Figure 6.

Site removal analysis. Figures (A) and (B) illustrate the bipartitions that were sought in the pool of trees generated by bootstrapped ML reconstructions, corresponding to the "LG" (blue) and "CAT" (red) relationships, respectively. The monitored relationships are indicated as followed: star: Foraminifera-Acantharea grouping; square: Gromia sister to Phytomyxea; diamond: basal position of the Foraminifera-Acantharea clade within Rhizaria; cross: Gromia sister to the Foraminifera-Acantharea clade; circle: basal position of Cercozoa to the rest of rhizarian lineages. (C) Dependence of the bootstrap support values (BP) for the monitored relationships on the number of removed fast-evolving sites, marked for each of the 14 shorter alignments. The blue and red lines correspond to the BP of nodes found in the "LG" and "CAT" trees, respectively. The black line corresponds to the BP for the Foraminifera-Acantharea grouping. The vertical dashed line shows the step (13'379 positions removed) where the supports for the sister position of Retaria reached a minimum and the support for the sister position of Cercozoa a maximum. Numbers next to the marks are PP obtained with the "CAT" model (PhyloBayes), resulting from the pooling of all trees after burnin of 2 independent chains and corresponding to the bifurcations found. At removal steps 1, 2, 4 and 5 only one PP value is shown next to the cross mark, indicating that the CAT model could not infer the position of Phytomyxea within Rhizaria (multifurcation). The y-axis represents the BP and the x-axis the length of the alignments after the removal of sites.