In previous years, we sequenced some samples of bees/wasps/butterflies/moths to study DNA taxonomy and species diversity. Besides barcodes, we have been also sequencing 28S D2. For most samples, we got only one copy of 28S D2 with very clean background shown in the ABI graphs. However, for some bees or butterflies species, we got several copies with variety of length or bps by cloning and sequencing. Why these species keep different copies of 28S in a same individual while most others conserve for the D2 region? If there are any papers relevant on this, please kindly let me know for references.
http://www.frontiersinzoology.com/content/4/1/6
The paper linked above mentions this problem
(Sonnenberg, R., Nolte, A. W., & Tautz, D. (2007). An evaluation of LSU rDNA D1-D2 sequences for their use in species identification. Frontiers in Zoology, 4(1), 6)
See page 2 under "Amplification efficiency"
And page 7, column 1
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