Maximum likelihood phylogenomic analyses of concatenated datasets demonstrate that Rhodelphis are sister to red algae

Maximum likelihood phylogenomic analyses were carried out for two very similar datasets: 153/253 (153 taxa, 253 proteins, 56,312 sites) and 151/253 (151 taxa, 253 proteins, 56,530 sites) using IQ-TREE under the LG+C60+F+G4 model. In each case, Rhodelphis were shown to be sister to red algae; in the 153/253 dataset, picozoa were shown to be sister to Rhodelphis + red algae. Unlike Bayesian analyses, maximum likelihood did not recover the monophyly of Archaeplastida, instead grouping Cryptista with green algae/plants and glaucophytes, though with only modest statistical support. The 153/253 tree corresponds to Extended Data Figure 3b, and the 151/253 tree corresponds to Extended Data Figure 4b.