title: Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees.
abstract: BACKGROUND
  In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking.
  
  
  RESULTS
  This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness.
  
  
  CONCLUSIONS
  Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion.
  
  
  METHODS
  This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin.
  
  
  BACKGROUND
  Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.
authors.affiliation: Department of Bioinformatics, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Keller
authors.forename: Frank
authors.initials: F
authors.lastname: Förster
authors.forename: Tobias
authors.initials: T
authors.lastname: Müller
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
authors.forename: Jörg
authors.initials: J
authors.lastname: Schultz
authors.forename: Matthias
authors.initials: M
authors.lastname: Wolf
mesh_terms: D003198:Computer Simulation; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D010944:Plants / Q000235:genetics*; D018749:RNA, Plant / Q000737:chemistry* / Q000235:genetics*
chemical_list: D018749:RNA, Plant