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Some recent publications about DNA barcoding


Fish survey finds many undescribed

More than a quarter of all freshwater fish species in North America could be undescribed in current taxonomy, according to a new study by a team of Canadian and US scientists.

In their paper Genetic Calibration of Species Diversity among North America's Freshwater Fishes, the research team reports on its project to generate a standard reference library of DNA barcodes derived from expert-identified museum specimens for 752 North American freshwater fish species.

From the 752 species analyzed, their survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28 percent increase in species diversity.

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The cryptic crustaceans of Churchill

Churchill, Manitoba, with its wide variety of habitats representing both boreal forest and arctic tundra, has been used as a model site for biodiversity studies for nearly seven decades. Although the Daphnia pulex species complex has been extensively studied, no one has used molecular markers to complete a wide-scale survey on the crustacean species that inhabit Churchill's aquatic ecosystems.

In the paper, Species Diversity and Phylogeographical Affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada, researchers describe how they used DNA barcoding to study the diversity of the Branchiopoda (Crustacea) in a wide variety of freshwater habitats and to determine the likely origins of the Churchill fauna following the last glaciation.

They sequenced 327 specimens and found 42 provisional and valid branchiopod species, including several cryptic lineages, in comparison with the 25 previously recorded from previous ecological works.

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Next-gen analysis of the diet of bats

The diversity of prey consumed by insectivorous bats makes it difficult to identify what they eat using morphological or conventional PCR-based analyses of their faeces.

In Molecular Diet Analysis of Two African Free-Tailed Bats (Molossidae) Using High Throughput Sequencing ,researchers describe how they used a powerful alternate tool, the Roche FLX sequencing platform, to deep-sequence uniquely tagged insect-generic COI fragments, that were PCR amplified from faecal pellets of two free-tailed bat species Chaerephon pumilus and Mops condylurus (family: Molossidae).

Despite the shortage of African insect barcodes in GenBank and BOLD, similarity to existing collections allowed the preliminary identification of 25 prey families from six orders of insects within the diet of C. pumilus, and 24 families from seven orders within the diet of M. condylurus.

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Cryptic diversity among shrews

Mitochondrial diversity of the white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in Vietnam reports that an analysis of COI and cytb gene fragments from 185 specimens of white-toothed shrews of the genus Crocidura from 14 localities across Vietnam revealed six deeply divergent lineages, corresponding to morphological species.

In addition to demonstrating the genetic separation of previously described species, substantial cryptic genetic diversity was revealed with two species having two subgroups that corresponded to geographically remote localities, while another contained two distinct subgroups that exhibited co-varying patterns of morphological and ecological differentiation.

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Genomics support for conservation biology

Scientific advancements in molecular sequencing can clarify and support the identifications needed for biodiversity assessment as the first step in protecting the diversity of species on Earth and in reaching the goals of conservation biology.

The authors of Biodiversity assessment: State-of-the-art techniques in phylogenomics and species identification, propose a combination of whole (or nearly whole) chloroplast genomes, mitochondrial genes, and nuclear repeat regions for both species identifications and phylogenetic analyses, obtained from a simple total DNA extraction and one run on massively parallel DNA sequencing machines.

They conclude that in combination with morphological and other data, this abundance of genomic information will not only help conservation biologists to understand ecosystem biodiversity, but also the evolutionary histories of organisms, mending damaged landscapes, and investigating interactions of plants with pollinators and pests.

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(Listed alphabetically by author)

Axel, B. G. K., & Peter, H. (2011). Pseudo-endemism and cryptic diversity in Lepidoptera - case studies from the Alps and the Abruzzi. eco.mont 11-18.

Baird, D. J., Pascoe, T. J., 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(1), 125-130.

Baird, D. J., & Sweeney, B. W. (2011). Applying DNA barcoding in benthology: the state of the science. Journal of the North American Benthological Society, 30(1), 122-124.

Becker, S., Hanner, R., & Steinke, D. (2011). Five years of FISH-BOL: Brief status report. Mitochondrial DNA Online early.

Bi, Y. H., & Chen, X. W. (2011). Mitochondrial genome of the American shad Alosa sapidissima. Mitochondrial DNA, 2011 Feb;22(1-2):9-11.

Boyer, S. L., Howe, A. A., Juergens, N. W., & Hove, M. C. (2011). A DNA-barcoding approach to identifying juvenile freshwater mussels (Bivalvia:Unionidae) recovered from naturally infested fishes. Journal of the North American Benthological Society, 30(1), 182-194.

Carr C.M., Hardy S.M., Brown T.M., Macdonald T.A., Hebert P.D.N. (2011). Tri-Oceanic Perspective: DNA Barcoding Reveals Geographic Structure and Cryptic Diversity in Canadian Polychaetes. PLoS ONE 6(7): e22232. doi:10.1371/journal.pone.0022232.

Chen J, Li Q, Kong L, Yu H (2011). How DNA Barcodes Complement Taxonomy and Explore Species Diversity: The Case Study of a Poorly Understood Marine Fauna. PLoS ONE 6(6): e21326. doi:10.1371/journal.pone.0021326.

Clare, E. L., Barber, B. R., Sweeney, B. W., Hebert, P. D. N., & Fenton, M. B. (2011). Eating local: influences of habitat on the diet of little brown bats (Myotis lucifugus). Molecular Ecology, Vol. 20, Issue 8, pages 1772-1780, April 2011.

de Groot, G. A., During, H. J., Maas, J. W., Schneider, H., Vogel, J. C., & Erkens, R. H. J. (2011). Use of rbcL and trnL-F as a Two-Locus DNA Barcode for Identification of NW-European Ferns: An Ecological Perspective. PLoS ONE, 6(1), e16371.

deWaard, J. R., Hebert, P. D. N., & Humble, L. M. (2011). A Comprehensive DNA Barcode Library for the Looper Moths (Lepidoptera: Geometridae) of British Columbia, Canada. PLoS ONE, 6(3), e18290.

DeWalt, R. E. (2011). DNA barcoding: a taxonomic point of view. Journal of the North American Benthological Society, 30(1), 174-181.

Doukakis, P., Hanner, R., Shivji, M., Bartholomew, C., Chapman, D., Wong, E., et al. (2011). Applying genetic techniques to study remote shark fisheries in northeastern Madagascar. Mitochondrial DNA, (doi:10.3109/19401736.2010.526112).

Geraci, C. J., Al-Saffar, M. A., & Zhou, X. (2011). DNA barcoding facilitates description of unknown faunas: a case study on Trichoptera in the headwaters of the Tigris River, Iraq. Journal of the North American Benthological Society, 30(1), 163-173.

Handy, S. M., Deeds, J., Ivanova, N. V., Hebert, P. D. N., Hanner, R., Ormos, A., et al. (2011). A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance. Journal of AOAC International, 94(1), 1-10.

Hausmann, A., Haszprunar, G., & Hebert, P. D. N. (2011). DNA Barcoding the Geometrid Fauna of Bavaria (Lepidoptera): Successes, Surprises, and Questions. PLoS ONE, 6(2), e17134.

Hollingsworth, P. M., Graham, S. W., & Little, D. P. (2011). Choosing and Using a Plant DNA Barcode. PLoS ONE, 6(5), e19254.

Jeanson ML, Labat JN and Little DP (2011). DNA barcoding: a new tool for palm taxonomists? Annals of Botany, 2011, Jul.14.

Jinbo, U., Kato, T., & Ito, M. (2011). Current progress in DNA barcoding and future implications for entomology. Entomological Science, 14(2), 107-124.

Jones, M., Ghoorah, A., & Blaxter, M. (2011). jMOTU and Taxonerator: Turning DNA Barcode Sequences into Annotated Operational Taxonomic Units. PLoS ONE, 6(4), e19259.

Kelly, L. J., Hollingsworth, P. M., Coppins, B. J., Ellis, C. J., Harrold, P., Tosh, J., et al. (2011). DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. New Phytologist, Vol.191, Issue 1, pages 288-300, July 2011.

Lowenstein, J. H., Osmundson, T. W., Becker, S., Hanner, R., & Stiassny, M. L. J. (2011). Incorporating DNA barcodes into a multi-year inventory of the fishes of the hyperdiverse Lower Congo River, with a multi-gene performance assessment of the genus Labeo as a case study. Mitochondrial DNA, (doi:10.3109/19401736.2010.537748).

Nwani, C. D., Becker, S., Braid, H. E., Ude, E. F., Okogwu, O. I., & Hanner, R. (2011). DNA barcoding discriminates freshwater fishes from southeastern Nigeria and provides river system-level phylogeographic resolution within some species. Mitochondrial DNA, (doi:10.3109/19401736.2010.536537).

Park, D.-S., Foottit, R., Maw, E., & Hebert, P. D. N. (2011). Barcoding Bugs: DNA-Based Identification of the True Bugs (Insecta: Hemiptera: Heteroptera). PLoS ONE, 6(4), e18749.

Pereira, L. H. G., Maia, G. u. M. G., Hanner, R., Foresti, F., & Oliveira, C. (2011). DNA barcodes discriminate freshwater fishes from the Paraba do Sul River Basin, Sao Paulo, Brazil. Mitochondrial DNA, (doi:10.3109/19401736.2010.532213).

Rasmussen-Hellberg, R., Naaum, A., Handy, S. M., Hanner, R., Yancy, H., Deeds, J., et al. (2011). Interlaboratory Evaluation of a Real-time Multiplex Polymerase Chain reaction method for Identification of Salmon and Trout Species in Commercial Products. Journal of Agricultural and Food Chemistry, 59, 879-884.

Robideau, G. P., De Cock, A. W., Coffey, M. D., Voglmayr, H., Brouwer, H., Bala, K., et al. (2011). DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer. Mol Ecol Resour, DOI: 10.1111/j.1755-0998.2011.03041.x.

Rougerie, R., Smith, M. A., Fernandez-Triana, J., Lopez-Vaamonde, C., Ratnasingham, S., & Hebert, P. D. (2011). Molecular analysis of parasitoid linkages (MAPL): gut contents of adult parasitoid wasps reveal larval host. Mol Ecol, 20(1), 179-186.

Smith, P. J., Steinke, D., McMillan, P., Stewart, A., & Ward, R. D. (2011). DNA barcoding of morid cods reveals deep divergence in the antitropical Halargyreus johnsoni but little distinction between Antimora rostrata and Antimora microlepis. Mitochondrial DNA, (doi:10.3109/19401736.2010.532329).

Steinke, D., & Hanner, R. (2011). The FISH-BOL collaborators’ protocol. Mitochondrial DNA, (doi:10.3109/19401736.2010.536538).

Sweeney, B. W., Battle, J. M., Jackson, J. K., & 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(1), 195-216.

Triantafyllidis, A., Bobori, D., Koliamitra, C., Gbandi, E., Mpanti, M., Petriki, O., et al. (2011). DNA barcoding analysis of fish species diversity in four north Greek lakes. Mitochondrial DNA, (doi:10.3109/19401736.2010.542242).

Valencia-Díaz, X., & Espinosa-Pérez, H. (2011). Comparative analysis of three species populations of Profundulus (Teleostei: Cyprinodontiformes) using two genetic markers. Mitochondrial DNA, Vol. 22, No. 1-2 , Pages 19-21.

Xiao, W. L., Motley, T. J., Unachukwu, U. J., Lau, C. B., Jiang, B., Hong, F., et al. (2011). Chemical and Genetic Assessment of Variability in Commercial Radix Astragali (Astragalus spp.) by Ion Trap LC-MS and Nuclear Ribosomal DNA Barcoding Sequence Analyses. Journal of Agricultural Food Chemistry, 59(5), 1548-1556.

Zhou, X., Robinson, J. L., Geraci, C. J., Parker, C. R., Flint, O. S., Etnier, D. A., 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(1), 131-162.

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