Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group

Abstract

Recent phylogenetic analyses position certain "orphan" protist lineages deep in the tree of eukaryotic life, but their exact placements are poorly resolved. We conducted phylogenomic analyses that incorporate deeply sequenced transcriptomes from representatives of collodictyonids (diphylleids), rigifilids, Mantamonas, and ancyromonads (planomonads). Analyses of 351 genes, using site-heterogeneous mixture models, strongly support a novel super-group-level clade that includes collodictyonids, rigifilids, and Mantamonas, which we name "CRuMs". Further, they robustly place CRuMs as the closest branch to Amorphea (including animals and fungi). Ancyromonads are strongly inferred to be more distantly related to Amorphea than are CRuMs. They emerge either as sister to malawimonads, or as a separate deeper branch. CRuMs and ancyromonads represent two distinct major groups that branch deeply on the lineage that includes animals, near the most commonly inferred root of the eukaryote tree. This makes both groups crucial in examinations of the deepest-level history of extant eukaryotes.

Keywords: concatenated phylogenetic analysis; eukaryote tree of life; protist; site-heterogeneous models.

Fig. 1.

—Phylogenetic tree for 61 eukaryotes, inferred from 351 proteins using Maximum Likelihood (LG + C60 + F+Γ-PMSF model). The numbers on branches show (in order) support values from 100 real bootstrap replicates (LG + C60 + F+Γ-PMSF model) and posterior probabilities from both sets of converged chains in Phylobayes-MPI under CAT-GTR+Γ model (i.e., MLBS/PP/PP). Filled circles represent maximum support with all methods; asterisks indicate a clade not recovered in the Phylobayes analysis. The dashed arrow indicates the placement of malawimonads inferred with Phylobayes-MPI (see also inset summary tree), and gray arrows indicate the placements of other lineages in the Phylobayes-MPI analyses.

Fig. 2.

—Effects of fast evolving sites and random subsampling of genes on our phylogenomic analyses. (A) Sites were sorted based on their rates of evolution estimated under the LG + F+Γ model and removed from the data set from highest to lowest rate. Each step has 4,000 of the fastest evolving sites removed progressively. The bootstrap values (UFBOOT; LG + C60 + F+Γ-PSMF model) for each bipartition of interest are plotted. (B and C) Effects of random subsampling of genes within the 351-gene data set. The following bipartitions were examined but received nearly 100% support across the fast site deletion series (data not shown); Amorphea, Obazoa, Amoebozoa, Ancryomonads, and Sar. The following bipartitions were examined but received nearly 0% support across the fast site deletion series (data not shown); Amoebozoa + CRuMs, Metamonada + Ancyromonads, Excavata (No Malawimonads), Excavata + Malawimonads, and Ancyromonads + Malawimonads + CRuMs. (B) Effects of random subsampling of genes on the bipartitions of interest. Inset panel is the calculation of the number of replicates (n) necessary for a 95% probability of sampling every gene when subsampling 20%, 40%, 60%, and 80% of genes using the formula: 0.95 = 1−(1−x/100)ⁿ, where x is the percentage of genes subsampled. UFBOOT support values for all nodes of interest with the variability of support values illustrated by box-and-whisker plots.