Supplementary dataset

Phylogenies - Directory with the main phylogeny presented in the manuscript (WGA-iqtree), and the alternative phylogenies presented in Figure S1. The text files in this main folder contain the species names and GAGA-IDs, as well as the files to rename and color the tree using iTol. 

	05a) WGA trees : Species trees reconstructed from intergenic regions extracted from the Cactus whole-genome alignment using iqtree and astral, and the respective sequence alignments. 

	05b) Ortholog trees : Species trees reconstructed from single copy ortholog alignments. The two presented trees in the manuscript are retrieved from codon alignments across 1000 genes selected with GeneSort using iqtree, or from all gene trees using Astral. The phylogenies resulting from alternative datasets and from protein alignments can be found in the Additional_trees folder. 

	05c) BUSCO trees : Protein alignment matrix based on genes from Hymenoptera_odb10 BUSCO dataset, and the phylogeny reconstructed using 1000 genes selected with GeneSort. Additional species trees can be found in the Additional_trees folder using the dna alignments in iqtree, and also Astral. 

	05d) UCE trees : Species tree based in UCE alignments. The Additional_trees folder contains phylogenies using different matrix occupancies. 

	05e) Dating : Folder containing the input alignment, the tree with fossil prior distributions and MCMCtree ctl, and the resulting calibrated ant phylogeny.