The accuracy of methods on Avian (a) and Mammalian (b) datasets using estimated gene trees. Left: number of genes is fixed (1000 for avian, 200 for mammalian) and ILS levels change. Right: ILS level is fixed (default 1X for avian and very high 0.2X for mammalian). We show average and standard error over 20 replicates, except for 1600 and 3200 genes, which have 10 and 5 replicates, respectively. For the mammalian dataset with 0.2X ILS, due to the large number of gene trees, running concatenation was not feasible