coverage for Lake Whitefish (Coregonus clupeaformis) across the three major basins of Lake Huron

Lauren M. Overdyk
  • Corresponding author
  • Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1
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/ Heather E. Braid
  • Institute for Applied Ecology New Zealand, Auckland University of Technology, Private Bag 92006, Auckland, New Zealand 1010
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/ Stephen S. Crawford
  • Chippewas of Nawash, Unceded First Nation, 135 Lakeshore Blvd, Nevaashiinigmiing, Ontario, Canada N1G 2W1
  • Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1
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/ Robert H. Hanner
  • Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1
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Published Online: 2015-11-26 | DOI: https://doi.org/10.1515/dna-2015-0007


DNA barcoding is a useful tool for both species identification and discovery, but the latter requires denser sampling than typically used in barcode studies. Lake Whitefish (Coregonus clupeaformis) is a valuable species, fished traditionally, commercially, and recreationally in Lake Huron. Based on the natural geographic and bathymetric separation of the three major basins in Lake Huron, the potential separation of Lake Whitefish within these basins, and the variation among life history (early and late spawning), we predicted that Lake Huron might harbour cryptic lineages of Lake Whitefish at the basin level. To test this prediction, DNA barcodes of the mitochondrial 5’ cytochrome c oxidase subunit I (COI) gene sequences were recovered from spawning phase Lake Whitefish (n = 5 per site), which were collected from sites (n = 28) around Lake Huron during Fall 2012. These sequences, combined with other publically available DNA barcodes from the Barcode of Life Data System (BOLD), revealed twelve unique haplotypes across North America, with seven unique to Lake Huron. The dominant haplotype was found throughout Lake Huron and east to the St. Lawrence River. No deep divergences were revealed. This comprehensive lake-wide sampling effort offers a new perspective on C. clupeaformis, and can provide insight for environmental assessments and fisheries management.

Keywords: haplotype; COI; Coregoninae


  • [1] Serrao N.R., Steinke D., Hanner R.H., Calibrating snakehead diversity with DNA barcodes: Expanding taxonomic coverage to enable identification of potential and established invasive species, PLoS One, 2014, 9, 6, e99546.Web of ScienceGoogle Scholar

  • [2] Hebert P.D.N., Cywinska A., Ball S.L., DeWaard J.R., Biological identifications through DNA barcodes, Proc. R. Soc. London, 2003, 270, 313-321.Google Scholar

  • [3] Ward R.D., Hanner R., Hebert P.D.N., The campaign to DNA barcode all fishes, FISH-BOL, J. Fish Biol., 2009, 74, 329-356.Web of ScienceGoogle Scholar

  • [4] Hubert N., Hanner R., Holm E., Mandrak N.E., Taylor E., Burridge M., et al., Identifying Canadian Freshwater Fishes through DNA Barcodes. PLoS One, 2008, 3, 6, e2490.Google Scholar

  • [5] Hubert N., Delrieu-Trottin E., Irisson J-O., Meyer C., Planes S., Identifiying coral reef fish larvae through DNA barcoding: a test case with the families Acanthuridae and Holocentridae, Mol. Phylogenet. Evol., 2010, 55, 1195-1203Web of ScienceCrossrefGoogle Scholar

  • [6] Hajibabei M., Singer G.A.C., Hebert P.D.N., Hickey D.A., DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics, TRENDS Gen., 2007, 23, 4, 167-172.Web of ScienceGoogle Scholar

  • [7] April J., Mayden R.L., Hanner R.H., Bernatchez L.,Genetic calibration of species diversity among North America’s freshwater fishes, PNAs, 2011, 108, 26, 10602-10607Google Scholar

  • [8] Young, M. K., K. S. McKelvey, K. L. Pilgrim and M. K. Schwartz. DNA barcoding at riverscape scales: assessing biodiversity among fishes of the genus Cottus (Teleostei) in northern Rocky Mountain streams, Mol. Ecol. Resour., 2013, 1-13.Web of ScienceGoogle Scholar

  • [9] Meier R., Zhang G., Ali F., The use of mean instead of smallest interspecific distance exaggerates the size of the ‘barcoding gap’ and leads to misidentification, Systematic Biol., 2008, 57, 809-813.Web of ScienceGoogle Scholar

  • [10] Knebelsberger T., Dunz A.R., Neumann D., Geiger M.F., Molecular diversity of Germany’s freshwater fishes and lampreys assessed by DNA barcoding, Mol. Ecol. Res., 2014, 1-11.Google Scholar

  • [11] Becker S., Hanner R., Steinke D., Five years of FISH-BOL: Brief Status Report. Mit. DNA, 2011, 22, S1, 3-9.Google Scholar

  • [12] April J., Hanner R.H., Dion-Cote A-M., Bernatchez L., Glacial cycles as an allopatric speciation pump in north-eastern American freshwater fishes. Mol. Ecol., 2013, 22, 409-422.Web of ScienceCrossrefGoogle Scholar

  • [13] Hanner R., Schindel D., Ward B., Hebert P., Fish barcode of life (FISH-BOL), 2005, 1-19.Google Scholar

  • [14] Beeton A.M., Saylor J.H., Limnology of Lake Huron, In Munawar M., Edsall T., Leach J., (Eds), The Lake Huron Ecosystem: Ecology, Fisheries and Management (pp.1-37), SPB Academic Publishing, Amsterdam, The Netherlands, 1995.Google Scholar

  • [15] Sloss P.W., Saylor J.H., Measurements of current flow during summer in Lake Huron. U.S. Department of Commerce, National Oceanic and Atmospheric Administration Environmental Research Laboratories ERL 353-GLERL 5, 1975, 1-45.Google Scholar

  • [16] Bohm E.U., Lake Huron Nearshore Currents in the Vicinity of Bruce NPD 1983-1984, Geotechnical and Hydraulic Engineering Department Report No 85301, 1985, 1-54.Google Scholar

  • [17] Loftus D.H., Interviews with Lake Huron commercial fishermen, Ontario Ministry of Natural Resources, Lake Huron Fisheries Assessment Unit Report 1-80. Owen Sound, Ontario, 1980.Google Scholar

  • [18] Stott W., Ebener M.P., Mohr L., Schaeffer J., Roseman E.F., Harford W.J., et al., Genetic structure of Lake Whitefish, Coregonus clupeaformis, populations in the northern main basin of Lake Huron, In Tallman R.F., Howland K.L., Rennie M.D., Mills K. (Eds) Biology and management of coregonid fishes - 2008; 10th International Symposium on the Biology and Management of Coregonid Fishes, Winnipeg, Canada. Advances in Limnology, 2012, 63, 241-260.Google Scholar

  • [19] Mat Jaafar T.N.A., Taylor M.I., Mohd Nor S.A., de Bruyn M., Carvalho G.R., DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes), PLoS ONE, 2012, 7, 11, e49623.Google Scholar

  • [20] Hubert N., Meyer C.P., Bruggemann H.J., Guerin F., Komeno R.J.L., Espiau B., et al., Cryptic diversity in Indo-Pacific Coral-Reef fishes revealed by DNA-Barcoding provides new support to the centre-of-overlap hypothesis, PLoS ONE, 2012, 7, 3, e28987. Google Scholar

  • [21] Winterbottom R., Hanner R.H., Burridge M., Zur M., A cornucopia of cryptic species - a DNA barcode analysis of the gobiid fish genus Trimma (Percomorpha, Gobiiformes), Zookeys, 2014, 381, 79-111.Web of ScienceGoogle Scholar

  • [22] Ratnasingham S., Hebert P.D.N., BOLD: The Barcode of Life Data System (http://www.barcodinglife.org), Mol. Ecol. Notes, 2007, 7, 3, 355-364.Web of ScienceCrossrefGoogle Scholar

  • [23] Ivanova N.V., Zemlak T.S., Hanner R.H., Hebert P.D.N., Universal primer cocktails for fish DNA barcoding, Mol. Ecol. Notes, 2007, 7, 544-548.Web of ScienceCrossrefGoogle Scholar

  • [24] Tamura K., Dudley J., Nei M., Kumar S., MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0, Mol. Biol. Evolution, 2007, 24, 1596-1599.Google Scholar

  • [25] Bandelt, H-J., Forster P., Rohl A., Median-joining networks for inferring intraspecific phylogenies, Mol. Biol. Evol., 1999, 16, 1, 37-48.CrossrefGoogle Scholar

  • [26] Abell R., Thieme M.L., Revenga C., Bryer M., Kottelat M., Bogutskaya N., et al., Freshwater ecoregions of the world: a new map of biogeographic units for freshwater biodiversity conservation, BioScience, 2008, 58, 5, 403-414.Google Scholar

  • [27] Ratnasingham S., Hebert P.D.N., A DNA-Based registry for all animal species: The Barcode Index Number (BIN) System, PLoS ONE, 2013, 8, 7, e66213.Google Scholar

  • [28] Hart M.W., Sunday J., Things fall apart: biological species form unconnected parsimony networks, Biol. Letters, 2007, 3, 5, 509-512.Web of ScienceCrossrefGoogle Scholar

  • [29] Spangler G.R., Factors of mortality in an exploited population of whitefish, Coregonus clupeaformis, in northern Lake Huron. In Lindsey C.C., Woods C.S. (Eds), Biology of Coregonid Fishes (pp. 515-529), University of Manitoba Press, Winnipeg, Manitoba, 1970.Google Scholar

  • [30] Carmichael K., Deary C., Filling a data gap- lake whitefish (Coregonus clupeaformis) index netting in the North Channel of Lake Huron, Aquatic Ecosys. Health Manag., 2009, 12, 23-28.Web of ScienceGoogle Scholar

  • [31] Casselman J.M., Collins J.J., Crossman E.J., Ihssen P.E., Spangler G.R. Lake whitefish (Coregonus clupeaformis) stocks of the Ontario waters of Lake Huron, Can. J. Fish Aquatic Sci., 1981, 38, 1772-1789.Google Scholar

  • [32] Crawford S.S., Muir A., McCann K., Ecological basis for recommendation of 2001 Saugeen Ojibway commercial harvest TACs for lake whitefish (Coregonus clupeaformis) in Lake Huron, report prepared for the Chippewas of Nawash First Nation, Wiarton, Ontario,2001.Google Scholar

  • [33] Bustin, S.A., Real-Time PCR. Encyclopedia of Diagnostic Genomics and Proteomics, University of London, London, U.K. 2005, 1117-1125. Google Scholar

About the article

Received: 2014-11-14

Accepted: 2015-06-08

Published Online: 2015-11-26

Published in Print: 2015-01-01

Citation Information: DNA Barcodes, ISSN (Online) 2299-1077, DOI: https://doi.org/10.1515/dna-2015-0007.

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© 2015. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

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