Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria

- Phylogenomic analyses of 147 proteins identify Rhizaria and Alveolata as sister taxa (R + A).
- A relative measure is used to estimate extreme long branch (xLB) content across genes and taxa.
- Removing xLB-rich genes increases support for R + A, suggesting this grouping is not a long branch attraction artifact.
- Some of the highest xLB content in a broad taxonomic sampling of eukaryotes is found in ribosomal proteins.

Rhizaria is a major eukaryotic group of tremendous diversity, including amoebae with spectacular skeletons or tests (Radiolaria and Foraminifera), plasmodial parasites (Plasmodiophorida) and secondary endosymbionts (Chlorarachniophyta). Current phylogeny places Rhizaria in an unresolved trichotomy with Stramenopila and Alveolata (supergroup “SAR”). We assembled a 147-protein data set with extensive rhizarian coverage (M147), including the first transcriptomic data for a euglyphid amoeba. Phylogenetic pre-screening of individual proteins indicated potential problems with radically misplaced sequences due either to contamination of rhizarian sequences amplified from wild collected material and/or extremely long branches (xLBs). Therefore, two data subsets were extracted containing either all proteins consistently recovering rhizarian monophyly (M34) or excluding all proteins with ⩾3 xLBs (defined as ⩾2× the average terminal branch length for the tree). Phylogenetic analyses of M147 give conflicting results depending on the outgroup and method of analysis but strongly support an exclusive Rhizaria + Alveolata (R + A) clade with both data subsets (M34 and M37) regardless of phylogenetic method used. Support for an R + A clade is most consistent when a close outgroup is used and decreases with more distant outgroups, suggesting that support for alternative SAR topologies may reflect a long-branch attraction artifact. A survey of xLB distribution among taxa and protein functional category indicates that small “informational” proteins in particular have highly variable evolutionary rates with no consistent pattern among taxa.

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