Figure 1A. displays the heat map for the archaeal dataset, Figure 1B. for the eukaryotic dataset. Heat maps include two kinds of markers: actual ones, indicated by a red rectangle at the left of the heat map, and artificial markers with extreme LGT (see main text), indicated in blue. They are based on a set of plausible topologies (see main text). The number of genes and topologies in the analysis are indicated on the heat map. These heat maps are double-clustered by genes and by topologies. The hierarchical clusters are represented by a tree of genes and a tree of topologies along the heat map. In the left band, the relative distribution of red and blue rectangles reflects the presence/absence of clustering of actual markers with artificial ones. Inside a heat map each dot of colour corresponds to the p-value for a given gene and a given topology. The p-values range from 0 (rejection) to 1 (support). The colour code associated with these p-values (from green for rejection to white for support) are reported above the heatmap. On the right of each heat map, the orange brackets indicate regions containing markers with a weak discriminatory power; the green brackets indicate regions containing markers with a stronger discriminatory power. Amongst the markers with a stronger phylogenetic signal, pink arrows point to some instances of conflicting signal in actual markers. They indicate different columns displaying a contrasting pattern of colour and contradictory p-values for several orthologues in a dataset.