Phylogenomic Analysis of Deep-Branching Telonemid

The evolutionary history of eukaryotic supergroups has been investigated primarily by large-scale phylogenomics, but one major hindrance to continued progress is that some major eukaryotic groups have extremely sparse sampling. The phylum Telonemia is one such group. Environmental sampling shows two major subgroups of Telonemia, but there are only multigene phylogenomic data from three closely related species belonging to one of the subgroups, TEL1. Here, a single cell was isolated from the pelagic Pacific Ocean, which SSU phylogenetic analysis reveals to be a telonemid of the TEL2 subgroup and distantly related to telonemids with multigene sequence data. Through single-cell transcriptome sequencing and phylogenomic analysis, we investigate the impact of this new telonemid on the relation of Telonemia to the Stramenopila-Alveolata-Rhizaria supergroup (SAR) and other sparsely sampled or historically unstable supergroups, namely, Hemimastigophora, Provora, and Haptista. Our maximum-likelihood (ML) analysis supports Telonemia as sister to Hemimastigophora, together as sister to SAR, with Haptista and Provora forming a clade and sister to all three. However, our Bayesian analysis failed to converge on a topology. Throughout different Telonemia sampling, gene sampling, alignment trimming, and site removal schemes, the sisterhood of Telonemia and Hemimastigophora remained largely supported in ML trees, even when their sisterhood to SAR dissolved, as was the sisterhood of Haptista and Provora. Inclusion of our TEL2 telonemid largely did not influence these relationships. However, our results also highlight the unstable placements of aforementioned groups throughout variations of our data, of which subsets give results consistent with other previously published analyses of this scale.