Multigene phylogenetic analyses including diverse radiolarian species support the “Retaria” hypothesis — The sister relationship of Radiolaria and Foraminifera

One of the large taxonomic assemblages in eukaryotes, Rhizaria, includes Filosa, Endomyxa, Foraminifera and Radiolaria based on phylogenetic analyses. However, the evolutionary interrelationships within these rhizarian members have not been resolved mainly due to the limitations in gene sequences and/or taxon sampling. In particular, the Radiolaria are the least studied group by molecular phylogenetic approaches among the rhizarian members. In the present study genes encoding small subunit ribosomal RNA (SSU rRNA), large subunit ribosomal RNA (LSU rRNA), actin, α-tubulin, β-tubulin, and heat shock protein 90 (HSP90) were isolated from spumellarian (Larcopyle butschlii) and collodarian species (Collozoum pelagicum, and Sphaerozoum punctatum) of the Radiolaria to achieve a better understanding of the evolution of the Radiolaria. Phylogenies based on combined sequences of two genes (SSU rRNA and LSU rRNA), and of three genes (SSU rRNA, LSU rRNA and HSP90) strongly supported the sister relationship of the Radiolaria and Foraminifera within the rhizarian lineage. In light of the sister relationship of the Radiolaria and Foraminifera, the complex evolution of actin, α-tubulin and β-tubulin in the rhizarian lineage can be reconciled by ancestral gene duplication followed by differential loss of one of the paralogues or lateral gene transfer. Our present findings lend support to the “Retaria” hypothesis uniting these two eukaryotic groups, as originally proposed by Cavalier-Smith (1999).