Fig. 2: Results of Syn-MRL on simulations.

a Simulation process. An evolutionary scenario for a single gene family is illustrated, involving gene duplication, loss, and rearrangement. Extant gene names are labeled at the bottom (left panel). Nodes and edges of synteny clusters are simulated in stages under the listed parameters, ‘snapshots’ of the evolution of the associated gene family synteny network are shown at three-time points right after a speciation event (right panel). For example, at t2, three connected components can be formed: a ‘conserved’ four-node cluster, and two ‘specific’ two-node clusters, which were formed as a result of the gene duplication or rearrangement events that happened between t1 and t2. b Proportions of inferred trees with a particular RF distance to the true 15 monocot species tree. Simulations were conducted for different numbers of total gene families, with 1000 replicates for each simulation. c Distribution of RF distances of the inferred trees to the true 62 plant species tree. A total of 1000 simulation replicates of 1000 gene families were conducted. The 10 most frequently recovered topologies are labeled within the corresponding bar of the histogram.