[Taxacom] DNA contamination

[Richard Zander]

Lynn:

On the other hand, regarding alternative cladograms, there is a difference between results if data are lumped or not.

If lumped, if all the data are about one phenomenon, then okay.

If lumped, and one of the data sets is about a wrong gene history (because it is not the species history) and the other sequences are about the right species history, then if the wrong data are larger than the right data, the wrong answer will obtain. Assuming you know which is the right answer.

If not lumped (generally recommended by intelligent people), then we get the following problem.

If we have three gene histories saying ((AB)C) and one saying ((AC)B), then do we have a sampling of two distributions (right vs wrong) or 4 distributions (4 gene histories). If of four gene histories, then do we have a 75% chance of being right by choosing the ((AB)C) cladogram supported by the three agreeing gene histories? 

OR suppose we do empirical Bayesian analysis: Say that all four are at 90% credibility. Three are 90% for ((AB)C) and one at 10% for ((AB)C. 

For ((AB)C, using first 50% prior, then the posterior of the last analysis as the prior of the next, we get .9875.

For ((AC)B, using the same but three at 10% and one at 90%, we get: 0.0125. 

So what is this? 0.9875 to 0.0125, or 0.25:0.75? which do you choose? If you think each gene sequence has it own history (and also one is correct), then you have ((AB)C) at 75% credibility. If you decide that the majority rule and when most gene sequences agree that must be the correct species tree, then 98% credibility for that. Your choice. You get mana from making the correct choice. 

R.



 
* * * * * * * * * * * * 
Richard H. Zander 
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA 
Web sites: http://www.mobot.org/plantscience/resbot/ and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site: http://www.mobot.org/plantscience/resbot/21EvSy.htm



-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Lynn Raw
Sent: Friday, April 01, 2011 5:22 PM
To: TAXACOM
Subject: Re: [Taxacom] DNA contamination

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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