Fig. 3

Phylogenetic inference using the coalescent-based summary method ASTRAL-II. a Phylogeny obtained using all 1040 gene trees. The phylogeny conflicts with that obtained using all other methods by placing Conolampas sigsbei inside Scutellina, sister to Scutelliformes. The neognathostomate section of a supernetwork built from gene tree quartets is also depicted, showing a reticulation involving Conolampas, Echinocyamus and scutelliforms. b Phylogeny obtained using 354 gene trees, selected to minimize the negative effects of saturation and across-lineage rate heterogeneity. The position of Conolampas shifts to become sister to Scutellina (as in all other methods), with relatively strong support. To emphasize the shift in topology between the two, only neognathostomate clades have been colored (as in Fig. 2), and nodes have maximum local posterior probability unless shown. c Values of the two potentially confounding factors across all genes. Genes in red were excluded from the analysis leading to the topology shown in b. Histograms for both variables are shown next to the axes. d Summary of the results obtained performing inference with ASTRAL-II after deleting 66% of genes selected at random (100 replicates). Most replicates showed the same topology as in a. Only 16% placed Conolampas as sister to Scutellina (top), and even among them the support for this resolution was generally weak (bottom)