Figure 3

Genome-wide incongruence. A, B, C, E, F, and G represent Oryza genome types and L represents the outgroup, Leersia. (a) Consensus network constructed from ML trees at a threshold of 0.15. The two boxes indicate the relatively high levels of incongruence among gene trees associated with internal branches I and IV. Branch length is proportional to the frequency of occurrence of a particular split of all gene trees. R represents the rest of the genome types, including A-, B-, C-, and E-genomes. Color schemes: for the box associated with branch I, blue, orange, and purple illustrate splits supporting alternative topologies, (AB)C, (BC)A, and (AC)B, respectively; for the box associated with branch IV, blue, orange, and purple illustrate splits supporting alternative topologies, (RF)G, (FG)R, and (RG)F, respectively. (b) Pie graphs indicate the proportions of gene trees that support alternative splits in the corresponding boxes at the left. Histograms at the right illustrate the distribution of ML bootstrap support for the corresponding split (in the corresponding colors). (c) Illustration of the relative physical locations of the 142 sampled genes on the 12 rice chromosomes based on rice genome sequences. The colors indicate genes supporting a split or topology coded in the same color in the corresponding boxes on the consensus network. Genes coded in gray are those that had no input in the topology illustrated in the pie graphs and those not included for the construction of the consensus network because of missing data.