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RE: Theropod phylogenies

> Well, to be fair, DNA analyses will often give
> wildly different topologies
> depending on the particular genes and the particular
> subset of taxa used...

Well protein data seems to be doing much better than
DNA at deeper levels, with 20 characters and lesser
chance for convergence and better opportunities for
alignments. However, it should be kept in mind that
molecular phylogenies also suffer from variable rates
of evolution of proteins/nucleic acids, long branch
attraction and at greater depths from lateral transfer
of genes and gene loss. For example the clade
ecdysozoa was much advertised in the tabloids based on
limited molecular analysis. However, more careful
molecular analysis showed that it was not supported by
much of the available data. Instead the traditional
coelmate clade makes much greater sense. So the lack
of correspondence between molecular and anatomical
phylogeny could in large part arise from reasons like
inadequacy of the data, errors of the practioners and
lack of careful analysis. Sometime back paleontologist
MS Lee* had published some really amateurish stuff
regarding molecular data. This illustrates to some
extant the lack of understanding amidst certain
paleontologists of related molecular phylogeny
methods. Conversely, I know from very realiable
sources that many card-carrying molecular
phyologeneticist are rather ignorant of certain
important aspects of protein evolution themselves. The
molecular phylogenies do not necessarily use
parsimony, in fact maximum likelihood and
neighbor-joining appear to work better. It may be good
for greater inter-disciplinary interaction between the
two flavor of phylogeneticists.


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