Figure S15: alignment and tree-file: Phylogenetic analyses of Rab and TBC proteins in Anaeramoeba

Phylogenetic analyses of Rab proteins of subfamilies containing endocytic Rabs <strong>a,</strong> Rabs 2, 4, and 14 <strong>b,</strong> and Rabs 1, 8, and 18 <strong>c,</strong>.<strong> d, </strong>Phylogenetic analysis of TBC proteins. <br> For membrane-trafficking proteins, <em>Anaeramoeba</em> datasets were searched by BLAST using queries from previous studies (Elias et al. 2012; Gabernet-Castello et al. 2013; Klinger, Klute, and Dacks 2013). Identified Rab and TBC proteins were subjected to orthologous clustering by OrthoFinder v2.0.0 (Emms and Kelly 2019) including proteins from human, cnidarian <em>Nematostella vectensis</em>, and heterolobosean <em>Naegleria gruberi</em>. Phylogenetic analyses for selected Rab sub-families and TBC proteins were conducted. Sequences were aligned by MAFFT v7.458 (Katoh and Standley 2013) under L-INS-i strategy, and poorly aligned positions were removed by trimAl v1.4.rev15 (Capella-Gutierrez, Silla-Martinez, and Gabaldon 2009) using -gt 0.8. Maximum-likelihood trees were inferred by IQ-TREE v1.6.8 (Nguyen et al. 2015) using the posterior mean site frequency method (H.-C. Wang et al. 2018) and the LG+C20+F+G model, with the guide tree inferred under the LG+F+G model. Branch supports were obtained by the ultrafast bootstrap approximation with 1,000 replicates.