“COI-like” Sequences are Becoming Problematic in Molecular Systematic and DNA Barcoding Studies

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DNA barcoding reveals new insights into the diversity of Antarctic species of Orchomene sensu lato (Crustacea: Amphipoda: Lysianassoidea) (2011, background): “Additionally, the phenomena of incomplete lineage sorting, genetic introgression, pseudogenes (e.g., Buhay, 2009) or bacterial infections (Wolbachia, e.g., Whitworth et al., 2007) can make species identification inadequate with this tool.”
Phylogenies without Synapomorphies—A Crisis in Fish Systematics: Time to Show Some Character (2010, background): “Some molecular workers consider that “data errors are not just negligible issues anymore—they are cause for serious concern” and that “it may be necessary to issue erratums or retractions for published studies that are based largely on erroneous data” (Buhay 2009: 108).”
Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? (2011, background): “2B) may reflect the presence of §2 emerging or very closely related congeneric species presently co-occurring in the stream or the presence of numts (nuclear copies of mitochondrial-derived genes that act as junk DNA; Buhay 2009, Moulton et al. 2010, Pfrender et al. 2010).”