Comprehensive Multigene Phylogenies of Excavate Protists Reveal the Evolutionary Positions of “Primitive” Eukaryotes

Abstract

Many of the protists thought to represent the deepest branches on the eukaryotic tree are assigned to a loose assemblage called the "excavates." This includes the mitochondrion-lacking diplomonads and parabasalids (e.g., Giardia and Trichomonas) and the jakobids (e.g., Reclinomonas). We report the first multigene phylogenetic analyses to include a comprehensive sampling of excavate groups (six nuclear-encoded protein-coding genes, nine of the 10 recognized excavate groups). Excavates coalesce into three clades with relatively strong maximum likelihood bootstrap support. Only the phylogenetic position of Malawimonas is uncertain. Diplomonads, parabasalids, and the free-living amitochondriate protist Carpediemonas are closely related to each other. Two other amitochondriate excavates, oxymonads and Trimastix, form the second monophyletic group. The third group is comprised of Euglenozoa (e.g., trypanosomes), Heterolobosea, and jakobids. Unexpectedly, jakobids appear to be specifically related to Heterolobosea. This tree topology calls into question the concept of Discicristata as a supergroup of eukaryotes united by discoidal mitochondrial cristae and makes it implausible that jakobids represent an independent early-diverging eukaryotic lineage. The close jakobids-Heterolobosea-Euglenozoa connection demands complex evolutionary scenarios to explain the transition between the presumed ancestral bacterial-type mitochondrial RNA polymerase found in jakobids and the phage-type protein in other eukaryotic lineages, including Euglenozoa and Heterolobosea.

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”

“…This corresponds well with the morphological similarities between Andalucia and other members of the Jakobida (51). Andalucia is a strikingly deep branch, however (the basal branch for Jakobida other than Andalucia is much longer than the basal branch for all jakobids), perhaps explaining why previous analyses based on 1-7 genes were unable to robustly resolve the position of this organism (15,55,56).…”

“…This analysis resolves previous doubts about the monophyly of Discicristata with respect to all Jakobida based on some smaller datasets (15). The grouping of Discicristata with Jakobida represents a still more significant clade than Discicristata, and we think it useful to have a taxon name for this clade.…”

“…A relationship between Jakobida, Heterolobosea, and Euglenozoa was recovered by several studies based on 1-6 genes, sometimes with strong statistical support (15,20,22), but the interrelationships among the 3 groups differed between datasets. Our results are consistent with those obtained recently by Rodriguez-Ezpeleta et al without Andalucia (20).…”

“…Finally, 2 small but crucial groups are of uncertain placement. The first, Malawimonas, exhibits a typical excavate morphology, but is not robustly associated with any one of the 3 main subclades in published molecular phylogenetic studies (15,53). The second, Andalucia, is morphologically similar to Jakobida, but an affiliation with jakobids is usually not recovered, nor statistically supported, in analyses of small subunit rRNA genes (53,55) or small multiprotein datasets (56).…”

“…Worse, in some cases single genes had been transferred laterally between the lineages under examination (12). More recently, the availability of vast quantities of data from genome-sequencing and expressed sequence tag (EST) projects over a wide range of eukaryotes has allowed phylogenetic estimation from ''supermatrices'' of moderate (13)(14)(15) to large (16)(17)(18)(19)(20)(21)(22)(23) numbers of genes. Although such phylogenomic approaches are less sensitive to stochastic error, they can, when the phylogenetic model is misspecified, reinforce systematic errors such as LBA, yielding apparently strong support for an incorrect phylogeny (16,19,24).…”