Figure 3

MP trees of spatangoid sea urchins from combined 28S rRNA, 16S rRNA, and mitochondrial COI sequences [25]. L.h.s. from original data, r.h.s. from a reduced alignment with cutoff q = 0.8. The latter tree matches the biological expectation and fits very well with those reported in [25] that were obtained from a manually reduced alignment. In particular, the noisy-reduced MP tree correctly shows Brissopsis and Allobrissus as sister groups and it correctly identifies the large monophyletic clade consisting of the Linopneustes/Metalia and Lovenia/Spatangus groups to the exclusion of Meoma and Archeopneustes. These major improvements are marked with a bullet. The included table compares the stability indices (HI = homoplasy index, RC = rescaled consistency index, RI = retention index) between the complete (unprocessed), Stockley's manually improved, and the noisy-reduced alignment.