Fig. 2

Topological accuracy of LD-based and breakpoint-based methods on datasets simulated using alternate model phylogenies. For each model phylogeny, coalescent simulation utilized a recombination rate ranging from 100 to 1000 which was uniform across loci. Topological accuracy of each method was measured using the RF distance between the inferred and model phylogenies [26]. In panel (i) on the left, results are shown for the set of 10 model phylogenies used in [5]. Following their study protocol, simulation was repeated for each model phylogeny to obtain 10 replicates, and averages and standard error bars are shown (n=10). In panel (ii) on the right, results are shown for simulations that utilized an empirical phylogeny. Averages and standard error bars are shown (n=20)