Posterior probability maps of genome quartets containing Synechocystis sp. Posterior probabilities were calculated according the maximum likelihood mapping approach described in [4, 17]. Tree topologies assigned to the vertices are depicted in New Hampshire tree format near the corresponding vertex of the triangle and they should be considered as unrooted tree topologies. The three numbers associated with each tree topology indicate how many QuartOPs fall into each of the three zones: "total" (i.e. posterior probability for the tree topology is larger than posterior probabilities for the other two topologies), 90% and 99% posterior probability respectively. A) Genome quartet consisting of Synechocystis sp., Halobacterium sp., Aquifex aeolicus and Thermotoga maritima. The majority of the QuartOPs support the grouping of the Halobacterium sp. with Synechocystis sp. B) Genome quartet consisting of Synechocystis sp., Archaeoglobus fulgidus, Aquifex aeolicus and Thermotoga maritima. The archaeon – Synechocystis sp. grouping is supported by fewer QuartOPs than in panel A.