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, Malawimonas jakobiformis, 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, Gefionella okellyi n. gen. n. sp. Electron microscopy revealed all canonical features of 'typical excavates', including flagellar vanes (as an opposed pair, unlike M. jakobiformis but like many metamonads) and a composite fibre. Initial phylogenomic analyses grouped malawimonads with the Amorphea-related orphan lineage Collodictyon, 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 strict 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.

Centre for Comparative Genomics and Evolutionary Bioinformatics Department of Biochemistry and Molecular Biology Dalhousie University Halifax Nova Scotia B3H 4R2 Canada

Centre for Comparative Genomics and Evolutionary Bioinformatics Department of Biology Dalhousie University Halifax Nova Scotia B3H 4R2 Canada

Department of Biological Sciences Mississippi State University Starkville MS 39762 USA

Department of Biology University of Copenhagen Universitetsparken 15 2100 Copenhagen Denmark

Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics American Museum of Natural History New York NY 10024 USA

Institute of Parasitology Biology Centre Czech Academy of Sciences Branišovská 31 370 05 České Budějovice Czech Republic

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Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system

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EukRef-excavates: seven curated SSU ribosomal RNA gene databases

Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis

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Dryad
10.5061/dryad.9mv6d51