Supplementary Figure 2 from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

Transmission electron microscopy (TEM) of <i>G. okellyi</i>; groove architecture

Supplementary Figure 6 from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

Heat map showing RAxML rapid bootstrap support for clade of Discoba and Metamonada with removal of fast-evolving sites (X-axis, in thousands) and fast-evolving taxa (Y-axis)

Supplementary Figure 5 from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

Full phylogenetic tree corresponding to the summary tree shown in Fig 4a, based on 159 genes, with all sites and 84 taxa included

Supplementary Figure 6 from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

Heat map showing RAxML rapid bootstrap support for clade of Discoba and Metamonada with removal of fast-evolving sites (X-axis, in thousands) and fast-evolving taxa (Y-axis)

Supplementary Materials Description from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

Modern syntheses of eukaryote diversity assign almost all taxa to one of three groups: Amorphea, Diaphoretickes and Excavata (comprising Discoba and Metamonada). The most glaring exception is Malawimonadidae, a group of small heterotrophic flagellates that resemble Excavata by morphology, but branch with Amorphea in most phylogenomic analyses. However, just one malawimonad, <i>Malawimonas jakobiformis</i>, has been studied with both morphological and molecular-phylogenetic approaches, raising the spectre of interpretation errors and phylogenetic artefacts from low taxon sampling. We report a morphological and phylogenomic study of a new deep-branching malawimonad, <i>Gefionella okellyi</i> n. gen. n. sp. Electron microscopy revealed all canonical features of ‘typical excavates’, including two opposed flagellar vanes (unlike <i>M. jakobiformis</i> but like many metamonads) and a composite fibre. Initial phylogenomic analyses grouped malawimonads with the Amorphea-related orphan lineage <i>Collodictyon</i>, separate from a Metamonada+Discoba clade. However, support for this topology weakened when more sophisticated evolutionary models were used, and/or fast-evolving sites and long-branching taxa (FS/LB) were excluded. Analyses of ‘–FS/LB’ datasets instead suggested a relationship between malawimonads and metamonads. The ‘malawimonad+metamonad signal’ in morphological and molecular data argues against a Metamonada+Discoba clade (i.e. the predominant concept of Excavata). A Metamonad+Discoba clade should therefore not be assumed when inferring deep-level evolutionary history in eukaryotes

Supplementary Figure 3 from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

Transmission electron microscopy (TEM) of <i>G. okellyi</i>; posterior portion of the cell

Supplementary Figure 3 from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

Transmission electron microscopy (TEM) of <i>G. okellyi</i>; posterior portion of the cell

Supplementary Materials Description from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

Modern syntheses of eukaryote diversity assign almost all taxa to one of three groups: Amorphea, Diaphoretickes and Excavata (comprising Discoba and Metamonada). The most glaring exception is Malawimonadidae, small heterotrophic flagellates that resemble Excavata by morphology, but group with Amorphea in most phylogenomic analyses. However, just one malawimonad, <i>Malawimonas jakobiformis</i>, has been studied with both morphological and molecular-phylogenetic approaches, raising the spectre of interpretation errors and phylogenetic artefacts from low taxon sampling. We report a morphological and phylogenomic study of a new deep-branching malawimonad, <i>Gefionella okellyi</i> n. gen. n. sp. Electron microscopy revealed all canonical features of ‘typical excavates’, including two opposed flagellar vanes (unlike <i>M. jakobiformis</i> but like many metamonads) and a composite fibre. Initial phylogenomic analyses grouped malawimonads with the Amorphea-related orphan lineage <i>Collodictyon</i>, separate from a Metamonada+Discoba clade. However, support for this topology weakened when more sophisticated evolutionary models were used, and/or fast-evolving sites and long-branching taxa (FS/LB) were excluded. Analyses of ‘-FS/LB’ datasets instead suggested a relationship between malawimonads and metamonads. The ‘malawimonad+metamonad signal’ in morphological and molecular data argues against a Metamonada+Discoba clade (i.e. the predominant concept of Excavata). A Metamonad+Discoba clade should therefore not be assumed when inferring deep-level evolutionary history in eukaryotes

Supplementary Figure 5 from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

Full phylogenetic tree corresponding to the summary tree shown in Fig 4a, based on 159 genes, with all sites and 84 taxa included

Supplementary Figure 4 from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

Alternative views of the model of the proximal portion of the flagellar apparatus, rendered from a 21-section series (See Fig. 3j); note compasses for orientatio