Fig. 3

Effects of removing fast evolving and heterotacheous sites, and random gene subsampling on apicomplexan relationships. a Colored schematic of the three possible relationships between Cryptosporidium spp., gregarines, and core apicomplexans. A+G (yellow) shows monophyly of core apicomplexans and gregarines, A+C (purple) shows monophyly of core apicomplexans and Cryptosporidium spp., and G+C (green) shows monophyly of gregarines and Cryptosporidium spp. b Box-and-whisker plots showing support for randomly sampled subsets of genes from each total dataset (dataset A on the left and dataset B on the right). Non-parametric bootstrap support (n = 100) values are on the y-axis and subsample percentage is shown on the x-axis. The number of individual datasets required to sample every gene with 95% probability of sampling every gene for each percentage of genes being sampled is shown in parentheses. Each bipartition of interest is shown in a different color with A+G, A+C, and G+C corresponding to the colors in a. c Graphs plotting support for bipartitions of interest after the stepwise removal of the 6000 fastest evolving sites (top) and 6000 most heterotachous sites (bottom) until all sites are removed from each dataset (dataset A on the left and dataset B on the right). Non-parametric bootstrap support (n = 100) values are on the y-axis and the number of sites removed, measured in thousands, is shown on the x-axis