Figure 3

Analyses of slices from the Nematoda dataset. The figure shows the results of analyses of automatically selected taxon subsets from the Nematoda dataset using various criteria for a three-gene supermatrix. (A) most_chars species (one per order) with most characters for the three genes; (B) least_bias species showing the lowest base composition bias; (C) slowest_rate species with the inferred slowest overall rate of evolution. (D) For comparison, we show the tree derived from alignment of full length SSU rRNA sequences for twelve of the fourteen species included in the iPhy slices in parts (A), (B) and (C). For two of the species (Caenorhabditis sp. 5 and Ditylenchus africanus) no SSU rRNA sequence was available so we have included closely-related species (Caenorhabditis briggsae and Ditylenchus angustus). Clade membership sensu Blaxter 1998 [36] is shown on the tree. For each iPhy subset the figure shows, from left to right, the tree resulting from phylogenetic analysis; a heat map showing the AT content of each of the three genes; a stacked bar chart showing the number of characters for each gene. Scale bars above each tree show the branch length associated with 0.1 changes per site. Order names are given in parentheses. The keys at the bottom of the figure show, from left to right, the mapping of colours to AT content for the heatmap, and the mapping of colours to loci for the bar chart. The scale bar shows the length of bar representing 1000 characters.