Phylogeny of Eukaryotes Based on Ribosomal RNA: Long-Branch Attraction and Models of Sequence Evolution

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Abstract
The molecular phylogeny of eukaryotes was first based on the comparison of the small-subunit ribosomal RNA (SSU rRNA) and quickly became a paradigm (Sogin 1991<$REFLINK> ). However, serious criticisms have recently been raised against it. In particular, it has been suggested that the various protist lineages that emerged first (e.g., microsporidia, trichomonads, mycetozoans) were misplaced because of the long-branch attraction (LBA) artifact (Philippe and Adoutte 1998<$REFLINK> ; Philippe and Laurent 1998<$REFLINK> ; Germot and Philippe 1999<$REFLINK> ; Moreira, Le Guyader, and Philippe 1999<$REFLINK> ; Roger et al. 1999<$REFLINK> ; Stiller and Hall 1999<$REFLINK> ). Indeed, simulation studies (unpublished data) showed that when a distant outgroup was used, all the standard methods of phylogenetic reconstruction artifactually inferred a phylogeny with an asymmetrical base containing the fast-evolving lineages, leading to a tree shape very similar to the rRNA one.

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