Topological incongruence of individual process partitions with the SA tree. The figure is a summary of bootstrap consensus trees (> 75% support) of individual (42 genes + morphology on red background) and broader (cell compartments on blue background; functional categories on yellow background) data partitions. Wide topological disagreement exists, as only one of the individual gene partitions (5, ribosomal protein S7) agrees with the simultaneous analysis (SA) tree. In broader partitions, only the nuclear data analysed together agrees with the SA tree at all nodes. Numbers in boxes indicate data partitions (see Additional File 5) represented by a particular tree. The "0 node" tree was obtained for 26 partitions (3, 4, 6, 10, 12, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31, 32, 34, 37, 40, 42). Abbreviations for functional partitions (yellow background) are as follows: SI:Signalling, PI:Photosynthesis, R: Respiration, ST:Structural, TF:Transcription Factors, UK:Unknown Function; 'LessN' (on pink background) indicates trees where process partitions for one, two and three taxa are missing in the alignment. Colors of taxa in the tree are as follows; orange = Arabidopsis, aqua = Oryza, red = Cycas, blue = Ginkgo, purple = Gnetum, green = Pinus, grey = outgroup Physcomitrella).