Table 1.
Parabasalian species used for the gene identification and phylogenetic analyses.
Figure 1.
Maximum likelihood phylogenetic analyses of parabasalids based on GAPDH (A), actin (B), and EF-1α (C) sequences.
Unambiguously aligned protein sequences of 278 (A), 280 (B) and 274 (C) sites were used for phylogenetic inference. The species names of the parabasalids except for the genus Trichonympha are shown in Table 1. The GAPDH sequences of Trichonympha acuta and Eucomonympha imla and the EF-1α sequence of Trichomonas tenax (not shown in Table 1) were also included in the analyses. Although the EF-1α sequences published for Pentatrichomonas and Tritrichomonas [57] were not included in C because of their shorter sequence length, the analysis with a reducing number of sites (219 sites) demonstrated that they were related very closely to the sequences from the same taxa shown in C. The sequence accession number was indicated for each taxon. The sequences used for the concatenation are in bold. The trees were estimated in RAxML and the numbers near the nodes indicate the bootstrap values. Values below 50% are not shown. Vertical bars to the right of the trees represent the parabasalian classes according to [26]: C, Cristamonadea; S, Spirotrichonymphea; Tn, Trichonymphea; Tt, Tritrichomonadea; H, Hypotrichomonadea; and Tm, Trichomonadea. Scale bars correspond to 0.10 substitutions per site.
Figure 2.
Phylogenetic relationship of parabasalids inferred from the concatenated dataset.
The concatenated dataset comprising 278 amino acid sites of GAPDH, 280 amino acid sites of actin, 274 amino acid sites of EF-1α, and 1338 nucleotide sites of SSU rRNA gene sequences was analyzed in 28 parabasalian species. The tree was estimated in RAxML using separate models with the parameters and branch length optimized for each gene partitions individually. The supporting values (bootstrap in RAxML/Bayesian posterior probability) are indicated at the nodes. Values below 50% or 0.5 are indicated with hyphens. When the site-heterogeneous CAT model was used in each partition, the identical tree topology with similar bootstrap values was obtained (data not shown). Vertical bars to the right of the tree represent the parabasalian classes. The scale bar corresponds to 0.10 substitutions per site.
Table 2.
Shimodaira-Hasegawa (SH) and approximately unbiased (AU) tests for alternative monophyletic relationships of parabasalian classes.
Figure 3.
Maximum likelihood tree based on concatenation of actin, EF-1α, and SSU rRNA gene sequences and rooted by diverse eukaryotes.
Unambiguously aligned amino acid sites of actin (268) and EF-1α (274), and nucleotide sites of SSU rRNA (1265) gene sequences were concatenated and analyzed in 30 parabasalian species and 23 diverse eukaryotes as outgroups. The tree was estimated with RAxML using the CAT model (CATMIX). The parameters and branch length were optimized for each gene partition individually. The supporting values (bootstrap in RAxML/Bayesian posterior probability) are indicated at the nodes. Values below 50% or 0.5 are indicated with hyphens. Vertical bars to the right of the tree represent the parabasalian classes. The 11 possible root positions are indicated in red letters. The scale bar corresponds to 0.10 substitutions per site.
Table 3.
Shimodaira-Hasegawa (SH) and approximately unbiased (AU) tests for parabasalian root positions.
Figure 4.
Maximum likelihood tree based on concatenation of GAPDH, actin, EF-1α, and SSU rRNA gene sequences and rooted by Trimastix.
Unambiguously aligned amino acid sites of GAPDH (257), actin (268), and EF-1α (274), and nucleotide sites of SSU rRNA (1338) gene sequences were concatenated and analyzed in 28 parabasalian species with Trimastix as an outgroup. The tree was estimated in RAxML using the CAT model (CATMIX). The parameters and branch length were optimized for each gene partition individually. The supporting values (bootstrap in RAxML/Bayesian posterior probability) are indicated at the nodes. Values below 50% or 0.5 are indicated by hyphens. Vertical bars to the right of the tree represent the parabasalian classes. The scale bar corresponds to 0.10 substitutions per site.
Table 4.
Exclusion of parabasalian taxa and the effect on their root.
Figure 5.
Proposed evolutionary relationships of parabasalids.
The tree shows the relationships of the six parabasalian classes. Flagellar multiplication in a single mastigont system has occurred independently in the boxed classes. The multiplications have occurred ancestrally in two classes (marked with filled circles) and probably twice within the other class (open circle). Triangles indicate the occurrence of cytoskeletal simplification in undulating membrane (UM) and costa. See the text for details.