aeb2 phylogenies

Aeb2 includes members of Bacteria, Archaea, and Eukarya. Methods of tree inference included maximum likelihood as implemented in RAxML, PhyML-4X (Le et al., 2012), and PhyML-Structure (Le and Gascuel, 2010) or Bayesian inference as implemented in PhyloBayes v. 3.3 or 3.3e (Lartillot et al., 2009). Aeb2 includes “Archezoan” (polyphyletic group of long branched eukaryotes such as Giardia, Trichomonas, Microsporidia, and Entamoeba) sequences; the subset “aeb2 Arch+” refers to the presence of Archezoa without Korarchaeota and Thaumarchaeota and the subset, “aeb2 KT+” refers to the presence of Korarchaeota and Thaumarchaeota without Archezoa. Aeb2 Arch+ and KT+ attempt to mitigate long-branch attraction (LBA) artifacts due to substitution rate saturation and allow us to assess the influence of taxonomic sampling on phylogenetic outcome. Gap removal occurred after the creation of the supermatrix (resulting in 13929 positions for aeb2 Arch+ and 13941 positions for aeb2 KT+).