Fig. 3: Results of Syn-MRL on empirical data sets.

a Distribution of the support values of all the nodes of the inferred trees for the four data sets under different settings of A_min (the number of required anchor pairs for regions to be called syntenic). The boxplots indicate the minimum, maximum, median (the middle hinge with red dots), first quartile (the lower hinge), and third quartile (the upper hinge) in the data sets (n = 16, 9, 10, and 18 for the data sets of YGOB, Drosophila, vertebrates, and yeast). The whiskers represent the 1.5 inter-quartile range (IQR) extending from the hinges and outliers are shown as individual points. b–e Pairwise RF distances of the inferred trees, sequence alignment-based tree, and the reported tree of the data sets of YGOB, Drosophila, vertebrates, and yeast, respectively. Note that for the yeast data set, the species ‘Yarrowia lipolytica’ (used as the root of the tree) was absent from the data matrices at A₁₁ and A₁₃ (no synteny detected), and we therefore manually added this species (as the root) to the inferred tree, in order to calculate the RF distances. f–i Tree comparisons between the reported tree and the Syn-MRL tree of YGOB, Drosophila, vertebrates, and yeast data sets, at parameter setting values of A₅G₂₅, A₅G₂₅, A₅G₆, and A₂G₂₅, respectively. Matrices of syntenic percentages of pairwise genome comparisons are aligned to the corresponding species. Each cell of the matrix represents an overall syntenic percentage of a genome comparison, which is calculated using the total number of syntenic genes relative to the total number of genes between two genomes. The color indicates the values and goes from low (blue) to high (red). Different branching patterns are highlighted in red, genome duplication events are labeled as blue dots. Branch lengths are not meaningful. Support values for certain nodes of the vertebrate and yeast trees are from Drillon et al.¹⁶.