[Taxacom] DNA contamination

[John Grehan]

So is this why the chimpanzee is matched up with humans? (this is just
rhetorical - although one might wonder). The beauty about morphogenetics
is that one can separately illustrate and identify claims for homology
for each character individually before an analysis. With sequences it
seems that even after one juggles the challenge of dealing with four
characters (not character states) and dream up all sort of theoretical
algorithms to create non-empirical homologies (i.e. that cannot be seen
in nature)that by their very nature are phenetic, we are also being told
that the data may be no good anyway, and there are such problems with
the theory of sequence systematics that just adding in more genes and
more sequences does not solve anything anyway.

It seems that the only biological basis for suggesting molecular
similarity might have any phylogenetic correlation is to say that it
makes some sort of morphogenetic sense (i.e creates groups that are seen
to be congruent - such as grouping birds with each other rather than
some birds for frogs for example) and on the other hand to create groups
that are morphogenetically incongruent (as with the chimpanzee-human
clade). One might add biogeography as an additional criterion where many
molecular phylogenies do product biogeographically sensible patterns of
spatial differentiation as demonstrated in several of Head's recent
papers.

John Grehan

-----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 3:13 AM
To: TAXACOM
Subject: [Taxacom] DNA contamination

I presume that most people on the Taxacom list are aware of this paper -
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.00164
10 .

I was wondering if contamination is a more general problem affecting
molecular phylogenies. It might explain one that I saw with an African
species nested within a set of apparently unrelated North American
species.

Lynn Raw
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