[Taxacom] DNA contamination

[Lynn Raw]

Thanks for everyone's comments and the links to further sources. I have another question. I have come across a case where morphologically very distinctive species cannot be separated using the standard molecular methods that separate other members of the group. Is this because the sequences examined have not diverged in these species but others have or is there some other explanation?

 In another case three geographically isolated populations, say A, B & C, group as (A B) C in terms of morphology but A (B C) in terms of molecular analysis. Geographically B lies between A and C.
Is this a case where insufficient different sequences have been examined and where additional sequences may show a different result?

I look forward to learning your views.

Thanks.

Lynn Raw

On 1 Apr 2011, at 18:48, David Campbell wrote:

> 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
> 
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