[Taxacom] DNA contamination

[bti at dsmz.de]

Lynn,
You might find this article of some help:
http://www.biology-direct.com/content/4/1/35/abstract

Brian


Quoting Lynn Raw <lynn at afriherp.org>:

> 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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