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Barcode: 28S rDNA D3 Expansion Segment

    A genetic barcode is a taxonomic tool that uses DNA for species diagnostics (Floyd et al 2002, Hebert et al 2003).  The barcode is a short segment of DNA that can be used to identify an individual to species level based on its nucleotide sequence.  A barcode can distinguish species when the differences between DNA sequences between species (interspecific variation) are greater than the differences within a species (intraspecific variation).

    This region of DNA can be amplified from an individual of an unknown species and compared to sequences from known species to aid in identification.  The genetic barcode is established by identifying individuals using morphological keys, sequencing DNA from those individuals and submitting ID vouchers for public access to verify correct identifications.  Comparisons of different species sequences ensure there is sufficient high interspecific variation and low intraspecific variation.

    Within species, individuals taken from the same population and different populations are compared to make sure the intraspecific variation does not increase with a wider geographic sampling range.  We determined that the D3 expansion segment of the large ribosomal subunit (28S rDNA) has promise as a genetic barcode for freshwater calanoid and cyclopoid copepods collected throughout New England.  To learn more about our methods for evaluating this barcode, click here.

    The utility of this genetic barcode was analyzed for nine species.  The five species of calanoids included were: Aglaodiaptomus spatulocrenatus, Epischura lacustris, Epischura nordenskioldi, Leptodiaptomus minutus, and Skistodiaptomus pygmeus.  The four species of cyclopoids included were: Cyclops scutifer, Diacyclops thomasi, Mesocyclops edax, and Tropocyclops prasinus mexicanus.  The global use of this barcode needs to be evaluated by including more species and more individuals of the same species representing a larger geographic range and greater morphological extremes.

    We have included the consensus barcode sequence and the National Center for Biotechnology Information (NCBI) GenBank accession (retrieval) numbers for each sequence.  The consensus sequences are the “average” barcode sequence for each species.  It shows all the possible nucleotides at each position for each species.  The following nucleotide codes are provided here.  NCBI GenBank is an online database that provides sequence information to the general public.  All of the high quality nucleotide sequences we generated were submitted to this database for public viewing.  Each sequence can be accessed via its accession number provided on each species page of this key.  


(1) Floyd, R., E. Abebe, A. Papert, M. Blaxter. 2002. Molecular barcodes for soil nematode identification. Molecular Ecology 11: 839-850.

(2) Hebert, P. D. N., A. Cywinksa, S. L. Ball, J. R. Dewaard. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society London B. 270: 313-321.

(3) Litvaitis, M. K., G. Nunn, W. K. Thomas, T. D. Kocher. (1994). A molecular approach for the identification of meiofaunal turbellarians (Platyhelminthes: Turbellaria). Marine Biology. 120: 437-442.