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Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.ORCID iD: 0000-0002-0440-5676
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
2016 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 101, 1-7 p.Article in journal (Refereed) Published
Abstract [en]

Rhizaria is a major eukaryotic group of tremendous diversity, including amoebae with spectacular skele- tons 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 exten- sive 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 P3 xLBs (defined as P2? 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.

Place, publisher, year, edition, pages
Elsevier, 2016. Vol. 101, 1-7 p.
Keyword [en]
SAR, Rhizaria, Phylogenomics, Eukaryote phylogeny
National Category
Evolutionary Biology
Research subject
Biology with specialization in Evolutionary Organismal Biology
Identifiers
URN: urn:nbn:se:uu:diva-292712DOI: 10.1016/j.ympev.2016.04.033ISI: 000378188100001PubMedID: 27132173OAI: oai:DiVA.org:uu-292712DiVA: diva2:926489
Funder
Swedish Research Council
Available from: 2016-05-08 Created: 2016-05-08 Last updated: 2016-07-27Bibliographically approved

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