From: Josh Bembenek (jbembe@hotmail.com)
Date: Fri Oct 24 2003 - 12:06:35 EDT
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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