Fig. 1

Topological accuracy of LD-based and breakpoint-based methods on simulated datasets. The model conditions had dataset size ranging from 8 to 25 taxa and 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]. Each of the three breakpoint-based methods utilized one of the following inputs: inferred breakpoints/inferred gene trees (“IBIG”), true breakpoints/inferred gene trees (“TBIG”), or true breakpoints/true gene trees (“TBTG”). Averages and standard error bars are shown (n=20)