[Taxacom] DNA contamination

[David Campbell]

Another example: Barcoding Bamboozled by Bacteria: Convergence to
Metazoan Mitochondrial Primer Targets by Marine Microbes
Syst Biol (2009) 58 (4): 445-451.

The bacterial "bivalve" sequences in question are conspicuously
divergent from actual bivalves, if you look at an alignment.  If you
don't actually look at the data, however...

In putting together data on the Bivalvia, I discovered that one paper
with environmental DNA sequenced from soil samples had the sequences
apparently randomly identified in GenBank as various metazoans, many
neither soil-dwelling nor similar in sequence.  It's now corrected,
but I don't know exactly what went wrong.  A data set with chironomid
sequences identified as snails, however, did not get corrected as far
as I know.

Parasites are common contaminants.  I also have amplified DNA for a
psocid booklouse from a freshwater mollusk sample.  Booklice are not
uncommon in the lab building.

Pseudogenes and paralogs provide additional complications.



-- 
Dr. David Campbell
The Paleontological Research Institution
1259 Trumansburg Road
Ithaca NY 14850