[Taxacom] DNA contamination

Sun Apr 3 10:45:32 CDT 2011

Since falsification is dependant upon some re-determined criterion, the support for molecular data cannot falsify morphological results simply through incongruence. In this respect I am in agreement.

At this time I have no objective recipe to offer in making a choice between molecular and morphological results. I have a personal preference for the morphology being more likely correct simply because the latter can be evaluated in terms of shared derived similarities for each character individually, and the orangutan result makes phylogenetic sense out of the orangutan features in early hominids. But of course that is just a personal preference and has no necessary scientific validity.

Perhaps others will create the kind of statistical proofs that will resolve the molecular - morphological incongruence ne way or the other. Or an early hominid fossil will turn up that has more dramatically obvious orangutan affinities (unfortunately I am not in a position to do anything about that and have to just sit by until someone finds the fossil associated with the isolated orangutan-type molars that have been found in Africa). Or something else will crop up.

John Grehan

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Richard Zander
Sent: Saturday, April 02, 2011 12:45 PM
To: Lynn Raw; TAXACOM
Subject: Re: [Taxacom] DNA contamination

Molecular data support ALL trees, just some more than others. They cannot falsify morphological results. If morphological results are so certain they falsify the probabilistic molecular tree, then a suboptimal molecular tree is required so both fit theory (unless you are theory-free, in which case you intuit that DNA has more manna).

Precision: 
Morphology: suppose you have a prior of 0.50, and a decision about a relationship at 0.90. The posterior is 0.90. Suppose somebody else does another study with somewhat different specimens and data, and gets the same answer at 0.90 credibility. Using the previous posterior as the prior (empirical Bayes analysis) you get 0.9878. A third study on the same relationship with different specimens and different data gives 0.90 credibility. Using the posterior from the previous study as the prior you get 0.9986. 

This is precision that aces molecular precision for an alternative relationship. You may ask, how the hell do you measure probabilities in morphological study? Well, maybe you can't, exactly, but suppose you have one relationship supported by several different studies by different people using different data (morphological cladistics, cytology, biogeography, etc.? The morphological and the molecular results may differ, but have very high credibility values. 

To conciliate the two different results you have to use scientific THEORY. For instance, if you have a taxon that is basal on a morphological tree but terminal on a molecular tree, a theory can be advanced that that taxon is a present-day surviving taxon that was the ancestral taxon of all lineages on the molecular dendrogram distal to the position of that taxon on the morphological cladogram. E.g. If the chimp/gorilla group is basal on a man/orang/chimp/gorilla morphological cladogram, and terminal in the molecular cladogram, maybe the chimp/gorilla morphotype is ancestral to the man/orang morphotype? Can we do a Dollo Rule analysis to gauge the probabilities of these sets of traits evolving in this direction? I think John Grehan has been saying this all along. Maybe.

ï»¿
* * * * * * * * * * * *
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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