From: Terry M. Gray (grayt@lamar.colostate.edu)
Date: Fri Oct 24 2003 - 13:21:12 EDT
Josh,
Thanks for the tip. I've argued all along that this would be case
once more complete data is out. This is the key trouble with the
Wells, Behe, Nelson, and the DI folks in general. They take a very
pessimistic look at the data and look at weaknesses based in lack of
information. This is because the optimistic look at the data goes
contrary to their strong anti-evolutionary biases. Strickly speaking
and at the moment and in the particular case, they may be correct.
But the trend is and always has been there with the molecular data,
the more we know the more evolutionary explanations make sense.
TG
>I think Wells' critique of molecular phylogenies will be much harder
>to sustain after papers like this (Nature 425, 798 - 804 (23 October
>2003):
>
>Genome-scale approaches to resolving incongruence in molecular phylogenies
>
>ANTONIS ROKAS*, BARRY L. WILLIAMS*, NICOLE KING & SEAN B. CARROLL
>
>Howard Hughes Medical Institute, Laboratory of Molecular Biology, R.
>M. Bock Laboratories, University of Wisconsin-Madison, 1525 Linden
>Drive, Madison, Wisconsin 53706, USA
>* These authors contributed equally to this work
>
>Correspondence and requests for materials should be addressed to
>S.B.C. (sbcarrol@wisc.edu).
>
>One of the most pervasive challenges in molecular phylogenetics is
>the incongruence between phylogenies obtained using different data
>sets, such as individual genes. To systematically investigate the
>degree of incongruence, and potential methods for resolving it, we
>screened the genome sequences of eight yeast species and selected
>106 widely distributed orthologous genes for phylogenetic analyses,
>singly and by concatenation. Our results suggest that data sets
>consisting of single or a small number of concatenated genes have a
>significant probability of supporting conflicting topologies. By
>contrast, analyses of the entire data set of concatenated genes
>yielded a single, fully resolved species tree with maximum support.
>Comparable results were obtained with a concatenation of a minimum
>of 20 genes; substantially more genes than commonly used but a small
>fraction of any genome. These results have important implications
>for resolving branches of the tree of life.
>
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-- _________________ Terry M. Gray, Ph.D., Computer Support Scientist Chemistry Department, Colorado State University Fort Collins, Colorado 80523 grayt@lamar.colostate.edu http://www.chm.colostate.edu/~grayt/ phone: 970-491-7003 fax: 970-491-1801
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