Additional file 2: Figure S2. of Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms

ML phylograms with bootstrap support values of all 55 genes (OGs) that were used to construct the 75% data matrix from which “?Haplotaxidae sp.” had been excluded. These genes passed through the TreSpEx and BaCoCa filters described in the text, and included all sites (i.e., sites comprising >50% gaps were not deleted). The title for each tree lists the tree number, the orthogroup number in the HaMStR Lophotrochozoa core ortholog set (e.g., “111,230” for tree 1) and the gene/transcript name (e.g., “C43H8.2” for tree 1). The gene/transcript name can be looked up in online databases (e.g., EnsemblMetazoa; http://metazoa.ensembl.org ). For example, for the first tree, C43H8 is a transcript of WBGene00016622, repressor of RNA polymerase III transcription MAF1. (PDF 14509 kb