Fig. 7.
Comparison of species tree estimation methods given estimated gene trees for the Miid model of missing data. Species tree estimation error (measured by the RF error rate) is shown for species trees estimated by giving increasing numbers of genes as inputs to ASTRAL (blue), ASTRID (orange), MP-EST (green), and SVDquartets (red). All three summary methods were given estimated gene trees, and SVDquartets was given the true multiple sequence alignment. Each column represents a different level of incomplete lineage sorting (ILS): panels (a), (d), and (g) show datasets with low ILS, panels (b), (e), and (h) show datasets with high ILS, and panels (c), (f), and (i) show datasets with very high ILS. Each row represents a different percentage of missing data: panels (a)-(c) show datasets with 0% missing data, panels (d)-(f) show datasets with 30% random missing data, and panels (g)-(i) show datasets with 60% random missing data. Lines represent the average over 20 replicate datasets, and filled regions indicate the standard error. Datasets shown here have deep speciation events; results for datasets with recent speciation are shown in Additional file 1