Eukaryotic phylogeny based on nuclear-encoded protein sequences plus nucleotide sequences of 18S rRNA genes using M 10:16 (modified from the data matrix by Parfrey et al.[<b>29</b>]), including (A) and excluding (B) intracellular endoparasite/ciliate OTUs.

<p>The analysis is based on the concatenated dataset of slowly evolving nuclear proteins (15 proteins; 5710 amino acid positions) and 18S rRNA genes (868 nucleotide positions). The tree was prepared using RAxML with the WAG+4G model (for amino acid positions) and the GTR+4G model (for nucleotide positions). Numbers at the left or right side at the branches represent BV (≥50%) obtained using 1,000 replicates with the RAxML or MP analysis, respectively. Asterisks at the branches indicate 100% BV by all three methods.