How Bayes tests of molecular phylogenies compare with frequentist approaches.
BACKGROUND
The desire to compare molecular phylogenies has stimulated the design of numerous tests. Most of these tests are formulated in a frequentist framework, and it is not known how they compare with Bayes procedures. I propose here two new Bayes tests that either compare pairs of trees (Bayes hypothesis test, BHT), or test each tree against an average of the trees included in the analysis (Bayes significance test, BST).


RESULTS
The algorithm, based on a standard Metropolis-Hastings sampler, integrates nuisance parameters out and estimates the probability of the data under each topology. These quantities are used to estimate Bayes factors for composite vs. composite hypotheses. Based on two data sets, the BHT and BST are shown to construct similar confidence sets to the bootstrap and the Shimodaira Hasegawa test, respectively. This suggests that the known difference among previous tests is mainly due to the null hypothesis considered.
Aris-Brosou
Stéphane
S
Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, USA. stephane@statgen.ncsu.edu
D000465:Algorithms; D001499:Bayes Theorem; D004252:DNA Mutational Analysis / Q000379:methods; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods; D015497:HIV-1 / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
D004272:DNA, Mitochondrial