Figure 5

Distributions of the Bowker's test statistics under various models. First column: number of pairwise tests significant at the 5% level. Second column: median of the pairwise statistics. First row: homogeneous model (H). Second row: one theta per branch non-homogeneous model (NH1). Third row: 3 thetas non-homogeneous model (NH2). Fourth row: 5 thetas non-homogeneous model (NH3). Fifth row: one kappa per branch non-homogeneous model (NH4). All models use the Tamura 1992 substitution model with a 4-classes discrete Gamma + invariant rate distribution. The arrows indicate the observed values from the real data set and the resulting p-values.