Fig. 2. Maximum likelihood (ML) phylogeny of Dorymyrmex inferred in IQ-TREE v2.1.2., with an identical topology to the Bayesian phylogeny (Supp Fig. S3 [online only]) inferred in ExaBayes v1.5.1. Clades are highlighted by color and main nodes and clades are numbered for easy reference in the text. All support values are at maximum (100% bootstrap, posterior probability of 1) except where indicated. For ML analysis, IQ-TREE included three independent runs, each with 1000 ultrafast bootstrap replicates, drawing on the data matrix of 904 partitions determined using the SWSC-EN method and using the best-fit models chosen by IQ-TREE ModelFinder. For Bayesian analysis, ExaBayes included 4 independent runs of 2 chains each, which continued for 1.5 million generations (first 100,000 generations discarded for diagnostics), under the same SWSC-EN partitioning scheme and a GTR+G model (full details in Methods).