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Syst. Biol. 52(6):781793, 2003 Copyright c Society of Systematic Biologists

Summary: Syst. Biol. 52(6):781­793, 2003
Copyright c Society of Systematic Biologists
ISSN: 1063-5157 print / 1076-836X online
DOI: 10.1080/10635150390258949
Least and Most Powerful Phylogenetic Tests to Elucidate the Origin of the Seed Plants in
the Presence of Conflicting Signals under Misspecified Models
Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695-7566, USA; E-mail: stephane@statgen.ncsu.edu
Abstract.--Several tests of molecular phylogenies have been proposed over the last decades, but most of them lead to
strikingly different P-values. I propose that such discrepancies are principally due to different forms of null hypotheses. To
support this hypothesis, two new tests are described. Both consider the composite null hypothesis that all the topologies are
equidistant from the true but unknown topology. This composite hypothesis can either be reduced to the simple hypothesis
at the least favorable distribution (frequentist significance test [FST]) or to the maximum likelihood topology (frequentist
hypothesis test [FHT]). In both cases, the reduced null hypothesis is tested against each topology included in the analysis.
The tests proposed have an information-theoretic justification, and the distribution of their test statistic is estimated by a
nonparametric bootstrap, adjusting P-values for multiple comparisons. I applied the new tests to the reanalysis of two
chloroplast genes, psaA and psbB, and compared the results with those of previously described tests. As expected, the FST
and the FHT behaved approximately like the Shimodaira­Hasegawa test and the bootstrap, respectively. Although the
tests give overconfidence in a wrong tree when an overly simple nucleotide substitution model is assumed, more complex
models incorporating heterogeneity among codon positions resolve some conflicts. To further investigate the influence


Source: Aris-Brosou, Stéphane - Department of Biology, University of Ottawa


Collections: Biology and Medicine