Phylogenetic dissection provides insights into the incongruity in the tree of Archaeplastida between the analyses of nucleus- and plastid-encoded proteins

Archaeplastida is defined as a taxonomic assemblage comprising three sub-clades, namely Chloroplastida, Glaucophyta, and Rhodophyta plus non-photosynthetic lineages sister to Rhodophyta (collectively termed “Rhodozoa” here). The members of Archaeplastida are the descendants of the eukaryote that took up and transformed a cyanobacterial endosymbiont into a primary plastid. Archaeplastida has been well studied as one of the major eukaryotic assemblages in science, as this assemblage initiated the diversity and evolution of eukaryotic phototrophs, and contains primary producers that are significant for the Earth’s environments. Recent phylogenetic analyses of multiple proteins (phylogenomic analyses) stably recovered the monophyly of Archaeplastida, but uncertainty remains in the relationship among the three sub-clades in this assemblage. The phylogenomic analyses of nucleus-encoded proteins (nuc-proteins) put Rhodozoa at the base of the Archaeplastida clade, albeit Glaucophyta was often inferred as the basal lineage in the phylogenomic analyses of plastid-encoded proteins (pld-proteins). In this study, we challenged the previously recognized but as-yet-explicitly addressed issue in the tree of Archaeplastida (ToA). The phylogenomic analyses of the nuc-protein and pld-protein supermatrices processed by the removal of fast-evolving, random, and heterotachious positions revealed that taxon sampling can invoke different types of phylogenetic artifacts into the inferences from both supermatrices examined here. In the end, we propose the basal branching of Rhodozoa as the working hypothesis for the ToA, redefine the issue in the internal relationship among the three sub-clades, and provide future perspectives toward resolving the ToA.