Amoebozoa is the eukaryotic supergroup sister to Obazoa, the lineage that contains the animals and Fungi, as well as their protistan relatives, and the breviate and apusomonad flagellates. Amoebozoa is extraordinarily diverse, encompassing important model organisms and significant pathogens. Although amoebozoans are integral to global nutrient cycles and present in nearly all environments, they remain vastly understudied. We present a robust phylogeny of Amoebozoa based on broad representative set of taxa in a phylogenomic framework (325 genes). By sampling 61 taxa using culture-based and single-cell transcriptomics, our analyses show two major clades of Amoebozoa, Discosea, and Tevosa. This phylogeny refutes previous studies in major respects. Our results support the hypothesis that the last common ancestor of Amoebozoa was sexual and flagellated, it also may have had the ability to disperse propagules from a sporocarp-type fruiting body. Overall, the main macroevolutionary patterns in Amoebozoa appear to result from the parallel losses of homologous characters of a multiphase life cycle that included flagella, sex, and sporocarps rather than independent acquisition of convergent features.

Centre for Comparative Genomics and Evolutionary Bioinformatics Department of Biochemistry and Molecular Biology Dalhousie University Halifax Canada

Department of Biological Sciences Mississippi State University Mississippi State MS

Department of Biological Sciences University of Arkansas Fayetteville AR

Department of Biology and Ecology University of Ostrava Ostrava Czech Republic

Department of Invertebrate Zoology Faculty of Biology Saint Petersburg State University Saint Petersburg Russia

Department of Parasitology University of South Bohemia Českě Budějovice Czech Republic

Department of Zoology Charles University Prague Czech Republic

Department of Zoology University of São Paulo São Paulo Brazil

Institute for Genomics Biocomputing and Biotechnology Mississippi State University Mississippi State MS

Institute of Parasitology Biology Centre of the Czech Academy of Sciences Českě Budějovice Czech Republic

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