Fig. 3.

Maximum likelihood phylogeny (TIM2 model allowing unequal base frequencies, with empirical base frequencies, invariable sites and the discrete gamma model) of Parabasalia-like EF-1α sequences from the macaque fecal metatranscriptome, alongside a range of Parabasalia species. Phylogeny is rooted using sequences from Giardia intestinalis (accession HQ179602.1) and Spironucleus barkhanus (accession AB665178.1) as an outgroup (not shown). Bootstrap values (1000 replicates) greater than 75% are shown on branches in red. Units for tree scale are inferred substitutions per base pair. Macaque-derived sequences (highlighted in orange) are named sequentially according to the animal from which they originated, e.g. Macaque1:1, Macaque1:2. The major Pentatrichomonas-like lineage of macaque-derived sequences is highlighted in yellow. Coloured dots indicate animal host taxa. Where available, Genbank accessions (Benson et al., 2015) are shown at the ends of tip labels.