Novel Predators Reshape Holozoan Phylogeny and Reveal the Presence of a Two-Component Signaling System in the Ancestor of Animals

Elisabeth Hehenberger, Denis V. Tikhonenkov, Martin Kolisko, Javier del Campo, Anton S. Esaulov, Alexander P. Mylnikov, Patrick J. Keeling
2017 Current Biology  
In Brief Hehenberger et al. describe three novel Holozoa and infer an updated phylogenomic framework for this group, in the course recovering a new lineage. Using comparative genomics, they show the presence of a two-component signaling system across all unicellular Holozoa and suggest the loss of this signaling system with the origin of animals. SUMMARY Our understanding of the origin of animals has been transformed by characterizing their most closely related, unicellular sisters: the
more » ... agellates, filastereans, and ichthyosporeans. Together with animals, these lineages make up the Holozoa [1, 2]. Many traits previously considered "animal specific" were subsequently found in other holozoans [3, 4] , showing that they evolved before animals, although exactly when is currently uncertain because several key relationships remain unresolved [2, 5] . Here we report the morphology and transcriptome sequencing from three novel unicellular holozoans: Pigoraptor vietnamica and Pigoraptor chileana, which are related to filastereans, and Syssomonas multiformis, which forms a new lineage with Corallochytrium in phylogenomic analyses. All three species are predatory flagellates that feed on large eukaryotic prey, and all three also appear to exhibit complex life histories with several distinct stages, including multicellular clusters. Examination of genes associated with multicellularity in animals showed that the new filastereans contain a cell-adhesion gene repertoire similar to those of other species in this group. Syssomonas multiformis possessed a smaller complement overall but does encode genes absent from the earlierbranching ichthyosporeans. Analysis of the T-box transcription factor domain showed expansion of T-box transcription factors based on combination with a non-T-box domain (a receiver domain), which has not been described outside of vertebrates. This domain and other domains we identified in all unicellular holozoans are part of the two-component signaling system that has been lost in animals, suggesting the continued use of this system in the closest relatives of animals and emphasizing the importance of studying loss of function as well as gain in major evolutionary transitions. RESULTS AND DISCUSSION Expanding the Phylogenomic Framework for Holozoa Three novel holozoan taxa were isolated from freshwater and/or freshwater sediments: Syssomonas multiformis, Pigoraptor vietnamica, and Pigoraptor chileana (see STAR Methods for formal taxonomic diagnosis). The most conspicuous characteristic of all of the three is their ability to readily feed on eukaryotic prey similar in size to themselves, an unusual if not unique feeding mechanism in unicellular holozoans (Figure 1C ). Although they capture only the cytoplasmic content of eukaryotic cells, reminiscent of the phagocytotic uptake of Schistosoma mansoni sporocyst content by the filasterean Capsaspora owczarzaki in lab conditions [6], they can also engulf bacteria and small detritus, similar to the phagocytotic uptake of bacteria in choanoflagellates [7] . These taxa are also morphologically plastic: all three form flagellates ( Figures 1A-1C , 1I, 1J, 1M, and 1N), but also cysts, and even multicellular clusters ( Figures 1F-1H, 1K, 1L, 1O, and 1P) . Syssomonas multiformis exists in amoeboflagellate and amoeboid stages ( Figures 1D and 1E) . The many forms of S. multiformis in particular indicate highly complex life cycles. To place the new species into a phylogenetic framework, we built on a previously published dataset of 263 genes [8], extensively expanding the taxon sampling for unicellular relatives of animals and also adding several early-branching animals. The final curated data matrix contained 255 genes (81,495 aa positions) from 38 taxa, with 12% missing data overall (Table S1 ). Using this 255-gene dataset, we resolved the position of the new species and also the branching order of holozoan subgroups as a whole with moderate to high support. Overall, this tree shows that filastereans are sister group to a clade containing animals and choanoflagellates, with high-confidence posterior probabilities and non-parametric maximum-likelihood (ML) bootstrap values (Figure 2A ). Similarly, significant support for the dermocystid Sphaerothecum destruens as sister to the Ichythophonida was found (Figure 2A) . Most importantly, however, we recovered a new
doi:10.1016/j.cub.2017.06.006 pmid:28648822 fatcat:tue6r2ymf5hpbk7wdpe4rtngrm