DOI: 10.5061/dryad.1v62kr3q
title: Data from: Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and phylogenetic analysis

description: This study presents a manually constructed alignment of nearly complete
 rRNA genes from most animal clades (371 taxa from ∼33 of the ∼36 metazoan
 phyla), expanded from the 197 sequences in a previous study. This
 thorough, taxon-rich alignment, available at
 http://www.wsu.edu/≃jmallatt/research/rRNAalignment.html and in the Dryad
 Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based
 rigidly on the secondary structure of the SSU and LSU rRNA molecules, and
 is annotated in detail, including labeling of the erroneous sequences
 (contaminants). The alignment can be used for future studies of the
 molecular evolution of rRNA. Here, we use it to explore if the larger
 number of sequences produces an improved phylogenetic tree of animal
 relationships. Disappointingly, the resolution did not improve, neither
 when the standard maximum-likelihood method was used, nor with more
 sophisticated methods that partitioned the rRNA into paired and unpaired
 sites (stem, loop, bulge, junction), or accounted for the evolution of the
 paired sites. For example, no doublet model of paired-site substitutions
 (16-state, 16A and 16B, 7A–F, or 6A–C models) corrected the placement of
 any rogue taxa or increased resolution. The following findings are from
 the simplest, standard, ML analysis. The 371-taxon tree only imperfectly
 supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this
 problem remained after 17 taxa with unstably positioned sequences were
 omitted from the analysis. The problem seems to stem from
 base-compositional heterogeneity across taxa and from an
 overrepresentation of highly divergent sequences among the newly added
 taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa).
 The rogue taxa continue to concentrate in two locations in the rRNA tree:
 near the base of Arthropoda and of Bilateria. The approximately uncertain
 (AU) test refuted the monophyly of Mollusca and of Chordata, probably due
 to long-branch attraction of the highly divergent cephalopod and
 urochordate sequences out of those clades. Unlikely to be correct, these
 refutations show for the first time that rRNA phylogeny can support some
 ‘wrong’ clades. Along with its weaknesses, the rRNA tree has strengths: It
 recovers many clades that are supported by independent evidence (e.g.,
 Metazoa, Bilateria, Hexapoda, Nonoculata, Ambulacraria, Syndermata, and
 Thecostraca with Malacostraca) and shows good resolution within certain
 groups (e.g., in Platyhelminthes, Insecta, Cnidaria). As another strength,
 the newly added rRNA sequences yielded the first rRNA-based support for
 Carnivora and Cetartiodactyla (dolphin + llama) in Mammalia, for basic
 subdivisions of Bryozoa (‘Gymnolaemata + Stenolaemata’ versus
 Phylactolaemata), and for Oligostraca (ostracods + branchiurans +
 pentastomids + mystacocarids). Future improvement could come from better
 sequence-evolution models that account for base-compositional
 heterogeneity, and from combining rRNA with protein-coding genes in
 phylogenetic reconstruction.
description: rRNA371animalsMarch252011Please see the ReadMe file.rRNA197animalsNov2008Please see the ReadMe file.